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27 pages, 12288 KiB

Open AccessArticle

Transcriptomic Approach for Investigation of Solanum spp. Resistance upon Early-Stage Broomrape Parasitism

by Maria Gerakari, Vasiliki Kotsira, Aliki Kapazoglou, Spyros Tastsoglou, Anastasios Katsileros, Demosthenis Chachalis, Artemis G. Hatzigeorgiou and Eleni Tani

Curr. Issues Mol. Biol. 2024, 46(8), 9047-9073; https://doi.org/10.3390/cimb46080535 - 18 Aug 2024

Viewed by 882

Abstract

Tomato (Solanum lycopersicum) is a major horticultural crop of high economic importance. Phelipanche and Orobanche genera (broomrapes) are parasitic weeds, constituting biotic stressors that impact tomato production. Developing varieties with tolerance to broomrapes has become imperative for sustainable agriculture. Solanum pennellii [...] Read more.

Tomato (Solanum lycopersicum) is a major horticultural crop of high economic importance. Phelipanche and Orobanche genera (broomrapes) are parasitic weeds, constituting biotic stressors that impact tomato production. Developing varieties with tolerance to broomrapes has become imperative for sustainable agriculture. Solanum pennellii, a wild relative of cultivated tomato, has been utilized as breeding material for S. lycopersicum. In the present study, it is the first time that an in-depth analysis has been conducted for these two specific introgression lines (ILs), IL6-2 and IL6-3 (S. lycopersicum X S. pennellii), which were employed to identify genes and metabolic pathways associated with resistance against broomrape. Comparative transcriptomic analysis revealed a multitude of differentially expressed genes (DEGs) in roots, especially in the resistant genotype IL6-3, several of which were validated by quantitative PCR. DEG and pathway enrichment analysis (PEA) revealed diverse molecular mechanisms that can potentially be implicated in the host’s defense response and the establishment of resistance. The identified DEGs were mostly up-regulated in response to broomrape parasitism and play crucial roles in various processes different from strigolactone regulation. Our findings indicate that, in addition to the essential role of strigolactone metabolism, multiple cellular processes may be involved in the tomato’s response to broomrapes. The insights gained from this study will enhance our understanding and facilitate molecular breeding methods regarding broomrape parasitism. Moreover, they will assist in developing sustainable strategies and providing alternative solutions for weed management in tomatoes and other agronomically important crops. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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16 pages, 3536 KiB

Open AccessArticle

miRNA Sequencing Analysis in Maize Roots Treated with Neutral and Alkaline Salts

by Ziqi Chen, Yang Liu, Qi Wang, Jianbo Fei, Xiangguo Liu, Chuang Zhang and Yuejia Yin

Curr. Issues Mol. Biol. 2024, 46(8), 8874-8889; https://doi.org/10.3390/cimb46080524 - 15 Aug 2024

Viewed by 687

Abstract

Soil salinization/alkalization is a complex environmental factor that includes not only neutral salt NaCl but also other components like Na₂CO₃. miRNAs, as small molecules that regulate gene expression post-transcriptionally, are involved in plant responses to abiotic stress. In this [...] Read more.

Soil salinization/alkalization is a complex environmental factor that includes not only neutral salt NaCl but also other components like Na₂CO₃. miRNAs, as small molecules that regulate gene expression post-transcriptionally, are involved in plant responses to abiotic stress. In this study, maize seedling roots were treated for 5 h with 100 mM NaCl, 50 mM Na₂CO₃, and H₂O, respectively. Sequencing analysis of differentially expressed miRNAs under these conditions revealed that the Na₂CO₃ treatment group had the most differentially expressed miRNAs. Cluster analysis indicated their main involvement in the regulation of ion transport, binding, metabolism, and phenylpropanoid and flavonoid biosynthesis pathways. The unique differentially expressed miRNAs in the NaCl treatment group were related to the sulfur metabolism pathway. This indicates a significant difference in the response patterns of maize to different treatment groups. This study provides theoretical evidence and genetic resources for further analysis of the molecular mechanisms behind maize’s salt–alkali tolerance. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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20 pages, 4178 KiB

Open AccessArticle

Transcriptome Analysis Reveals That FvPAP1 Genes Are Related to the Prolongation of Red-Leaf Period in Ficus virens

by Qingchao Ma, Shuhua Zhong, Tianci Ma, Yajie Yue, Shihui Zou, Shunzhao Sui, Lijiao Ai and Yulong Guo

Curr. Issues Mol. Biol. 2024, 46(6), 5724-5743; https://doi.org/10.3390/cimb46060343 - 8 Jun 2024

Cited by 1 | Viewed by 1140

Abstract

Ficus virens is a deciduous tree that is highly valuable both economically and medicinally. Like other plants with ‘red young leaves’, the red-leaf period of most F. virens trees lasts only a few days, and the red leaves have little ornamental value. However, [...] Read more.

Ficus virens is a deciduous tree that is highly valuable both economically and medicinally. Like other plants with ‘red young leaves’, the red-leaf period of most F. virens trees lasts only a few days, and the red leaves have little ornamental value. However, in recent years, some lines of F. virens with bright red young leaves and a prolonged red-leaf period have been utilized for urban greening. To explore the mechanism of the different lengths of the duration of F. virens leaves, we analyzed the physiology and changes in gene expression during the development of two varieties of leaves. The detection of anthocyanin in different developmental stages of the F. virens leaves showed that the changes in color of the red leaves of F. virens were primarily caused by the change in anthocyanin content. A transcriptome analysis showed that the expression of genes related to the biosynthesis of anthocyanin changed significantly during the development of leaves. A MYB gene FvPAP1, which was consistent with the change in anthocyanin content, was identified. A real-time quantitative reverse transcription PCR analysis and heterologous expression transgenic studies showed that FvPAP1 promoted the biosynthesis of anthocyanins. The difference in the expression of FvPAP1 in time and intensity in the young leaves may be the reason for the difference in the duration of the red-leaf period in different lines of F. virens. A sequence analysis showed that the cDNA sequence of FvPAP1 was polymorphic, and possible reasons were discussed. These results can provide insight for similar studies on the mechanism of the formation of red coloring in other woody plant leaves and provide molecular targets to breed new materials with more prolonged red-leaf periods in F. virens. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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15 pages, 7282 KiB

Open AccessArticle

Functional Validation of Different Alternative Splicing Variants of the Chrysanthemum lavandulifolium ClNUM1 Gene in Tobacco

by Wenxin Zhang, Hai Wang, Yuning Guo, Xueying Hao, Yanxi Li, Wenting He, Xiang Zhao, Shiyi Cai and Xuebin Song

Curr. Issues Mol. Biol. 2024, 46(6), 5242-5256; https://doi.org/10.3390/cimb46060314 - 25 May 2024

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Abstract

The Asteraceae are widely distributed throughout the world, with diverse functions and large genomes. Many of these genes remain undiscovered and unstudied. In this study, we discovered a new gene ClNUM1 in Chrysanthemum lavandulifolium and studied its function. In this study, bioinformatics, RT-qPCR, [...] Read more.

The Asteraceae are widely distributed throughout the world, with diverse functions and large genomes. Many of these genes remain undiscovered and unstudied. In this study, we discovered a new gene ClNUM1 in Chrysanthemum lavandulifolium and studied its function. In this study, bioinformatics, RT-qPCR, paraffin sectioning, and tobacco transgenics were utilized to bioinformatically analyze and functionally study the three variable splice variants of the unknown gene ClNUM1 cloned from C. lavandulifolium. The results showed that ClNUM1.1 and ClNUM1.2 had selective 3′ splicing and selective 5′ splicing, and ClNUM1.3 had selective 5′ splicing. When the corresponding transgenic tobacco plants were subjected to abiotic stress treatment, in the tobacco seedlings, the ClNUM1.1 gene and the ClNUM1.2 gene enhanced salt and low-temperature tolerance and the ClNUM1.3 gene enhanced low-temperature tolerance; in mature tobacco plants, the ClNUM1.1 gene was able to enhance salt and low-temperature tolerance, and the ClNUM1.2 and ClNUM1.3 genes were able to enhance low-temperature tolerance. In summary, there are differences in the functions of the different splice variants and the different seedling stages of transgenic tobacco, but all of them enhanced the resistance of tobacco to a certain extent. The analysis and functional characterization of the ClNUM1 gene provided new potential genes and research directions for abiotic resistance breeding in Chrysanthemum. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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11 pages, 3084 KiB

Open AccessArticle

Enhancing Yield and Improving Grain Quality in Japonica Rice: Targeted EHD1 Editing via CRISPR-Cas9 in Low-Latitude Adaptation

by Jian Song, Liqun Tang, Honghuan Fan, Xiaozheng Xu, Xinlu Peng, Yongtao Cui and Jianjun Wang

Curr. Issues Mol. Biol. 2024, 46(4), 3741-3751; https://doi.org/10.3390/cimb46040233 - 22 Apr 2024

Cited by 2 | Viewed by 1534

Abstract

The “Indica to Japonica” initiative in China focuses on adapting Japonica rice varieties from the northeast to the unique photoperiod and temperature conditions of lower latitudes. While breeders can select varieties for their adaptability, the sensitivity to light and temperature often [...] Read more.

The “Indica to Japonica” initiative in China focuses on adapting Japonica rice varieties from the northeast to the unique photoperiod and temperature conditions of lower latitudes. While breeders can select varieties for their adaptability, the sensitivity to light and temperature often complicates and prolongs the process. Addressing the challenge of cultivating high-yield, superior-quality Japonica rice over expanded latitudinal ranges swiftly, in the face of these sensitivities, is critical. Our approach harnesses the CRISPR-Cas9 technology to edit the EHD1 gene in the premium northeastern Japonica cultivars Jiyuanxiang 1 and Yinongxiang 12, which are distinguished by their exceptional grain quality—increased head rice rates, gel consistency, and reduced chalkiness and amylose content. Field trials showed that these new ehd1 mutants not only surpass the wild types in yield when grown at low latitudes but also retain the desirable traits of their progenitors. Additionally, we found that disabling Ehd1 boosts the activity of Hd3a and RFT1, postponing flowering by approximately one month in the ehd1 mutants. This research presents a viable strategy for the accelerated breeding of elite northeastern Japonica rice by integrating genomic insights with gene-editing techniques suitable for low-latitude cultivation. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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18 pages, 5375 KiB

Open AccessArticle

Biochemical and Molecular Basis of Chemically Induced Defense Activation in Maize against Banded Leaf and Sheath Blight Disease

by Shah Mahmood Hamidi, Shweta Meshram, Aundy Kumar, Archana Singh, Rajbir Yadav and Robin Gogoi

Curr. Issues Mol. Biol. 2024, 46(4), 3063-3080; https://doi.org/10.3390/cimb46040192 - 2 Apr 2024

Viewed by 1937

Abstract

Maize is the third most vital global cereal, playing a key role in the world economy and plant genetics research. Despite its leadership in production, maize faces a severe threat from banded leaf and sheath blight, necessitating the urgent development of eco-friendly management [...] Read more.

Maize is the third most vital global cereal, playing a key role in the world economy and plant genetics research. Despite its leadership in production, maize faces a severe threat from banded leaf and sheath blight, necessitating the urgent development of eco-friendly management strategies. This study aimed to understand the resistance mechanisms against banded leaf and sheath blight (BLSB) in maize hybrid “Vivek QPM-9”. Seven fungicides at recommended doses (1000 and 500 ppm) and two plant defense inducers, salicylic acid (SA) and jasmonic acid (JA) at concentrations of 50 and 100 ppm, were applied. Fungicides, notably Azoxystrobin and Trifloxystrobin + Tebuconazole, demonstrated superior efficacy against BLSB, while Pencycuron showed limited effectiveness. Field-sprayed Azoxystrobin exhibited the lowest BLSB infection, correlating with heightened antioxidant enzyme activity (SOD, CAT, POX, β-1,3-glucanase, PPO, PAL), similar to the Validamycin-treated plants. The expression of defense-related genes after seed priming with SA and JA was assessed via qRT-PCR. Lower SA concentrations down-regulated SOD, PPO, and APX genes but up-regulated CAT and β-1,3-glucanase genes. JA at lower doses up-regulated CAT and APX genes, while higher doses up-regulated PPO and β-1,3-glucanase genes; SOD gene expression was suppressed at both JA doses. This investigation elucidates the effectiveness of certain fungicides and plant defense inducers in mitigating BLSB in maize hybrids and sheds light on the intricate gene expression mechanisms governing defense responses against this pathogen. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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15 pages, 3382 KiB

Open AccessArticle

Rapid Visual Detection of Elite Erect Panicle Dense and Erect Panicle 1 Allele for Marker-Assisted Improvement in Rice (Oryza sativa L.) Using the Loop-Mediated Isothermal Amplification Method

by Yonghang Tian, Xiyi Chen, Peizhou Xu, Yuping Wang, Xianjun Wu, Kun Wu, Xiangdong Fu, Yaoxian Chin and Yongxiang Liao

Curr. Issues Mol. Biol. 2024, 46(1), 498-512; https://doi.org/10.3390/cimb46010032 - 4 Jan 2024

Viewed by 1367

Abstract

Molecular-assisted breeding is an effective way to improve targeted agronomic traits. dep1 (dense and erect panicle 1) is a pleiotropic gene that regulates yield, quality, disease resistance, and stress tolerance, traits that are of great value in rice (Oryza sativa [...] Read more.

Molecular-assisted breeding is an effective way to improve targeted agronomic traits. dep1 (dense and erect panicle 1) is a pleiotropic gene that regulates yield, quality, disease resistance, and stress tolerance, traits that are of great value in rice (Oryza sativa L.) breeding. In this study, a colorimetric LAMP (loop-mediated isothermal amplification) assay was developed for the detection of the dep1 allele and tested for the screening and selection of the heavy-panicle hybrid rice elite restorer line SHUHUI498, modified with the allele. InDel (Insertion and Deletion) primers (DEP1_F and DEP1_R) and LAMP primers (F3, B3, FIP, and BIP) for genotyping were designed using the Primer3 Plus (version 3.3.0) and PrimerExplore (version 5) software. Our results showed that both InDel and LAMP markers could be used for accurate genotyping. After incubation at a constant temperature of 65 °C for 60 min with hydroxynaphthol blue (HNB) as a color indicator, the color of the LAMP assay containing the dep1 allele changed to sky blue. The SHUHUI498 rice line that was detected in our LAMP assay displayed phenotypes consistent with the dep1 allele such as having a more compact plant architecture, straight stems and leaves, and a significant increase in the number of effective panicles and spikelets, demonstrating the effectiveness of our method in screening for the dep1 allele in rice breeding. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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20 pages, 5100 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analyses of the FAR1/FHY3 Gene Family Provide Insight into Inflorescence Development in Maize

by Huaijun Tang, De Jing, Cheng Liu, Xiaoqing Xie, Lei Zhang, Xunji Chen and Changyu Li

Curr. Issues Mol. Biol. 2024, 46(1), 430-449; https://doi.org/10.3390/cimb46010027 - 2 Jan 2024

Cited by 2 | Viewed by 1888

Abstract

As transcription factors derived from transposase, FAR-RED IMPAIRED RESPONSE1 (FAR1) and its homolog FHY3 play crucial roles in the regulation of light signaling and various stress responses by coordinating the expression of downstream target genes. Despite the extensive investigation of the [...] Read more.

As transcription factors derived from transposase, FAR-RED IMPAIRED RESPONSE1 (FAR1) and its homolog FHY3 play crucial roles in the regulation of light signaling and various stress responses by coordinating the expression of downstream target genes. Despite the extensive investigation of the FAR1/FHY3 family in Arabidopsis thaliana and other species, a comprehensive examination of these genes in maize has not been conducted thus far. In this study, we employed a genomic mining approach to identify 16 ZmFAR1 genes in the maize inbred line B73, which were further classified into five subgroups based on their phylogenetic relationships. The present study characterized the predicted polypeptide sequences, molecular weights, isoelectric points, chromosomal distribution, gene structure, conserved motifs, subcellular localizations, phylogenetic relationships, and cis-regulatory elements of all members belonging to the ZmFAR1 family. Furthermore, the tissue-specific expression of the 16 ZmFAR1 genes was analyzed using RNA-seq, and their expression patterns under far-red light conditions were validated in the ear and tassel through qRT-qPCR. The observed highly temporal and spatial expression patterns of these ZmFAR1 genes were likely associated with their specific functional capabilities under different light conditions. Further analysis revealed that six ZmFAR1 genes (ZmFAR1-1, ZmFAR1-10, ZmFAR1-11, ZmFAR1-12, ZmFAR1-14, and ZmFAR1-15) exhibited a response to simulated shading treatment and actively contributed to the development of maize ears. Through the integration of expression quantitative trait loci (eQTL) analyses and population genetics, we identified the presence of potential causal variations in ZmFAR1-14 and ZmFAR1-9, which play a crucial role in regulating the kernel row number and kernel volume weight, respectively. In summary, this study represents the initial identification and characterization of ZmFAR1 family members in maize, uncovering the functional variation in candidate regulatory genes associated with the improvement of significant agronomic traits during modern maize breeding. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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17 pages, 8946 KiB

Open AccessArticle

Overexpression of KvCHX Enhances Salt Tolerance in Arabidopsis thaliana Seedlings

by Yuqi Guo, Chengrong Zhu and Zengyuan Tian

Curr. Issues Mol. Biol. 2023, 45(12), 9692-9708; https://doi.org/10.3390/cimb45120605 - 1 Dec 2023

Cited by 1 | Viewed by 1453

Abstract

The CHX (cation/H⁺ exchanger) family plays an important role in the transmembrane transport of cation/H⁺ in plants. The aim of this study was to identify and functionally analyze the KvCHX gene in the halophyte Kosteletzkya virginica to investigate its role in [...] Read more.

The CHX (cation/H⁺ exchanger) family plays an important role in the transmembrane transport of cation/H⁺ in plants. The aim of this study was to identify and functionally analyze the KvCHX gene in the halophyte Kosteletzkya virginica to investigate its role in regulating the K⁺/Na⁺ ratio under salinity tolerance. Based on a partial gene sequence of EST from K. virginica, the full-length DNA sequence of the KvCHX gene was obtained using genome walking technology. Structural analysis and phylogenetic relationship analysis showed that the KvCHX gene was closely related to the AtCHX17 gene. The KvCHX overexpression vector was successfully constructed and transformed into Arabidopsis via floral dipping. Arabidopsis seedlings overexpressing KvCHX showed an enhanced tolerance to salt stress compared with wild-type plants. Transgenic Arabidopsis seedlings grew better under K⁺ deficiency than WT. The results showed that KvCHX could promote the uptake of K⁺, increase the ratio of K⁺/Na⁺, and promote the growth of plants under K⁺ deficiency and treatment with NaCl solution. KvCHX is involved in K⁺ transport and improves plant salt tolerance by coordinating K⁺ acquisition and homeostasis. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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22 pages, 3231 KiB

Open AccessArticle

Identification of Multiple Genetic Loci Related to Low-Temperature Tolerance during Germination in Maize (Zea maize L.) through a Genome-Wide Association Study

by Tao Yu, Jianguo Zhang, Jingsheng Cao, Shujun Li, Quan Cai, Xin Li, Sinan Li, Yunlong Li, Changan He and Xuena Ma

Curr. Issues Mol. Biol. 2023, 45(12), 9634-9655; https://doi.org/10.3390/cimb45120602 - 29 Nov 2023

Cited by 1 | Viewed by 1072

Abstract

Low-temperature stress during the germination stage is an important abiotic stress that affects the growth and development of northern spring maize and seriously restricts maize yield and quality. Although some quantitative trait locis (QTLs) related to low-temperature tolerance in maize have been detected, [...] Read more.

Low-temperature stress during the germination stage is an important abiotic stress that affects the growth and development of northern spring maize and seriously restricts maize yield and quality. Although some quantitative trait locis (QTLs) related to low-temperature tolerance in maize have been detected, only a few can be commonly detected, and the QTL intervals are large, indicating that low-temperature tolerance is a complex trait that requires more in-depth research. In this study, 296 excellent inbred lines from domestic and foreign origins (America and Europe) were used as the study materials, and a low-coverage resequencing method was employed for genome sequencing. Five phenotypic traits related to low-temperature tolerance were used to assess the genetic diversity of maize through a genome-wide association study (GWAS). A total of 14 SNPs significantly associated with low-temperature tolerance were detected (−log10(P) > 4), and an SNP consistently linked to low-temperature tolerance in the field and indoors during germination was utilized as a marker. This SNP, 14,070, was located on chromosome 5 at position 2,205,723, which explained 4.84–9.68% of the phenotypic variation. The aim of this study was to enrich the genetic theory of low-temperature tolerance in maize and provide support for the innovation of low-temperature tolerance resources and the breeding of new varieties. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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13 pages, 2151 KiB

Open AccessArticle

Optimization of Plant Growth Regulators for In Vitro Mass Propagation of a Disease-Free ‘Shine Muscat’ Grapevine Cultivar

by Si-Hong Kim, Mewuleddeg Zebro, Dong-Cheol Jang, Jeong-Eun Sim, Han-Kyeol Park, Kyeong-Yeon Kim, Hyung-Min Bae, Shimeles Tilahun and Sung-Min Park

Curr. Issues Mol. Biol. 2023, 45(10), 7721-7733; https://doi.org/10.3390/cimb45100487 - 22 Sep 2023

Cited by 6 | Viewed by 2613

Abstract

This study addresses the propagation challenges faced by ‘Shine Muscat’, a newly introduced premium grapevine cultivar in South Korea, where multiple viral infections pose considerable economic loss. The primary objective was to establish a robust in vitro propagation method for producing disease-free grapes [...] Read more.

This study addresses the propagation challenges faced by ‘Shine Muscat’, a newly introduced premium grapevine cultivar in South Korea, where multiple viral infections pose considerable economic loss. The primary objective was to establish a robust in vitro propagation method for producing disease-free grapes and to identify effective plant growth regulators to facilitate large-scale mass cultivation. After experimentation, 2.0 µM 6-benzyladenine (BA) exhibited superior shoot formation in the Murashige and Skoog medium compared with kinetin and thidiazuron. Conversely, α-naphthaleneacetic acid (NAA) hindered shoot growth and induced callus formation, while indole-3-butyric acid (IBA) and indole-3-acetic acid (IAA) demonstrated favorable root formation, with IBA showing better results overall. Furthermore, inter simple sequence repeat analysis confirmed the genetic stability of in vitro-cultivated seedlings using 2.0 μM BA and 1.0 μM IBA, validating the suitability of the developed propagation method for generating disease-free ‘Shine Muscat’ grapes. These findings offer promising prospects for commercial grape cultivation, ensuring a consistent supply of healthy grapes in the market. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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20 pages, 5340 KiB

Open AccessArticle

QTL Mapping and Genome-Wide Association Study Reveal Genetic Loci and Candidate Genes Related to Soluble Solids Content in Melon

by Honglang Yan, Kang Wang, Manman Wang, Lulu Feng, Huimin Zhang and Xiaoyun Wei

Curr. Issues Mol. Biol. 2023, 45(9), 7110-7129; https://doi.org/10.3390/cimb45090450 - 26 Aug 2023

Cited by 2 | Viewed by 1873

Abstract

Melon (Cucumis melo L.) is an economically important Cucurbitaceae crop grown around the globe. The sweetness of melon is a significant factor in fruit quality and consumer appeal, and the soluble solids content (SSC) is a key index of melon sweetness. In [...] Read more.

Melon (Cucumis melo L.) is an economically important Cucurbitaceae crop grown around the globe. The sweetness of melon is a significant factor in fruit quality and consumer appeal, and the soluble solids content (SSC) is a key index of melon sweetness. In this study, 146 recombinant inbred lines (RILs) derived from two oriental melon materials with different levels of sweetness containing 1427 bin markers, and 213 melon accessions containing 1,681,775 single nucleotide polymorphism (SNP) markers were used to identify genomic regions influencing SSC. Linkage mapping detected 10 quantitative trait loci (QTLs) distributed on six chromosomes, seven of which were overlapped with the reported QTLs. A total of 211 significant SNPs were identified by genome-wide association study (GWAS), 138 of which overlapped with the reported QTLs. Two new stable, co-localized regions on chromosome 3 were identified by QTL mapping and GWAS across multiple environments, which explained large phenotypic variance. Five candidate genes related to SSC were identified by QTL mapping, GWAS, and qRT-PCR, two of which were involved in hydrolysis of raffinose and sucrose located in the new stable loci. The other three candidate genes were involved in raffinose synthesis, sugar transport, and production of substrate for sugar synthesis. The genomic regions and candidate genes will be helpful for molecular breeding programs and elucidating the mechanisms of sugar accumulation. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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15 pages, 2488 KiB

Open AccessArticle

Exploring Genetic and Epigenetic Changes in Lingonberry Using Molecular Markers: Implications for Clonal Propagation

by Umanath Sharma, Arindam Sikdar, Abir U. Igamberdiev and Samir C. Debnath

Curr. Issues Mol. Biol. 2023, 45(8), 6296-6310; https://doi.org/10.3390/cimb45080397 - 28 Jul 2023

Viewed by 2134

Abstract

Lingonberry (Vaccinium vitis-idaea L.) is an important and valuable horticultural crop due to its high antioxidant properties. Plant tissue culture is an advanced propagation system employed in horticultural crops. However, the progeny derived using this technique may not be true-to-type. In order [...] Read more.

Lingonberry (Vaccinium vitis-idaea L.) is an important and valuable horticultural crop due to its high antioxidant properties. Plant tissue culture is an advanced propagation system employed in horticultural crops. However, the progeny derived using this technique may not be true-to-type. In order to obtain the maximum return of any agricultural enterprise, uniformity of planting materials is necessary, which sometimes is not achieved due to genetic and epigenetic instabilities under in vitro culture. Therefore, we analyzed morphological traits and genetic and epigenetic variations under tissue-culture and greenhouse conditions in lingonberry using molecular markers. Leaf length and leaf width under greenhouse conditions and shoot number per explant, shoot height and shoot vigor under in vitro conditions were higher in hybrid H1 compared to the cultivar Erntedank. Clonal fidelity study using one expressed sequence tag (EST)—polymerase chain reaction (PCR), five EST—simple sequence repeat (SSR) and six genomic (G)—SSR markers revealed monomorphic bands in micropropagated shoots and plants in lingonberry hybrid H1 and cultivar Erntedank conforming genetic integrity. Epigenetic variation was studied by quantifying cytosine methylation using a methylation-sensitive amplification polymorphism (MSAP) technique. DNA methylation ranged from 32% in greenhouse-grown hybrid H1 to 44% in cultivar Erntedank under a tissue culture system. Although total methylation was higher in in vitro grown shoots, fully methylated bands were observed more in the greenhouse-grown plants. On the contrary, hemimethylated DNA bands were more prominent in tissue culture conditions as compared to the greenhouse-grown plants. The study conclude that lingonberry maintains its genetic integrity but undergoes variable epigenetic changes during in vitro and ex vitro conditions. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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22 pages, 2600 KiB

Open AccessArticle

Genome-Wide SNP and Indel Discovery in Abaca (Musa textilis Née) and among Other Musa spp. for Abaca Genetic Resources Management

by Cris Francis C. Barbosa, Jayson C. Asunto, Rhosener Bhea L. Koh, Daisy May C. Santos, Dapeng Zhang, Ernelea P. Cao and Leny C. Galvez

Curr. Issues Mol. Biol. 2023, 45(7), 5776-5797; https://doi.org/10.3390/cimb45070365 - 12 Jul 2023

Cited by 2 | Viewed by 2916

Abstract

Abaca (Musa textilis Née) is an economically important fiber crop in the Philippines. Its economic potential, however, is hampered by biotic and abiotic stresses, which are exacerbated by insufficient genomic resources for varietal identification vital for crop improvement. To address these gaps, [...] Read more.

Abaca (Musa textilis Née) is an economically important fiber crop in the Philippines. Its economic potential, however, is hampered by biotic and abiotic stresses, which are exacerbated by insufficient genomic resources for varietal identification vital for crop improvement. To address these gaps, this study aimed to discover genome-wide polymorphisms among abaca cultivars and other Musa species and analyze their potential as genetic marker resources. This was achieved through whole-genome Illumina resequencing of abaca cultivars and variant calling using BCFtools, followed by genetic diversity and phylogenetic analyses. A total of 20,590,381 high-quality single-nucleotide polymorphisms (SNP) and DNA insertions/deletions (InDels) were mined across 16 abaca cultivars. Filtering based on linkage disequilibrium (LD) yielded 130,768 SNPs and 13,620 InDels, accounting for 0.396 ± 0.106 and 0.431 ± 0.111 of gene diversity across these cultivars. LD-pruned polymorphisms across abaca, M. troglodytarum, M. acuminata and M. balbisiana enabled genetic differentiation within abaca and across the four Musa spp. Phylogenetic analysis revealed the registered varieties Abuab and Inosa to accumulate a significant number of mutations, eliciting further studies linking mutations to their advantageous phenotypes. Overall, this study pioneered in producing marker resources in abaca based on genome-wide polymorphisms vital for varietal authentication and comparative genotyping with the more studied Musa spp. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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18 pages, 1662 KiB

Open AccessArticle

Genetic Dissection of Salt Tolerance and Yield Traits of Geng (japonica) Rice by Selective Subspecific Introgression

by Simin Li, Ting Feng, Chenyang Zhang, Fanlin Zhang, Hua Li, Yanjun Chen, Lunping Liang, Chaopu Zhang, Wei Zeng, Erbao Liu, Yingyao Shi, Min Li and Lijun Meng

Curr. Issues Mol. Biol. 2023, 45(6), 4796-4813; https://doi.org/10.3390/cimb45060305 - 31 May 2023

Cited by 1 | Viewed by 1699

Abstract

Salinity is a major factor limiting rice productivity, and developing salt-tolerant (ST) varieties is the most efficient approach. Seventy-eight ST introgression lines (ILs), including nine promising lines with improved ST and yield potential (YP), were developed from four BC₂F₄ populations [...] Read more.

Salinity is a major factor limiting rice productivity, and developing salt-tolerant (ST) varieties is the most efficient approach. Seventy-eight ST introgression lines (ILs), including nine promising lines with improved ST and yield potential (YP), were developed from four BC₂F₄ populations from inter-subspecific crosses between an elite Geng (japonica) recipient and four Xian (indica) donors at the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences. Genome-wide characterization of donor introgression identified 35 ST QTLs, 25 of which harbor 38 cloned ST genes as the most likely QTL candidates. Thirty-four are Xian-Geng differentiated ones with the donor (Xian) alleles associated with ST, suggesting differentiated responses to salt stress were one of the major phenotypic differences between the two subspecies. At least eight ST QTLs and many others affecting yield traits were identified under salt/non-stress conditions. Our results indicated that the Xian gene pool contains rich ‘hidden’ genetic variation for developing superior Geng varieties with improved ST and YP, which could be efficiently exploited by selective introgression. The developed ST ILs and their genetic information on the donor alleles for ST and yield traits would provide a useful platform for developing superior ST and high-yield Geng varieties through breeding by design in the future. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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18 pages, 9454 KiB

Open AccessArticle

Transcriptome Analysis and VIGS Identification of Key Genes Regulating Citric Acid Metabolism in Citrus

by Tianxin Chen, Juan Niu, Zhimin Sun, Jing Chen, Yue Wang, Jianhua Chen and Mingbao Luan

Curr. Issues Mol. Biol. 2023, 45(6), 4647-4664; https://doi.org/10.3390/cimb45060295 - 28 May 2023

Cited by 4 | Viewed by 2107

Abstract

Citrus (Citrus reticulata) is one of the world’s most widely planted and highest-yielding fruit trees. Citrus fruits are rich in a variety of nutrients. The content of citric acid plays a decisive role in the flavor quality of the fruit. There [...] Read more.

Citrus (Citrus reticulata) is one of the world’s most widely planted and highest-yielding fruit trees. Citrus fruits are rich in a variety of nutrients. The content of citric acid plays a decisive role in the flavor quality of the fruit. There is a high organic acid content in early-maturing and extra-precocious citrus varieties. Reducing the amount of organic acid after fruit ripening is significant to the citrus industry. In this study, we selected a low-acid variety, “DF4”, and a high-acid variety, “WZ”, as research materials. Through WGCNA analysis, two differentially expressed genes, citrate synthase (CS) and ATP citrate-pro-S-lyase (ACL), were screened out, which related to the changing citric acid. The two differentially expressed genes were preliminarily verified by constructing a virus-induced gene-silencing (VIGS) vector. The VIGS results showed that the citric acid content was negatively correlated with CS expression and positively correlated with ACL expression, while CS and ACL oppositely control citric acid and inversely regulate each other. These results provide a theoretical basis for promoting the breeding of early-maturing and low-acid citrus varieties. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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Review

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22 pages, 1852 KiB

Open AccessReview

Exploring Plant Meiosis: Insights from the Kinetochore Perspective

by Kang-Di Zhou, Cai-Xia Zhang, Fu-Rong Niu, Hao-Chen Bai, Dan-Dan Wu, Jia-Cheng Deng, Hong-Yuan Qian, Yun-Lei Jiang and Wei Ma

Curr. Issues Mol. Biol. 2023, 45(10), 7974-7995; https://doi.org/10.3390/cimb45100504 - 28 Sep 2023

Cited by 1 | Viewed by 4859

Abstract

The central player for chromosome segregation in both mitosis and meiosis is the macromolecular kinetochore structure, which is assembled by >100 structural and regulatory proteins on centromere DNA. Kinetochores play a crucial role in cell division by connecting chromosomal DNA and microtubule polymers. [...] Read more.

The central player for chromosome segregation in both mitosis and meiosis is the macromolecular kinetochore structure, which is assembled by >100 structural and regulatory proteins on centromere DNA. Kinetochores play a crucial role in cell division by connecting chromosomal DNA and microtubule polymers. This connection helps in the proper segregation and alignment of chromosomes. Additionally, kinetochores can act as a signaling hub, regulating the start of anaphase through the spindle assembly checkpoint, and controlling the movement of chromosomes during anaphase. However, the role of various kinetochore proteins in plant meiosis has only been recently elucidated, and these proteins differ in their functionality from those found in animals. In this review, our current knowledge of the functioning of plant kinetochore proteins in meiosis will be summarized. In addition, the functional similarities and differences of core kinetochore proteins in meiosis between plants and other species are discussed, and the potential applications of manipulating certain kinetochore genes in meiosis for breeding purposes are explored. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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15 pages, 1697 KiB

Open AccessReview

Research Progress on Anthocyanin-Mediated Regulation of ‘Black’ Phenotypes of Plant Organs

by Fei Wang, Jinliao Chen, Ruonan Tang, Ruixin Wang, Sagheer Ahmad, Zhongjian Liu and Donghui Peng

Curr. Issues Mol. Biol. 2023, 45(9), 7242-7256; https://doi.org/10.3390/cimb45090458 - 1 Sep 2023

Cited by 3 | Viewed by 2505

Abstract

The color pattern is one of the most important characteristics of plants. Black stands out among the vibrant colors due to its rare and distinctive nature. While some plant organs appear black, they are, in fact, dark purple. Anthocyanins are the key compounds [...] Read more.

The color pattern is one of the most important characteristics of plants. Black stands out among the vibrant colors due to its rare and distinctive nature. While some plant organs appear black, they are, in fact, dark purple. Anthocyanins are the key compounds responsible for the diverse hues in plant organs. Cyanidin plays an important role in the deposition of black pigments in various plant organs, such as flower, leaf, and fruit. A number of structural genes and transcription factors are involved in the metabolism of anthocyanins in black organs. It has been shown that the high expression of R2R3-MYB transcription factors, such as PeMYB7, PeMYB11, and CsMYB90, regulates black pigmentation in plants. This review provides a comprehensive overview of the anthocyanin pathways that are involved in the regulation of black pigments in plant organs, including flower, leaf, and fruit. It is a great starting point for further investigation into the molecular regulation mechanism of plant color and the development of novel cultivars with black plant organs. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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Other

Jump to: Research, Review

11 pages, 2286 KiB

Open AccessBrief Report

Yeast One-Hybrid Screening to Identify Transcription Factors for IbMYB1-4 in the Purple-Fleshed Sweet Potato (Ipomoea batatas [L.] Lam.)

by Danwen Fu, Shaohua Yang, Rui Liu and Feng Gao

Curr. Issues Mol. Biol. 2023, 45(7), 5765-5775; https://doi.org/10.3390/cimb45070364 - 12 Jul 2023

Cited by 1 | Viewed by 1932

Abstract

IbMYB1 is a transcription factor involved in the biosynthesis of anthocyanin in the purple-fleshed sweet potato. So far, few studies have investigated transcription factors that are upstream of the promoter IbMYB1-4. In this study, a yeast one-hybrid screening aimed at identifying transcription [...] Read more.

IbMYB1 is a transcription factor involved in the biosynthesis of anthocyanin in the purple-fleshed sweet potato. So far, few studies have investigated transcription factors that are upstream of the promoter IbMYB1-4. In this study, a yeast one-hybrid screening aimed at identifying transcription factors upstream of the promoter IbMYB1-4 was performed in the storage roots of the purple-fleshed sweet potato, and IbPDC, IbERF1, and IbPGP19 were identified as upstream binding proteins for the promoter IbMYB1-4. A dual luciferase reporter assay, and yeast one-hybrid assays, were employed to confirm the interaction of these binding proteins with promoters. IbERF1 was found to be an upstream transcription factor for the promoter IbMYB1, and is implicated in the biosynthesis of anthocyanin in the purple-fleshed sweet potato. IbERF1 plays a major role in the biosynthesis of anthocyanin in the purple-fleshed sweet potato. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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