Editorial

5 pages, 195 KiB

Open AccessEditorial

by Jie Huang, Zhiyong Li and Jian Zhang

Int. J. Mol. Sci. 2023, 24(20), 15298; https://doi.org/10.3390/ijms242015298 - 18 Oct 2023

Viewed by 777

In recent years, plant genomics has made significant progress following the development of biotechnology [...] Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

Research

Jump to: Editorial, Review

15 pages, 4135 KiB

Open AccessArticle

Fine Mapping and Candidate Gene Analysis of Rice Grain Length QTL qGL9.1

by Luomiao Yang, Peng Li, Jingguo Wang, Hualong Liu, Hongliang Zheng, Wei Xin and Detang Zou

Int. J. Mol. Sci. 2023, 24(14), 11447; https://doi.org/10.3390/ijms241411447 - 14 Jul 2023

Cited by 1 | Viewed by 1203

Abstract

Grain length (GL) is one of the crucial determinants of rice yield and quality. However, there is still a shortage of knowledge on the major genes controlling the inheritance of GL in japonica rice, which severely limits the improvement of japonica rice yields. [...] Read more.

Grain length (GL) is one of the crucial determinants of rice yield and quality. However, there is still a shortage of knowledge on the major genes controlling the inheritance of GL in japonica rice, which severely limits the improvement of japonica rice yields. Here, we systemically measured the GL of 667 F₂ and 1570 BC₃F₃ individuals derived from two cultivated rice cultivars, Pin20 and Songjing15, in order to identify the major genomic regions associated with GL. A novel major QTL, qGL9.1, was mapped on chromosome 9, which is associated with the GL, using whole-genome re-sequencing with bulked segregant analysis. Local QTL linkage analysis with F₂ and fine mapping with the recombinant plant revealed a 93-kb core region on qGL9.1 encoding 15 protein-coding genes. Only the expression level of LOC_Os09g26970 was significantly different between the two parents at different stages of grain development. Moreover, haplotype analysis revealed that the alleles of Pin20 contribute to the optimal GL (9.36 mm) and GL/W (3.31), suggesting that Pin20 is a cultivated species carrying the optimal GL variation of LOC_Os09g26970. Furthermore, a functional-type mutation (16398989-bp, G>A) located on an exon of LOC_Os09g26970 could be used as a molecular marker to distinguish between long and short grains. Our experiments identified LOC_Os09g26970 as a novel gene associated with GL in japonica rice. This result is expected to further the exploration of the genetic mechanism of rice GL and improve GL in rice japonica varieties by marker-assisted selection. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

14 pages, 2301 KiB

Open AccessArticle

Effectiveness of TaDreb-B1 and 1-FEH w3 KASP Markers in Spring and Winter Wheat Populations for Marker-Assisted Selection to Improve Drought Tolerance

by Shamseldeen Eltaher, Mostafa Hashem, Asmaa A. M. Ahmed, P. Stephen Baenziger, Andreas Börner and Ahmed Sallam

Int. J. Mol. Sci. 2023, 24(10), 8986; https://doi.org/10.3390/ijms24108986 - 19 May 2023

Cited by 4 | Viewed by 1458

Abstract

Due to the advances in DNA markers, kompetitive allele-specific PCR (KASP) markers could accelerate breeding programs and genetically improve drought tolerance. Two previously reported KASP markers, TaDreb-B1 and 1-FEH w3, were investigated in this study for the marker-assisted selection (MAS) of drought [...] Read more.

Due to the advances in DNA markers, kompetitive allele-specific PCR (KASP) markers could accelerate breeding programs and genetically improve drought tolerance. Two previously reported KASP markers, TaDreb-B1 and 1-FEH w3, were investigated in this study for the marker-assisted selection (MAS) of drought tolerance. Two highly diverse spring and winter wheat populations were genotyped using these two KASP markers. The same populations were evaluated for drought tolerance at seedling (drought stress) and reproductive (normal and drought stress) growth stages. The single-marker analysis revealed a high significant association between the target allele of 1-FEH w3 and drought susceptibility in the spring population, while the marker–trait association was not significant in the winter population. The TaDreb-B1 marker did not have any highly significant association with seedling traits, except the sum of leaf wilting in the spring population. For field experiments, SMA revealed very few negative and significant associations between the target allele of the two markers and yield traits under both conditions. The results of this study revealed that the use of TaDreb-B1 provided better consistency in improving drought tolerance than 1-FEH w3. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

24 pages, 5474 KiB

Open AccessArticle

Transgenerational Paternal Inheritance of TaCKX GFMs Expression Patterns Indicate a Way to Select Wheat Lines with Better Parameters for Yield-Related Traits

by Karolina Szala, Marta Dmochowska-Boguta, Joanna Bocian, Waclaw Orczyk and Anna Nadolska-Orczyk

Int. J. Mol. Sci. 2023, 24(9), 8196; https://doi.org/10.3390/ijms24098196 - 03 May 2023

Cited by 4 | Viewed by 1332

Abstract

Members of the TaCKX gene family (GFMs) encode the cytokinin oxygenase/dehydrogenase enzyme (CKX), which irreversibly degrades cytokinins in the organs of wheat plants; therefore, these genes perform a key role in the regulation of yield-related traits. The purpose of the investigation was to [...] Read more.

Members of the TaCKX gene family (GFMs) encode the cytokinin oxygenase/dehydrogenase enzyme (CKX), which irreversibly degrades cytokinins in the organs of wheat plants; therefore, these genes perform a key role in the regulation of yield-related traits. The purpose of the investigation was to determine how expression patterns of these genes, together with the transcription factor-encoding gene TaNAC2-5A, and yield-related traits are inherited to apply this knowledge to speed up breeding processes. The traits were tested in 7 days after pollination (DAP) spikes and seedling roots of maternal and paternal parents and their F₂ progeny. The expression levels of most of them and the yield were inherited in F₂ from the paternal parent. Some pairs or groups of genes cooperated, and some showed opposite functions. Models of up- or down-regulation of TaCKX GFMs and TaNAC2-5A in low-yielding maternal plants crossed with higher-yielding paternal plants and their high-yielding F₂ progeny reproduced gene expression and yield of the paternal parent. The correlation coefficients between TaCKX GFMs, TaNAC2-5A, and yield-related traits in high-yielding F₂ progeny indicated which of these genes were specifically correlated with individual yield-related traits. The most common was expressed in 7 DAP spikes TaCKX2.1, which positively correlated with grain number, grain yield, spike number, and spike length, and seedling root mass. The expression levels of TaCKX1 or TaNAC2-5A in the seedling roots were negatively correlated with these traits. In contrast, the thousand grain weight (TGW) was negatively regulated by TaCKX2.2.2, TaCKX2.1, and TaCKX10 in 7 DAP spikes but positively correlated with TaCKX10 and TaNAC2-5A in seedling roots. Transmission of TaCKX GFMs and TaNAC2-5A expression patterns and yield-related traits from parents to the F₂ generation indicate their paternal imprinting. These newly shown data of nonmendelian epigenetic inheritance shed new light on crossing strategies to obtain a high-yielding F₂ generation. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

12 pages, 2285 KiB

Open AccessArticle

OsLPR5 Encoding Ferroxidase Positively Regulates the Tolerance to Salt Stress in Rice

by Juan Zhao, Xin Meng, Zhaonian Zhang, Mei Wang, Fanhao Nie and Qingpo Liu

Int. J. Mol. Sci. 2023, 24(9), 8115; https://doi.org/10.3390/ijms24098115 - 30 Apr 2023

Cited by 1 | Viewed by 1492

Abstract

Salinity is a major abiotic stress that harms rice growth and productivity. Low phosphate roots (LPRs) play a central role in Pi deficiency-mediated inhibition of primary root growth and have ferroxidase activity. However, the function of LPRs in salt stress response and tolerance [...] Read more.

Salinity is a major abiotic stress that harms rice growth and productivity. Low phosphate roots (LPRs) play a central role in Pi deficiency-mediated inhibition of primary root growth and have ferroxidase activity. However, the function of LPRs in salt stress response and tolerance in plants remains largely unknown. Here, we reported that the OsLPR5 was induced by NaCl stress and positively regulates the tolerance to salt stress in rice. Under NaCl stress, overexpression of OsLPR5 led to increased ferroxidase activity, more green leaves, higher levels of chlorophyll and lower MDA contents compared with the WT. In addition, OsLPR5 could promote the accumulation of cell osmotic adjustment substances and promote ROS-scavenging enzyme activities. Conversely, the mutant lpr5 had a lower ferroxidase activity and suffered severe damage under salt stress. Moreover, knock out of OsLPR5 caused excessive Na⁺ levels and Na⁺/K⁺ ratios. Taken together, our results exemplify a new molecular link between ferroxidase and salt stress tolerance in rice. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

15 pages, 7214 KiB

Open AccessArticle

Systematic Analysis of NRAMP Family Genes in Areca catechu and Its Response to Zn/Fe Deficiency Stress

by Guangzhen Zhou, Qiyuan An, Zheng Liu, Yinglang Wan and Wenlong Bao

Int. J. Mol. Sci. 2023, 24(8), 7383; https://doi.org/10.3390/ijms24087383 - 17 Apr 2023

Cited by 3 | Viewed by 1042

Abstract

Areca catechu is a commercially important medicinal plant widely cultivated in tropical regions. The natural resistance-associated macrophage protein (NRAMP) is widespread in plants and plays critical roles in transporting metal ions, plant growth, and development. However, the information on NRAMPs in A. catechu [...] Read more.

Areca catechu is a commercially important medicinal plant widely cultivated in tropical regions. The natural resistance-associated macrophage protein (NRAMP) is widespread in plants and plays critical roles in transporting metal ions, plant growth, and development. However, the information on NRAMPs in A. catechu is quite limited. In this study, we identified 12 NRAMPs genes in the areca genome, which were classified into five groups by phylogenetic analysis. Subcellular localization analysis reveals that, except for NRAMP2, NRAMP3, and NRAMP11, which are localized in chloroplasts, all other NRAMPs are localized on the plasma membrane. Genomic distribution analysis shows that 12 NRAMPs genes are unevenly spread on seven chromosomes. Sequence analysis shows that motif 1 and motif 6 are highly conserved motifs in 12 NRAMPs. Synteny analysis provided deep insight into the evolutionary characteristics of AcNRAMP genes. Among the A. catechu and the other three representative species, we identified a total of 19 syntenic gene pairs. Analysis of Ka/Ks values indicates that AcNRAMP genes are subjected to purifying selection in the evolutionary process. Analysis of cis-acting elements reveals that AcNRAMP genes promoter sequences contain light-responsive elements, defense- and stress-responsive elements, and plant growth/development-responsive elements. Expression profiling confirms distinct expression patterns of AcNRAMP genes in different organs and responses to Zn/Fe deficiency stress in leaves and roots. Taken together, our results lay a foundation for further exploration of the AcNRAMPs regulatory function in areca response to Fe and Zn deficiency. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

18 pages, 10412 KiB

Open AccessArticle

Comprehensive Analysis of bHLH Transcription Factors in Ipomoea aquatica and Its Response to Anthocyanin Biosynthesis

by Zheng Liu, Xiaoai Fu, Hao Xu, Yuxin Zhang, Zhidi Shi, Guangzhen Zhou and Wenlong Bao

Int. J. Mol. Sci. 2023, 24(6), 5652; https://doi.org/10.3390/ijms24065652 - 15 Mar 2023

Cited by 3 | Viewed by 1581

Abstract

The basic helix-loop-helix (bHLH) proteins compose one of the largest transcription factor (TF) families in plants, which play a vital role in regulating plant biological processes including growth and development, stress response, and secondary metabolite biosynthesis. Ipomoea aquatica is one of the most [...] Read more.

The basic helix-loop-helix (bHLH) proteins compose one of the largest transcription factor (TF) families in plants, which play a vital role in regulating plant biological processes including growth and development, stress response, and secondary metabolite biosynthesis. Ipomoea aquatica is one of the most important nutrient-rich vegetables. Compared to the common green-stemmed I. aquatica, purple-stemmed I. aquatica has extremely high contents of anthocyanins. However, the information on bHLH genes in I. aquatica and their role in regulating anthocyanin accumulation is still unclear. In this study, we confirmed a total of 157 bHLH genes in the I. aquatica genome, which were classified into 23 subgroups according to their phylogenetic relationship with the bHLH of Arabidopsis thaliana (AtbHLH). Of these, 129 IabHLH genes were unevenly distributed across 15 chromosomes, while 28 IabHLH genes were spread on the scaffolds. Subcellular localization prediction revealed that most IabHLH proteins were localized in the nucleus, while some were in the chloroplast, extracellular space, and endomembrane system. Sequence analysis revealed conserved motif distribution and similar patterns of gene structure within IabHLH genes of the same subfamily. Analysis of gene duplication events indicated that DSD and WGD played a vital role in the IabHLH gene family expansion. Transcriptome analysis showed that the expression levels of 13 IabHLH genes were significantly different between the two varieties. Of these, the IabHLH027 had the highest expression fold change, and its expression level was dramatically higher in purple-stemmed I. aquatica than that in green-stemmed I. aquatica. All upregulated DEGs in purple-stemmed I. aquatica exhibited the same expression trends in both qRT-PCR and RNA-seq. Three downregulated genes including IabHLH142, IabHLH057, and IabHLH043 determined by RNA-seq had opposite expression trends of those detected by qRT-PCR. Analysis of the cis-acting elements in the promoter region of 13 differentially expressed genes indicated that light-responsive elements were the most, followed by phytohormone-responsive elements and stress-responsive elements, while plant growth and development-responsive elements were the least. Taken together, this work provides valuable clues for further exploring IabHLH function and facilitating the breeding of anthocyanin-rich functional varieties of I. aquatica. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

23 pages, 4595 KiB

Open AccessArticle

Development of a Multi-Criteria Decision-Making Approach for Evaluating the Comprehensive Application of Herbaceous Peony at Low Latitudes

by Xiaobin Wang, Runlong Zhang, Kaijing Zhang, Lingmei Shao, Tong Xu, Xiaohua Shi, Danqing Li, Jiaping Zhang and Yiping Xia

Int. J. Mol. Sci. 2022, 23(22), 14342; https://doi.org/10.3390/ijms232214342 - 18 Nov 2022

Cited by 3 | Viewed by 1335

Abstract

The growing region of herbaceous peony (Paeonia lactiflora) has been severely constrained due to the intensification of global warming and extreme weather events, especially at low latitudes. Assessing and selecting stress-tolerant and high-quality peony germplasm is essential for maintaining the normal [...] Read more.

The growing region of herbaceous peony (Paeonia lactiflora) has been severely constrained due to the intensification of global warming and extreme weather events, especially at low latitudes. Assessing and selecting stress-tolerant and high-quality peony germplasm is essential for maintaining the normal growth and application of peonies under adverse conditions. This study proposed a modified multi-criteria decision-making (MCDM) model for assessing peonies adapted to low-latitude climates based on our previous study. This model is low-cost, timesaving and suitable for screening the adapted peony germplasm under hot and humid climates. The evaluation was conducted through the analytic hierarchy process (AHP), three major criteria, including adaptability-related, ornamental feature-related and growth habits-related criteria, and eighteen sub-criteria were proposed and constructed in this study. The model was validated on fifteen herbaceous peonies cultivars from different latitudes. The results showed that ‘Meiju’, ‘Hang Baishao’, ‘Hongpan Tuojin’ and ‘Bo Baishao’ were assessed as Level I, which have strong growth adaptability and high ornamental values, and were recommended for promotion and application at low latitudes. The reliability and stability of the MCDM model were further confirmed by measuring the chlorophyll fluorescence of the selected adaptive cultivars ‘Meiju’ and ‘Hang Baishao’ and one maladaptive cultivar ‘Zhuguang’. This study could provide a reference for the introduction, breeding and application of perennials under everchanging unfavorable climatic conditions. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

19 pages, 3583 KiB

Open AccessArticle

Identification of Genetic Variations and Candidate Genes Responsible for Stalk Sugar Content and Agronomic Traits in Fresh Corn via GWAS across Multiple Environments

by Jianjian Chen, Jinming Cao, Yunlong Bian, Hui Zhang, Xiangnan Li, Zhenxing Wu, Guojin Guo and Guihua Lv

Int. J. Mol. Sci. 2022, 23(21), 13490; https://doi.org/10.3390/ijms232113490 - 04 Nov 2022

Cited by 3 | Viewed by 1484

Abstract

The stem and leaves of fresh corn plants can be used as green silage or can be converted to biofuels, and the stalk sugar content and yield directly determine the application value of fresh corn. To identify the genetic variations and candidate genes [...] Read more.

The stem and leaves of fresh corn plants can be used as green silage or can be converted to biofuels, and the stalk sugar content and yield directly determine the application value of fresh corn. To identify the genetic variations and candidate genes responsible for the related traits in fresh corn, the genome-wide scan and genome-wide association analysis (GWAS) were performed. A total of 32 selective regions containing 172 genes were detected between sweet and waxy corns. Using the stalk sugar content and seven other agronomic traits measured in four seasons over two years, the GWAS identified ninety-two significant single nucleotide polymorphisms (SNPs). Most importantly, seven SNPs associated with the stalk sugar content were detected across multiple environments, which could explain 13.68–17.82% of the phenotypic variation. Accessions differing in genotype for certain significant SNPs showed significant variation in the stalk sugar content and other agronomic traits, and the expression levels of six important candidate genes were significantly different between two materials with different stalk sugar content. The genetic variations and candidate genes provide valuable resources for future studies of the molecular mechanism of the stalk sugar content and establish the foundation for molecular marker-assisted breeding of fresh corn. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

15 pages, 2913 KiB

Open AccessArticle

Sucrose Facilitates Rhizome Development of Perennial Rice (Oryza longistaminata)

by Zhiquan Fan, Guanwen Huang, Yourong Fan and Jiangyi Yang

Int. J. Mol. Sci. 2022, 23(21), 13396; https://doi.org/10.3390/ijms232113396 - 02 Nov 2022

Cited by 6 | Viewed by 1911

Abstract

Compared with annual crops, perennial crops with longer growing seasons and deeper root systems can fix more sunlight energy, and have advantages in reducing soil erosion and saving water, fertilizer and pesticide inputs. Rice is one of the most important food crops in [...] Read more.

Compared with annual crops, perennial crops with longer growing seasons and deeper root systems can fix more sunlight energy, and have advantages in reducing soil erosion and saving water, fertilizer and pesticide inputs. Rice is one of the most important food crops in the world. Perennial rice can be of great significance for protecting the ecological environment and coping with the shortage of young farmers due to urbanization. Oryza longistaminata (OL) is a rhizomatous wild rice with an AA genome and has strong biotic and abiotic resistances. The AA genome makes OL easy to cross with cultivated rice, thus making it an ideal donor material for perennial rice breeding. Sucrose plays an important role in the development and growth of plants. In this study, OL seedlings were cultured in medium with different concentrations of sucrose, and it was found that sucrose of appropriate concentrations can promote the sprout of basal axillary buds and the subsequent development of rhizomes. In order to explore the molecular mechanism, comparative transcriptome analysis was carried out with OL cultured under two concentrations of sucrose, 20 g/L and 100 g/L, respectively. The results showed that the boost of sucrose to rhizome elongation may be due to the glucose and fructose, hydrolyzed from the absorbed sucrose by vacuolar acid invertase. In addition, the consequent increased osmotic pressure of the cells would promote water absorption, which is benefit for the cell elongation, eventually causing the rhizome elongation. These results may provide a reference for elucidating the regulatory mechanism of sucrose on the rhizome development of OL. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

17 pages, 3167 KiB

Open AccessArticle

The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice

by Guilian Xiao, Junzhi Zhou, Zhiheng Huo, Tong Wu, Yingchun Li, Yajing Li, Yanxia Wang and Mengcheng Wang

Int. J. Mol. Sci. 2022, 23(21), 12860; https://doi.org/10.3390/ijms232112860 - 25 Oct 2022

Cited by 3 | Viewed by 966

Abstract

The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- [...] Read more.

The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- and guanidine-ending (NNC and NNG) synonymous codons (SCs) were more pronounced than adenosine- and thymine-ending SCs (NNA and NNT) in both wild and cultivated species of Asian and African rice. The ratios of NNC/G to NNA/T codons gradually decreased following the rise in the number of introns, and the preference for NNA/T codons became more obvious in genes with more introns in cultivated rice when compared with those in wild rice. SCUB frequencies were heterogeneous across the exons, with a higher preference for NNA/T in internal exons than in terminal exons. The preference for NNA/T in internal but not terminal exons was more predominant in cultivated rice than in wild rice, with the difference between wild and cultivated rice becoming more remarkable with the rise in exon numbers. The difference in the ratios of codon combinations representing DNA methylation-mediated conversion from cytosine to thymine between wild and cultivated rice coincided with their difference in SCUB frequencies, suggesting that SCUB reveals the possible association between genetic and epigenetic variation during the domestication of rice. Similar patterns of SCUB shift in Asian and African rice indicate that genomic variation occurs in the same non-random manner. SCUB representing non-neutral synonymous mutations can provide insight into the mechanism of genomic variation in domestication and can be used for the genetic dissection of agricultural traits in rice and other crops. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

29 pages, 5676 KiB

Open AccessArticle

Genome-Wide Identification of Maize Protein Arginine Methyltransferase Genes and Functional Analysis of ZmPRMT1 Reveal Essential Roles in Arabidopsis Flowering Regulation and Abiotic Stress Tolerance

by Qiqi Ling, Jiayao Liao, Xiang Liu, Yue Zhou and Yexiong Qian

Int. J. Mol. Sci. 2022, 23(21), 12793; https://doi.org/10.3390/ijms232112793 - 24 Oct 2022

Cited by 4 | Viewed by 1608

Abstract

Histone methylation, as one of the important epigenetic regulatory mechanisms, plays a significant role in growth and developmental processes and stress responses of plants, via altering the methylation status or ratio of arginine and lysine residues of histone tails, which can affect the [...] Read more.

Histone methylation, as one of the important epigenetic regulatory mechanisms, plays a significant role in growth and developmental processes and stress responses of plants, via altering the methylation status or ratio of arginine and lysine residues of histone tails, which can affect the regulation of gene expression. Protein arginine methyltransferases (PRMTs) have been revealed to be responsible for histone methylation of specific arginine residues in plants, which is important for maintaining pleiotropic development and adaptation to abiotic stresses in plants. Here, for the first time, a total of eight PRMT genes in maize have been identified and characterized in this study, named as ZmPRMT1-8. According to comparative analyses of phylogenetic relationship and structural characteristics among PRMT gene family members from several representative species, all maize 8 PRMT proteins were categorized into three distinct subfamilies. Further, schematic structure and chromosome location analyses displayed evolutionarily conserved structure features and an unevenly distribution on maize chromosomes of ZmPRMT genes, respectively. The expression patterns of ZmPRMT genes in different tissues and under various abiotic stresses (heat, drought, and salt) were determined. The expression patterns of ZmPRMT genes indicated that they play a role in regulating growth and development and responses to abiotic stress. Eventually, to verify the biological roles of ZmPRMT genes, the transgenic Arabidopsis plants overexpressing ZmPRMT1 gene was constructed as a typical representative. The results demonstrated that overexpression of ZmPRMT1 can promote earlier flowering time and confer enhanced heat tolerance in transgenic Arabidopsis. Taken together, our results are the first to report the roles of ZmPRMT1 gene in regulating flowering time and resisting heat stress response in plants and will provide a vital theoretical basis for further unraveling the functional roles and epigenetic regulatory mechanism of ZmPRMT genes in maize growth, development and responses to abiotic stresses. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

19 pages, 3914 KiB

Open AccessArticle

Transcriptome Analysis Reveals the Genes Related to Pollen Abortion in a Cytoplasmic Male-Sterile Soybean (Glycine max (L.) Merr.)

by Zhiyuan Bai, Xianlong Ding, Ruijun Zhang, Yuhua Yang, Baoguo Wei, Shouping Yang and Junyi Gai

Int. J. Mol. Sci. 2022, 23(20), 12227; https://doi.org/10.3390/ijms232012227 - 13 Oct 2022

Cited by 6 | Viewed by 1607

Abstract

Cytoplasmic male sterility (CMS) lays a foundation for the utilization of heterosis in soybean. The soybean CMS line SXCMS5A is an excellent CMS line exhibiting 100% male sterility. Cytological analysis revealed that in SXCMS5A compared to its maintainer SXCMS5B, its tapetum was vacuolated [...] Read more.

Cytoplasmic male sterility (CMS) lays a foundation for the utilization of heterosis in soybean. The soybean CMS line SXCMS5A is an excellent CMS line exhibiting 100% male sterility. Cytological analysis revealed that in SXCMS5A compared to its maintainer SXCMS5B, its tapetum was vacuolated and abnormally developed. To identify the genes and metabolic pathways involving in pollen abortion of SXCMS5A, a comparative transcriptome analysis was conducted between SXCMS5A and SXCMS5B using flower buds. A total of 372,973,796 high quality clean reads were obtained from 6 samples (3 replicates for each material), and 840 differentially expressed genes (DEGs) were identified, including 658 downregulated and 182 upregulated ones in SXCMS5A compared to SXCMS5B. Among them, 13 DEGs, i.e., 12 open reading frames (ORFs) and 1 COX2, were mitochondrial genome genes in which ORF178 and ORF103c were upregulated in CMS lines and had transmembrane domain(s), therefore, identified as CMS candidate mitochondrial genes of SXCMS5A. Furthermore, numerous DEGs were associated with pollen wall development, carbohydrate metabolism, sugar transport, reactive oxygen species (ROS) metabolism and transcription factor. Some of them were further confirmed by quantitative real time PCR analysis between CMS lines with the same cytoplasmic source as SXCMS5A and their respective maintainer lines. The amount of soluble sugar and adenosine triphosphate and the activity of catalase and ascorbic acid oxidase showed that energy supply and ROS scavenging decreased in SXCMS5A compared to SXCMS5B. These findings provide valuable information for further understanding the molecular mechanism regulating the pollen abortion of soybean CMS. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

14 pages, 1983 KiB

Open AccessArticle

A Mutation in the MYBL2-1 Gene Is Associated with Purple Pigmentation in Brassica oleracea

by Emil Khusnutdinov, Alexander Artyukhin, Yuliya Sharifyanova and Elena V. Mikhaylova

Int. J. Mol. Sci. 2022, 23(19), 11865; https://doi.org/10.3390/ijms231911865 - 06 Oct 2022

Cited by 4 | Viewed by 1575

Abstract

Anthocyanins are well-known antioxidants that are beneficial for plants and consumers. Dihydroflavonol-4-reductase (DFR) is a key gene of anthocyanin biosynthesis, controlled by multiple transcription factors. Its expression can be enhanced by mutations in the negative regulator of anthocyanin biosynthesis myeloblastosis family [...] Read more.

Anthocyanins are well-known antioxidants that are beneficial for plants and consumers. Dihydroflavonol-4-reductase (DFR) is a key gene of anthocyanin biosynthesis, controlled by multiple transcription factors. Its expression can be enhanced by mutations in the negative regulator of anthocyanin biosynthesis myeloblastosis family transcription factor-like 2 (MYBL2). The expression profiles of the DFR gene were examined in 43 purple and green varieties of Brassica oleracea L., Brassica napus L., Brassica juncea L., and Brassica rapa L. MYBL2 gene expression was significantly reduced in purple varieties of B. oleracea, and green varieties of B. juncea. The MYBL2 gene sequences were screened for mutations that can affect pigmentation. Expression of the DFR gene was cultivar-specific, but in general it correlated with anthocyanin content and was higher in purple plants. Two single nucleotide polymorphysms (SNPs) were found at the beginning of the DNA-binding domain of MYBL2 gene in all purple varieties of B. oleracea. This mutation, leading to an amino acid substitution and the formation of a mononucleotide repeat (A)₈, significantly affects RNA structure. No other noteworthy mutations were found in the MYBL2 gene in green varieties of B. oleracea and other studied species. These results bring new insights into the regulation of anthocyanin biosynthesis in genus Brassica and provide opportunities for generation of new purple varieties with precise mutations introduced via genetic engineering and CRISPR/Cas. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

21 pages, 3520 KiB

Open AccessArticle

Physiological and Biochemical Regulation Mechanism of Exogenous Hydrogen Peroxide in Alleviating NaCl Stress Toxicity in Tartary Buckwheat (Fagopyrum tataricum (L.) Gaertn)

by Xin Yao, Meiliang Zhou, Jingjun Ruan, Yan Peng, Chao Ma, Weijiao Wu, Anjing Gao, Wenfeng Weng and Jianping Cheng

Int. J. Mol. Sci. 2022, 23(18), 10698; https://doi.org/10.3390/ijms231810698 - 14 Sep 2022

Cited by 8 | Viewed by 1535

Abstract

We aimed to elucidate the physiological and biochemical mechanism by which exogenous hydrogen peroxide (H₂O₂) alleviates salt stress toxicity in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn). Tartary buckwheat “Chuanqiao-2” under 150 mmol·L⁻¹ salt (NaCl) stress was treated [...] Read more.

We aimed to elucidate the physiological and biochemical mechanism by which exogenous hydrogen peroxide (H₂O₂) alleviates salt stress toxicity in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn). Tartary buckwheat “Chuanqiao-2” under 150 mmol·L⁻¹ salt (NaCl) stress was treated with 5 or 10 mmol·L⁻¹ H₂O₂, and seedling growth, physiology and biochemistry, and related gene expression were studied. Treatment with 5 mmol·L⁻¹ H₂O₂ significantly increased plant height (PH), fresh and dry weights of shoots (SFWs/SDWs) and roots (RFWs/RDWs), leaf length (LL) and area (LA), and relative water content (LRWC); increased chlorophyll a (Chl a) and b (Chl b) contents; improved fluorescence parameters; enhanced antioxidant enzyme activity and content; and reduced malondialdehyde (MDA) content. Expressions of all stress-related and enzyme-related genes were up-regulated. The F3′H gene (flavonoid synthesis pathway) exhibited similar up-regulation under 10 mmol·L⁻¹ H₂O₂ treatment. Correlation and principal component analyses showed that 5 mmol·L⁻¹ H₂O₂ could significantly alleviate the toxic effect of salt stress on Tartary buckwheat. Our results show that exogenous 5 mmol·L⁻¹ H₂O₂ can alleviate the inhibitory or toxic effects of 150 mmol·L⁻¹ NaCl stress on Tartary buckwheat by promoting growth, enhancing photosynthesis, improving enzymatic reactions, reducing membrane lipid peroxidation, and inducing the expression of related genes. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

18 pages, 8859 KiB

Open AccessArticle

Ectopic Expression of AeNAC83, a NAC Transcription Factor from Abelmoschus esculentus, Inhibits Growth and Confers Tolerance to Salt Stress in Arabidopsis

by Xuan Zhao, Tingting Wu, Shixian Guo, Junling Hu and Yihua Zhan

Int. J. Mol. Sci. 2022, 23(17), 10182; https://doi.org/10.3390/ijms231710182 - 05 Sep 2022

Cited by 6 | Viewed by 1621

Abstract

NAC transcription factors play crucial roles in plant growth, development and stress responses. Previously, we preliminarily identified that the transcription factor AeNAC83 gene was significantly up-regulated under salt stress in okra (Abelmoschus esculentus). Herein, we cloned the nuclear-localized AeNAC83 from okra [...] Read more.

NAC transcription factors play crucial roles in plant growth, development and stress responses. Previously, we preliminarily identified that the transcription factor AeNAC83 gene was significantly up-regulated under salt stress in okra (Abelmoschus esculentus). Herein, we cloned the nuclear-localized AeNAC83 from okra and identified its possible role in salt stress response and plant growth. The down-regulation of AeNAC83 caused by virus-induced gene silencing enhanced plant sensitivity to salt stress and increased the biomass accumulation of okra seedlings. Meanwhile, AeNAC83-overexpression Arabidopsis lines improved salt tolerance and exhibited many altered phenotypes, including small rosette, short primary roots, and promoted crown roots and root hairs. RNA-seq showed numerous genes at the transcriptional level that changed significantly in the AeNAC83-overexpression transgenic and the wild Arabidopsis with or without NaCl treatment, respectively. The expression of most phenylpropanoid and flavonoid biosynthesis-related genes was largely induced by salt stress. While genes encoding key proteins involved in photosynthesis were almost declined dramatically in AeNAC83-overexpression transgenic plants, and NaCl treatment further resulted in the down-regulation of these genes. Furthermore, DEGs encoding various plant hormone signal pathways were also identified. These results indicate that AeNAC83 is involved in resistance to salt stress and plant growth. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

18 pages, 3917 KiB

Open AccessArticle

LEAF TIP RUMPLED 1 Regulates Leaf Morphology and Salt Tolerance in Rice

by Jiajia Wang, Yiting Liu, Songping Hu, Jing Xu, Jinqiang Nian, Xiaoping Cao, Minmin Chen, Jiangsu Cen, Xiong Liu, Zhihai Zhang, Dan Liu, Li Zhu, Jiang Hu, Deyong Ren, Zhenyu Gao, Lan Shen, Guojun Dong, Qiang Zhang, Qing Li, Sibin Yu, Qian Qian and Guangheng Zhang Show full author list Hide full author list

Int. J. Mol. Sci. 2022, 23(15), 8818; https://doi.org/10.3390/ijms23158818 - 08 Aug 2022

Cited by 6 | Viewed by 2130

Abstract

Leaf morphology is one of the important traits related to ideal plant architecture and is an important factor determining rice stress resistance, which directly affects yield. Wax layers form a barrier to protect plants from different environmental stresses. However, the regulatory effect of [...] Read more.

Leaf morphology is one of the important traits related to ideal plant architecture and is an important factor determining rice stress resistance, which directly affects yield. Wax layers form a barrier to protect plants from different environmental stresses. However, the regulatory effect of wax synthesis genes on leaf morphology and salt tolerance is not well-understood. In this study, we identified a rice mutant, leaf tip rumpled 1 (ltr1), in a mutant library of the classic japonica variety Nipponbare. Phenotypic investigation of NPB and ltr1 suggested that ltr1 showed rumpled leaf with uneven distribution of bulliform cells and sclerenchyma cells, and disordered vascular bundles. A decrease in seed-setting rate in ltr1 led to decreased per-plant grain yield. Moreover, ltr1 was sensitive to salt stress, and LTR1 was strongly induced by salt stress. Map-based cloning of LTR1 showed that there was a 2-bp deletion in the eighth exon of LOC_Os02g40784 in ltr1, resulting in a frameshift mutation and early termination of transcription. Subsequently, the candidate gene was confirmed using complementation, overexpression, and knockout analysis of LOC_Os02g40784. Functional analysis of LTR1 showed that it was a wax synthesis gene and constitutively expressed in entire tissues with higher relative expression level in leaves and panicles. Moreover, overexpression of LTR1 enhanced yield in rice and LTR1 positively regulates salt stress by affecting water and ion homeostasis. These results lay a theoretical foundation for exploring the molecular mechanism of leaf morphogenesis and stress response, providing a new potential strategy for stress-tolerance breeding. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

15 pages, 1412 KiB

Open AccessArticle

Insights into the Genomic Regions and Candidate Genes of Senescence-Related Traits in Upland Cotton via GWAS

by Qibao Liu, Zhen Feng, Chenjue Huang, Jia Wen, Libei Li and Shuxun Yu

Int. J. Mol. Sci. 2022, 23(15), 8584; https://doi.org/10.3390/ijms23158584 - 02 Aug 2022

Cited by 4 | Viewed by 1751

Abstract

Senescence is the last stage of plant development and is controlled by both internal and external factors. Premature senescence significantly affects the yield and quality of cotton. However, the genetic architecture underlying cotton senescence remains unclear. In this study, genome-wide association studies (GWAS) [...] Read more.

Senescence is the last stage of plant development and is controlled by both internal and external factors. Premature senescence significantly affects the yield and quality of cotton. However, the genetic architecture underlying cotton senescence remains unclear. In this study, genome-wide association studies (GWAS) were performed based on 3,015,002 high-quality SNP markers from the resequencing data of 355 upland cotton accessions to detect genomic regions for cotton senescence. A total of 977 candidate genes within 55 senescence-related genomic regions (SGRs), SGR1–SGR55, were predicted. Gene ontology (GO) analysis of candidate genes revealed that a set of biological processes was enriched, such as salt stress, ethylene processes, and leaf senescence. Furthermore, in the leaf senescence GO term, one candidate gene was focused on: Gohir.A12G270900 (GhMKK9), located in SGR36, which encodes a protein of the MAP kinase kinase family. Quantitative real-time PCR (qRT-PCR) analysis showed that GhMKK9 was up-regulated in old cotton leaves. Overexpression of GhMKK9 in Arabidopsis accelerated natural leaf senescence. Virus-induced gene silencing (VIGS) of GhMKK9 in cotton increased drought tolerance. These results suggest that GhMKK9 is a positive regulator and might be involved in drought-induced senescence in cotton. The results provide new insights into the genetic basis of cotton senescence and will be useful for improving cotton breeding in the future. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

12 pages, 2563 KiB

Open AccessArticle

Five Rice Seed-Specific NF-YC Genes Redundantly Regulate Grain Quality and Seed Germination via Interfering Gibberellin Pathway

by Huayu Xu, Shufan Li, Bello Babatunde Kazeem, Abolore Adijat Ajadi, Jinjin Luo, Man Yin, Xinyong Liu, Lijuan Chen, Jiezheng Ying, Xiaohong Tong, Yifeng Wang, Baixiao Niu, Chen Chen, Xiaoshan Zeng and Jian Zhang

Int. J. Mol. Sci. 2022, 23(15), 8382; https://doi.org/10.3390/ijms23158382 - 29 Jul 2022

Cited by 4 | Viewed by 1930

Abstract

NF-YCs are important transcription factors with diverse functions in the plant kingdoms including seed development. NF-YC8, 9, 10, 11 and 12 are close homologs with similar seed-specific expression patterns. Despite the fact that some of the NF-YCs are functionally known; [...] Read more.

NF-YCs are important transcription factors with diverse functions in the plant kingdoms including seed development. NF-YC8, 9, 10, 11 and 12 are close homologs with similar seed-specific expression patterns. Despite the fact that some of the NF-YCs are functionally known; their biological roles have not been systematically explored yet, given the potential functional redundancy. In this study, we generated pentuple mutant pnfyc of NF-YC8-12 and revealed their functions in the regulation of grain quality and seed germination. pnfyc grains displayed significantly more chalkiness with abnormal starch granule packaging. pnfyc seed germination and post-germination growth are much slower than the wild-type NIP, largely owing to the GA-deficiency as exogenous GA was able to fully recover the germination phenotype. The RNA-seq experiment identified a total of 469 differentially expressed genes, and several GA-, ABA- and grain quality control-related genes might be transcriptionally regulated by the five NF-YCs, as revealed by qRT-PCR analysis. The results demonstrated the redundant functions of NF-YC8-12 in regulating GA pathways that underpin rice grain quality and seed germination, and shed a novel light on the functions of the seed-specific NF-YCs. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

18 pages, 6287 KiB

Open AccessArticle

Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress

by Nazir Ahmad, Bin Su, Sani Ibrahim, Lieqiong Kuang, Ze Tian, Xinfa Wang, Hanzhong Wang and Xiaoling Dun

Int. J. Mol. Sci. 2022, 23(14), 7958; https://doi.org/10.3390/ijms23147958 - 19 Jul 2022

Cited by 10 | Viewed by 2044

Abstract

An excellent root system is responsible for crops with high nitrogen-use efficiency (NUE). The current study evaluated the natural variations in 13 root- and biomass-related traits under a low nitrogen (LN) treatment in a rapeseed association panel. The studied traits exhibited significant phenotypic [...] Read more.

An excellent root system is responsible for crops with high nitrogen-use efficiency (NUE). The current study evaluated the natural variations in 13 root- and biomass-related traits under a low nitrogen (LN) treatment in a rapeseed association panel. The studied traits exhibited significant phenotypic differences with heritabilities ranging from 0.53 to 0.66, and most of the traits showed significant correlations with each other. The genome-wide association study (GWAS) found 51 significant and 30 suggestive trait–SNP associations that integrated into 14 valid quantitative trait loci (QTL) clusters and explained 5.7–21.2% phenotypic variance. In addition, RNA sequencing was performed at two time points to examine the differential expression of genes (DEGs) between high and low NUE lines. In total, 245, 540, and 399 DEGs were identified as LN stress-specific, high nitrogen (HN) condition-specific, and HNLN common DEGs, respectively. An integrated analysis of GWAS, weighted gene co-expression network, and DEGs revealed 16 genes involved in rapeseed root development under LN stress. Previous studies have reported that the homologs of seven out of sixteen potential genes control root growth and NUE. These findings revealed the genetic basis underlying nitrogen stress and provided worthwhile SNPs/genes information for the genetic improvement of NUE in rapeseed. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

Review

Jump to: Editorial, Research

10 pages, 664 KiB

Open AccessReview

Studies on Lotus Genomics and the Contribution to Its Breeding

by Huanhuan Qi, Feng Yu, Jiao Deng and Pingfang Yang

Int. J. Mol. Sci. 2022, 23(13), 7270; https://doi.org/10.3390/ijms23137270 - 30 Jun 2022

Cited by 3 | Viewed by 1872

Abstract

Lotus (Nelumbo nucifera), under the Nelumbonaceae family, is one of the relict plants possessing important scientific research and economic values. Because of this, much attention has been paid to this species on both its biology and breeding among the scientific community. [...] Read more.

Lotus (Nelumbo nucifera), under the Nelumbonaceae family, is one of the relict plants possessing important scientific research and economic values. Because of this, much attention has been paid to this species on both its biology and breeding among the scientific community. In the last decade, the genome of lotus has been sequenced, and several high-quality genome assemblies are available, which have significantly facilitated functional genomics studies in lotus. Meanwhile, re-sequencing of the natural and genetic populations along with different levels of omics studies have not only helped to classify the germplasm resources but also to identify the domestication of selected regions and genes controlling different horticultural traits. This review summarizes the latest progress of all these studies on lotus and discusses their potential application in lotus breeding. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Research on Plant Genomics and Breeding

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Related Special Issue

Published Papers (21 papers)

Editorial

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI