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15 pages, 1696 KiB

Open AccessArticle

Mapping and Functional Analysis of QTL for Kernel Number per Row in Tropical and Temperate–Tropical Introgression Lines of Maize (Zea mays L.)

by Yuling Wang, Yaqi Bi, Fuyan Jiang, Ranjan Kumar Shaw, Jiachen Sun, Can Hu, Ruijia Guo and Xingming Fan

Curr. Issues Mol. Biol. 2023, 45(5), 4416-4430; https://doi.org/10.3390/cimb45050281 - 18 May 2023

Cited by 6 | Viewed by 2190

Abstract

Kernel number per row (KNR) is an essential component of maize (Zea mays L.) grain yield (GY), and understanding its genetic mechanism is crucial to improve GY. In this study, two F₇ recombinant inbred line (RIL) populations were created using a [...] Read more.

Kernel number per row (KNR) is an essential component of maize (Zea mays L.) grain yield (GY), and understanding its genetic mechanism is crucial to improve GY. In this study, two F₇ recombinant inbred line (RIL) populations were created using a temperate–tropical introgression line TML418 and a tropical inbred line CML312 as female parents and a backbone maize inbred line Ye107 as the common male parent. Bi-parental quantitative trait locus (QTL) mapping and genome-wide association analysis (GWAS) were then performed on 399 lines of the two maize RIL populations for KNR in two different environments using 4118 validated single nucleotide polymorphism (SNP) markers. This study aimed to: (1) detect molecular markers and/or the genomic regions associated with KNR; (2) identify the candidate genes controlling KNR; and (3) analyze whether the candidate genes are useful in improving GY. The authors reported a total of 7 QTLs tightly linked to KNR through bi-parental QTL mapping and identified 21 SNPs significantly associated with KNR through GWAS. Among these, a highly confident locus qKNR7-1 was detected at two locations, Dehong and Baoshan, with both mapping approaches. At this locus, three novel candidate genes (Zm00001d022202, Zm00001d022168, Zm00001d022169) were identified to be associated with KNR. These candidate genes were primarily involved in the processes related to compound metabolism, biosynthesis, protein modification, degradation, and denaturation, all of which were related to the inflorescence development affecting KNR. These three candidate genes were not reported previously and are considered new candidate genes for KNR. The progeny of the hybrid Ye107 × TML418 exhibited strong heterosis for KNR, which the authors believe might be related to qKNR7-1. This study provides a theoretical foundation for future research on the genetic mechanism underlying KNR in maize and the use of heterotic patterns to develop high-yielding hybrids. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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17 pages, 4060 KiB

Open AccessArticle

Genome-Wide Identification of Candidate Genes Associated with Heat Stress in Mulberry (Morus alba L.)

by Xin Jin, Michael Ackah, Adolf Acheampong, Qiaonan Zhang, Lei Wang, Qiang Lin, Changyu Qiu and Weiguo Zhao

Curr. Issues Mol. Biol. 2023, 45(5), 4151-4167; https://doi.org/10.3390/cimb45050264 - 8 May 2023

Cited by 3 | Viewed by 1932

Abstract

Mulberry (Morus alba L.) is an economically important plant for the silk industry and has the possibility of contributing immensely to Chinese pharmacopeia because of its health benefits. Domesticated silkworms feed only on mulberry leaves, meaning that the worms’ survival depends on [...] Read more.

Mulberry (Morus alba L.) is an economically important plant for the silk industry and has the possibility of contributing immensely to Chinese pharmacopeia because of its health benefits. Domesticated silkworms feed only on mulberry leaves, meaning that the worms’ survival depends on the mulberry tree. Mulberry production is threatened by climate change and global warming. However, the regulatory mechanisms of mulberry responses to heat are poorly understood. We performed transcriptome analysis of high-temperature-stressed (42 °C) M. alba seedlings using RNA-Seq technologies. A total of 703 differentially expressed genes (DEGs) were discovered from 18,989 unigenes. Among these, 356 were up-regulated, and 347 were down-regulated. KEGG analysis revealed that most DEGs were enriched in valine, leucine and isoleucine degradation, and in starch and sucrose metabolism, alpha-linolenic acid metabolism, carotenoid biosynthesis and galactose metabolism, among others. In addition, TFs such as the NAC, HSF, IAA1, MYB, AP2, GATA, WRKY, HLH and TCP families were actively involved in response to high temperatures. Moreover, we used RT-qPCR to confirm the expression changes of eight genes under heat stress observed in the RNA-Seq analysis. This study provides M. alba transcriptome profiles under heat stress and provides theoretical bases to researchers for better understanding mulberry heat response mechanisms and breeding heat-tolerant mulberry plants. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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15 pages, 3385 KiB

Open AccessArticle

Characteristics, Comparative Analysis, and Phylogenetic Relationships of Chloroplast Genomes of Cultivars and Wild Relatives of Eggplant (Solanum melongena)

by Qihong Yang, Ye Li, Liangyu Cai, Guiyun Gan, Peng Wang, Weiliu Li, Wenjia Li, Yaqin Jiang, Dandan Li, Mila Wang, Cheng Xiong, Riyuan Chen and Yikui Wang

Curr. Issues Mol. Biol. 2023, 45(4), 2832-2846; https://doi.org/10.3390/cimb45040185 - 1 Apr 2023

Cited by 6 | Viewed by 2216

Abstract

The eggplant (Solanum melongena) is a popular vegetable around the world. However, the origin and evolution of eggplant has long been considered complex and unclear, which has become the barrier to improvements in eggplant breeding. Sequencing and comparative analyses of 13 [...] Read more.

The eggplant (Solanum melongena) is a popular vegetable around the world. However, the origin and evolution of eggplant has long been considered complex and unclear, which has become the barrier to improvements in eggplant breeding. Sequencing and comparative analyses of 13 complete chloroplast (cp) genomes of seven Solanum species were performed. Genome sizes were between 154,942 and 156,004 bp, the smallest genome was from S. torvum and the largest from S. macrocapon. Thirteen cp genomes showed highly conserved sequences and GC contents, particularly at the subgenus level. All genes in the 13 genomes were annotated. The cp genomes in this study comprised 130 genes (i.e., 80 protein-coding genes, 8 rRNA genes, and 42 tRNA genes), apart from S. sisymbriifolium, which had 129 (79 protein-coding genes, 8 rRNA genes, and 42 tRNA genes.). The rps16 was absent from the cp genome of S. sisymbriifolium, resulting in a nonsense mutation. Twelve hotspot regions of the cp genome were identified, which showed a series of sequence variations and differed significantly in the inverted repeat/single-copy boundary regions. Furthermore, phylogenetic analysis was conducted using 46 cp genomic sequences to determine interspecific genetic and phylogenetic relationships in Solanum species. All species formed two branches, one of which contained all cultivars of the subgenus Leptostemonum. The cp genome data and phylogenetic analysis provides molecular evidence revealing the origin and evolutionary relationships of S. melongena and its wild relatives. Our findings suggest precise intra- and interspecies relatedness within the subgenus Leptostemonum, which has positive implications for work on improvements in eggplant breeding, particularly in producing heterosis, expanding the source of species variation, and breeding new varieties. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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15 pages, 4608 KiB

Open AccessArticle

Sucrose Transporter StSUT2 Affects Potato Plants Growth, Flowering Time, and Tuber Yield

by Hui-Ling Gong, Jin-Bao Liu, Clement Igiraneza and Leonce Dusengemungu

Curr. Issues Mol. Biol. 2023, 45(3), 2629-2643; https://doi.org/10.3390/cimb45030172 - 22 Mar 2023

Cited by 4 | Viewed by 1980

Abstract

Background: Sucrose transporters (SUTs) mediate sucrose phloem loading in source tissue and sucrose unloading into sink tissue in potatoes and higher plants, thus playing a crucial role in plant growth and development. In potatoes, the physiological function of the sucrose transporters StSUT1 and [...] Read more.

Background: Sucrose transporters (SUTs) mediate sucrose phloem loading in source tissue and sucrose unloading into sink tissue in potatoes and higher plants, thus playing a crucial role in plant growth and development. In potatoes, the physiological function of the sucrose transporters StSUT1 and StSUT4 has been clarified, whereas the physiological role of StSUT2 is not yet fully understood. Methods and Results: This study analyzed the relative expression of StSUT2 compared to that of StSUT1 and StSUT4 in different tissues from potatoes and its impact on different physiological characteristics by using StSUT2-RNA interference lines. Here, we report a negative effect of StSUT2-RNA interference on plant height, fresh weight, internodes number, leaf area, flowering time, and tuber yield. However, our data indicate that StSUT2 is not involved in carbohydrate accumulation in potato leaves and tubers. In addition, the data of the RNA-seq between the StSUT2-RNA interference line and WT showed that 152 genes were differentially expressed, of which 128 genes were upregulated and 24 genes were downregulated, and the GO and KEGG analyses revealed that differentially expressed genes were mainly related to cell wall composition metabolism. Conclusions: Thus, StSUT2 functions in potato plant growth, flowering time, and tuber yield without affecting carbohydrate accumulation in the leaves and tubers but may be involved in cell wall composition metabolism. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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9 pages, 2186 KiB

Open AccessArticle

Early Fruit Development Regulation-Related Genes Concordantly Expressed with TCP Transcription Factors in Tomato (Solanum lycopersicum)

by Sherif Edris, Aala A. Abulfaraj, Rania M. Makki, Salah Abo-Aba, Mardi M. Algandaby, Jamal Sabir, Robert K. Jansen, Fotouh M. El Domyati and Ahmed Bahieldin

Curr. Issues Mol. Biol. 2023, 45(3), 2372-2380; https://doi.org/10.3390/cimb45030153 - 13 Mar 2023

Cited by 2 | Viewed by 2038

Abstract

The tomato (Solanum lycopersicum L.) is considered one of the most important vegetable crops globally, both agronomically and economically; however, its fruit development regulation network is still unclear. The transcription factors serve as master regulators, activating many genes and/or metabolic pathways throughout [...] Read more.

The tomato (Solanum lycopersicum L.) is considered one of the most important vegetable crops globally, both agronomically and economically; however, its fruit development regulation network is still unclear. The transcription factors serve as master regulators, activating many genes and/or metabolic pathways throughout the entire plant life cycle. In this study, we identified the transcription factors that are coordinated with TCP gene family regulation in early fruit development by making use of the high-throughput sequencing of RNA (RNAseq) technique. A total of 23 TCP-encoding genes were found to be regulated at various stages during the growth of the fruit. The expression patterns of five TCPs were consistent with those of other transcription factors and genes. There are two unique subgroups of this larger family: class I and class II TCPs. Others were directly associated with the growth and/or ripening of fruit, while others were involved in the production of the hormone auxin. Moreover, it was discovered that TCP18 had an expression pattern that was similar to that of the ethylene-responsive transcription factor 4 (ERF4). Tomato fruit set and overall development are under the direction of a gene called auxin response factor 5 (ARF5). TCP15 revealed an expression that was in sync with this gene. This study provides insight into the potential processes that help in acquiring superior fruit qualities by accelerating fruit growth and ripening. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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12 pages, 3665 KiB

Open AccessArticle

Cloning of Three Cytokinin Oxidase/Dehydrogenase Genes in Bambusa oldhamii

by Chun-Yen Hsieh and Lu-Sheng Hsieh

Curr. Issues Mol. Biol. 2023, 45(3), 1902-1913; https://doi.org/10.3390/cimb45030123 - 27 Feb 2023

Cited by 1 | Viewed by 1720

Abstract

Cytokinin oxidase/dehydrogenase (CKX) catalyzes the irreversible breakdown of active cytokinins, which are a class of plant hormones that regulate cell division. According to conserved sequences of CKX genes from monocotyledons, PCR primers were designed to synthesize a probe for screening a bamboo genomic [...] Read more.

Cytokinin oxidase/dehydrogenase (CKX) catalyzes the irreversible breakdown of active cytokinins, which are a class of plant hormones that regulate cell division. According to conserved sequences of CKX genes from monocotyledons, PCR primers were designed to synthesize a probe for screening a bamboo genomic library. Cloned results of three genes encoding cytokinin oxidase were named as follows: BoCKX1, BoCKX2, and BoCKX3. In comparing the exon-intron structures among the above three genes, there are three exons and two introns in BoCKX1 and BoCKX3 genes, whereas BoCKX2 contains four exons and three introns. The amino acid sequence of BoCKX2 protein shares 78% and 79% identity with BoCKX1 and BoCKX3 proteins, respectively. BoCKX1 and BoCKX3 genes are particularly closely related given that the amino acid and nucleotide sequence identities are more than 90%. These three BoCKX proteins carried putative signal peptide sequences typical of secretion pathway, and a GHS-motif was found at N-terminal flavin adenine dinucleotide (FAD) binding domain, suggesting that BoCKX proteins might covalently conjugate with an FAD cofactor through a predicted histidine residue. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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10 pages, 1205 KiB

Open AccessArticle

Genetic Diversity Analysis of Banana Cultivars (Musa sp.) in Saudi Arabia Based on AFLP Marker

by Fatmah Ahmed Safhi, Salha Mesfer Alshamrani, Dalal Sulaiman Alshaya, Mohammed A. A. Hussein and Diaa Abd El-Moneim

Curr. Issues Mol. Biol. 2023, 45(3), 1810-1819; https://doi.org/10.3390/cimb45030116 - 22 Feb 2023

Cited by 12 | Viewed by 2716

Abstract

Banana plantation has been introduced recently to a temperate zone in the southeastern parts of Saudi Arabia (Fifa, Dhamadh, and Beesh, located in Jazan province). The introduced banana cultivars were of a clear origin without a recorded genetic background. In the current study, [...] Read more.

Banana plantation has been introduced recently to a temperate zone in the southeastern parts of Saudi Arabia (Fifa, Dhamadh, and Beesh, located in Jazan province). The introduced banana cultivars were of a clear origin without a recorded genetic background. In the current study, the genetic variability and structure of five common banana cultivars (i.e., Red, America, Indian, French, and Baladi) were analyzed using the fluorescently labeled AFLP technique. Nine different primer pairs combinations yielded 1468 loci with 88.96% polymorphism. Among all locations, high expected heterozygosity under the Hardy–Weinberg assumption was found (0.249 ± 0.003), where Dhamadh was the highest, followed by Fifa and Beesh, respectively. Based on the PCoA and Structure analysis, the samples were not clustered by location but in pairs in accordance with the cultivar’s names. However, the Red banana cultivar was found to be a hybrid between the American and Indian cultivars. Based on Φ_ST, 162 molecular markers (i.e., loci under selection) were detected among cultivars. Identifying those loci using NGS techniques can reveal the genetic bases and molecular mechanisms involved in the domestication and selection indicators among banana cultivars. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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19 pages, 4294 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of Calmodulin-Like Gene Family in Paspalums vaginatium Revealed Their Role in Response to Salt and Cold Stress

by Meizhen Yang, Jingjin Chen, Tingting Liu, Leilei Xiang and Biao-Feng Zhou

Curr. Issues Mol. Biol. 2023, 45(2), 1693-1711; https://doi.org/10.3390/cimb45020109 - 16 Feb 2023

Cited by 5 | Viewed by 1902

Abstract

The calmodulin-like (CML) family is an important calcium (Ca²⁺) sensor in plants and plays a pivotal role in the response to abiotic and biotic stresses. As one of the most salt-tolerant grass species, Paspalums vaginatum is resistant to multiple abiotic stresses, [...] Read more.

The calmodulin-like (CML) family is an important calcium (Ca²⁺) sensor in plants and plays a pivotal role in the response to abiotic and biotic stresses. As one of the most salt-tolerant grass species, Paspalums vaginatum is resistant to multiple abiotic stresses, such as salt, cold, and drought. However, investigations of PvCML proteins in P. vaginatum have been limited. Based on the recently published P. vaginatum genome, we identified forty-nine PvCMLs and performed a comprehensive bioinformatics analysis of PvCMLs. The main results showed that the PvCMLs were unevenly distributed on all chromosomes and that the expansion of PvCMLs was shaped by tandem and segmental duplications. In addition, cis-acting element analysis, expression profiles, and qRT–PCR analysis revealed that PvCMLs were involved in the response to salt and cold stress. Most interestingly, we found evidence of a tandem gene cluster that independently evolved in P. vaginatum and may participate in cold resistance. In summary, our work provides important insight into how grass species are resistant to abiotic stresses such as salt and cold and could be the basis of further gene function research on CMLs in P. vaginatum. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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9 pages, 606 KiB

Open AccessArticle

In Silico Integrated Analysis of Genomic, Transcriptomic, and Proteomic Data Reveals QTL-Specific Genes for Bacterial Canker Resistance in Tomato (Solanum lycopersicum L.)

by Ibrahim Celik

Curr. Issues Mol. Biol. 2023, 45(2), 1387-1395; https://doi.org/10.3390/cimb45020090 - 6 Feb 2023

Cited by 2 | Viewed by 1810

Abstract

Bacterial canker of tomato, caused by Clavibacter michiganensis subsp. michiganensis (Cmm), is a devasting disease that leads to significant yield losses. Although QTLs originating from three wild species (Solanum arcanum, S. habrochaites, and S. pimpinellifolium) were identified, [...] Read more.

Bacterial canker of tomato, caused by Clavibacter michiganensis subsp. michiganensis (Cmm), is a devasting disease that leads to significant yield losses. Although QTLs originating from three wild species (Solanum arcanum, S. habrochaites, and S. pimpinellifolium) were identified, none of the QTLs was annotated for candidate gene identification. In the present study, a QTL-based physical map was constructed to reveal the meta-QTLs for Cmm resistance. As a result, seven major QTLs were mapped. Functional annotation of QTLs revealed 48 candidate genes. Additionally, experimentally validated Cmm resistance-related genes based on transcriptomic and proteomic studies were mapped in the genome and 25 genes were found to be located in the QTL regions. The present study is the first report to construct a physical map for Cmm resistance QTLs and identify QTL-specific candidate genes. The candidate genes identified in the present study are valuable targets for fine mapping and developing markers for marker-assisted selection in tomatoes for Cmm resistance breeding. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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13 pages, 2497 KiB

Open AccessArticle

Analysis of the Chloroplast Genome of Ficus simplicissima Lour Collected in Vietnam and Proposed Barcodes for Identifying Ficus Plants

by Thuy Thi Thu Vu, Lien Thi Kim Vu, Lam Tung Le, Thu Thi Mai Lo and Mau Hoang Chu

Curr. Issues Mol. Biol. 2023, 45(2), 1024-1036; https://doi.org/10.3390/cimb45020067 - 27 Jan 2023

Cited by 2 | Viewed by 2204

Abstract

Ficus simplicissima Lour. is an Asian species of fig tree in the family Moraceae. The chloroplast (cp) genome of F. simplicissima m3 was sequenced using the Pacbio sequel platform. The F. simplicissima cpDNA has a size of 160,321 bp in length, of which [...] Read more.

Ficus simplicissima Lour. is an Asian species of fig tree in the family Moraceae. The chloroplast (cp) genome of F. simplicissima m3 was sequenced using the Pacbio sequel platform. The F. simplicissima cpDNA has a size of 160,321 bp in length, of which GC content accounts for 36.13%. The cp genome of F. simplicissima consists of a single large copy (LSC) with a size of 91,346 bp, a single small copy (SSC) with a size of 20,131 bp, and a pair of inverted repeats with a size of 24,421 to 24,423 bp. The cp genome of F. simplicissima has 127 genes, including 85 protein-coding genes, eight rRNA genes, and 34 tRNA genes; 92 simple sequence repeats and 39 long repeats were detected in the cpDNA of F. simplicissim. A comparative cp genome analysis among six species in the Ficus genus indicated that the genome structure and gene content were highly conserved. The non-coding regions show more differentiation than the coding regions, and the LSC and SSC regions show more differences than the inverted repeat regions. Phylogenetic analysis supported that F. simplicissima m3 had a close relationship with F. hirta. The complete cp genome of F. simplicissima was proposed as a chloroplast DNA barcoding for genus-level in the Moraceae family and the psbA-trnH gene region for species-level identification. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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16 pages, 3940 KiB

Open AccessArticle

BSR and Full-Length Transcriptome Approaches Identified Candidate Genes for High Seed Ratio in Camellia vietnamensis

by Bing-Qing Hao, Hong-Ze Liao, Ying-Ying Xia, Dong-Xue Wang and Hang Ye

Curr. Issues Mol. Biol. 2023, 45(1), 311-326; https://doi.org/10.3390/cimb45010022 - 31 Dec 2022

Cited by 2 | Viewed by 1636

Abstract

(1) Background: C. vietnamensis is very suitable for growth in the low hilly areas of southern subtropical regions. Under appropriate conditions, the oil yield of C. vietnamensis can reach 1125 kg/ha (the existing varieties can reach 750 kg/ha). Moreover, the fruit of C. [...] Read more.

(1) Background: C. vietnamensis is very suitable for growth in the low hilly areas of southern subtropical regions. Under appropriate conditions, the oil yield of C. vietnamensis can reach 1125 kg/ha (the existing varieties can reach 750 kg/ha). Moreover, the fruit of C. vietnamensis is large and the pericarp is thick (>5 cm). Therefore, a high seed ratio has become the main target economic trait for the breeding of C. vietnamensis. (2) Methods: A half-sibling population of C. vietnamensis plants with a combination of high and low seed ratios was constructed by crossing a C. vietnamensis female parent. Bulked segregant RNA analysis and full-length transcriptome sequencing were performed to determine the molecular mechanisms underlying a high seed ratio. (3) Results: Seed ratio is a complex quantitative trait with a normal distribution, which is significantly associated with four other traits of fruit (seed weight, seed number, fruit diameter, and pericarp thickness). Two candidate regions related to high seed ratio (HSR) were predicted. One spanned 140.8–148.4 Mb of chromosome 2 and was associated with 97 seed-yield-related candidate genes ranging in length from 278 to 16,628 bp. The other spanned 35.3–37.3 Mb on chromosome 15 and was associated with 38 genes ranging in length from 221 to 16,928 bp. Using the full-length transcript as a template, a total of 115 candidate transcripts were obtained, and 78 transcripts were predicted to be functionally annotated. The DEGs from two set pairs of cDNA sequencing bulks were enriched to cytochrome p450 CYP76F14 (KOG0156; GO:0055114, HSR4, HSR7), the gibberellin phytohormone pathway (GO:0016787, HSR5), the calcium signaling pathway (GO:0005509, HSR6), the polyubiquitin-PPAR signaling pathway (GO:0005515, HSR2, HSR3), and several main transcription factors (bZIP transcription factor, HSR1) in C. vietnamensis. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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12 pages, 2308 KiB

Open AccessArticle

Genome-Wide Identification of Brassica napus PEN1-LIKE Genes and Their Expression Profiling in Insect-Susceptible and Resistant Cultivars

by Lei Sheng, Zengbei Feng, Zhongping Hao and Shumin Hou

Curr. Issues Mol. Biol. 2022, 44(12), 6385-6396; https://doi.org/10.3390/cimb44120435 - 15 Dec 2022

Viewed by 1812

Abstract

Recently, it has been reported that a gene (PEN1) in Arabidopsis thaliana is highly resistant to Plutella xylostella. We screened all the homologous genes of PEN1 in Arabidopsis thaliana and found that the motif of these genes was very conserved. At present, [...] Read more.

Recently, it has been reported that a gene (PEN1) in Arabidopsis thaliana is highly resistant to Plutella xylostella. We screened all the homologous genes of PEN1 in Arabidopsis thaliana and found that the motif of these genes was very conserved. At present, few insect resistance genes have been identified and characterized in Brassica napus. Therefore, we screened all the homologous genes containing this motif in the Brassica napus genome and systematically analyzed the basic information, conserved domain, evolutionary relationship, chromosomal localization and expression analysis of these genes. In this study, 12 PEN1 homologous genes were identified in the Brassica napus genome, which is more than the number in Arabidopsis thaliana. These genes are unevenly distributed on the 12 chromosomes in Brassica napus. Furthermore, all the PEN1 homologous genes contained light responsiveness elements, and most of the genes contained gibberellin-responsive elements, meJA-responsive elements and abscisic-acid-responsive elements. The results will provide a theoretical basis for screening insect resistance genes from the genome of Brassica napus and analyzing the molecular mechanism of insect resistance in Brassica napus. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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16 pages, 4029 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the NAC Gene Family in Kandelia obovata, a Typical Mangrove Plant

by Man-Man Sun, Xiu Liu, Xiao-Juan Huang, Jing-Jun Yang, Pei-Ting Qin, Hao Zhou, Ming-Guo Jiang and Hong-Ze Liao

Curr. Issues Mol. Biol. 2022, 44(11), 5622-5637; https://doi.org/10.3390/cimb44110381 - 13 Nov 2022

Cited by 12 | Viewed by 2578

Abstract

The NAC (NAM, ATAF1/2, and CUC2) gene family, one of the largest transcription factor families in plants, acts as positive or negative regulators in plant response and adaption to various environmental stresses, including cold stress. Multiple reports on the [...] Read more.

The NAC (NAM, ATAF1/2, and CUC2) gene family, one of the largest transcription factor families in plants, acts as positive or negative regulators in plant response and adaption to various environmental stresses, including cold stress. Multiple reports on the functional characterization of NAC genes in Arabidopsis thaliana and other plants are available. However, the function of the NAC genes in the typical woody mangrove (Kandelia obovata) remains poorly understood. Here, a comprehensive analysis of NAC genes in K. obovata was performed with a pluri-disciplinary approach including bioinformatic and molecular analyses. We retrieved a contracted NAC family with 68 genes from the K. obovata genome, which were unevenly distributed in the chromosomes and classified into ten classes. These KoNAC genes were differentially and preferentially expressed in different organs, among which, twelve up-regulated and one down-regulated KoNAC genes were identified. Several stress-related cis-regulatory elements, such as LTR (low-temperature response), STRE (stress response element), ABRE (abscisic acid response element), and WUN (wound-responsive element), were identified in the promoter regions of these 13 KoNAC genes. The expression patterns of five selected KoNAC genes (KoNAC6, KoNAC15, KoNAC20, KoNAC38, and KoNAC51) were confirmed by qRT-PCR under cold treatment. These results strongly implied the putative important roles of KoNAC genes in response to chilling and other stresses. Collectively, our findings provide valuable information for further investigations on the function of KoNAC genes. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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18 pages, 2657 KiB

Open AccessArticle

De Novo Transcriptome Assembly, Gene Annotations, and Characterization of Functional Profiling Reveal Key Genes for Lead Alleviation in the Pb Hyperaccumulator Greek Mustard (Hirschfeldia incana L.)

by Said El Hasnaoui, Mouna Fahr, Mohamed Zouine and Abdelaziz Smouni

Curr. Issues Mol. Biol. 2022, 44(10), 4658-4675; https://doi.org/10.3390/cimb44100318 - 4 Oct 2022

Cited by 3 | Viewed by 2241

Abstract

Lead (Pb) contamination is a widespread environmental problem due to its toxicity to living organisms. Hirschfeldia incana L., a member of the Brassicaceae family, commonly found in the Mediterranean regions, is characterized by its ability to tolerate and accumulate Pb in soils and [...] Read more.

Lead (Pb) contamination is a widespread environmental problem due to its toxicity to living organisms. Hirschfeldia incana L., a member of the Brassicaceae family, commonly found in the Mediterranean regions, is characterized by its ability to tolerate and accumulate Pb in soils and hydroponic cultures. This plant has been reported as an excellent model to assess the response of plants to Pb. However, the lack of genomic data for H. incana hinders research at the molecular level. In the present study, we carried out RNA deep transcriptome sequencing (RNA-seq) of H. incana under two conditions, control without Pb(NO₃)₂ and treatment with 100 µM of Pb(NO₃)₂ for 15 days. A total of 797.83 million reads were generated using Illumina sequencing technology. We assembled 77,491 transcript sequences with an average length of 959 bp and N50 of 1330 bp. Sequence similarity analyses and annotation of these transcripts were performed against the Arabidopsis thaliana nr protein database, Gene Ontology (GO), and KEGG databases. As a result, 13,046 GO terms and 138 KEGG maps were created. Under Pb stress, 577 and 270 genes were differentially expressed in roots and aboveground parts, respectively. Detailed elucidation of regulation of metal transporters, transcription factors (TFs), and plant hormone genes described the role of actors that allow the plant to fine-tune Pb stress responses. Our study revealed that several genes related to jasmonic acid biosynthesis and alpha-linoleic acid were upregulated, suggesting these components’ implication in Hirschfeldia incana L responses to Pb stress. This study provides data for further genomic analyses of the biological and molecular mechanisms leading to Pb tolerance and accumulation in Hirschfeldia incana L. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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20 pages, 4213 KiB

Open AccessArticle

Genome-Wide Association Study Reveals Candidate Genes for Root-Related Traits in Rice

by Jun Xiang, Chaopu Zhang, Nansheng Wang, Zhaojie Liang, Zheng Zhenzhen, Lunping Liang, Hongyan Yuan and Yingyao Shi

Curr. Issues Mol. Biol. 2022, 44(10), 4386-4405; https://doi.org/10.3390/cimb44100301 - 21 Sep 2022

Cited by 4 | Viewed by 2896

Abstract

Root architecture is a determinant factor of drought resistance in rice and plays essential roles in the absorption of water and nutrients for the survival of rice plants. Dissection of the genetic basis for root structure can help to improve stress-resistance and grain [...] Read more.

Root architecture is a determinant factor of drought resistance in rice and plays essential roles in the absorption of water and nutrients for the survival of rice plants. Dissection of the genetic basis for root structure can help to improve stress-resistance and grain yield in rice breeding. In this study, a total of 391 rice (Oryz asativa L.) accessions were used to perform a genome-wide association study (GWAS) on three root-related traits in rice, including main root length (MRL), average root length (ARL), and total root number (TRN). As a result, 13 quantitative trait loci (QTLs) (qMRL1.1, qMRL1.2, qMRL3.1, qMRL3.2, qMRL3.3, qMRL4.1, qMRL7.1, qMRL8.1, qARL1.1, qARL9.1, qTRN9.1, qTRN9.2, and qTRN11.1) significantly associated with the three traits were identified, among which three (qMRL3.2, qMRL4.1 and qMRL8.1) were overlapped with OsGNOM1, OsARF12 and qRL8.1, respectively, and ten were novel QTLs. Moreover, we also detected epistatic interactions affecting root-related traits and identified 19 related genetic interactions. These results lay a foundation for cloning the corresponding genes for rice root structure, as well as provide important genomic resources for breeding high yield rice varieties. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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14 pages, 5507 KiB

Open AccessArticle

Genome-Wide Association Study of Partial Resistance to P. sojae in Wild Soybeans from Heilongjiang Province, China

by Wei Li, Miao Liu, Yong-Cai Lai, Jian-Xin Liu, Chao Fan, Guang Yang, Ling Wang, Wen-Wei Liang, Shu-Feng Di, De-Yue Yu and Ying-Dong Bi

Curr. Issues Mol. Biol. 2022, 44(7), 3194-3207; https://doi.org/10.3390/cimb44070221 - 17 Jul 2022

Cited by 3 | Viewed by 2475

Abstract

Phytophthora root rot (PRR) is a destructive disease of soybeans (Glycine max (L.) Merr) caused by Phytophthora sojae (P. sojae). The most effective way to prevent the disease is growing resistant or tolerant varieties. Partial resistance provides a more durable [...] Read more.

Phytophthora root rot (PRR) is a destructive disease of soybeans (Glycine max (L.) Merr) caused by Phytophthora sojae (P. sojae). The most effective way to prevent the disease is growing resistant or tolerant varieties. Partial resistance provides a more durable resistance against the pathogen compared to complete resistance. Wild soybean (Glycine soja Sieb. & Zucc.) seems to be an extraordinarily important gene pool for soybean improvement due to its high level of genetic variation. In this study, 242 wild soybean germplasms originating from different regions of Heilongjiang province were used to identify resistance genes to P. sojae race 1 using a genome-wide association study (GWAS). A total of nine significant SNPs were detected, repeatedly associated with P. sojae resistance and located on chromosomes 1, 10, 12, 15, 17, 19 and 20. Among them, seven favorable allelic variations associated with P. sojae resistance were evaluated by a t-test. Eight candidate genes were predicted to explore the mechanistic hypotheses of partial resistance, including Glysoja.19G051583, which encodes an LRR receptor-like serine/threonine protein kinase protein, Glysoja.19G051581, which encodes a receptor-like cytosolic serine/threonine protein kinase protein. These findings will provide additional insights into the genetic architecture of P. sojae resistance in a large sample of wild soybeans and P. sojae-resistant breeding through marker-assisted selection. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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Review

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18 pages, 1893 KiB

Open AccessReview

Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding

by Yizhen Li, Jing Liang, Bufang Deng, Yingli Jiang, Jingyan Zhu, Like Chen, Min Li and Juan Li

Curr. Issues Mol. Biol. 2023, 45(2), 918-935; https://doi.org/10.3390/cimb45020059 - 19 Jan 2023

Cited by 12 | Viewed by 5214

Abstract

The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 system (Cas9) has been used at length to optimize multiple aspects of germplasm resources. However, large-scale genomic research has indicated that novel variations in crop plants are attributed to single-nucleotide polymorphisms (SNPs). Therefore, [...] Read more.

The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 system (Cas9) has been used at length to optimize multiple aspects of germplasm resources. However, large-scale genomic research has indicated that novel variations in crop plants are attributed to single-nucleotide polymorphisms (SNPs). Therefore, substituting single bases into a plant genome may produce desirable traits. Gene editing by CRISPR/Cas9 techniques frequently results in insertions–deletions (indels). Base editing allows precise single-nucleotide changes in the genome in the absence of double-strand breaks (DSBs) and donor repair templates (DRTs). Therefore, BEs have provided a new way of thinking about genome editing, and base editing techniques are currently being utilized to edit the genomes of many different organisms. As traditional breeding techniques and modern molecular breeding technologies complement each other, various genome editing technologies have emerged. How to realize the greater potential of BE applications is the question we need to consider. Here, we explain various base editings such as CBEs, ABEs, and CGBEs. In addition, the latest applications of base editing technologies in agriculture are summarized, including crop yield, quality, disease, and herbicide resistance. Finally, the challenges and future prospects of base editing technologies are presented. The aim is to provide a comprehensive overview of the application of BE in crop breeding to further improve BE and make the most of its value. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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12 pages, 906 KiB

Open AccessReview

Rice Lesion Mimic Gene Cloning and Association Analysis for Disease Resistance

by Anpeng Zhang, Hongzhen Jiang, Huangwei Chu, Liming Cao and Jingguang Chen

Curr. Issues Mol. Biol. 2022, 44(5), 2350-2361; https://doi.org/10.3390/cimb44050160 - 22 May 2022

Cited by 4 | Viewed by 3237

Abstract

Lesion mimic mutants refer to a class of mutants that naturally form necrotic lesions similar to allergic reactions on leaves in the absence of significant stress or damage and without being harmed by pathogens. Mutations in most lesion mimic genes, such as OsACL-A2 [...] Read more.

Lesion mimic mutants refer to a class of mutants that naturally form necrotic lesions similar to allergic reactions on leaves in the absence of significant stress or damage and without being harmed by pathogens. Mutations in most lesion mimic genes, such as OsACL-A2 and OsSCYL2, can enhance mutants’ resistance to pathogens. Lesion mimic mutants are ideal materials for studying programmed cell death (PCD) and plant defense mechanisms. Studying the genes responsible for the rice disease-like phenotype is of great significance for understanding the disease resistance mechanism of rice. In this paper, the nomenclature, occurrence mechanism, genetic characteristics, regulatory pathways, and the research progress on the cloning and disease resistance of rice lesion mimic mutant genes were reviewed, in order to further analyze the various lesion mimic mutants of rice. The mechanism lays a theoretical foundation and provides a reference for rice breeding. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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Other

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9 pages, 884 KiB

Open AccessBrief Report

Mitogenomic Research of Silverleaf Sunflower (Helianthus argophyllus) and Its Interspecific Hybrids

by Maksim S. Makarenko, Kirill V. Azarin and Vera A. Gavrilova

Curr. Issues Mol. Biol. 2023, 45(6), 4841-4849; https://doi.org/10.3390/cimb45060308 - 2 Jun 2023

Cited by 2 | Viewed by 1753

Abstract

Interspecific hybridization is widespread for sunflowers, both in wild populations and commercial breeding. One of the most common species that can efficiently cross with Helianthus annuus is the Silverleaf sunflower—Helianthus argophyllus. The current study carried out structural and functional organization analyses of [...] Read more.

Interspecific hybridization is widespread for sunflowers, both in wild populations and commercial breeding. One of the most common species that can efficiently cross with Helianthus annuus is the Silverleaf sunflower—Helianthus argophyllus. The current study carried out structural and functional organization analyses of mitochondrial DNA in H. argophyllus and the interspecific hybrid, H. annuus (VIR114A line) × H. argophyllus. The complete mitogenome of H. argophyllus counts 300,843 bp, has a similar organization to the mitogenome of cultivated sunflower, and holds SNPs typical for wild sunflowers. RNA editing analysis predicted 484 sites in H. argophyllus mitochondrial CDS. The mitochondrial genome of the H. annuus × H. argophyllus hybrid is identical to the maternal line (VIR114A). We expected that significant rearrangements in the mitochondrial DNA of the hybrid would occur, due to the frequent recombination. However, the hybrid mitogenome lacks rearrangements, presumably due to the preservation of nuclear–cytoplasmic interaction paths. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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