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Zhao Q, Zhao D, Wang Y, Li Y, Ni C, Su Z, Lian P, Liu S, Liu H, Zhang J, Yao D. Exploration of GmDof11- lncRNA13082 Module Regulating Oil Synthesis in Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39021146 DOI: 10.1021/acs.jafc.4c03084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Soybean (Glycine max [Linn.] Merr.) is an important oilseed crop. Although transcription factors (TFs) can coordinate the expression of mRNA and lncRNA, their coordination in the soybean oil synthesis pathway remains unclear. This study examined the interaction between the TF GmDof11 and lncRNA13082 and found that overexpression of GmDof11 led to an increase in the number of Arabidopsis seeds, thousand seed weight, crude protein, hydrolysis amino acid, and soluble sugar. Additionally, it reduced the triglyceride and starch contents and affected the proportion of fatty acids, increasing the contents of palmitic acid, stearic acid, and linolenic acid. The yeast two-hybrid experiments revealed that GmDof11 interacts with GmBCCP1, GmLEC1b, and GmFAB2 proteins. In the RT-qPCR analysis of transgenic soybean roots, it was found that GmDof11 can activate the production of lncRNA13082 and work in conjunction with lncRNA13082 to oversee oil synthesis and nutrient storage. Our research provides robust theoretical evidence for a comprehensive resolution of TF-lncRNA regulation in the soybean oil synthesis network.
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Affiliation(s)
- Qiuzhu Zhao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Dingyi Zhao
- College of Agronomy, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yashuo Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yuxin Li
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Chang Ni
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Zitong Su
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Panhang Lian
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
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Li Y, Zhao W, Tang J, Yue X, Gu J, Zhao B, Li C, Chen Y, Yuan J, Lin Y, Li Y, Kong F, He J, Wang D, Zhao TJ, Wang ZY. Identification of the domestication gene GmCYP82C4 underlying the major quantitative trait locus for the seed weight in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:62. [PMID: 38418640 DOI: 10.1007/s00122-024-04571-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
KEY MESSAGE A major quantitative trait locus (QTL) for the hundred-seed weight (HSW) was identified and confirmed in the two distinct soybean populations, and the target gene GmCYP82C4 underlying this locus was identified that significantly associated with soybean seed weight, and it was selected during the soybean domestication and improvement process. Soybean is a major oil crop for human beings and the seed weight is a crucial goal of soybean breeding. However, only a limited number of target genes underlying the quantitative trait loci (QTLs) controlling seed weight in soybean are known so far. In the present study, six loci associated with hundred-seed weight (HSW) were detected in the first population of 573 soybean breeding lines by genome-wide association study (GWAS), and 64 gene models were predicted in these candidate QTL regions. The QTL qHSW_1 exhibits continuous association signals on chromosome four and was also validated by region association study (RAS) in the second soybean population (409 accessions) with wild, landrace, and cultivar soybean accessions. There were seven genes in qHSW_1 candidate region by linkage disequilibrium (LD) block analysis, and only Glyma.04G035500 (GmCYP82C4) showed specifically higher expression in flowers, pods, and seeds, indicating its crucial role in the soybean seed development. Significant differences in HSW trait were detected when the association panels are genotyped by single-nucleotide polymorphisms (SNPs) in putative GmCYP82C4 promoter region. Eight haplotypes were generated by six SNPs in GmCYP82C4 in the second soybean population, and two superior haplotypes (Hap2 and Hap4) of GmCYP82C4 were detected with average HSW of 18.27 g and 18.38 g, respectively. The genetic diversity of GmCYP82C4 was analyzed in the second soybean population, and GmCYP82C4 was most likely selected during the soybean domestication and improvement process, leading to the highest proportion of Hap2 of GmCYP82C4 both in landrace and cultivar subpopulations. The QTLs and GmCYP82C4 identified in this study provide novel genetic resources for soybean seed weight trait, and the GmCYP82C4 could be used for soybean molecular breeding to develop desirable seed weight in the future.
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Affiliation(s)
- Yang Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Wenqian Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jiajun Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xiuli Yue
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Biyao Zhao
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Cong Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yanhang Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Jianbo Yuan
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yan Lin
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jin He
- College of Agriculture, Guizhou University, Guiyang, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, China
| | - Tuan-Jie Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China.
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Pinky, Jain R, Yadav A, Sharma R, Dhaka N. Emerging roles of long non-coding RNAs in regulating agriculturally important seed traits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108019. [PMID: 37714026 DOI: 10.1016/j.plaphy.2023.108019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
Seeds have enormous economic importance as source of calories, nutrition, edible oil, and biofuels. Therefore, seed traits like seed size and shape, weight, micronutrient content, oil content, quality, post-harvest sprouting, etc., are some of the main targets in crop improvement. Designing the strategies for their improvement benefits heavily from understanding the regulatory aspects of seed development. Recent studies indicate that long non-coding RNAs (lncRNAs) are one of the important regulators of seed development. They played a significant role in crop domestication by influencing seed traits. LncRNAs are conventionally defined as non-coding RNAs greater than 200 bp in length but lacking protein coding potential. Here we highlight the emerging pieces of evidence of lncRNA-mediated regulation of seed development through diverse mechanisms, for instance, by acting as target mimics or precursors of regulatory small RNAs or through chromatin remodeling and post-transcriptional repression. We also enumerate the insights from high-throughput transcriptomic studies from developing seeds of cereal, oilseed, biofuel, and pulse crops. We highlight the lncRNA candidates and lncRNA-mediated regulatory networks regulating seed development and related agronomic traits. Further, we discuss the potential of lncRNAs for improvement of agriculturally important seed traits through marker-assisted breeding and/or transgenic approaches.
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Affiliation(s)
- Pinky
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rubi Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhinandan Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
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Khemka N, Rajkumar MS, Garg R, Jain M. Genome-wide analysis suggests the potential role of lncRNAs during seed development and seed size/weight determination in chickpea. PLANTA 2022; 256:79. [PMID: 36094579 DOI: 10.1007/s00425-022-03986-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The integrated transcriptome data analyses suggested the plausible roles of lncRNAs during seed development in chickpea. The candidate lncRNAs associated with QTLs and those involved in miRNA-mediated seed size/weight determination in chickpea have been identified. Long non-coding RNAs (lncRNAs) are important regulators of various biological processes. Here, we identified lncRNAs at seven successive stages of seed development in small-seeded and large-seeded chickpea cultivars. In total, 4751 lncRNAs implicated in diverse biological processes were identified. Most of lncRNAs were conserved between the two cultivars, whereas only a few of them were conserved in other plants, suggesting their species-specificity. A large number of lncRNAs differentially expressed between the two chickpea cultivars associated with seed development-related processes were identified. The lncRNAs acting as precursors of miRNAs and those mimicking target protein-coding genes of miRNAs involved in seed size/weight determination, including HAIKU1, BIG SEEDS1, and SHB1, were also revealed. Further, lncRNAs located within seed size/weight associated quantitative trait loci were also detected. Overall, we present a comprehensive resource and identified candidate lncRNAs that may play important roles during seed development and seed size/weight determination in chickpea.
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Affiliation(s)
- Niraj Khemka
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mohan Singh Rajkumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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5
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Ma B, Zhang A, Zhao Q, Li Z, Lamboro A, He H, Li Y, Jiao S, Guan S, Liu S, Yao D, Zhang J. Genome-wide identification and analysis of long non-coding RNAs involved in fatty acid biosynthesis in young soybean pods. Sci Rep 2021; 11:7603. [PMID: 33828134 PMCID: PMC8027399 DOI: 10.1038/s41598-021-87048-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs of more than 200 nucleotides. To date, the roles of lncRNAs in soybean fatty acid synthesis have not been fully studied. Here, the low-linolenic acid mutant 'MT72' and the wild-type control 'JN18' were used as materials. The lncRNAs in young pods at 30 and 40 days (d) after flowering were systematically identified and analyzed using transcriptome sequencing technology combined with bioinformatics tools. A total of 39,324 lncRNAs and 561 differentially expressed lncRNAs were identified. A lncRNAs-miRNAs-protein-coding genes (mRNAs) network was constructed, and 46 lncRNAs, 46 miRNAs and 137 mRNAs were found to be correlated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 12 targeted mRNAs in the competing endogenous RNA network showed that these lncRNAs may be involved in the biological processes of fatty acid transport, lipid synthesis and cell division. Finally, the expression levels of differentially expressed lncRNAs, miRNAs and mRNAs were verified using qRT-PCR. The expression patterns of most genes were consistent with the sequencing results. In conclusion, new information was provided for the study of fatty acid synthesis by lncRNAs in young soybean pods.
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Affiliation(s)
- Bohan Ma
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Aijing Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Qiuzhu Zhao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Zeyuan Li
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Abraham Lamboro
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Haobo He
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yue Li
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Suqi Jiao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Shuyan Guan
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Siyan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, China.
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6
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Li M, Chen L, Zeng J, Razzaq MK, Xu X, Xu Y, Wang W, He J, Xing G, Gai J. Identification of Additive-Epistatic QTLs Conferring Seed Traits in Soybean Using Recombinant Inbred Lines. FRONTIERS IN PLANT SCIENCE 2020; 11:566056. [PMID: 33362807 PMCID: PMC7758492 DOI: 10.3389/fpls.2020.566056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/29/2020] [Indexed: 05/31/2023]
Abstract
Seed weight and shape are important agronomic traits that affect soybean quality and yield. In the present study, we used image analysis software to evaluate 100-seed weight and seed shape traits (length, width, perimeter, projection area, length/width, and weight/projection area) of 155 novel recombinant inbred soybean lines (NJRISX) generated by crossing "Su88-M21" and "XYXHD". We examined quantitative trait loci (QTLs) associated with the six traits (except seed weight per projection area), and identified 42 additive QTLs (5-8 QTLs per trait) accounting for 24.9-37.5% of the phenotypic variation (PV). Meanwhile, 2-4 epistatic QTL pairs per trait out of a total of 18 accounted for 2.5-7.2% of the PV; and unmapped minor QTLs accounted for the remaining 35.0-56.7% of the PV. A total of 28 additive and 11 epistatic QTL pairs were concentrated in nine joint QTL segments (JQSs), indicating that QTLs associated with seed weight and shape are closely related and interacted. An interaction was also detected between additive and epistatic QTL pairs and environment, which made significant contributions of 1.4-9.5% and 0.4-0.8% to the PV, respectively. We annotated 18 candidate genes in the nine JQSs, which were important for interpreting the close relationships among the six traits. These findings indicate that examining the interactions between closely related traits rather than only analyzing individual trait provides more useful insight into the genetic system of the interrelated traits for which there has been limited QTL information.
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7
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Kang X, Cai J, Chen Y, Yan Y, Yang S, He R, Wang D, Zhu Y. Pod-shattering characteristics differences between two groups of soybeans are associated with specific changes in gene expression. Funct Integr Genomics 2020; 20:201-210. [PMID: 31456133 DOI: 10.1007/s10142-019-00702-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/10/2019] [Accepted: 07/22/2019] [Indexed: 12/01/2022]
Abstract
Soybean is an economically important leguminous crop, and pod dehiscence of soybean could cause huge yield loss. In this study, we measured fruit-cracking forces and percentages of dehisced pods for ten soybean accessions, then separated them into two groups as shattering-sensitive (SS) and shattering-resistant (SR) soybeans. Pod transcriptomes from these two groups were analyzed, and 225 differentially expressed genes (DEGs) were identified between SS and SR soybeans. Some of these DEGs have been previously reported to be associated with pod dehiscence in soybean. The expression patterns of selected DEGs were validated by real-time quantitative reverse transcription PCR, which confirmed the expression changes found in RNA-seq analysis. We also de novo identified 246 soybean pod-long intergenic ncRNAs (lincRNAs), 401 intronic lncRNAs, and 23 antisense lncRNAs from these transcriptomes. Furthermore, genes and lincRNAs co-expression network analysis showed that there are distinct expression patterns between SS and SR soybeans in some co-expression modules. In conclusion, we systematically investigated potential genes and molecular pathways as candidates for differences in soybean pod dehiscence and will provide a useful resource for molecular breeding of soybeans.
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Affiliation(s)
- Xiang Kang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Jingjing Cai
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yexin Chen
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yuchuan Yan
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Songtao Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China.
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China.
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Karikari B, Chen S, Xiao Y, Chang F, Zhou Y, Kong J, Bhat JA, Zhao T. Utilization of Interspecific High-Density Genetic Map of RIL Population for the QTL Detection and Candidate Gene Mining for 100-Seed Weight in Soybean. FRONTIERS IN PLANT SCIENCE 2019; 10:1001. [PMID: 31552060 PMCID: PMC6737081 DOI: 10.3389/fpls.2019.01001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/17/2019] [Indexed: 05/26/2023]
Abstract
Seed-weight is one of the most important traits determining soybean yield. Hence, it is prerequisite to have detailed understanding of the genetic basis regulating seed-weight for the development of improved cultivars. In this regard, the present study used high-density interspecific linkage map of NJIR4P recombinant inbred population evaluated in four different environments to detect stable Quantitative trait loci (QTLs) as well as mine candidate genes for 100-seed weight. In total, 19 QTLs distributed on 12 chromosomes were identified in all individual environments plus combined environment, out of which seven were novel and eight are stable identified in more than one environment. However, all the novel QTLs were minor (R 2 < 10%). The remaining 12 QTLs detected in this study were co-localized with the earlier reported QTLs with narrow genomic regions, and out of these only 2 QTLs were major (R 2 > 10%) viz., qSW-17-1 and qSW-17-4. Beneficial alleles of all identified QTLs were derived from cultivated soybean parent (Nannong493-1). Based on Protein ANalysis THrough Evolutionary Relationships, gene annotation information, and literature search, 29 genes within 5 stable QTLs were predicted to be possible candidate genes that might regulate seed-weight/size in soybean. However, it needs further validation to confirm their role in seed development. In conclusion, the present study provides better understanding of trait genetics and candidate gene information through the use high-density inter-specific bin map, and also revealed considerable scope for genetic improvement of 100-seed weight in soybean using marker-assisted breeding.
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Affiliation(s)
| | | | | | | | | | | | - Javaid Akhter Bhat
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tuanjie Zhao
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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9
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Czajkowska BI, Jones G, Brown TA. Diversity of a wall-associated kinase gene in wild and cultivated barley. PLoS One 2019; 14:e0218526. [PMID: 31247008 PMCID: PMC6597065 DOI: 10.1371/journal.pone.0218526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/04/2019] [Indexed: 11/18/2022] Open
Abstract
Domestication of barley and other cereals was accompanied by an increase in seed size which has been ascribed to human selection, large seeds being preferred by early farmers or favoured by cultivation practices such as deep sowing. An alternative suggestion is that the increase in seed size was an indirect consequence of selection for plants with more vigorous growth. To begin to address the latter hypothesis we studied the diversity of HvWAK1, a wall-associated kinase gene involved in root proliferation, in 220 wild barley accessions and 200 domesticated landraces. A 3655-bp sequence comprising the gene and upstream region contained 69 single nucleotide polymorphisms (SNPs), one indel and four short tandem repeats. A network of 50 haplotypes revealed a complex evolutionary relationship, but with landraces largely restricted to two parts of the topology. SNPs in the HvWAK1 coding region resulted in nonsynonymous substitutions at nine positions in the translation product, but none of these changes were predicted to have a significant effect on the protein structure. In contrast, the region upstream of the coding sequence contained five SNPs that were invariant in the domesticated population, fixation of these SNPs decreasing the likelihood that the upstream of a pair of TATA boxes and transcription start sites would be used to promote transcription of HvWAK1. The sequence diversity therefore suggests that the cis-regulatory region of HvWAK1 might have been subject to selection during barley domestication. The extent of root proliferation has been linked with traits such as above-ground biomass, so selection for particular cis-regulatory variants of HvWAK1 would be consistent with the hypothesis that seed size increases during domestication were the indirect consequence of selection for plants with increased growth vigour.
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Affiliation(s)
- Beata I. Czajkowska
- School of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Glynis Jones
- Department of Archaeology, University of Sheffield, Northgate House, Sheffield, United Kingdom
| | - Terence A. Brown
- School of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
- * E-mail:
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10
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Wu J, Liu C, Liu Z, Li S, Li D, Liu S, Huang X, Liu S, Yukawa Y. Pol III-Dependent Cabbage BoNR8 Long ncRNA Affects Seed Germination and Growth in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:421-435. [PMID: 30462304 DOI: 10.1093/pcp/pcy220] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/02/2018] [Indexed: 05/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts longer than 200 nt that are distributed widely in organisms and play many physiological roles. The BoNR8 lncRNA is a 272 nt long transcript yielded by RNA polymerase III in cabbage that was identified as the closest homolog of the AtR8 lncRNA in Arabidopsis. The BoNR8 lncRNA was expressed extensively in the epidermal tissue in the root elongation zone of germinated seeds, and its accumulation was induced by abiotic stresses, auxins and ABA. To investigate the correlation between the BoNR8 lncRNA and germination, BoNR8-overexpressing Arabidopsis plants (BoNR8-AtOX) were prepared. Three independent BoNR8-AtOX lines showed less primary root elongation, incomplete silique development and decreased germination rates. The germination efficiencies were affected strongly by ABA and slightly by salt stress, and ABA-related gene expression was changed in the BoNR8-AtOX lines.
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Affiliation(s)
- Juan Wu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, PR, Harbin, China
| | - Chunxiao Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Ziguang Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, PR, Harbin, China
| | - Shuang Li
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Dandan Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Shengyi Liu
- Mudanjiang Medical University, Mudanjiang, Heilongjiang, China
| | - Xiaoqing Huang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - ShenKui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Lin'an, Hangzhou, China
| | - Yasushi Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
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