International Journal of Molecular Sciences

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9 pages, 295 KiB

Open AccessEditorial

Molecular Genetics Enhances Plant Breeding

by Andrés J. Cortés and Hai Du

Int. J. Mol. Sci. 2023, 24(12), 9977; https://doi.org/10.3390/ijms24129977 - 9 Jun 2023

Cited by 5 | Viewed by 1818

Abstract

Human-driven plant selection, a practice as ancient as agriculture itself, has laid the foundations of plant breeding and contemporary farming [...] Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

Research

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19 pages, 4796 KiB

Open AccessArticle

Resequencing of 410 Sesame Accessions Identifies SINST1 as the Major Underlying Gene for Lignans Variation

by Senouwa Segla Koffi Dossou, Shengnan Song, Aili Liu, Donghua Li, Rong Zhou, Muez Berhe, Yanxin Zhang, Chen Sheng, Zhijian Wang, Jun You and Linhai Wang

Int. J. Mol. Sci. 2023, 24(2), 1055; https://doi.org/10.3390/ijms24021055 - 5 Jan 2023

Cited by 8 | Viewed by 2378

Abstract

Sesame is a promising oilseed crop that produces specific lignans of clinical importance. Hence, a molecular description of the regulatory mechanisms of lignan biosynthesis is essential for crop improvement. Here, we resequence 410 sesame accessions and identify 5.38 and 1.16 million SNPs (single [...] Read more.

Sesame is a promising oilseed crop that produces specific lignans of clinical importance. Hence, a molecular description of the regulatory mechanisms of lignan biosynthesis is essential for crop improvement. Here, we resequence 410 sesame accessions and identify 5.38 and 1.16 million SNPs (single nucleotide polymorphisms) and InDels, respectively. Population genomic analyses reveal that sesame has evolved a geographic pattern categorized into northern (NC), middle (MC), and southern (SC) groups, with potential origin in the southern region and subsequent introduction to the other regions. Selective sweeps analysis uncovers 120 and 75 significant selected genomic regions in MC and NC groups, respectively. By screening these genomic regions, we unveiled 184 common genes positively selected in these subpopulations for exploitation in sesame improvement. Genome-wide association study identifies 17 and 72 SNP loci for sesamin and sesamolin variation, respectively, and 11 candidate causative genes. The major pleiotropic SNP^C/A locus for lignans variation is located in the exon of the gene SiNST1. Further analyses revealed that this locus was positively selected in higher lignan content sesame accessions, and the “C” allele is favorable for a higher accumulation of lignans. Overexpression of SiNST1^C in sesame hairy roots significantly up-regulated the expression of SiMYB58, SiMYB209, SiMYB134, SiMYB276, and most of the monolignol biosynthetic genes. Consequently, the lignans content was significantly increased, and the lignin content was slightly increased. Our findings provide insights into lignans and lignin regulation in sesame and will facilitate molecular breeding of elite varieties and marker-traits association studies. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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17 pages, 3614 KiB

Open AccessArticle

Evolution and Phylogeny of Soybean Mosaic Virus Based on 143 Complete Genomes

by Hoseong Choi, Yeonhwa Jo, Soo Yeon Choi, Sang-Min Kim, Yu Mi Choi, Jin-Sung Hong, Bong Choon Lee and Won Kyong Cho

Int. J. Mol. Sci. 2023, 24(1), 22; https://doi.org/10.3390/ijms24010022 - 20 Dec 2022

Cited by 2 | Viewed by 2158

Abstract

Soybean mosaic virus (SMV) of the genus Potyvirus is an important virus in cultivated soybeans. Here, we obtained 7 SMV genomes from soybean germplasms using RNA sequencing and conducted a comprehensive evolutionary and phylogenetic study of 143 SMV genomes derived from 10 plant [...] Read more.

Soybean mosaic virus (SMV) of the genus Potyvirus is an important virus in cultivated soybeans. Here, we obtained 7 SMV genomes from soybean germplasms using RNA sequencing and conducted a comprehensive evolutionary and phylogenetic study of 143 SMV genomes derived from 10 plant species and 12 countries. The phylogenetic tree we constructed using coding DNA sequences revealed the existence of nine clades of SMV isolates/strains. Recombination analysis revealed 76 recombinant events and 141 recombinants in total. Clades 1 and 3 contain the most common SMV pathotypes, including G1 through G7, which are distributed worldwide. Clade 2 includes several Chinese SMV pathotypes. The SMV isolates were further divided into two groups. The SMV isolates in the first group, including clades 8 and 9, were identified from Pinellia and Atractylodes species, whereas those in the second group (clades 1 through 7) were mostly found in cultivated soybeans. The SMV polyprotein undergoes positive selection, whereas most mature proteins, except for the P1 protein, undergo negative selection. The P1 protein of SMV isolates in group 1 may be highly correlated with host adaptation. This study provides strong evidence that recombination and plant hosts are powerful forces driving the genetic diversity of the SMV genome. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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19 pages, 4204 KiB

Open AccessArticle

Effect of Overexpression of γ-Tocopherol Methyltransferase on α-Tocopherol and Fatty Acid Accumulation and Tolerance to Salt Stress during Seed Germination in Brassica napus L.

by Yuan Guo, Dong Li, Tiantian Liu, Meifang Liao, Yuxin Li, Weitang Zhang, Zijin Liu and Mingxun Chen

Int. J. Mol. Sci. 2022, 23(24), 15933; https://doi.org/10.3390/ijms232415933 - 14 Dec 2022

Cited by 7 | Viewed by 1783

Abstract

Rapeseed (Brassica napus L.) is an important oil crop and a major source of tocopherols, also known as vitamin E, in human nutrition. Enhancing the quality and composition of fatty acids (FAs) and tocopherols in seeds has long been a target for [...] Read more.

Rapeseed (Brassica napus L.) is an important oil crop and a major source of tocopherols, also known as vitamin E, in human nutrition. Enhancing the quality and composition of fatty acids (FAs) and tocopherols in seeds has long been a target for rapeseed breeding. The gene γ-Tocopherol methyltransferase (γ-TMT) encodes an enzyme catalysing the conversion of γ-tocopherol to α-tocopherol, which has the highest biological activity. However, the genetic basis of γ-TMT in B. napus seeds remains unclear. In the present study, BnaC02.TMT.a, one paralogue of Brassica napus γ-TMT, was isolated from the B. napus cultivar “Zhongshuang11” by nested PCR, and two homozygous transgenic overexpression lines were further characterised. Our results demonstrated that the overexpression of BnaC02.TMT.a mediated an increase in the α- and total tocopherol content in transgenic B. napus seeds. Interestingly, the FA composition was also altered in the transgenic plants; a reduction in the levels of oleic acid and an increase in the levels of linoleic acid and linolenic acid were observed. Consistently, BnaC02.TMT.a promoted the expression of BnFAD2 and BnFAD3, which are involved in the biosynthesis of polyunsaturated fatty acids during seed development. In addition, BnaC02.TMT.a enhanced the tolerance to salt stress by scavenging reactive oxygen species (ROS) during seed germination in B. napus. Our results suggest that BnaC02.TMT.a could affect the tocopherol content and FA composition and play a positive role in regulating the rapeseed response to salt stress by modulating the ROS scavenging system. This study broadens our understanding of the function of the Bnγ-TMT gene and provides a novel strategy for genetic engineering in rapeseed breeding. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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20 pages, 6368 KiB

Open AccessArticle

Conservation and Divergence of the Trihelix Genes in Brassica and Expression Profiles of BnaTH Genes in Brassica napus under Abiotic Stresses

by Cuiping Zhang, Lijing Lu, Ruolin Gong, Xing Su, Fengbo Liu, Ru Zhang and Jihong Hu

Int. J. Mol. Sci. 2022, 23(24), 15766; https://doi.org/10.3390/ijms232415766 - 12 Dec 2022

Cited by 7 | Viewed by 1962

Abstract

Trihelix (TH) proteins are a family of plant-specific transcription factors that play a role in light response and are extensively involved in plant growth and development, as well as in various stress responses. However, the function of TH genes in Brassica napus ( [...] Read more.

Trihelix (TH) proteins are a family of plant-specific transcription factors that play a role in light response and are extensively involved in plant growth and development, as well as in various stress responses. However, the function of TH genes in Brassica napus (B. napus) remains unclear, as does the evolution and differentiation pattern of TH genes in Brassica plants. Here, we identified a total of 455 TH genes in seven species, including six Brassica species and Arabidopsis, which were grouped into five clades, GT-1, GT-2, GTγ, SH4, and SIP1, each with 69, 142, 44, 55, and 145 members, respectively. The types and distributions of motifs of the TH proteins and the structures of the TH genes are conserved in the same subgroup, and some variations in certain amino acid residues occur in B. napus when inheriting motifs from Brassica rapa (B. rapa) and Brassica oleracea (B. oleracea). Collinearity analysis revealed that the massive expansion of TH genes in tetraploid species was attributed to the hetero-tetraploidization of diploid ancestors and gene duplication events within the tetraploid species. Comparative analysis of the membership numbers of five subgroups in different species revealed that the GT-2 and SIP1 genes underwent significant expansion during evolution, possibly to support the better adaptation of plants to their environments. The differential expression of the BnaTH genes under five stresses indicates that the BnaTH genes are involved in plant responses to stresses such as drought, cold, and heat. The presence of different stress-responsive cis-elements in the upstream promoter region of the genes indicated that BnaTH genes have the potential to cope with variable environments. Meanwhile, qRT-PCR analyses also confirmed that five TH genes respond to different abiotic stresses. Our results provide information and candidates for further studies on the role of TH genes in stress resistance of B. napus. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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21 pages, 8134 KiB

Open AccessArticle

Genome-Wide Association Analysis for Hybrid Breeding in Wheat

by Monika Mokrzycka, Stefan Stojałowski, Mirosław Tyrka, Przemysław Matysik, Barbara Żmijewska, Rafał Marcinkowski, Urszula Woźna-Pawlak, Róża Martofel, Michał Rokicki, Monika Rakoczy-Trojanowska and Paweł Krajewski

Int. J. Mol. Sci. 2022, 23(23), 15321; https://doi.org/10.3390/ijms232315321 - 5 Dec 2022

Cited by 3 | Viewed by 2275

Abstract

Disclosure of markers that are significantly associated with plant traits can help develop new varieties with desirable properties. This study determined the genome-wide associations based on DArTseq markers for six agronomic traits assessed in eight environments for wheat. Moreover, the association study for [...] Read more.

Disclosure of markers that are significantly associated with plant traits can help develop new varieties with desirable properties. This study determined the genome-wide associations based on DArTseq markers for six agronomic traits assessed in eight environments for wheat. Moreover, the association study for heterosis and analysis of the effects of markers grouped by linkage disequilibrium were performed based on mean values over all experiments. All results were validated using data from post-registration trials. GWAS revealed 1273 single nucleotide polymorphisms with biologically significant effects. Most polymorphisms were predicted to be modifiers of protein translation, with only two having a more pronounced effect. Markers significantly associated with the considered set of features were clustered within chromosomes based on linkage disequilibrium in 327 LD blocks. A GWAS for heterosis revealed 1261 markers with significant effects. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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20 pages, 4780 KiB

Open AccessArticle

Mapping and Validation of BrGOLDEN: A Dominant Gene Regulating Carotenoid Accumulation in Brassica rapa

by Lei Zhang, Shifan Zhang, Yun Dai, Shaoxing Wang, Chenggang Wang, Fei Li, Hui Zhang, Guohu Chen, Lingyun Yuan, Jinfeng Hou, Xiaoyan Tang, Shidong Zhu, Rifei Sun, Guoliang Li and Shujiang Zhang

Int. J. Mol. Sci. 2022, 23(20), 12442; https://doi.org/10.3390/ijms232012442 - 18 Oct 2022

Cited by 5 | Viewed by 2130

Abstract

In plants, the accumulation of carotenoids can maintain the balance of the photosystem and improve crop nutritional quality. Therefore, the molecular mechanisms underlying carotenoid synthesis and accumulation should be further explored. In this study, carotenoid accumulation differed significantly among parental Brassica rapa. [...] Read more.

In plants, the accumulation of carotenoids can maintain the balance of the photosystem and improve crop nutritional quality. Therefore, the molecular mechanisms underlying carotenoid synthesis and accumulation should be further explored. In this study, carotenoid accumulation differed significantly among parental Brassica rapa. Genetic analysis was carried out using the golden inner leaf ‘1900264′ line and the light−yellow inner leaf ‘1900262′ line, showing that the golden inner leaf phenotype was controlled by a single dominant gene. Using bulked−segregant analysis sequencing, BraA09g007080.3C encoding the ORANGE protein was selected as a candidate gene. Sequence alignment revealed that a 4.67 kb long terminal repeat insertion in the third exon of the BrGOLDEN resulted in three alternatively spliced transcripts. The spatiotemporal expression results indicated that BrGOLDEN might regulate the expression levels of carotenoid−synthesis−related genes. After transforming BrGOLDEN into Arabidopsis thaliana, the seed−derived callus showed that BrGOLDEN_Ins and BrGOLDEN_Del lines presented a yellow color and the BrGOLDEN_Ldel line presented a transparent phenotype. In addition, using the yeast two−hybrid assay, BrGOLDEN_Ins, BrGOLDEN_Ldel, and Brgolden_wt exhibited strong interactions with BrPSY1, but BrGOLDEN_Del did not interact with BrPSY1 in the split−ubiquitin membrane system. In the secondary and 3D structure analysis, BrGOLDEN_Del was shown to have lost the PNFPSFIPFLPPL sequences at the 125 amino acid position, which resulted in the α−helices of BrGOLDEN_Del being disrupted, restricting the formation of the 3D structure and affecting the functions of the protein. These findings may provide new insights into the regulation of carotenoid synthesis in B. rapa. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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17 pages, 5397 KiB

Open AccessArticle

Genome-Wide Identification of DOF Gene Family and the Mechanism Dissection of SbDof21 Regulating Starch Biosynthesis in Sorghum

by Qianlin Xiao, Tingting Liu, Min Ling, Qiannan Ma, Wan Cao, Fangyu Xing, Tianhui Huang, Yingyi Zhang, Hong Duan and Zhizhai Liu

Int. J. Mol. Sci. 2022, 23(20), 12152; https://doi.org/10.3390/ijms232012152 - 12 Oct 2022

Cited by 9 | Viewed by 1974

Abstract

Starch is one of the main utilization products of sorghum (Sorghum bicolor L.), the fifth largest cereal crop in the world. Up to now, the regulation mechanism of starch biosynthesis is rarely documented in sorghum. In the present study, we identified 30 [...] Read more.

Starch is one of the main utilization products of sorghum (Sorghum bicolor L.), the fifth largest cereal crop in the world. Up to now, the regulation mechanism of starch biosynthesis is rarely documented in sorghum. In the present study, we identified 30 genes encoding the C2-C2 zinc finger domain (DOF), with one to three exons in the sorghum genome. The DOF proteins of sorghum were divided into two types according to the results of sequence alignment and evolutionary analysis. Based on gene expressions and co-expression analysis, we identified a regulatory factor, SbDof21, that was located on chromosome 5. SbDof21 contained two exons, encoding a 36.122 kD protein composed of 340 amino acids. SbDof21 co-expressed with 15 genes involved in the sorghum starch biosynthesis pathway, and the Pearson correlation coefficients (PCCs) with 11 genes were greater than 0.9. The results of qRT-PCR assays indicated that SbDof21 is highly expressed in sorghum grains, exhibiting low relative expression levels in the tissues of roots, stems and leaves. SbDOF21 presented as a typical DOF transcription factor (TF) that was localized to the nucleus and possessed transcriptional activation activity. Amino acids at positions 182–231 of SbDOF21 formed an important structure in its activation domain. The results of EMSA showed that SbDOF21 could bind to four tandem repeats of P-Box (TGTAAAG) motifs in vitro, such as its homologous proteins of ZmDOF36, OsPBF and TaPBF. Meanwhile, we also discovered that SbDOF21 could bind and transactivate SbGBSSI, a key gene in sorghum amylose biosynthesis. Collectively, the results of the present study suggest that SbDOF21 acts as an important regulator in sorghum starch biosynthesis, exhibiting potential values for the improvement of starch contents in sorghum. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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11 pages, 2127 KiB

Open AccessArticle

Sequencing and Genomic Analysis of Sorghum DNA Introgression Variant Line R21 and Recipient Rice Jin Hui 1 Revealed Repetitive Element Variation

by Ting Zhang, Xiaodong Li, Zijun Zhao, Renhong Wu, Zhenglin Yang and Guanghua He

Int. J. Mol. Sci. 2022, 23(19), 11864; https://doi.org/10.3390/ijms231911864 - 6 Oct 2022

Cited by 2 | Viewed by 1720

Abstract

Transferring the genome of distant species to crops is an efficient way to create new germplasms. However, the molecular mechanisms involved are unclear. In this study, a new rice restorer line R21 with heat tolerance was created by introgressing the genomic DNA of [...] Read more.

Transferring the genome of distant species to crops is an efficient way to create new germplasms. However, the molecular mechanisms involved are unclear. In this study, a new rice restorer line R21 with heat tolerance was created by introgressing the genomic DNA of sorghum into the recipient restorer line Jin Hui 1. Assembly of rice R21 and Jin Hui 1 genomes was performed using PacBio sequencing technology. Comparative genome analysis and coverage statistics showed that the repetitive sequence atr0026 was a candidate introgression fragment of sorghum DNA. Sequence similarity analysis revealed that atr0026 was distributed at different copy numbers on the telomeric position of chromosomes 9 or 10 in R21, Jin Hui 1, and several rice varieties, indicating that the repetitive sequence from sorghum was highly conserved in rice. The repeat annotation in Gramineae indicated that ribosomal DNA loci that existed in atr0026 may be cause a rearrangement of chromosomes 9 and 10 of the R21 genome, resulting in a copy number variation at the 5′ end of it. Our study lays the foundation for further elucidation of the molecular mechanisms underlying the heat tolerance of sorghum DNA introgression variant line R21, which is of great significance for guiding crop genetic breeding. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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17 pages, 2933 KiB

Open AccessArticle

Identification of Quantitative Trait Locus and Candidate Genes for Drought Tolerance in a Soybean Recombinant Inbred Line Population

by Wenqi Ouyang, Limiao Chen, Junkui Ma, Xiaorong Liu, Haifeng Chen, Hongli Yang, Wei Guo, Zhihui Shan, Zhonglu Yang, Shuilian Chen, Yong Zhan, Hengbin Zhang, Dong Cao and Xinan Zhou

Int. J. Mol. Sci. 2022, 23(18), 10828; https://doi.org/10.3390/ijms231810828 - 16 Sep 2022

Cited by 11 | Viewed by 2259

Abstract

With global warming and regional decreases in precipitation, drought has become a problem worldwide. As the number of arid regions in the world is increasing, drought has become a major factor leading to significant crop yield reductions and food crises. Soybean is a [...] Read more.

With global warming and regional decreases in precipitation, drought has become a problem worldwide. As the number of arid regions in the world is increasing, drought has become a major factor leading to significant crop yield reductions and food crises. Soybean is a crop that is relatively sensitive to drought. It is also a crop that requires more water during growth and development. The aim of this study was to identify the quantitative trait locus (QTL) that affects drought tolerance in soybean by using a recombinant inbred line (RIL) population from a cross between the drought-tolerant cultivar ‘Jindou21’ and the drought-sensitive cultivar ‘Zhongdou33’. Nine agronomic and physiological traits were identified under drought and well-watered conditions. Genetic maps were constructed with 923,420 polymorphic single nucleotide polymorphism (SNP) markers distributed on 20 chromosomes at an average genetic distance of 0.57 centimorgan (cM) between markers. A total of five QTLs with a logarithm of odds (LOD) value of 4.035–8.681 were identified on five chromosomes. Under well-watered conditions and drought-stress conditions, one QTL related to the main stem node number was located on chromosome 16, accounting for 17.177% of the phenotypic variation. Nine candidate genes for drought resistance were screened from this QTL, namely Glyma.16G036700, Glyma.16G036400, Glyma.16G036600, Glyma.16G036800, Glyma.13G312700, Glyma.13G312800, Glyma.16G042900, Glyma.16G043200, and Glyma.15G100700. These genes were annotated as NAC transport factor, GATA transport factor, and BTB/POZ-MATH proteins. This result can be used for molecular marker-assisted selection and provide a reference for breeding for drought tolerance in soybean. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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13 pages, 2785 KiB

Open AccessArticle

Increasing the Grain Yield and Grain Protein Content of Common Wheat (Triticum aestivum) by Introducing Missense Mutations in the Q Gene

by Qing Chen, Zhenru Guo, Xiaoli Shi, Meiqiao Wei, Yazhen Fan, Jing Zhu, Ting Zheng, Yan Wang, Li Kong, Mei Deng, Xinyou Cao, Jirui Wang, Yuming Wei, Qiantao Jiang, Yunfeng Jiang, Guoyue Chen, Youliang Zheng and Pengfei Qi

Int. J. Mol. Sci. 2022, 23(18), 10772; https://doi.org/10.3390/ijms231810772 - 15 Sep 2022

Cited by 6 | Viewed by 3583

Abstract

Grain yield (GY) and grain protein content (GPC) are important traits for wheat breeding and production; however, they are usually negatively correlated. The Q gene is the most important domestication gene in cultivated wheat because it influences many traits, including GY and GPC. [...] Read more.

Grain yield (GY) and grain protein content (GPC) are important traits for wheat breeding and production; however, they are usually negatively correlated. The Q gene is the most important domestication gene in cultivated wheat because it influences many traits, including GY and GPC. Allelic variations in the Q gene may positively affect both GY and GPC. Accordingly, we characterized two new Q alleles (Q^s1 and Q^c1-N8) obtained through ethyl methanesulfonate-induced mutagenesis. Compared with the wild-type Q allele, Q^s1 contains a missense mutation in the sequence encoding the first AP₂ domain, whereas Q^c1-N8 has two missense mutations: one in the sequence encoding the second AP₂ domain and the other in the microRNA172-binding site. The Q^s1 allele did not significantly affect GPC or other processing quality parameters, but it adversely affected GY by decreasing the thousand kernel weight and grain number per spike. In contrast, Q^c1-N8 positively affected GPC and GY by increasing the thousand kernel weight and grain number per spike. Thus, we generated novel germplasm relevant for wheat breeding. A specific molecular marker was developed to facilitate the use of the Q^c1-N8 allele in breeding. Furthermore, our findings provide useful new information for enhancing cereal crops via non-transgenic approaches. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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18 pages, 6570 KiB

Open AccessArticle

Viromes of 15 Pepper (Capsicum annuum L.) Cultivars

by Yeonhwa Jo, Hoseong Choi, Jeong Hun Lee, Sang Hyun Moh and Won Kyong Cho

Int. J. Mol. Sci. 2022, 23(18), 10507; https://doi.org/10.3390/ijms231810507 - 10 Sep 2022

Cited by 11 | Viewed by 3916

Abstract

Pepper (Capsicum annuum L.) plants produce berry fruits that are used as spices. Here, we examined the viromes of 15 pepper cultivars through RNA sequencing. We obtained 1,325 virus-associated contigs derived from 8 virus species. Bean broad wilt virus 2 (BBWV2) and [...] Read more.

Pepper (Capsicum annuum L.) plants produce berry fruits that are used as spices. Here, we examined the viromes of 15 pepper cultivars through RNA sequencing. We obtained 1,325 virus-associated contigs derived from 8 virus species. Bean broad wilt virus 2 (BBWV2) and cucumber mosaic virus (CMV) were identified as the major viruses infecting pepper plants, followed by potato virus Y, bell pepper endornavirus, and hot pepper endornavirus. The proportion of viral reads in each transcriptome ranged from 0.04% to 24.5%. BBWV2 was the dominant virus in seven cultivars, whereas CMV was dominant in five cultivars. All the bell pepper cultivars showed severe viral disease symptoms, whereas the commercially developed hot pepper cultivars were asymptomatic or had mild symptoms. In addition, 111 complete viral segments were obtained from 7 viruses. Based on the obtained viral genomes, the genetic relationship between the identified viruses and quasispecies of BBWV2 and CMV in each pepper plant was determined. Newly designed primers for nine viruses confirmed the results of RNA sequencing. Taken together, this study, for the first time, provides a comprehensive overview of viromes in 15 major pepper cultivars through RNA sequencing. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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20 pages, 3285 KiB

Open AccessArticle

Integrated Transcriptome and Proteome Analysis Provides Insight into the Ribosome Inactivating Proteins in Plukenetia volubilis Seeds

by Guo Liu, Zhihua Wu, Yan Peng, Xiuhua Shang and Liqiong Gao

Int. J. Mol. Sci. 2022, 23(17), 9562; https://doi.org/10.3390/ijms23179562 - 24 Aug 2022

Cited by 1 | Viewed by 1981

Abstract

Plukenetia volubilis is a highly promising plant with high nutritional and economic values. In our previous studies, the expression levels of ricin encoded transcripts were the highest in the maturation stage of P. volubilis seeds. The present study investigated the transcriptome and proteome [...] Read more.

Plukenetia volubilis is a highly promising plant with high nutritional and economic values. In our previous studies, the expression levels of ricin encoded transcripts were the highest in the maturation stage of P. volubilis seeds. The present study investigated the transcriptome and proteome profiles of seeds at two developmental stages (Pv-1 and Pv-2) using RNA-Seq and iTRAQ technologies. A total of 53,224 unigenes and 6026 proteins were identified, with functional enrichment analyses, including GO, KEGG, and KOG annotations. At two development stages of P. volubilis seeds, 8815 unique differentially expressed genes (DEGs) and 4983 unique differentially abundant proteins (DAPs) were identified. Omics-based association analysis showed that ribosome-inactivating protein (RIP) transcripts had the highest expression and abundance levels in Pv-2, and those DEGs/DAPs of RIPs in the GO category were involved in hydrolase activity. Furthermore, 21 RIP genes and their corresponding amino acid sequences were obtained from libraries produced with transcriptome analysis. The analysis of physicochemical properties showed that 21 RIPs of P. volubilis contained ricin, the ricin_B_lectin domain, or RIP domains and could be divided into three subfamilies, with the largest number for type II RIPs. The expression patterns of 10 RIP genes indicated that they were mostly highly expressed in Pv-2 and 4 transcripts encoding ricin_B_like lectins had very low expression levels during the seed development of P. volubilis. This finding would represent valuable evidence for the safety of oil production from P. volubilis for human consumption. It is also notable that the expression level of the Unigene0030485 encoding type I RIP was the highest in roots, which would be related to the antiviral activity of RIPs. This study provides a comprehensive analysis of the physicochemical properties and expression patterns of RIPs in different organs of P. volubilis and lays a theoretical foundation for further research and utilization of RIPs in P. volubilis. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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12 pages, 3668 KiB

Open AccessArticle

De Novo Transcriptome Analysis of R. nigrum cv. Aldoniai in Response to Blackcurrant Reversion Virus Infection

by Ingrida Mažeikienė, Ana Dovilė Juškytė, Vidmantas Bendokas and Vidmantas Stanys

Int. J. Mol. Sci. 2022, 23(17), 9560; https://doi.org/10.3390/ijms23179560 - 24 Aug 2022

Cited by 6 | Viewed by 2037

Abstract

The most damaging pathogen in blackcurrant plantations is mite-transmitted blackcurrant reversion virus (BRV). Some Ribes species have an encoded genetic resistance to BRV. We performed RNA sequencing analysis of BRV-resistant blackcurrant cv. Aldoniai to evaluate the molecular mechanisms related to the BRV infection [...] Read more.

The most damaging pathogen in blackcurrant plantations is mite-transmitted blackcurrant reversion virus (BRV). Some Ribes species have an encoded genetic resistance to BRV. We performed RNA sequencing analysis of BRV-resistant blackcurrant cv. Aldoniai to evaluate the molecular mechanisms related to the BRV infection response. The RNA of virus-inoculated and mock-inoculated microshoots was sequenced, and the transcriptional changes at 2- and 4-days post inoculation (dpi) were analyzed. The accumulation and expression of BRV RNA1 were detected in infected plants. In total, 159,701 transcripts were obtained and 30.7% were unigenes, annotated in 7 databases. More than 25,000 differentially expressed genes (DEGs) according to FPKM were upregulated or downregulated. We observed 221 and 850 DEGs at 2 and 4 dpi, respectively, in BRV-infected microshoots related to the stress response. The proportion of upregulated DEGs at 4 dpi was about 3.5 times higher than at 2 dpi. Pathways of the virus defense response were activated, and key candidate genes were identified. The phenylpropanoid and the cutin, suberine, and wax biosynthesis pathways were activated in infected plants. Our comparative de novo analysis of the R. nigrum transcriptome provides clues not only for understanding the molecular BRV resistance mechanisms but also for breeding BRV-tolerant genotypes. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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13 pages, 1758 KiB

Open AccessArticle

AtEAU1 and AtEAU2, Two EAR Motif-Containing ABA Up-Regulated Novel Transcription Repressors Regulate ABA Response in Arabidopsis

by Na Zhang, Siyu Chen, Adnan, Xutong Wang, Saddam Hussain, Yuxin Cheng, Yingying Li, Yuan Yuan, Chen Wang, Rao Lin, Huiyuan Zhang, Jiachen Wang, Tianya Wang and Shucai Wang

Int. J. Mol. Sci. 2022, 23(16), 9053; https://doi.org/10.3390/ijms23169053 - 13 Aug 2022

Cited by 2 | Viewed by 2108

Abstract

EAR (Ethylene-responsive element binding factor-associated Amphiphilic Repression) motif-containing transcription repressors have been shown to regulate plant growth and development, and plant responses to plant hormones and environmental stresses including biotic and abiotic stresses. However, the functions of most EAR-motif-containing proteins remain largely uncharacterized. [...] Read more.

EAR (Ethylene-responsive element binding factor-associated Amphiphilic Repression) motif-containing transcription repressors have been shown to regulate plant growth and development, and plant responses to plant hormones and environmental stresses including biotic and abiotic stresses. However, the functions of most EAR-motif-containing proteins remain largely uncharacterized. The plant hormone abscisic acid (ABA) also plays important roles in regulating plant responses to abiotic stresses via activation/repression of ABA-responsive genes. We report here the identification and functional characterization of two ABA-responsive EAR motif-containing protein genes, AtEAU1 (Arabidopsis thaliana EAR motif-containing ABAUp-regulated 1) and AtEAU2. Quantitative RT-PCR results show that the expressions of AtEAU1 and AtEAU2 were increased by ABA treatment, and were decreased in the ABA biosynthesis mutant aba1-5. Assays in transfected Arabidopsis protoplasts show that both AtEAU1 and AtEAU2 were specifically localized in the nucleus, and when recruited to the promoter region of the reporter gene by a fused DNA binding domain, repressed reporter gene expression. By using T-DNA insertion mutants and a gene-edited transgene-free mutant generated by CRISPR/Cas9 gene editing, we performed ABA sensitivity assays, and found that ABA sensitivity in the both ateau1 and ateau2 single mutants was increased in seedling greening assays. ABA sensitivity in the ateau1 ateau2 double mutants was also increased, but was largely similar to the ateau1 single mutants. On the other hand, all the mutants showed a wild type response to ABA in root elongation assays. Quantitative RT-PCR results show that the expression level of PYL4, an ABA receptor gene was increased, whereas that of ABI2, a PP2C gene was decreased in the ateau1 and ateau1 single, and the ateau1 ateau2 double mutants. In summary, our results suggest that AtEAU1 and AtEAU2 are ABA-response genes, and AtEAU1 and AtEAU2 are novel EAR motif-containing transcription repressors that negatively regulate ABA responses in Arabidopsis, likely by regulating the expression of some ABA signaling key regulator genes. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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14 pages, 2344 KiB

Open AccessArticle

A WRKY Protein, MfWRKY40, of Resurrection Plant Myrothamnus flabellifolia Plays a Positive Role in Regulating Tolerance to Drought and Salinity Stresses of Arabidopsis

by Zhuo Huang, Jiatong Wang, Yuan Li, Li Song, Duo’er Chen, Ling Liu and Cai-Zhong Jiang

Int. J. Mol. Sci. 2022, 23(15), 8145; https://doi.org/10.3390/ijms23158145 - 24 Jul 2022

Cited by 11 | Viewed by 2035

Abstract

WRKY transcription factors (TFs), one of the largest transcription factor families in plants, play an important role in abiotic stress responses. The resurrection plant, Myrothamnus flabellifolia, has a strong tolerance to dehydration, but only a few WRKY proteins related to abiotic stress [...] Read more.

WRKY transcription factors (TFs), one of the largest transcription factor families in plants, play an important role in abiotic stress responses. The resurrection plant, Myrothamnus flabellifolia, has a strong tolerance to dehydration, but only a few WRKY proteins related to abiotic stress response have been identified and functionally characterized in M. flabellifolia. In this study, we identified an early dehydration-induced gene, MfWRKY40, of M. flabellifolia. The deduced MfWRKY40 protein has a conserved WRKY motif but lacks a typical zinc finger motif in the WRKY domain and is localized in the nucleus. To investigate its potential roles in abiotic stresses, we overexpressed MfWRKY40 in Arabidopsis and found that transgenic lines exhibited better tolerance to both drought and salt stresses. Further detailed analysis indicated that MfWRKY40 promoted primary root length elongation and reduced water loss rate and stomata aperture (width/length) under stress, which may provide Arabidopsis the better water uptake and retention abilities. MfWRKY40 also facilitated osmotic adjustment under drought and salt stresses by accumulating more osmolytes, such as proline, soluble sugar, and soluble protein. Additionally, the antioxidation ability of transgenic lines was also significantly enhanced, represented by higher chlorophyll content, less malondialdehyde and reactive oxygen species accumulations, as well as higher antioxidation enzyme activities. All these results indicated that MfWRKY40 might positively regulate tolerance to drought and salinity stresses. Further investigation on the relationship of the missing zinc finger motif of MfWRKY40 and its regulatory role is necessary to obtain a better understanding of the mechanism underlying the excellent drought tolerance of M. flabellifolia. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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19 pages, 6002 KiB

Open AccessArticle

The Q^c5 Allele Increases Wheat Bread-Making Quality by Regulating SPA and SPR

by Zhenru Guo, Qing Chen, Jing Zhu, Yan Wang, Yang Li, Qingcheng Li, Kan Zhao, Yue Li, Rui Tang, Xiaoli Shi, Kenan Tan, Li Kong, Yunfeng Jiang, Qiantao Jiang, Jirui Wang, Guoyue Chen, Yuming Wei, Youliang Zheng and Pengfei Qi

Int. J. Mol. Sci. 2022, 23(14), 7581; https://doi.org/10.3390/ijms23147581 - 8 Jul 2022

Cited by 3 | Viewed by 3138

Abstract

Common wheat (Triticum aestivum L.) is an important food crop with a unique processing quality. The Q gene positively regulates the processing quality of wheat, but the underlying mechanism remains unclear. Here, a new Q allele (Q^c5) responsible for [...] Read more.

Common wheat (Triticum aestivum L.) is an important food crop with a unique processing quality. The Q gene positively regulates the processing quality of wheat, but the underlying mechanism remains unclear. Here, a new Q allele (Q^c5) responsible for compact spikes and good bread performance was identified. Compared with the Q allele widely distributed in modern common wheat cultivars, Q^c5 had a missense mutation outside the miRNA172-binding site. This missense mutation led to a more compact messenger RNA (mRNA) secondary structure around the miRNA172-binding region, resulting in increased Q^c5 expression during the spike development stage and a consequent increase in spike density. Furthermore, this missense mutation weakened the physical interaction between Q^c5 and storage protein activator (SPA) in seeds and suppressed the expression of storage protein repressor (SPR). These changes increased the grain protein content and improved the bread-making quality of wheat. In conclusion, a missense mutation increases Q expression because of the resulting highly folded mRNA secondary structure around the miRNA172-binding site. Furthermore, this mutation improves the bread-making quality of wheat by repressing the expression of SPR and influencing the physical interaction between Q and SPA. These findings provide new insights into the miRNA172-directed regulation of gene expression, with implications for wheat breeding. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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13 pages, 2377 KiB

Open AccessArticle

Silencing GmBIR1 in Soybean Results in Activated Defense Responses

by Dan-Dan Liu, Hu-Jiao Lan, Hashimi Said Masoud, Mei-Yan Ye, Xian-Yong Dai, Chen-Li Zhong, Sheng-Nan Tian and Jian-Zhong Liu

Int. J. Mol. Sci. 2022, 23(13), 7450; https://doi.org/10.3390/ijms23137450 - 5 Jul 2022

Cited by 9 | Viewed by 2327

Abstract

Receptor-like kinases (RLKs) are a large group of pattern recognition receptors (PRRs) and play a critical role in recognizing pathogens, transducing defense signals, and mediating the activation of immune defense responses. Although extensively studied in the model plant Arabidopsis, studies of RLKs in [...] Read more.

Receptor-like kinases (RLKs) are a large group of pattern recognition receptors (PRRs) and play a critical role in recognizing pathogens, transducing defense signals, and mediating the activation of immune defense responses. Although extensively studied in the model plant Arabidopsis, studies of RLKs in crops, including soybean, are limited. When a BAK1-interacting receptor-like kinase (BIR1) homolog (referred to as GmBIR1 hereafter) was silenced by the BPMV (Bean pod mottle virus)-induced gene silencing (BPMV-VIGS), it resulted in phenotypes that were reminiscent of constitutively activated defense responses, including a significantly stunted stature with observable cell death on the leaves of the silenced plants. In addition, both SA and H₂O₂ were over-accumulated in the leaves of the GmBIR1-silenced plants. Consistent with this autoimmune phenotype, GmBIR1-silenced plants exhibited significantly enhanced resistance to both Pseudomonas syringae pv. glycinea (Psg) and Soybean mosaic virus (SMV), two different types of pathogens, compared to the vector control plants. Together, our results indicated that GmBIR1 is a negative regulator of immunity in soybean and the function of BIR1 homologs is conserved in different plant species. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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14 pages, 7088 KiB

Open AccessArticle

QTL Mapping and Candidate Gene Analysis for Seed Germination Response to Low Temperature in Rice

by Nari Kim, Rahmatullah Jan, Jae-Ryoung Park, Saleem Asif, Dan-Dan Zhao, Eun-Gyeong Kim, Yoon-Hee Jang, Gyu-Hyeon Eom, Gang-Seob Lee and Kyung-Min Kim

Int. J. Mol. Sci. 2022, 23(13), 7379; https://doi.org/10.3390/ijms23137379 - 2 Jul 2022

Cited by 5 | Viewed by 2494

Abstract

Low temperature is a serious threat to the seed emergence of rice, which has become one of the main limiting factors affecting rice production in the world. It is of great significance to find the candidate genes controlling low-temperature tolerance during seed germination [...] Read more.

Low temperature is a serious threat to the seed emergence of rice, which has become one of the main limiting factors affecting rice production in the world. It is of great significance to find the candidate genes controlling low-temperature tolerance during seed germination and study their functions for breeding new rice cultivars with immense low-temperature tolerance during seed germination. In the current experiment, 120 lines of the Cheongcheong Nagdong Double Haploid (CNDH) population were used for quantitative trait locus (QTL) analysis of low-temperature germinability. The results showed a significant difference in germination under low different temperature (LDT) (15 °C, 20 °C) conditions. In total, four QTLs were detected on chromosome 3, 6, and 8. A total of 41 genes were identified from all the four QTLs, among them, 25 genes were selected by gene function annotation and further screened through quantitative real-time polymerase chain reaction (qRT-PCR). Based on gene function annotation and level of expression under low-temperature, our study suggested the OsGPq3 gene as a candidate gene controlling viviparous germination, ABA and GA signaling under low-temperature. This study will provide a theoretical basis for marker-assisted breeding and lay the basis for further mining molecular mechanisms of low-temperature germination tolerance in rice. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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19 pages, 6190 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of Ariadne Gene Family Reveal Its Genetic Effects on Agronomic Traits of Brassica napus

by Sumbal Wahid, Meili Xie, Sehrish Sarfraz, Jie Liu, Chuanji Zhao, Zetao Bai, Chaobo Tong, Xiaohui Cheng, Feng Gao and Shengyi Liu

Int. J. Mol. Sci. 2022, 23(11), 6265; https://doi.org/10.3390/ijms23116265 - 3 Jun 2022

Cited by 7 | Viewed by 2392

Abstract

E3 ligases promote protein ubiquitination and degradation, which regulate every aspect of eukaryotic life. The Ariadne (ARI) proteins of RBR (ring between ring fingers) protein subfamily has been discovered as a group of potential E3 ubiquitin ligases. Only a few available research studies [...] Read more.

E3 ligases promote protein ubiquitination and degradation, which regulate every aspect of eukaryotic life. The Ariadne (ARI) proteins of RBR (ring between ring fingers) protein subfamily has been discovered as a group of potential E3 ubiquitin ligases. Only a few available research studies show their role in plant adaptations processes against the external environment. Presently, the functions of ARI proteins are largely unknown in plants. Therefore, in this study, we performed genome-wide analysis to identify the ARI gene family and explore their potential importance in B. napus. A total of 39 ARI genes were identified in the B. napus genome and were classified into three subfamilies (A, B and C) based on phylogenetic analysis. The protein–protein interaction networks and enrichment analysis indicated that BnARI genes could be involved in endoreduplication, DNA repair, proteasome assembly, ubiquitination, protein kinase activity and stress adaptation. The transcriptome data analysis in various tissues provided us an indication of some BnARI genes’ functional importance in tissue development. We also identified potential BnARI genes that were significantly responsive towards the abiotic stresses. Furthermore, eight BnARI genes were identified as candidate genes for multiple agronomic traits through association mapping analysis in B. napus; among them, BnaA02g12100D, which is the ortholog of AtARI8, was significantly associated with ten agronomic traits. This study provided useful information on BnARI genes, which could aid targeted functional research and genetic improvement for breeding in B. napus. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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20 pages, 4884 KiB

Open AccessArticle

PIF4 Promotes Expression of HSFA2 to Enhance Basal Thermotolerance in Arabidopsis

by Jiaheng Yang, Xiao Qu, Li Ji, Guanhui Li, Chen Wang, Changyu Wang, Yan Zhang, Lanjie Zheng, Wanchen Li and Xu Zheng

Int. J. Mol. Sci. 2022, 23(11), 6017; https://doi.org/10.3390/ijms23116017 - 27 May 2022

Cited by 16 | Viewed by 3719

Abstract

Heat stress (HS) seriously restricts the growth and development of plants. When plants are exposed to extreme high temperature, the heat stress response (HSR) is activated to enable plants to survive. Sessile plants have evolved multiple strategies to sense and cope with HS. [...] Read more.

Heat stress (HS) seriously restricts the growth and development of plants. When plants are exposed to extreme high temperature, the heat stress response (HSR) is activated to enable plants to survive. Sessile plants have evolved multiple strategies to sense and cope with HS. Previous studies have established that PHYTOCHROME INTERACTING FACTOR 4 (PIF4) acts as a key component in thermomorphogenesis; however, whether PIF4 regulates plant thermotolerance and the molecular mechanism linking this light transcriptional factor and HSR remain unclear. Here, we show that the overexpression of PIF4 indeed provides plants with a stronger basal thermotolerance and greatly improves the survival ability of Arabidopsis under severe HS. Via phylogenetic analysis, we identified two sets (six) of PIF4 homologs in wheat, and the expression patterns of the PIF4 homologs were conservatively induced by heat treatment in both wheat and Arabidopsis. Furthermore, the PIF4 protein was accumulated under heat stress and had an identical expression level. Additionally, we found that the core regulator of HSR, HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2), was highly responsive to light and heat. Followed by promoter analysis and ChIP-qPCR, we further found that PIF4 can bind directly to the G-box motifs of the HSFA2 promoter. Via effector–reporter assays, we found that PIF4 binding could activate HSFA2 gene expression, thereby resulting in the activation of other HS-inducible genes, such as heat shock proteins. Finally, the overexpression of PIF4 led to a stronger basal thermotolerance under non-heat-treatment conditions, thereby resulting in an enhanced tolerance to severe heat stress. Taken together, our findings propose that PIF4 is linked to heat stress signaling by directly binding to the HSFA2 promoter and triggering the HSR at normal temperature conditions to promote the basal thermotolerance. These functions of PIF4 provide a candidate direction for breeding heat-resistant crop cultivars. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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15 pages, 1478 KiB

Open AccessArticle

Whole Transcriptome Sequencing Unveils the Genomic Determinants of Putative Somaclonal Variation in Mint (Mentha L.)

by Felipe López-Hernández and Andrés J. Cortés

Int. J. Mol. Sci. 2022, 23(10), 5291; https://doi.org/10.3390/ijms23105291 - 10 May 2022

Cited by 11 | Viewed by 2827

Abstract

Mint (Mentha L., Lamiaceae) is a strongly scented herb of the family Lamiaceae that is grown mostly by clonal propagation, making it a valuable species for the study of somaclonal variation and its phenotypic consequences. The recent introduction of a few species [...] Read more.

Mint (Mentha L., Lamiaceae) is a strongly scented herb of the family Lamiaceae that is grown mostly by clonal propagation, making it a valuable species for the study of somaclonal variation and its phenotypic consequences. The recent introduction of a few species of mint in South America, followed by a presumably rampant propagation, make this region particularly ideal for studying the extent of somaclonal genetic diversity. Hence, the objective of this work was to offer a preliminary characterization of somaclonal genetically coding diversity of the mint in the northern Andes in order to address the question of whether somaclonal variants may have emerged despite relatively recent introductions in a region where mint is not native. A total of 29 clonally propagated specimens, collected in mint export farms in the province of Antioquia, a major region for mint production in the northwest Andes of Colombia, were genotyped using RNA sequencing (RNA-Seq). SNP calling was carried out from the leaves’ transcriptome profiles of each plant by combining the GATK4 and TRINITY protocols, obtaining a total of 2033 loci across 912 transcripts with a minimum read depth of 20X and 4% of missing data. Unsupervised machine learning algorithms considered the K-means, AGNES and UPGMA approaches, all of which suggested three genetic clusters for M. spicata and a unique cluster for M. × piperita. The results indicate that at least two different origins of M. spicata reached the eastern region of the Antioquia province, clonally propagated in the locality ever since for local consumption and export. One of these ancestries had more population structure, possibly due to environmental or anthropological pressures that intervened in the fragmentation of this genetic group or to a higher somaclonal mutation rate. This work offers a first step into the study of the accumulation and transmission of presumably quasi-neutral somatic mutations at coding regions in an herbaceous clonally propagated scented species such as mint, likely favored by an expected population expansion after its Andean introduction. These ad hoc hypotheses warrant further study as part of future research. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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18 pages, 32528 KiB

Open AccessArticle

Global DNA Methylation and mRNA-miRNA Variations Activated by Heat Shock Boost Early Microspore Embryogenesis in Cabbage (Brassica oleracea)

by Congcong Kong, Henan Su, Siping Deng, Jialei Ji, Yong Wang, Yangyong Zhang, Limei Yang, Zhiyuan Fang and Honghao Lv

Int. J. Mol. Sci. 2022, 23(9), 5147; https://doi.org/10.3390/ijms23095147 - 5 May 2022

Cited by 6 | Viewed by 2489

Abstract

Microspore culture, a type of haploid breeding, is extensively used in the cultivation of cruciferous crops such as cabbage. Heat shock (HS) treatment is essential to improve the embryo rate during the culture process; however, its molecular role in boosting early microspore embryogenesis [...] Read more.

Microspore culture, a type of haploid breeding, is extensively used in the cultivation of cruciferous crops such as cabbage. Heat shock (HS) treatment is essential to improve the embryo rate during the culture process; however, its molecular role in boosting early microspore embryogenesis (ME) remains unknown. Here we combined DNA methylation levels, miRNAs, and transcriptome profiles in isolated microspores of cabbage ‘01-88’ under HS (32 °C for 24 h) and normal temperature (25 °C for 24 h) to investigate the regulatory roles of DNA methylation and miRNA in early ME. Global methylation levels were significantly different in the two pre-treatments, and 508 differentially methylated regions (DMRs) were identified; 59.92% of DMRs were correlated with transcripts, and 39.43% of miRNA locus were associated with methylation levels. Significantly, the association analysis revealed that 31 differentially expressed genes (DEGs) were targeted by methylation and miRNA and were mainly involved in the reactive oxygen species (ROS) response and abscisic acid (ABA) signaling, indicating that HS induced DNA methylation, and miRNA might affect ME by influencing ROS and ABA. This study revealed that DNA methylation and miRNA interfered with ME by modulating key genes and pathways, which could broaden our understanding of the molecular regulation of ME induced by HS pre-treatment. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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19 pages, 3990 KiB

Open AccessArticle

Genome-Wide Characterization of High-Affinity Nitrate Transporter 2 (NRT2) Gene Family in Brassica napus

by Run-Jie Du, Ze-Xuan Wu, Zhao-Xi Yu, Peng-Feng Li, Jian-Yu Mu, Jie Zhou, Jia-Na Li and Hai Du

Int. J. Mol. Sci. 2022, 23(9), 4965; https://doi.org/10.3390/ijms23094965 - 29 Apr 2022

Cited by 7 | Viewed by 2569

Abstract

Nitrate transporter 2 (NRT2) plays an essential role in Nitrogen (N) uptake, transport, utilization, and stress resistance. In this study, the NRT2 gene family in two sequenced Brassica napus ecotypes were identified, including 31 genes in ‘Zhongshuang11’ (BnaZSNRT2s) and 19 in [...] Read more.

Nitrate transporter 2 (NRT2) plays an essential role in Nitrogen (N) uptake, transport, utilization, and stress resistance. In this study, the NRT2 gene family in two sequenced Brassica napus ecotypes were identified, including 31 genes in ‘Zhongshuang11’ (BnaZSNRT2s) and 19 in ‘Darmor-bzh’ (BnaDarNRT2s). The candidate genes were divided into three groups (Group I−III) based on phylogenetic analyses, supported by a conserved intron-exon structure in each group. Collinearity analysis revealed that the large expansion of BnaZSNRT2s attributed to allopolyploidization of ancestors Brassica rapa and Brassica oleracea, and small-scale duplication events in B. napus. Transcription factor (TF) binding site prediction, cis-element analysis, and microRNA prediction suggested that the expressions of BnaZSNRT2s are regulated by multiple factors, and the regulatory pattern is relatively conserved in each group and is tightly connected between groups. Expression assay showed the diverse and differentiated spatial-temporal expression profiles of BnaZSNRT2s in Group I, but conserved patterns were observed in Group II/III; and the low nitrogen (LN) stress up-regulated expression profiles were presented in Group I−III, based on RNA-seq data. RT-qPCR analyses confirmed that BnaZSNRT2.5A-1 and BnaZSNRT2.5C-1 in Group II were highly up-regulated under LN stress in B. napus roots. Our results offer valid information and candidates for further functional BnaZSNRT2s studies. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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19 pages, 3722 KiB

Open AccessArticle

Comparative Study of Starch Phosphorylase Genes and Encoded Proteins in Various Monocots and Dicots with Emphasis on Maize

by Guowu Yu, Noman Shoaib, Ying Xie, Lun Liu, Nishbah Mughal, Yangping Li, Huanhuan Huang, Na Zhang, Junjie Zhang, Yinghong Liu, Yufeng Hu, Hanmei Liu and Yubi Huang

Int. J. Mol. Sci. 2022, 23(9), 4518; https://doi.org/10.3390/ijms23094518 - 20 Apr 2022

Cited by 9 | Viewed by 2293

Abstract

Starch phosphorylase (PHO) is a multimeric enzyme with two distinct isoforms: plastidial starch phosphorylase (PHO1) and cytosolic starch phosphorylase (PHO2). PHO1 specifically resides in the plastid, while PHO2 is found in the cytosol. Both play a critical role in the synthesis and degradation [...] Read more.

Starch phosphorylase (PHO) is a multimeric enzyme with two distinct isoforms: plastidial starch phosphorylase (PHO1) and cytosolic starch phosphorylase (PHO2). PHO1 specifically resides in the plastid, while PHO2 is found in the cytosol. Both play a critical role in the synthesis and degradation of starch. This study aimed to report the detailed structure, function, and evolution of genes encoding PHO1 and PHO2 and their protein ligand-binding sites in eight monocots and four dicots. “True” orthologs of PHO1 and PHO2 of Oryza sativa were identified, and the structure of the enzyme at the protein level was studied. The genes controlling PHO2 were found to be more conserved than those controlling PHO1; the variations were mainly due to the variable sequence and length of introns. Cis-regulatory elements in the promoter region of both genes were identified, and the expression pattern was analyzed. The real-time quantitative polymerase chain reaction indicated that PHO2 was expressed in all tissues with a uniform pattern of transcripts, and the expression pattern of PHO1 indicates that it probably contributes to the starch biosynthesis during seed development in Zea mays. Under abscisic acid (ABA) treatment, PHO1 was found to be downregulated in Arabidopsis and Hordeum vulgare. However, we found that ABA could up-regulate the expression of both PHO1 and PHO2 within 12 h in Zea mays. In all monocots and dicots, the 3D structures were highly similar, and the ligand-binding sites were common yet fluctuating in the position of aa residues. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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14 pages, 2277 KiB

Open AccessArticle

Development and Validation of SNP and InDel Markers for Pod-Shattering Tolerance in Soybean

by Jeong-Hyun Seo, Sanjeev Kumar Dhungana, Beom-Kyu Kang, In-Youl Baek, Jung-Sook Sung, Jee-Yeon Ko, Chan-Sik Jung, Ki-Seung Kim and Tae-Hwan Jun

Int. J. Mol. Sci. 2022, 23(4), 2382; https://doi.org/10.3390/ijms23042382 - 21 Feb 2022

Cited by 11 | Viewed by 3608

Abstract

Pod-shattering causes a significant yield loss in many soybean cultivars. Shattering-tolerant cultivars provide the most effective approach to minimizing this loss. We developed molecular markers for pod-shattering and validated them in soybeans with diverse genetic backgrounds. The genes Glyma.16g141200, Glyma.16g141500, and [...] Read more.

Pod-shattering causes a significant yield loss in many soybean cultivars. Shattering-tolerant cultivars provide the most effective approach to minimizing this loss. We developed molecular markers for pod-shattering and validated them in soybeans with diverse genetic backgrounds. The genes Glyma.16g141200, Glyma.16g141500, and Glyma.16g076600, identified in our previous study by quantitative trait locus (QTL) mapping and whole-genome resequencing, were selected for marker development. The whole-genome resequencing of three parental lines (one shattering-tolerant and two shattering-susceptible) identified single nucleotide polymorphism (SNP) and/or insertion/deletion (InDel) regions within or near the selected genes. Two SNPs and one InDel were converted to Kompetitive Allele-Specific PCR (KASP) and InDel markers, respectively. The accuracy of the markers was examined in the two recombinant inbred line populations used for the QTL mapping, as well as the 120 varieties and elite lines, through allelic discrimination and phenotyping by the oven-drying method. Both types of markers successfully discriminated the pod shattering-tolerant and shattering-susceptible genotypes. The prediction accuracy, which was as high as 90.9% for the RILs and was 100% for the varieties and elite lines, also supported the accuracy and usefulness of these markers. Thus, the markers can be used effectively for genetic and genomic studies and the marker-assisted selection for pod-shattering tolerance in soybean. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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19 pages, 44972 KiB

Open AccessArticle

HuNAC20 and HuNAC25, Two Novel NAC Genes from Pitaya, Confer Cold Tolerance in Transgenic Arabidopsis

by Xinglong Hu, Fangfang Xie, Wenwei Liang, Yinhao Liang, Zhike Zhang, Jietang Zhao, Guibing Hu and Yonghua Qin

Int. J. Mol. Sci. 2022, 23(4), 2189; https://doi.org/10.3390/ijms23042189 - 16 Feb 2022

Cited by 17 | Viewed by 2271

Abstract

NAC transcription factors are one of the largest families of transcriptional regulators in plants, and members of the gene family play vital roles in regulating plant growth and development processes including biotic/abiotic stress responses. However, little information is available about the NAC family [...] Read more.

NAC transcription factors are one of the largest families of transcriptional regulators in plants, and members of the gene family play vital roles in regulating plant growth and development processes including biotic/abiotic stress responses. However, little information is available about the NAC family in pitaya. In this study, we conducted a genome-wide analysis and a total of 64 NACs (named HuNAC1-HuNAC64) were identified in pitaya (Hylocereus). These genes were grouped into fifteen subgroups with diversities in gene proportions, exon–intron structures, and conserved motifs. Genome mapping analysis revealed that HuNAC genes were unevenly scattered on all eleven chromosomes. Synteny analysis indicated that the segmental duplication events played key roles in the expansion of the pitaya NAC gene family. Expression levels of these HuNAC genes were analyzed under cold treatments using qRT-PCR. Four HuNAC genes, i.e., HuNAC7, HuNAC20, HuNAC25, and HuNAC30, were highly induced by cold stress. HuNAC7, HuNAC20, HuNAC25, and HuNAC30 were localized exclusively in the nucleus. HuNAC20, HuNAC25, and HuNAC30 were transcriptional activators while HuNAC7 was a transcriptional repressor. Overexpression of HuNAC20 and HuNAC25 in Arabidopsis thaliana significantly enhanced tolerance to cold stress through decreasing ion leakage, malondialdehyde (MDA), and H₂O₂ and O₂⁻ accumulation, accompanied by upregulating the expression of cold-responsive genes (AtRD29A, AtCOR15A, AtCOR47, and AtKIN1). This study presents comprehensive information on the understanding of the NAC gene family and provides candidate genes to breed new pitaya cultivars with tolerance to cold conditions through genetic transformation. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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12 pages, 1357 KiB

Open AccessArticle

Identification and Validation of Quantitative Trait Loci Mapping for Spike-Layer Uniformity in Wheat

by Kunyu Zhou, Yu Lin, Xiaojun Jiang, Wanlin Zhou, Fangkun Wu, Caixia Li, Yuming Wei and Yaxi Liu

Int. J. Mol. Sci. 2022, 23(3), 1052; https://doi.org/10.3390/ijms23031052 - 19 Jan 2022

Cited by 3 | Viewed by 2230

Abstract

Spike-layer uniformity (SLU), the consistency of the spike distribution in the vertical space, is an important trait. It directly affects the yield potential and appearance. Revealing the genetic basis of SLU will provide new insights into wheat improvement. To map the SLU-related quantitative [...] Read more.

Spike-layer uniformity (SLU), the consistency of the spike distribution in the vertical space, is an important trait. It directly affects the yield potential and appearance. Revealing the genetic basis of SLU will provide new insights into wheat improvement. To map the SLU-related quantitative trait loci (QTL), 300 recombinant inbred lines (RILs) that were derived from a cross between H461 and Chinese Spring were used in this study. The RILs and parents were tested in fields from two continuous years from two different pilots. Phenotypic analysis showed that H461 was more consistent in the vertical spatial distribution of the spike layer than in Chinese Spring. Based on inclusive composite interval mapping, four QTL were identified for SLU. There were two major QTL on chromosomes 2BL and 2DL and two minor QTL on chromosomes 1BS and 2BL that were identified. The additive effects of QSlu.sicau-1B, Qslu.sicau-2B-2, and QSlu.sicau-2D were all from the parent, H461. The major QTL, QSlu.sicau-2B-2 and QSlu.sicau-2D, were detected in each of the conducted trials. Based on the best linear unbiased prediction values, the two loci explained 23.97% and 15.98% of the phenotypic variation, respectively. Compared with previous studies, the two major loci were potentially novel and the two minor loci were overlapped. Based on the kompetitive allele-specific PCR (KASP) marker, the genetic effects for QSlu.sicau-2B-2 were validated in an additional RIL population. The genetic effects ranged from 26.65% to 32.56%, with an average value of 30.40%. In addition, QSlu.sicau-2B-2 showed a significant (p < 0.01) and positive influence on the spike length, spikelet number, and thousand kernel weight. The identified QTL and the developed KASP marker will be helpful for fine-mapping these loci, finally contributing to wheat breeding programs in a marker-assisted selection way. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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Review

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18 pages, 1693 KiB

Open AccessReview

Advances in Biological Control and Resistance Genes of Brassicaceae Clubroot Disease-The Study Case of China

by Chaoying Zhang, Chunyu Du, Yuwei Li, Huiying Wang, Chunyu Zhang and Peng Chen

Int. J. Mol. Sci. 2023, 24(1), 785; https://doi.org/10.3390/ijms24010785 - 2 Jan 2023

Cited by 10 | Viewed by 3308

Abstract

Clubroot disease is a soil-borne disease caused by Plasmodiophora brassicae. It occurs in cruciferous crops exclusively, and causes serious damage to the economic value of cruciferous crops worldwide. Although different measures have been taken to prevent the spread of clubroot disease, the [...] Read more.

Clubroot disease is a soil-borne disease caused by Plasmodiophora brassicae. It occurs in cruciferous crops exclusively, and causes serious damage to the economic value of cruciferous crops worldwide. Although different measures have been taken to prevent the spread of clubroot disease, the most fundamental and effective way is to explore and use disease-resistance genes to breed resistant varieties. However, the resistance level of plant hosts is influenced both by environment and pathogen race. In this work, we described clubroot disease in terms of discovery and current distribution, life cycle, and race identification systems; in particular, we summarized recent progress on clubroot control methods and breeding practices for resistant cultivars. With the knowledge of these identified resistance loci and R genes, we discussed feasible strategies for disease-resistance breeding in the future. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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13 pages, 1319 KiB

Open AccessReview

Applications of Artificial Intelligence in Climate-Resilient Smart-Crop Breeding

by Muhammad Hafeez Ullah Khan, Shoudong Wang, Jun Wang, Sunny Ahmar, Sumbul Saeed, Shahid Ullah Khan, Xiaogang Xu, Hongyang Chen, Javaid Akhter Bhat and Xianzhong Feng

Int. J. Mol. Sci. 2022, 23(19), 11156; https://doi.org/10.3390/ijms231911156 - 22 Sep 2022

Cited by 31 | Viewed by 11072

Abstract

Recently, Artificial intelligence (AI) has emerged as a revolutionary field, providing a great opportunity in shaping modern crop breeding, and is extensively used indoors for plant science. Advances in crop phenomics, enviromics, together with the other “omics” approaches are paving ways for elucidating [...] Read more.

Recently, Artificial intelligence (AI) has emerged as a revolutionary field, providing a great opportunity in shaping modern crop breeding, and is extensively used indoors for plant science. Advances in crop phenomics, enviromics, together with the other “omics” approaches are paving ways for elucidating the detailed complex biological mechanisms that motivate crop functions in response to environmental trepidations. These “omics” approaches have provided plant researchers with precise tools to evaluate the important agronomic traits for larger-sized germplasm at a reduced time interval in the early growth stages. However, the big data and the complex relationships within impede the understanding of the complex mechanisms behind genes driving the agronomic-trait formations. AI brings huge computational power and many new tools and strategies for future breeding. The present review will encompass how applications of AI technology, utilized for current breeding practice, assist to solve the problem in high-throughput phenotyping and gene functional analysis, and how advances in AI technologies bring new opportunities for future breeding, to make envirotyping data widely utilized in breeding. Furthermore, in the current breeding methods, linking genotype to phenotype remains a massive challenge and impedes the optimal application of high-throughput field phenotyping, genomics, and enviromics. In this review, we elaborate on how AI will be the preferred tool to increase the accuracy in high-throughput crop phenotyping, genotyping, and envirotyping data; moreover, we explore the developing approaches and challenges for multiomics big computing data integration. Therefore, the integration of AI with “omics” tools can allow rapid gene identification and eventually accelerate crop-improvement programs. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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15 pages, 1239 KiB

Open AccessReview

The miR393-Target Module Regulates Plant Development and Responses to Biotic and Abiotic Stresses

by Jinjin Jiang, Haotian Zhu, Na Li, Jacqueline Batley and Youping Wang

Int. J. Mol. Sci. 2022, 23(16), 9477; https://doi.org/10.3390/ijms23169477 - 22 Aug 2022

Cited by 20 | Viewed by 2921

Abstract

MicroRNAs (miRNAs), a class of endogenous small RNAs, are broadly involved in plant development, morphogenesis and responses to various environmental stresses, through manipulating the cleavage, translational expression, or DNA methylation of target mRNAs. miR393 is a conserved miRNA family present in many plants, [...] Read more.

MicroRNAs (miRNAs), a class of endogenous small RNAs, are broadly involved in plant development, morphogenesis and responses to various environmental stresses, through manipulating the cleavage, translational expression, or DNA methylation of target mRNAs. miR393 is a conserved miRNA family present in many plants, which mainly targets genes encoding the transport inhibitor response1 (TIR1)/auxin signaling F-box (AFB) auxin receptors, and thus greatly affects the auxin signal perception, Aux/IAA degradation, and related gene expression. This review introduces the advances made on the miR393/target module regulating plant development and the plant’s responses to biotic and abiotic stresses. This module is valuable for genetic manipulation of optimized conditions for crop growth and development and would also be helpful in improving crop yield through molecular breeding. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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16 pages, 1467 KiB

Open AccessReview

MYB Transcription Factors Becoming Mainstream in Plant Roots

by Zhuo Chen, Zexuan Wu, Wenyu Dong, Shiying Liu, Lulu Tian, Jiana Li and Hai Du

Int. J. Mol. Sci. 2022, 23(16), 9262; https://doi.org/10.3390/ijms23169262 - 17 Aug 2022

Cited by 17 | Viewed by 3674

Abstract

The function of the root system is crucial for plant survival, such as anchoring plants, absorbing nutrients and water from the soil, and adapting to stress. MYB transcription factors constitute one of the largest transcription factor families in plant genomes with structural and [...] Read more.

The function of the root system is crucial for plant survival, such as anchoring plants, absorbing nutrients and water from the soil, and adapting to stress. MYB transcription factors constitute one of the largest transcription factor families in plant genomes with structural and functional diversifications. Members of this superfamily in plant development and cell differentiation, specialized metabolism, and biotic and abiotic stress processes are widely recognized, but their roles in plant roots are still not well characterized. Recent advances in functional studies remind us that MYB genes may have potentially key roles in roots. In this review, the current knowledge about the functions of MYB genes in roots was summarized, including promoting cell differentiation, regulating cell division through cell cycle, response to biotic and abiotic stresses (e.g., drought, salt stress, nutrient stress, light, gravity, and fungi), and mediate phytohormone signals. MYB genes from the same subfamily tend to regulate similar biological processes in roots in redundant but precise ways. Given their increasing known functions and wide expression profiles in roots, MYB genes are proposed as key components of the gene regulatory networks associated with distinct biological processes in roots. Further functional studies of MYB genes will provide an important basis for root regulatory mechanisms, enabling a more inclusive green revolution and sustainable agriculture to face the constant changes in climate and environmental conditions. Full article

(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)

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