1
|
Ma R, Huang W, Hu Q, Tian G, An J, Fang T, Liu J, Hou J, Zhao M, Sun L. Tandemly duplicated MYB genes are functionally diverged in the regulation of anthocyanin biosynthesis in soybean. PLANT PHYSIOLOGY 2024; 194:2549-2563. [PMID: 38235827 DOI: 10.1093/plphys/kiae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/13/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
Gene duplications have long been recognized as a driving force in the evolution of genes, giving rise to novel functions. The soybean (Glycine max) genome is characterized by a large number of duplicated genes. However, the extent and mechanisms of functional divergence among these duplicated genes in soybean remain poorly understood. In this study, we revealed that 4 MYB genes (GmMYBA5, GmMYBA2, GmMYBA1, and Glyma.09g235000)-presumably generated by tandem duplication specifically in the Phaseoleae lineage-exhibited a stronger purifying selection in soybean compared to common bean (Phaseolus vulgaris). To gain insights into the diverse functions of these tandemly duplicated MYB genes in anthocyanin biosynthesis, we examined the expression, transcriptional activity, induced metabolites, and evolutionary history of these 4 MYB genes. Our data revealed that Glyma.09g235000 is a pseudogene, while the remaining 3 MYB genes exhibit strong transcriptional activation activity, promoting anthocyanin biosynthesis in different soybean tissues. GmMYBA5, GmMYBA2, and GmMYBA1 induced anthocyanin accumulation by upregulating the expression of anthocyanin pathway-related genes. Notably, GmMYBA5 showed a lower capacity for gene induction compared to GmMYBA2 and GmMYBA1. Metabolomics analysis further demonstrated that GmMYBA5 induced distinct anthocyanin accumulation in Nicotiana benthamiana leaves and soybean hairy roots compared to GmMYBA2 and GmMYBA1, suggesting their functional divergence leading to the accumulation of different metabolites accumulation following gene duplication. Together, our data provide evidence of functional divergence within the MYB gene cluster following tandem duplication, which sheds light on the potential evolutionary directions of gene duplications during legume evolution.
Collapse
Affiliation(s)
- Ruirui Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Wenxuan Huang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Quan Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Guo Tian
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie An
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ting Fang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jia Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jingjing Hou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lianjun Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
2
|
Biová J, Kaňovská I, Chan YO, Immadi MS, Joshi T, Bilyeu K, Škrabišová M. Natural and artificial selection of multiple alleles revealed through genomic analyses. Front Genet 2024; 14:1320652. [PMID: 38259621 PMCID: PMC10801239 DOI: 10.3389/fgene.2023.1320652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
Genome-to-phenome research in agriculture aims to improve crops through in silico predictions. Genome-wide association study (GWAS) is potent in identifying genomic loci that underlie important traits. As a statistical method, increasing the sample quantity, data quality, or diversity of the GWAS dataset positively impacts GWAS power. For more precise breeding, concrete candidate genes with exact functional variants must be discovered. Many post-GWAS methods have been developed to narrow down the associated genomic regions and, ideally, to predict candidate genes and causative mutations (CMs). Historical natural selection and breeding-related artificial selection both act to change the frequencies of different alleles of genes that control phenotypes. With higher diversity and more extensive GWAS datasets, there is an increased chance of multiple alleles with independent CMs in a single causal gene. This can be caused by the presence of samples from geographically isolated regions that arose during natural or artificial selection. This simple fact is a complicating factor in GWAS-driven discoveries. Currently, none of the existing association methods address this issue and need to identify multiple alleles and, more specifically, the actual CMs. Therefore, we developed a tool that computes a score for a combination of variant positions in a single candidate gene and, based on the highest score, identifies the best number and combination of CMs. The tool is publicly available as a Python package on GitHub, and we further created a web-based Multiple Alleles discovery (MADis) tool that supports soybean and is hosted in SoyKB (https://soykb.org/SoybeanMADisTool/). We tested and validated the algorithm and presented the utilization of MADis in a pod pigmentation L1 gene case study with multiple CMs from natural or artificial selection. Finally, we identified a candidate gene for the pod color L2 locus and predicted the existence of multiple alleles that potentially cause loss of pod pigmentation. In this work, we show how a genomic analysis can be employed to explore the natural and artificial selection of multiple alleles and, thus, improve and accelerate crop breeding in agriculture.
Collapse
Affiliation(s)
- Jana Biová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| | - Ivana Kaňovská
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| | - Yen On Chan
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
| | - Manish Sridhar Immadi
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
| | - Trupti Joshi
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
- Department of Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri-Columbia, Columbia, MO, United States
| | - Kristin Bilyeu
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, Columbia, MO, United States
| | - Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| |
Collapse
|
3
|
Lemay MA, de Ronne M, Bélanger R, Belzile F. k-mer-based GWAS enhances the discovery of causal variants and candidate genes in soybean. THE PLANT GENOME 2023; 16:e20374. [PMID: 37596724 DOI: 10.1002/tpg2.20374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/19/2023] [Indexed: 08/20/2023]
Abstract
Genome-wide association studies (GWAS) are powerful statistical methods that detect associations between genotype and phenotype at genome scale. Despite their power, GWAS frequently fail to pinpoint the causal variant or the gene controlling a given trait in crop species. Assessing genetic variants other than single-nucleotide polymorphisms (SNPs) could alleviate this problem. In this study, we tested the potential of structural variant (SV)- and k-mer-based GWAS in soybean by applying these methods as well as conventional SNP/indel-based GWAS to 13 traits. We assessed the performance of each GWAS approach based on loci for which the causal genes or variants were known from previous genetic studies. We found that k-mer-based GWAS was the most versatile approach and the best at pinpointing causal variants or candidate genes. Moreover, k-mer-based analyses identified promising candidate genes for loci related to pod color, pubescence form, and resistance to Phytophthora sojae. In our dataset, SV-based GWAS did not add value compared to k-mer-based GWAS and may not be worth the time and computational resources invested. Despite promising results, significant challenges remain regarding the downstream analysis of k-mer-based GWAS. Notably, better methods are needed to associate significant k-mers with sequence variation. Our results suggest that coupling k-mer- and SNP/indel-based GWAS is a powerful approach for discovering candidate genes in crop species.
Collapse
Affiliation(s)
- Marc-André Lemay
- Département de phytologie, Université Laval, Québec, QC, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, QC, Canada
- Centre de recherche et d'innovation sur les végétaux, Université Laval, Québec, QC, Canada
| | - Maxime de Ronne
- Département de phytologie, Université Laval, Québec, QC, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, QC, Canada
- Centre de recherche et d'innovation sur les végétaux, Université Laval, Québec, QC, Canada
| | - Richard Bélanger
- Département de phytologie, Université Laval, Québec, QC, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, QC, Canada
- Centre de recherche et d'innovation sur les végétaux, Université Laval, Québec, QC, Canada
| | - François Belzile
- Département de phytologie, Université Laval, Québec, QC, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, QC, Canada
- Centre de recherche et d'innovation sur les végétaux, Université Laval, Québec, QC, Canada
| |
Collapse
|
4
|
Song J, Xu R, Guo Q, Wu C, Li Y, Wang X, Wang J, Qiu LJ. An omics strategy increasingly improves the discovery of genetic loci and genes for seed-coat color formation in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:71. [PMID: 37663546 PMCID: PMC10471558 DOI: 10.1007/s11032-023-01414-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/13/2023] [Indexed: 09/05/2023]
Abstract
The phenotypic color of seeds is a complex agronomic trait and has economic and biological significance. The genetic control and molecular regulation mechanisms have been extensively studied. Here, we used a multi-omics strategy to explore the color formation in soybean seeds at a big data scale. We identified 13 large quantitative trait loci (QTL) for color with bulk segregating analysis in recombinant inbreeding lines. GWAS analysis of colors and decomposed attributes in 763 germplasms revealed associated SNP sites perfectly falling in five major QTL, suggesting inherited regulation on color during natural selection. Further transcriptomics analysis before and after color accumulation revealed 182 differentially expression genes (DEGs) in the five QTL, including known genes CHS, MYB, and F3'H involved in pigment accumulation. More DEGs with consistently upregulation or downregulation were identified as shared regulatory genes for two or more color formations while some DEGs were only for a specific color formation. For example, five upregulated DEGs in QTL qSC-3 were in flavonoid biosynthesis responsible for black and brown seed. The DEG (Glyma.08G085400) was identified in the purple seed only, which encodes gibberellin 2-beta-dioxygenase in the metabolism of colorful terpenoids. The candidate genes are involved in flavonoid biosynthesis, transcription factor regulation, gibberellin and terpenoid metabolism, photosynthesis, ascorbate and aldarate metabolism, and lipid metabolism. Seven differentially expressed transcription factors were also speculated that may regulate color formation, including a known MYB. The finds expand QTL and gene candidates for color formation, which could guide to breed better cultivars with designed colors. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01414-z.
Collapse
Affiliation(s)
- Jian Song
- Yangtze University, Jingzhou, 434025 Hubei P.R. China
| | - Ruixin Xu
- Yangtze University, Jingzhou, 434025 Hubei P.R. China
| | - Qingyuan Guo
- Yangtze University, Jingzhou, 434025 Hubei P.R. China
| | - Caiyu Wu
- Yangtze University, Jingzhou, 434025 Hubei P.R. China
| | - Yinghui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
| | - Jun Wang
- Yangtze University, Jingzhou, 434025 Hubei P.R. China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| |
Collapse
|
5
|
Lyu X, Li YH, Li Y, Li D, Han C, Hong H, Tian Y, Han L, Liu B, Qiu LJ. The domestication-associated L1 gene encodes a eucomic acid synthase pleiotropically modulating pod pigmentation and shattering in soybean. MOLECULAR PLANT 2023:S1674-2052(23)00169-7. [PMID: 37433301 DOI: 10.1016/j.molp.2023.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/23/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023]
Abstract
Pod coloration is a domestication-related trait in soybean, with modern cultivars typically displaying brown or tan pods, while their wild relative, Glycine soja, possesses black pods. However, the factors regulating this color variation remain unknown. In this study, we cloned and characterized L1, the classical locus responsible for black pods in soybean. By using map-based cloning and genetic analyses, we identified the causal gene of L1 and revealed that it encodes a hydroxymethylglutaryl-coenzyme A (CoA) lyase-like (HMGL-like) domain protein. Biochemical assays showed that L1 functions as a eucomic acid synthase and facilitates the synthesis of eucomic acid and piscidic acid, both of which contribute to coloration of pods and seed coats in soybean. Interestingly, we found that L1 plants are more prone to pod shattering under light exposure than l1 null mutants because dark pigmentation increases photothermal efficiency. Hence, pleiotropic effects of L1 on pod color and shattering, as well as seed pigmentation, likely contributed to the preference for l1 alleles during soybean domestication and improvement. Collectively, our study provides new insights into the mechanism of pod coloration and identifies a new target for future de novo domestication of legume crops.
Collapse
Affiliation(s)
- Xiangguang Lyu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Yanfei Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People''s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Delin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Chao Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Huilong Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Yu Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Lida Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
| |
Collapse
|
6
|
Kafer JM, Molinari MDC, Henning FA, Koltun A, Marques VV, Marin SRR, Nepomuceno AL, Mertz-Henning LM. Transcriptional Profile of Soybean Seeds with Contrasting Seed Coat Color. PLANTS (BASEL, SWITZERLAND) 2023; 12:1555. [PMID: 37050181 PMCID: PMC10097363 DOI: 10.3390/plants12071555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Soybean is the primary source of vegetable protein and is used for various purposes, mainly to feed animals. This crop can have diverse seed coat colors, varying from yellow, black, brown, and green to bicolor. Black seed coat cultivars have already been assigned as favorable for both seed and grain production. Thus, this work aimed to identify genes associated with soybean seed quality by comparing the transcriptomes of soybean seeds with contrasting seed coat colors. The results from RNA-seq analyses were validated with real-time PCR using the cultivar BRS 715A (black seed coat) and the cultivars BRS 413 RR and DM 6563 IPRO (yellow seed coat). We found 318 genes differentially expressed in all cultivars (freshly harvested seeds and seeds stored in cold chamber). From the in silico analysis of the transcriptomes, the following genes were selected and validated with RT-qPCR: ACS1, ACSF3, CYP90A1, CYP710A1, HCT, CBL, and SAHH. These genes are genes induced in the black seed coat cultivar and are part of pathways responsible for ethylene, lipid, brassinosteroid, lignin, and sulfur amino acid biosynthesis. The BRSMG 715A gene has almost 4times more lignin than the yellow seed coat cultivars. These attributes are related to the BRSMG 715A cultivar's higher seed quality, which translates to more longevity and resistance to moisture and mechanical damage. Future silencing studies may evaluate the knockout of these genes to better understand the biology of soybean seeds with black seed coat.
Collapse
Affiliation(s)
- João M. Kafer
- Biotechnology Department, Londrina State University, Londrina 86057-970, PR, Brazil
| | - Mayla D. C. Molinari
- Arthur Bernardes Foundation, Embrapa Soja, Londrina 86085-981, PR, Brazil; (M.D.C.M.); (V.V.M.)
| | - Fernando A. Henning
- Embrapa Soja, Londrina 86085-981, PR, Brazil; (F.A.H.); (S.R.R.M.); (A.L.N.)
| | - Alessandra Koltun
- Agronomy Department, State University of Maringá, Maringá 87020-900, PR, Brazil;
| | - Viviani V. Marques
- Arthur Bernardes Foundation, Embrapa Soja, Londrina 86085-981, PR, Brazil; (M.D.C.M.); (V.V.M.)
| | - Silvana R. R. Marin
- Embrapa Soja, Londrina 86085-981, PR, Brazil; (F.A.H.); (S.R.R.M.); (A.L.N.)
| | | | | |
Collapse
|
7
|
Chan YO, Dietz N, Zeng S, Wang J, Flint-Garcia S, Salazar-Vidal MN, Škrabišová M, Bilyeu K, Joshi T. The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis. BMC Genomics 2023; 24:107. [PMID: 36899307 PMCID: PMC10007842 DOI: 10.1186/s12864-023-09161-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/31/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize. RESULTS The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes. CONCLUSIONS The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species.
Collapse
Affiliation(s)
- Yen On Chan
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, USA.,Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA
| | - Nicholas Dietz
- Division of Plant Science and Technology, University of Missouri-Columbia, Columbia, MO, USA
| | - Shuai Zeng
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA
| | - Juexin Wang
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA.,Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA
| | - Sherry Flint-Garcia
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, Columbia, MO, USA
| | - M Nancy Salazar-Vidal
- Division of Plant Science and Technology, University of Missouri-Columbia, Columbia, MO, USA.,Department of Evolution and Ecology, University of California-Davis, Davis, CA, USA
| | - Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacky University in Olomouc, Olomouc, Czech Republic
| | - Kristin Bilyeu
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, Columbia, MO, USA.
| | - Trupti Joshi
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, USA. .,Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA. .,Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA. .,Department of Health Management and Informatics, University of Missouri-Columbia, Columbia, MO, USA.
| |
Collapse
|
8
|
Wang H, Cui C, Liu Y, Zheng Y, Zhao Y, Chen X, Wang X, Jing B, Mei H, Wang Z. Genetic mapping of QTLs controlling brown seed coat traits by genome resequencing in sesame ( Sesamum indicum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1131975. [PMID: 36909448 PMCID: PMC9995652 DOI: 10.3389/fpls.2023.1131975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Sesame seeds have become an irreplaceable source of edible oils and food products with rich nutrients and a unique flavor, and their metabolite contents and physiological functions vary widely across different seed coat colors. Although the quantitative trait loci (QTLs) for genetic variation in seed coat color have been extensively investigated, the identification of unique genetic loci for intermediate colors such as brown has not been reported due to their complexity. METHODS Here, we crossed the white sesame 'Yuzhi No. 8' (YZ8) and the brown sesame 'Yanzhou Erhongpi' (YZEHP) to construct a recombinant inbred line (RIL) population with consecutive self-fertilization for ten generations. RESULTS The selfed F1 seeds were brown which was controlled by a dominant gene. Based on the genotyping by whole-genome resequencing of the RILs, a major-effect QTL for brown coat color was identified through both bulk segregant analysis (BSA) and genetic linkage mapping in sesame, which was located within a 1.19 Mb interval on chromosome 6 (qBSCchr6). Moreover, we found that the YZEHP seed coat initially became pigmented at 20 days post-anthesis (DPA) and was substantially colored at 30 DPA. We screened 13 possible candidate genes based on the effects of genetic variants on protein coding and predicted gene functions. Furthermore, qRT‒PCR was used to verify the expression patterns of these genes in different post-anthesis developmental periods. We noted that in comparison to YZ8 seeds, YZEHP seeds had expression of SIN_1023239 that was significantly up-regulated 2.5-, 9.41-, 6.0-, and 5.9-fold at 15, 20, 25, and 30 DPA, respectively, which was consistent with the pattern of brown seed coat pigment accumulation. DISCUSSION This study identified the first major-effect QTL for the control of the brown seed coat trait in sesame. This finding lays the foundation for further fine mapping and cloning as well as investigating the regulatory mechanism of seed coat color in sesame.
Collapse
Affiliation(s)
- Han Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Chengqi Cui
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Yanyang Liu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Yiqing Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xiaoqin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xueqi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Bing Jing
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Hongxian Mei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| |
Collapse
|
9
|
Duraiswamy A, Sneha A. NM, Jebakani K. S, Selvaraj S, Pramitha J. L, Selvaraj R, Petchiammal K. I, Kather Sheriff S, Thinakaran J, Rathinamoorthy S, Kumar P. R. Genetic manipulation of anti-nutritional factors in major crops for a sustainable diet in future. FRONTIERS IN PLANT SCIENCE 2023; 13:1070398. [PMID: 36874916 PMCID: PMC9976781 DOI: 10.3389/fpls.2022.1070398] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
The consumption of healthy food, in order to strengthen the immune system, is now a major focus of people worldwide and is essential to tackle the emerging pandemic concerns. Moreover, research in this area paves the way for diversification of human diets by incorporating underutilized crops which are highly nutritious and climate-resilient in nature. However, although the consumption of healthy foods increases nutritional uptake, the bioavailability of nutrients and their absorption from foods also play an essential role in curbing malnutrition in developing countries. This has led to a focus on anti-nutrients that interfere with the digestion and absorption of nutrients and proteins from foods. Anti-nutritional factors in crops, such as phytic acid, gossypol, goitrogens, glucosinolates, lectins, oxalic acid, saponins, raffinose, tannins, enzyme inhibitors, alkaloids, β-N-oxalyl amino alanine (BOAA), and hydrogen cyanide (HCN), are synthesized in crop metabolic pathways and are interconnected with other essential growth regulation factors. Hence, breeding with the aim of completely eliminating anti-nutrition factors tends to compromise desirable features such as yield and seed size. However, advanced techniques, such as integrated multi-omics, RNAi, gene editing, and genomics-assisted breeding, aim to breed crops in which negative traits are minimized and to provide new strategies to handle these traits in crop improvement programs. There is also a need to emphasize individual crop-based approaches in upcoming research programs to achieve smart foods with minimum constraints in future. This review focuses on progress in molecular breeding and prospects for additional approaches to improve nutrient bioavailability in major crops.
Collapse
Affiliation(s)
- Aishwarya Duraiswamy
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Nancy Mano Sneha A.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Sherina Jebakani K.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Sellakumar Selvaraj
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Lydia Pramitha J.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Ramchander Selvaraj
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Indira Petchiammal K.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Sharmili Kather Sheriff
- Agronomy, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Jenita Thinakaran
- Horticulture, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Samundeswari Rathinamoorthy
- Crop Physiology, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Ramesh Kumar P.
- Plant Biochemistry, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| |
Collapse
|
10
|
Yuan B, Yuan C, Wang Y, Liu X, Qi G, Wang Y, Dong L, Zhao H, Li Y, Dong Y. Identification of genetic loci conferring seed coat color based on a high-density map in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:968618. [PMID: 35979081 PMCID: PMC9376438 DOI: 10.3389/fpls.2022.968618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/11/2022] [Indexed: 05/26/2023]
Abstract
Seed coat color is a typical evolutionary trait. Identification of the genetic loci that control seed coat color during the domestication of wild soybean could clarify the genetic variations between cultivated and wild soybean. We used 276 F10 recombinant inbred lines (RILs) from the cross between a cultivated soybean (JY47) and a wild soybean (ZYD00321) as the materials to identify the quantitative trait loci (QTLs) for seed coat color. We constructed a high-density genetic map using re-sequencing technology. The average distance between adjacent markers was 0.31 cM on this map, comprising 9,083 bin markers. We identified two stable QTLs (qSC08 and qSC11) for seed coat color using this map, which, respectively, explained 21.933 and 26.934% of the phenotypic variation. Two candidate genes (CHS3C and CHS4A) in qSC08 were identified according to the parental re-sequencing data and gene function annotations. Five genes (LOC100786658, LOC100801691, LOC100806824, LOC100795475, and LOC100787559) were predicted in the novel QTL qSC11, which, according to gene function annotations, might control seed coat color. This result could facilitate the identification of beneficial genes from wild soybean and provide useful information to clarify the genetic variations for seed coat color in cultivated and wild soybean.
Collapse
Affiliation(s)
- Baoqi Yuan
- College of Agronomy, Jilin Agricultural University, Changchun, China
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Cuiping Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Yumin Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Xiaodong Liu
- Crop Germplasm Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Guangxun Qi
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Yingnan Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Lingchao Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Hongkun Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Yuqiu Li
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Yingshan Dong
- College of Agronomy, Jilin Agricultural University, Changchun, China
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| |
Collapse
|
11
|
Lin Y, Laosatit K, Liu J, Chen J, Yuan X, Somta P, Chen X. The mungbean VrP locus encoding MYB90, an R2R3-type MYB protein, regulates anthocyanin biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:895634. [PMID: 35937322 PMCID: PMC9355716 DOI: 10.3389/fpls.2022.895634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/27/2022] [Indexed: 05/30/2023]
Abstract
Anthocyanins are water-soluble pigments present in several tissues/parts of plants. The pigments provide color and are wildly known for health benefits for human, insect attraction for plant pollination, and stress resistance in plants. Anthocyanin content variations in mungbean [Vigna radiata (L.) Wilczek] were first noticed a long time ago, but the genetic mechanism controlling the anthocyanins in mungbean remains unknown. An F2 population derived from the cross between purple-hypocotyl (V2709) and green-hypocotyl (Sulv1) mungbeans was used to map the VrP locus controlling purple hypocotyl. The VrP locus was mapped to a 78.9-kb region on chromosome 4. Sequence comparison and gene expression analysis identified an R2R3-MYB gene VrMYB90 as the candidate gene for the VrP locus. Haplotype analysis using 124 mungbean accessions suggested that 10 single nucleotide polymorphisms (SNPs) in exon 3 may lead to an abolished expression of VrMYB90 and an absence of anthocyanin accumulation in the hypocotyl of Sulv1 and KPS2. The overexpression of VrMYB90 in mungbean hairy root, tobacco leaf, and Arabidopsis resulted in anthocyanin accumulation (purple color). Gene expression analysis demonstrated that VrMYB90 regulated anthocyanin accumulation in the hypocotyl, stem, petiole, and flowers, and the expression was sensitive to light. VrMYB90 protein may upregulate VrDFR encoding dihydroflavonol 4-reductase at the late biosynthesis step of anthocyanins in mungbeans. These results suggest that VrMYB90 is the dominator in the spatiotemporal regulation of anthocyanin biosynthesis. Our results provide insight into the biosynthesis mechanism of anthocyanin and a theoretical basis for breeding mungbeans.
Collapse
Affiliation(s)
- Yun Lin
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Thailand
| | - Jinyang Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jingbing Chen
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xingxing Yuan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Thailand
| | - Xin Chen
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| |
Collapse
|
12
|
Škrabišová M, Dietz N, Zeng S, Chan YO, Wang J, Liu Y, Biová J, Joshi T, Bilyeu KD. A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes. J Adv Res 2022; 42:117-133. [PMID: 36513408 PMCID: PMC9788956 DOI: 10.1016/j.jare.2022.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Genome-Wide Association Studies (GWAS) identify tagging variants in the genome that are statistically associated with the phenotype because of their linkage disequilibrium (LD) relationship with the causative mutation (CM). When both low-density genotyped accession panels with phenotypes and resequenced data accession panels are available, tagging variants can assist with post-GWAS challenges in CM discovery. OBJECTIVES Our objective was to identify additional GWAS evaluation criteria to assess correspondence between genomic variants and phenotypes, as well as enable deeper analysis of the localized landscape of association. METHODS We used genomic variant positions as Synthetic phenotypes in GWAS that we named "Synthetic phenotype association study" (SPAS). The extreme case of SPAS is what we call an "Inverse GWAS" where we used CM positions of cloned soybean genes. We developed and validated the Accuracy concept as a measure of the correspondence between variant positions and phenotypes. RESULTS The SPAS approach demonstrated that the genotype status of an associated variant used as a Synthetic phenotype enabled us to explore the relationships between tagging variants and CMs, and further, that utilizing CMs as Synthetic phenotypes in Inverse GWAS illuminated the landscape of association. We implemented the Accuracy calculation for a curated accession panel to an online Accuracy calculation tool (AccuTool) as a resource for gene identification in soybean. We demonstrated our concepts on three examples of soybean cloned genes. As a result of our findings, we devised an enhanced "GWAS to Genes" analysis (Synthetic phenotype to CM strategy, SP2CM). Using SP2CM, we identified a CM for a novel gene. CONCLUSION The SP2CM strategy utilizing Synthetic phenotypes and the Accuracy calculation of correspondence provides crucial information to assist researchers in CM discovery. The impact of this work is a more effective evaluation of landscapes of GWAS associations.
Collapse
Affiliation(s)
- Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacky University Olomouc, Olomouc 78371, Czech Republic
| | - Nicholas Dietz
- Division of Plant Sciences, University of Missouri, Columbia, MO 65201, USA
| | - Shuai Zeng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65212, USA,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA
| | - Yen On Chan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA,MU Data Science and Informatics Institute, University of Missouri, Columbia, MO 65212, USA
| | - Juexin Wang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65212, USA,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA
| | - Yang Liu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA,MU Data Science and Informatics Institute, University of Missouri, Columbia, MO 65212, USA
| | - Jana Biová
- Department of Biochemistry, Faculty of Science, Palacky University Olomouc, Olomouc 78371, Czech Republic
| | - Trupti Joshi
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65212, USA,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA,MU Data Science and Informatics Institute, University of Missouri, Columbia, MO 65212, USA,Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA,Corresponding authors at: Department of Health Management and Informatics, School of Medicine, 1201 E Rollins St, 271B Life Science Center, Columbia, MO 65201, USA (T. Joshi). Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, 110 Waters Hall, University of Missouri, Columbia, MO 65211, USA (K.D. Bilyeu).
| | - Kristin D. Bilyeu
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA,Corresponding authors at: Department of Health Management and Informatics, School of Medicine, 1201 E Rollins St, 271B Life Science Center, Columbia, MO 65201, USA (T. Joshi). Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, 110 Waters Hall, University of Missouri, Columbia, MO 65211, USA (K.D. Bilyeu).
| |
Collapse
|
13
|
Hu Z, Shi X, Chen X, Zheng J, Zhang A, Wang H, Fu Q. Fine-mapping and identification of a candidate gene controlling seed coat color in melon (Cucumis melo L. var. chinensis Pangalo). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:803-815. [PMID: 34825925 DOI: 10.1007/s00122-021-03999-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
MELO3C019554 encoding a homeobox protein (PHD transcription factor) is a candidate gene that involved in the formation of seed coat color in melon. Seed coat color is related to flavonoid content which is closely related to seed dormancy. According to the genetic analysis of a six-generation population derived from two parents (IC2508 with a yellow seed coat and IC2518 with a brown seed coat), we discovered that the yellow seed coat trait in melon is controlled by a single dominant gene, named CmBS-1. Bulked segregant analysis sequencing (BSA-Seq) revealed that the gene is located at 11,860,000-15,890,000 bp (4.03 Mb) on Chr 6. The F2 population was genotyped using insertion-deletions (InDels), from which cleaved amplified polymorphic sequence (dCAPS) markers were derived to construct a genetic map. The gene was then fine-mapped to a 233.98 kb region containing 12 genes. Based on gene sequence analysis with two parents, we found that the MELO3C019554 gene encoding a homeobox protein (PHD transcription factor) had a nonsynonymous single nucleotide polymorphism (SNP) mutation in the coding sequence (CDS), and the SNP mutation resulted in the conversion of an amino acid (A → T) at residue 534. In addition, MELO3C019554 exhibited lower relative expression levels in the yellow seed coat than in the brown seed coat. Furthermore, we found that MELO3C019554 is related to 12 flavonoid metabolites. Thus, we predicted that MELO3C019554 is a candidate gene controlling seed coat color in melon. The study lays a foundation for further cloning projects and functional analysis of this gene, as well as marker-assisted selection breeding.
Collapse
Affiliation(s)
- Zhicheng Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueyin Shi
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuemiao Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Aiai Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huaisong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Qiushi Fu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
14
|
Tokumitsu Y, Kozu T, Yamatani H, Ito T, Nakano H, Hase A, Sasada H, Takada Y, Kaga A, Ishimoto M, Kusaba M, Nakashima T, Abe J, Yamada T. Functional Divergence of G and Its Homologous Genes for Green Pigmentation in Soybean Seeds. FRONTIERS IN PLANT SCIENCE 2022; 12:796981. [PMID: 35069653 PMCID: PMC8766641 DOI: 10.3389/fpls.2021.796981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
The degradation of chlorophyll in mature soybean seeds is closely related to the development of their yellow color. In this study, we examined G, its homologue G-like (GL), and their mutant alleles and investigated the relationship between these genes and chlorophyll accumulation in the seed coats of mature seeds. Transient expression of G and GL proteins fused with green fluorescent protein revealed that both were localized in plastids. Overexpression of G resulted in the accumulation of chlorophyll in the seed coats and cotyledons of mature seeds, indicating that high expression levels of G result in chlorophyll accumulation that exceeds its metabolism in the seeds of yellow soybean. Analysis of near isogenic lines at the G locus demonstrated a significant difference in the chlorophyll content of the seed coats and cotyledons of mature seeds when G and mutant g alleles were expressed in the d1d2 stay-green genetic background, indicating that the G protein might repress the SGR-independent degradation of chlorophyll. We examined the distribution of mutant alleles at the G and GL loci among cultivated and wild soybean germplasm. The g allele was widely distributed in cultivated soybean germplasm, except for green seed coat soybean lines, all of which contained the G allele. The gl alleles were much fewer in number than the g alleles and were mainly distributed in the genetic resources of cultivated soybean from Japan. None of the landraces and breeding lines investigated in this study were observed to contain both the g and gl alleles. Therefore, in conclusion, the mutation of the G locus alone is essential for establishing yellow soybeans, which are major current soybean breeding lines.
Collapse
Affiliation(s)
- Yusuke Tokumitsu
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Takuto Kozu
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hiroshi Yamatani
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takeshi Ito
- Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| | - Haruna Nakano
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Ayaka Hase
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hiroki Sasada
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yoshitake Takada
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Japan
| | - Akito Kaga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Masao Ishimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Makoto Kusaba
- Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| | - Taiken Nakashima
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Jun Abe
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Tetsuya Yamada
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| |
Collapse
|
15
|
Yamaguchi N, Suzuki C, Yamashita Y, Senda M. A pubescence color gene enhances tolerance to cold-induced seed cracking in yellow soybean. BREEDING SCIENCE 2021; 71:467-473. [PMID: 34912173 PMCID: PMC8661493 DOI: 10.1270/jsbbs.21035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 06/14/2023]
Abstract
In yellow soybean, severe cold weather causes seed cracking on the dorsal side. Yellow soybeans carry the I or ii allele of the I locus and have a yellow (I) or pigmented (ii ) hilum. We previously isolated an additional allele, designated as Ic, of the I locus, and reported that yellow soybeans with the IcIc genotype may be tolerant to cold-induced seed cracking. The Ic allele by itself, however, does not confer high tolerance. The association of a pubescence color gene (T) with suppression of low-temperature-induced seed coat deterioration has been previously reported. In the present study, we tested whether T is effective for the suppression of cold-induced seed cracking using two pairs of near-isogenic lines for the T locus in the iiii or IcIc background. In both backgrounds, the cracked seed rate of the near-isogenic line with the TT genotype was significantly lower than that with the tt genotype, which indicates that T has an inhibitory effect on cold-induced seed cracking. Furthermore, we also showed that gene pyramiding of Ic and T can improve tolerance to cold-induced seed cracking. Our findings should aid the development of highly SC-tolerant cultivars in soybean breeding programs.
Collapse
Affiliation(s)
- Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, 2, Minami 9 sen, Shinsei, Memuro-cho, Kasai-gun, Hokkaido 082-0081, Japan
| | - Chika Suzuki
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, 2, Minami 9 sen, Shinsei, Memuro-cho, Kasai-gun, Hokkaido 082-0081, Japan
| | - Yoko Yamashita
- Hokkaido Research Organization Central Agricultural Experiment Station, Higashi 6 Kita 15, Naganuma, Hokkaido 069-1395, Japan
| | - Mineo Senda
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| |
Collapse
|
16
|
Biosynthetic Pathway of Proanthocyanidins in Major Cash Crops. PLANTS 2021; 10:plants10091792. [PMID: 34579325 PMCID: PMC8472070 DOI: 10.3390/plants10091792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 01/10/2023]
Abstract
Proanthocyanidins (PAs) are a group of oligomers or polymers composed of monomeric flavanols. They offer many benefits for human fitness, such as antioxidant, anticancer, and anti-inflammatory activities. To date, three types of PA have been observed in nature: procyanidins, propelargonidins, and prodelphinidins. These are synthesized as some of the end-products of the flavonoid pathway by different consecutive enzymatic activities, from the same precursor—naringenin. Although the general biosynthetic pathways of PAs have been reported in a few model plant species, little is known about the species-specific pathways in major crops containing different types of PA. In the present study, we identified the species-specific pathways in 10 major crops, based on the presence/absence of flavanol-based intermediates in the metabolic pathway, and found 202 orthologous genes in the reference genomic database of each species, which may encode for key enzymes involved in the biosynthetic pathways of PAs. Parallel enzymatic reactions in the pathway are responsible for the ratio between PAs and anthocyanins, as well as among the three types of PAs. Our study suggests a promising strategy for molecular breeding, to regulate the content of PAs and anthocyanins and improve the nutritional quality of food sources globally.
Collapse
|
17
|
Alseekh S, Scossa F, Wen W, Luo J, Yan J, Beleggia R, Klee HJ, Huang S, Papa R, Fernie AR. Domestication of Crop Metabolomes: Desired and Unintended Consequences. TRENDS IN PLANT SCIENCE 2021; 26:650-661. [PMID: 33653662 DOI: 10.1016/j.tplants.2021.02.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 05/02/2023]
Abstract
The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.
Collapse
Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy
| | - Weiwei Wen
- Key laboratory of Horticultural Plant Biology (MOE),College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Hubei, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China; College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-, CI), 71122 Foggia, Italy
| | - Harry J Klee
- Horticultural Sciences, University of Florida, Gainesville, FL, USA
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture - Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
| |
Collapse
|
18
|
Gao R, Han T, Xun H, Zeng X, Li P, Li Y, Wang Y, Shao Y, Cheng X, Feng X, Zhao J, Wang L, Gao X. MYB transcription factors GmMYBA2 and GmMYBR function in a feedback loop to control pigmentation of seed coat in soybean. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4401-4418. [PMID: 33825878 DOI: 10.1093/jxb/erab152] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Soybean has undergone extensive selection pressures for seed nutrient composition and seed color during domestication, but the major genetic loci controlling seed coat color have not been completely understood, and the transcriptional regulation relationship among the loci remains elusive. Here, two major regulators, GmMYBA2 and GmMYBR, were functionally characterized as an anthocyanin activator and repressor, respectively. Ectopic expression of GmMYBA2 in soybean hairy roots conferred the enhanced accumulation of delphinidin and cyanidin types of anthocyanins in W1t and w1T backgrounds, respectively, through activating anthocyanin biosynthetic genes in the reported loci. The seed coat pigmentation of GmMYBA2-overexpressing transgenic plants in the W1 background mimicked the imperfect black phenotype (W1/w1, i, R, t), suggesting that GmMYBA2 was responsible for the R locus. Molecular and biochemical analysis showed that GmMYBA2 interacted with GmTT8a to directly activate anthocyanin biosynthetic genes. GmMYBA2 and GmMYBR might form a feedback loop to fine-tune seed coat coloration, which was confirmed in transgenic soybeans. Both GmTT8a and GmMYBR that were activated by GmMYBA2 in turn enhanced and obstructed the formation of the GmMYBA2-GmTT8a module, respectively. The results revealed the sophisticated regulatory network underlying the soybean seed coat pigmentation loci and shed light on the understanding of the seed coat coloration and other seed inclusions.
Collapse
Affiliation(s)
- Ruifang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Taotao Han
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Hongwei Xun
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Agro-Biotechnology Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiangsheng Zeng
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Yueqing Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Yanan Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Yan Shao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Xin Cheng
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| |
Collapse
|
19
|
Yang X, Li X, Shan J, Li Y, Zhang Y, Wang Y, Li W, Zhao L. Overexpression of GmGAMYB Accelerates the Transition to Flowering and Increases Plant Height in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:667242. [PMID: 34040624 PMCID: PMC8141843 DOI: 10.3389/fpls.2021.667242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/07/2021] [Indexed: 05/27/2023]
Abstract
The flowering time and plant height of soybean are important agronomic characters, which control the adaptability and yield of soybean. R2R3 MYB transcription factor plays an important regulatory role in plant growth and development. In this study, soybean GmGAMYB gene of R2R3-MYB type was induced by long-days (LDs). GmGAMYB showed higher transcriptional levels in the flowers, leaves and pods of soybean. Overexpression of GmGAMYB in transgenic soybean showed earlier flowering time and maturity in LDs and short-days (SDs). GmGAMYB interacted with GmGBP1 and might promote flowering time by up-regulating the expression of GmFULc gene in soybean. Moreover, the expression level of GmGAMYB was also induced by gibberellins (GAs) and the plant height of GmGAMYB-ox plants was significantly increased, which was caused by the enlargement of internode cell in stem. Furthermore, GmGAMYB overexpression led to increased GA sensitivity in the hypocotyl of soybean seedlings compared with WT. GmGAMYB may be a positive regulator of GA response of promoting plant height by up-regulating the expression of GmGA20ox gene in soybean. Together, our studies preliminarily showed that the partial functions of GmGAMYB in regulating flowering time and GA pathway.
Collapse
|
20
|
Kajiya-Kanegae H, Nagasaki H, Kaga A, Hirano K, Ogiso-Tanaka E, Matsuoka M, Ishimori M, Ishimoto M, Hashiguchi M, Tanaka H, Akashi R, Isobe S, Iwata H. Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections. DNA Res 2021; 28:dsaa032. [PMID: 33492369 PMCID: PMC7934572 DOI: 10.1093/dnares/dsaa032] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/04/2021] [Indexed: 12/11/2022] Open
Abstract
We performed whole-genome Illumina resequencing of 198 accessions to examine the genetic diversity and facilitate the use of soybean genetic resources and identified 10 million single nucleotide polymorphisms and 2.8 million small indels. Furthermore, PacBio resequencing of 10 accessions was performed, and a total of 2,033 structure variants were identified. Genetic diversity and structure analysis congregated the 198 accessions into three subgroups (Primitive, World, and Japan) and showed the possibility of a long and relatively isolated history of cultivated soybean in Japan. Additionally, the skewed regional distribution of variants in the genome, such as higher structural variations on the R gene clusters in the Japan group, suggested the possibility of selective sweeps during domestication or breeding. A genome-wide association study identified both known and novel causal variants on the genes controlling the flowering period. Novel candidate causal variants were also found on genes related to the seed coat colour by aligning together with Illumina and PacBio reads. The genomic sequences and variants obtained in this study have immense potential to provide information for soybean breeding and genetic studies that may uncover novel alleles or genes involved in agronomically important traits.
Collapse
Affiliation(s)
- Hiromi Kajiya-Kanegae
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hideki Nagasaki
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Akito Kaga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Eri Ogiso-Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Motoyuki Ishimori
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Masao Ishimoto
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | | | - Hidenori Tanaka
- Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Ryo Akashi
- Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| |
Collapse
|
21
|
Kim JH, Park JS, Lee CY, Jeong MG, Xu JL, Choi Y, Jung HW, Choi HK. Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 Glycine accessions. PLoS One 2020; 15:e0243085. [PMID: 33259564 PMCID: PMC7707508 DOI: 10.1371/journal.pone.0243085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/15/2020] [Indexed: 11/19/2022] Open
Abstract
The soybean is agro-economically the most important among all cultivated legume crops, and its seed color is considered one of the most attractive factors in the selection-by-breeders. Thus, genome-wide identification of genes and loci associated with seed colors is critical for the precision breeding of crop soybeans. To dissect seed pigmentation-associated genomic loci and genes, we employed dual approaches by combining reference-based genome-wide association study (rbGWAS) and k-mer-based reference-free GWAS (rfGWAS) with 438 Glycine accessions. The dual analytical strategy allowed us to identify four major genomic loci (designated as SP1-SP4 in this study) associated with the seed colors of soybeans. The k-mer analysis enabled us to find an important recombination event that occurred between subtilisin and I-cluster B in the soybean genome, which could describe a special structural feature of ii allele within the I locus (SP3). Importantly, mapping analyses of both mRNAs and small RNAs allowed us to reveal that the subtilisin-CHS1/CHS3 chimeric transcripts generate and act as an initiator towards 'mirtron (i.e., intron-harboring miRNA precursor)'-triggered silencing of chalcone synthase (CHS) genes. Consequently, the results led us to propose a working model of 'mirtron-triggered gene silencing (MTGS)' to elucidate a long-standing puzzle in the genome-wide CHS gene silencing mechanism. In summary, our study reports four major genomic loci, lists of key genes and genome-wide variations that are associated with seed pigmentation in soybeans. In addition, we propose that the MTGS mechanism plays a crucial role in the genome-wide silencing of CHS genes, thereby suggesting a clue to currently predominant soybean cultivars with the yellow seed coat. Finally, this study will provide a broad insight into the interactions and correlations among seed color-associated genes and loci within the context of anthocyanin biosynthetic pathways.
Collapse
Affiliation(s)
- Jin-Hyun Kim
- Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Joo-Seok Park
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Chae-Young Lee
- Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea
| | - Min-Gyun Jeong
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Jiu Liang Xu
- Systems Biotechnology Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Yongsoo Choi
- Systems Biotechnology Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Ho-Won Jung
- Department of Molecular Genetics, Dong-A University, Busan, Republic of Korea
| | - Hong-Kyu Choi
- Department of Molecular Genetics, Dong-A University, Busan, Republic of Korea
| |
Collapse
|
22
|
Zabala G, Kour A, Vodkin LO. Overexpression of an ethylene-forming ACC oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max. BMC Genomics 2020; 21:716. [PMID: 33066734 PMCID: PMC7566151 DOI: 10.1186/s12864-020-07130-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/08/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a smaller hilum region where the seed attaches to the pod and also results in seed coat cracking surrounding the hilum region. RESULTS RNAs were extracted from immature seed from an extended hilum region (i.e., the hilum and a small ring of tissue surrounding the hilum in which the cracks form) at three different developmental stages:10-25, 25-50 and 50-100 mg seed fresh weight in two independent replicates for each stage. The transcriptomes of these samples from both the Clark isoline containing the mi allele (PI 547628, UC413, ii R t mi G), and its recurrent Clark 63 parent isoline (PI 548532, UC7, ii R T Mi g), which was used for six generations of backcrossing, were compared for differential expression of 88,648 Glyma models of the soybean genome Wm82.a2. The RNA sequence data obtained from the 12 cDNA libraries were subjected to padj value < 0.05 and at least two-fold expression differences to select with confidence genes differentially expressed in the hilum-containing tissue of the seed coat between the two lines. Glyma.09G008400 annotated as encoding an ethylene forming enzyme, ACC oxidase (ACO), was found to be highly overexpressed in the mi hilum region at 165 RPKMs (reads per kilobase per million mapped reads) compared to the standard line at just 0.03 RPKMs. Evidence of changes in expression of genes downstream of the ethylene pathway included those involved in auxin and gibberellin hormone action and extensive differences in expression of cell wall protein genes. These changes are postulated to determine the restricted hilum size and cracking phenotypes. CONCLUSIONS We present transcriptome and phenotypic evidence that substantially higher expression of an ethylene-forming ACO gene likely shifts hormone balance and sets in motion downstream changes resulting in a smaller hilum phenotype and the cracks observed in the minute hilum (mi) isoline as compared to its recurrent parent.
Collapse
Affiliation(s)
- Gracia Zabala
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61981, USA
| | - Anupreet Kour
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61981, USA
- Present address: Robert M. Berne Cardiovascular Research Institute, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Lila O Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61981, USA.
| |
Collapse
|
23
|
Bian S, Jin D, Sun G, Shan B, Zhou H, Wang J, Zhai L, Li X. Characterization of the soybean R2R3-MYB transcription factor GmMYB81 and its functional roles under abiotic stresses. Gene 2020; 753:144803. [PMID: 32446917 DOI: 10.1016/j.gene.2020.144803] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 11/20/2022]
Abstract
R2R3-type MYBs are a key group of regulatory factors that control diverse developmental processes and stress tolerance in plants. Soybean is a major legume crop with the richness of seed protein and edible vegetable oil, and 244 R2R3-type MYBs have been identified in soybean. However, the knowledge regarding their functional roles has been greatly limited as yet. In this study, a novel R2R3-type MYB (GmMYB81) was functionally characterized in soybean, and it is closely related to two abiotic stress-associated regulators (AtMYB44 and AtMYB77). GmMYB81 transcripts not only differentially accumulated in soybean tissues and during embryo development, but also were significantly enhanced by drought, salt and cold stress. Histochemical GUS assay in Arabidopsis indicated that GmMYB81 promoter showed high activity in seedlings, rosette leaves, inflorescences, silique wall, mature anthers, roots, and germinating seeds. Further investigation indicated that over-expression of GmMYB81 in Arabidopsis caused auxin-associated phenotypes, including small flower and silique, more branch, and weakened apical dominance. Moreover, over-expression of GmMYB81 significantly elevated the rates of seed germination and green seedling under salt and drought stress, indicating that GmMYB81 might confer plant tolerance to salt and drought stress during seed germination. Additionally, protein interaction analysis showed that GmMYB81 interacts with the abiotic stress regulator GmSGF14l. Further observation indicated that they displayed similar expression patterns under drought and salt stress, suggesting GmMYB81 and GmSGF14l might cooperatively affect stress tolerance. These findings will facilitate future investigations of the regulatory mechanisms of GmMYB81 in response to plant stress tolerance, especially seed germination under abiotic stresses.
Collapse
Affiliation(s)
- Shaomin Bian
- College of Plant Science, Jilin University, Changchun 130062, Jilin, China
| | - Donghao Jin
- College of Plant Science, Jilin University, Changchun 130062, Jilin, China
| | - Guoqing Sun
- College of Plant Science, Jilin University, Changchun 130062, Jilin, China
| | - Binghui Shan
- College of Plant Science, Jilin University, Changchun 130062, Jilin, China
| | - Huina Zhou
- National Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, Henan, China
| | - Jingying Wang
- College of Plant Science, Jilin University, Changchun 130062, Jilin, China
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun 130062, Jilin, China
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun 130062, Jilin, China.
| |
Collapse
|
24
|
Li Y, Chen Q, Xie X, Cai Y, Li J, Feng Y, Zhang Y. Integrated Metabolomics and Transcriptomics Analyses Reveal the Molecular Mechanisms Underlying the Accumulation of Anthocyanins and Other Flavonoids in Cowpea Pod ( Vigna unguiculata L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9260-9275. [PMID: 32709199 DOI: 10.1021/acs.jafc.0c01851] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As an important vegetable crop of the legume family, cowpea (Vigna unguiculata L.) is grown widely for its tender pod with good taste and nutrition. The purple cowpea pods attract more attention mainly for the eye-catching color and health-promoting ingredients. Initially, large quantities of two major anthocyanins (delphinidin 3-O-glucoside and cyanidin 3-O-glucoside) and nine kinds of flavonoids (most are quercetin-based flavonol glycosides) were separated and identified from purple cowpea pod by ultra-high performance liquid chromatography coupled with quadrupole Orbitrap high-resolution mass spectrometry. To study them systematically, two representative cowpea cultivars with a drastic difference in anthocyanin accumulation were further analyzed by the integration of metabolomics and transcriptomics. A total of 56 differentially accumulated metabolites and 4142 differentially expressed genes were identified, respectively. On the basis of the comprehensive analysis of multiomic data, it was shown that VuMYB90-1, VuMYB90-2, VuMYB90-3, VuCPC, VuMYB4, and endogenous bHLH and WD40 proteins coordinately control anthocyanin and flavonoid accumulation via transcriptional regulation of structural genes in purple cowpea pod.
Collapse
Affiliation(s)
- Yan Li
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan 450001, People's Republic of China
| | - Qiyan Chen
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan 450001, People's Republic of China
| | - Xiaodong Xie
- Zhengzhou Tobacco Research Institute of CNTC, China Tobacco Gene Research Center, Fengyang Avenue, Zhengzhou, Henan 450001, People's Republic of China
| | - Yu Cai
- School of Life Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan 450001, People's Republic of China
| | - Jiangfeng Li
- School of Life Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan 450001, People's Republic of China
| | - Yiling Feng
- School of Life Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan 450001, People's Republic of China
| | - Yanjie Zhang
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan 450001, People's Republic of China
| |
Collapse
|
25
|
Ibrahim AEC, van Dolleweerd CJ, Drake PMW, Ma JKC. Development of a minigenome cassette for Lettuce necrotic yellows virus: A first step in rescuing a plant cytorhabdovirus. PLoS One 2020; 15:e0229877. [PMID: 32134974 PMCID: PMC7058326 DOI: 10.1371/journal.pone.0229877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/15/2020] [Indexed: 12/12/2022] Open
Abstract
Rhabdoviruses are enveloped negative-sense RNA viruses that have numerous biotechnological applications. However, recovering plant rhabdoviruses from cDNA remains difficult due to technical difficulties such as the need for concurrent in planta expression of the viral genome together with the viral nucleoprotein (N), phosphoprotein (P) and RNA-dependent RNA polymerase (L) and viral genome instability in E. coli. Here, we developed a negative-sense minigenome cassette for Lettuce necrotic yellows virus (LNYV). We introduced introns into the unstable viral ORF and employed Agrobacterium tumefaciens to co-infiltrate Nicotiana with the genes for the N, P, and L proteins together with the minigenome cassette. The minigenome cassette included the Discosoma sp. red fluorescent protein gene (DsRed) cloned in the negative-sense between the viral trailer and leader sequences which were placed between hammerhead and hepatitis delta ribozymes. In planta DsRed expression was demonstrated by western blotting while the appropriate splicing of introduced introns was confirmed by sequencing of RT-PCR product.
Collapse
Affiliation(s)
- Ahmad E. C. Ibrahim
- Institute for Infection and Immunity, St. George’s University of London, London, United Kingdom
| | - Craig J. van Dolleweerd
- Institute for Infection and Immunity, St. George’s University of London, London, United Kingdom
| | - Pascal M. W. Drake
- Institute for Infection and Immunity, St. George’s University of London, London, United Kingdom
| | - Julian K-C. Ma
- Institute for Infection and Immunity, St. George’s University of London, London, United Kingdom
| |
Collapse
|
26
|
Yan F, Githiri SM, Liu Y, Sang Y, Wang Q, Takahashi R. Loss-of-Function Mutation of Soybean R2R3 MYB Transcription Factor Dilutes Tawny Pubescence Color. FRONTIERS IN PLANT SCIENCE 2020; 10:1809. [PMID: 32082354 PMCID: PMC7005258 DOI: 10.3389/fpls.2019.01809] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/24/2019] [Indexed: 06/10/2023]
Abstract
Pubescence color of soybean is controlled by two genes, T and Td. In the presence of a dominant T allele, dominant and recessive alleles of the Td locus generate tawny and light tawny (or near-gray) pubescence, respectively. Flavones, responsible for pubescence color, are synthesized via two copies of flavone synthase II genes (FNS II-1 and FNS II-2). This study was conducted to map and clone the Td gene. Genetic and linkage analysis using an F2 population and F3 families derived from a cross between a Clark near-isogenic line with light tawny pubescence (genotype: TT tdtd) and a Harosoy near-isogenic line with tawny pubescence (TT TdTd) revealed a single gene for pubescence color around the end of chromosome 3. Genome sequence alignment of plant introductions revealed an association between premature stop codons in Glyma.03G258700 (R2R3 MYB transcription factor) and recessive td allele. Cultivars and lines having near-gray or light tawny pubescence and a gray pubescence cultivar with td allele had premature stop codons in the gene. These results suggest that Glyma.03G258700 corresponds to the Td gene. It was predominantly expressed in pubescence. Compared to a tawny pubescence line, a near-isogenic line with td allele produced extremely small amounts of transcripts of Glyma.03G258700, FNS II-1, and FNS II-2 in pubescence. The promoter of FNS II-1 and FNS II-2 shared cis-acting regulatory elements for binding of MYB proteins. These results suggest that the wild type of Glyma.03G258700 protein may bind to the promoter of FNS II genes and upregulate their expression, resulting in increased flavone content and deeper pubescence color. In contrast, mutated Glyma.03G258700 protein may fail to upregulate the expression of FNS II genes, resulting in decreased flavone content and dilute pubescence color.
Collapse
Affiliation(s)
- Fan Yan
- College of Plant Science, Jilin University, Changchun, China
| | - Stephen M. Githiri
- Horticulture Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Yajing Liu
- College of Plant Science, Jilin University, Changchun, China
| | - Yu Sang
- College of Plant Science, Jilin University, Changchun, China
| | - Qingyu Wang
- College of Plant Science, Jilin University, Changchun, China
| | | |
Collapse
|
27
|
Woodhouse MR, Hufford MB. Parallelism and convergence in post-domestication adaptation in cereal grasses. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180245. [PMID: 31154975 DOI: 10.1098/rstb.2018.0245] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The selection of desirable traits in crops during domestication has been well studied. Many crops share a suite of modified phenotypic characteristics collectively known as the domestication syndrome. In this sense, crops have convergently evolved. Previous work has demonstrated that, at least in some instances, convergence for domestication traits has been achieved through parallel molecular means. However, both demography and selection during domestication may have placed limits on evolutionary potential and reduced opportunities for convergent adaptation during post-domestication migration to new environments. Here we review current knowledge regarding trait convergence in the cereal grasses and consider whether the complexity and dynamism of cereal genomes (e.g., transposable elements, polyploidy, genome size) helped these species overcome potential limitations owing to domestication and achieve broad subsequent adaptation, in many cases through parallel means. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
Collapse
Affiliation(s)
- M R Woodhouse
- Iowa State University, Ecology, Evolution, and Organismal Biology , Ames, IA 50011 , USA
| | - M B Hufford
- Iowa State University, Ecology, Evolution, and Organismal Biology , Ames, IA 50011 , USA
| |
Collapse
|
28
|
Jeong SC, Moon JK, Park SK, Kim MS, Lee K, Lee SR, Jeong N, Choi MS, Kim N, Kang ST, Park E. Genetic diversity patterns and domestication origin of soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1179-1193. [PMID: 30588539 PMCID: PMC6449312 DOI: 10.1007/s00122-018-3271-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/19/2018] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Genotyping data of a comprehensive Korean soybean collection obtained using a large SNP array were used to clarify global distribution patterns of soybean and address the evolutionary history of soybean. Understanding diversity and evolution of a crop is an essential step to implement a strategy to expand its germplasm base for crop improvement research. Accessions intensively collected from Korea, which is a small but central region in the distribution geography of soybean, were genotyped to provide sufficient data to underpin population genetic questions. After removing natural hybrids and duplicated or redundant accessions, we obtained a non-redundant set comprising 1957 domesticated and 1079 wild accessions to perform population structure analyses. Our analysis demonstrates that while wild soybean germplasm will require additional sampling from diverse indigenous areas to expand the germplasm base, the current domesticated soybean germplasm is saturated in terms of genetic diversity. We then showed that our genome-wide polymorphism map enabled us to detect genetic loci underlying flower color, seed-coat color, and domestication syndrome. A representative soybean set consisting of 194 accessions was divided into one domesticated subpopulation and four wild subpopulations that could be traced back to their geographic collection areas. Population genomics analyses suggested that the monophyletic group of domesticated soybeans was likely originated at a Japanese region. The results were further substantiated by a phylogenetic tree constructed from domestication-associated single nucleotide polymorphisms identified in this study.
Collapse
Affiliation(s)
- Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea.
| | - Jung-Kyung Moon
- Agricultural Genome Center, National Academy of Agricultural Sciences, Rural Development Administration, Jeonju, Jeonbuk, 55365, Korea.
| | - Soo-Kwon Park
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Myung-Shin Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Kwanghee Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Soo Rang Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Namhee Jeong
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Man Soo Choi
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Namshin Kim
- Epigenomics Research Center, Genome Institute, Institute of Bioscience and Biotechnology, Korea Research, Taejon, 34141, Korea
| | - Sung-Taeg Kang
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, Chungnam, 31116, Korea
| | - Euiho Park
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Korea
| |
Collapse
|
29
|
Ha J, Kang YG, Lee T, Kim M, Yoon MY, Lee E, Yang X, Kim D, Kim YJ, Lee TR, Kim MY, Lee SH. Comprehensive RNA sequencing and co-expression network analysis to complete the biosynthetic pathway of coumestrol, a phytoestrogen. Sci Rep 2019; 9:1934. [PMID: 30760815 PMCID: PMC6374408 DOI: 10.1038/s41598-018-38219-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 12/17/2018] [Indexed: 01/22/2023] Open
Abstract
Coumestrol (CMS), a coumestan isoflavone, plays key roles in nodulation through communication with rhizobia, and has been used as phytoestrogens for hormone replacement therapy in humans. Because CMS content is controlled by multiple genetic factors, the genetic basis of CMS biosynthesis has remained unclear. We identified soybean genotypes with consistently high (Daewonkong) or low (SS0903-2B-21-1-2) CMS content over 2 years. We performed RNA sequencing of leaf samples from both genotypes at developmental stage R7, when CMS levels are highest. Within the phenylpropanoid biosynthetic pathway, 41 genes were tightly connected in a functional co-expression gene network; seven of these genes were differentially expressed between two genotypes. We identified 14 candidate genes involved in CMS biosynthesis. Among them, seven were annotated as encoding oxidoreductases that may catalyze the transfer of electrons from daidzein, a precursor of CMS. Two of the other genes, annotated as encoding a MYB domain protein and a MLP-like protein, may increase CMS accumulation in response to stress conditions. Our results will help to complete our understanding of the CMS biosynthetic pathway, and should facilitate development of soybean cultivars with high CMS content that could be used to promote the fitness of plants and human beings.
Collapse
Affiliation(s)
- Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Young-Gyu Kang
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Taeyoung Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Myoyeon Kim
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Min Young Yoon
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Eunsoo Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Xuefei Yang
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyun Kim
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Yong-Jin Kim
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Tae Ryong Lee
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Moon Young Kim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea.
| |
Collapse
|
30
|
Deokar A, Sagi M, Daba K, Tar'an B. QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:275-288. [PMID: 29890030 PMCID: PMC6330535 DOI: 10.1111/pbi.12964] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/17/2018] [Accepted: 06/07/2018] [Indexed: 05/21/2023]
Abstract
Whole-genome sequencing-based bulked segregant analysis (BSA) for mapping quantitative trait loci (QTL) provides an efficient alternative approach to conventional QTL analysis as it significantly reduces the scale and cost of analysis with comparable power to QTL detection using full mapping population. We tested the application of next-generation sequencing (NGS)-based BSA approach for mapping QTLs for ascochyta blight resistance in chickpea using two recombinant inbred line populations CPR-01 and CPR-02. Eleven QTLs in CPR-01 and six QTLs in CPR-02 populations were mapped on chromosomes Ca1, Ca2, Ca4, Ca6 and Ca7. The QTLs identified in CPR-01 using conventional biparental mapping approach were used to compare the efficiency of NGS-based BSA in detecting QTLs for ascochyta blight resistance. The QTLs on chromosomes Ca1, Ca4, Ca6 and Ca7 overlapped with the QTLs previously detected in CPR-01 using conventional QTL mapping method. The QTLs on chromosome Ca4 were detected in both populations and overlapped with the previously reported QTLs indicating conserved region for ascochyta blight resistance across different chickpea genotypes. Six candidate genes in the QTL regions identified using NGS-based BSA on chromosomes Ca2 and Ca4 were validated for their association with ascochyta blight resistance in the CPR-02 population. This study demonstrated the efficiency of NGS-based BSA as a rapid and cost-effective method to identify QTLs associated with ascochyta blight in chickpea.
Collapse
Affiliation(s)
- Amit Deokar
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSKCanada
| | - Mandeep Sagi
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSKCanada
| | - Ketema Daba
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSKCanada
| | - Bunyamin Tar'an
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSKCanada
| |
Collapse
|
31
|
Patil G, Vuong TD, Kale S, Valliyodan B, Deshmukh R, Zhu C, Wu X, Bai Y, Yungbluth D, Lu F, Kumpatla S, Shannon JG, Varshney RK, Nguyen HT. Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1939-1953. [PMID: 29618164 PMCID: PMC6181215 DOI: 10.1111/pbi.12929] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 03/09/2018] [Accepted: 03/21/2018] [Indexed: 05/04/2023]
Abstract
The cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil, and high sucrose. In this study, an interspecific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3× depth. Based on 91 342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4070 bins). In addition to bin mapping, quantitative trait loci (QTL) analysis for protein, oil, and sucrose was performed using 3343 polymorphic SNPs (3K-SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared, and a significant concordance was observed between bin and 3K-SNP markers. Importantly, the bin map derived from next-generation sequencing technology enhanced mapping resolution (from 1325 to 50 Kb). A total of five, nine, and four QTLs were identified for protein, oil, and sucrose content, respectively, and some of the QTLs coincided with soybean domestication-related genomic loci. The major QTL for protein and oil were mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL were identified on Chr. 8 (qSuc_08) and harbours putative genes involved in sugar transport. In addition, genome-wide association using 91 342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL-based haplotype using whole-genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean.
Collapse
Affiliation(s)
- Gunvant Patil
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
- Present address:
Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMN55108USA
| | - Tri D. Vuong
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Sandip Kale
- Center of Excellence in GenomicsInternational Crops Research Institute for the Semi‐Arid TropicsHyderabadIndia
- Present address:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GateslebenD‐06466StadtSeelandGermany
| | - Babu Valliyodan
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | | | - Chengsong Zhu
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Xiaolei Wu
- Crop Science DivisionBayer CropScienceMorrisvilleNCUSA
| | - Yonghe Bai
- Dow AgroSciencesIndianapolisINUSA
- Present address:
Nuseed Americas10 N. East Street, Suite 101WoodlandCA95776USA
| | | | - Fang Lu
- Dow AgroSciencesIndianapolisINUSA
- Present address:
AmgenOne Amgen Center DriveThousand OaksCA91320USA
| | | | | | - Rajeev K. Varshney
- Center of Excellence in GenomicsInternational Crops Research Institute for the Semi‐Arid TropicsHyderabadIndia
| | - Henry T. Nguyen
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| |
Collapse
|
32
|
Ha J, Kim M, Kim MY, Lee T, Yoon MY, Lee J, Lee YH, Kang YG, Park JS, Lee JH, Lee SH. Transcriptomic variation in proanthocyanidin biosynthesis pathway genes in soybean (Glycine spp.). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:2138-2146. [PMID: 28960323 DOI: 10.1002/jsfa.8698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/29/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Proanthocyanidins are oligomeric or polymeric end products of flavonoid metabolic pathways starting with the central phenylpropanoid pathway. Although soybean (Glycine spp.) seeds represent a major source of nutrients for the human diet, as well as components for the cosmetics industry as a result of their high levels of flavonoid metabolites, including isoflavonoids, anthocyanins and proanthocyanidins, the genetic regulatory mechanisms underlying proanthocyanidin biosynthesis in soybean remain unclear. RESULTS We evaluated interspecific and intraspecific variability in flavonoid components in soybean using 43 cultivars, landraces and wild soybean accessions. We performed transcriptomic profiling of genes encoding enzymes involved in flavonoid biosynthesis using three soybean genotypes, Hwangkeum (elite cultivar), IT109098 (landrace) and IT182932 (wild accession), in seeds. We identified a Glycine max landrace, IT109098, with a proanthocyanidin content as high as that of wild soybean. Different homologous genes for anthocyanidin reductase, which is involved in proanthocyanidin biosynthesis, were detected as differentially expressed genes between IT109098 and IT182932 compared to Hwangkeum. CONCLUSION We detected major differences in the transcriptional levels of genes involved in the biosynthesis of proanthocyanidin and anthocyanin among genotypes beginning at the early stage of seed development. The results of the present study provide insights into the underlying genetic variation in proanthocyanidin biosynthesis among soybean genotypes. © 2017 Society of Chemical Industry.
Collapse
Affiliation(s)
- Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Myoyeon Kim
- Applied Technology & Research Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Moon Young Kim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Taeyoung Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Min Young Yoon
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Jayern Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yeong-Ho Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young-Gyu Kang
- Applied Technology & Research Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Jun Seong Park
- Applied Technology & Research Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - John Hwan Lee
- Applied Technology & Research Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
33
|
Yang H, Xue Q, Zhang Z, Du J, Yu D, Huang F. GmMYB181, a Soybean R2R3-MYB Protein, Increases Branch Number in Transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1027. [PMID: 30065741 PMCID: PMC6056663 DOI: 10.3389/fpls.2018.01027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/25/2018] [Indexed: 05/11/2023]
Abstract
Soybean (Glycine max) is an important economic crop that provides abundant oil and high quality protein for human beings. As the process of reproductive growth directly determines the crop seed yield and quality, we initiated studies to identify genes that regulate soybean floral organ development. One R2R3-MYB transcription factor gene, designated as GmMYB181, was found to be enriched in flowers based on microarray analysis and was further functionally investigated in transgenic Arabidopsis. GmMYB181 protein contains two MYB domains, which localized to the nucleus and displayed transcriptional activation in yeast hybrid system. Real-time quantitative PCR (qRT-PCR) results suggested GmMYB181 exclusively expressed in flower tissue. In Arabidopsis, overexpression of GmMYB181 altered the morphology of floral organs, fruit size and plant architecture, including outward curly sepals, smaller siliques, increased lateral branches and reduced plant height, indicating that GmMYB181 is involved in the development of reproductive organs and plays an important role in controlling plant architecture. Further, microarray analysis revealed that overexpressing GmMYB181 in Arabidopsis affected the expression of 3450 genes in mature flowers, including those involved in floral organ, seed/fruit development, and responded to different hormone signals.
Collapse
|
34
|
Gillman JD, Kim WS, Song B, Oehrle NW, Tawari NR, Liu S, Krishnan HB. Whole-Genome Resequencing Identifies the Molecular Genetic Cause for the Absence of a Gy5 Glycinin Protein in Soybean PI 603408. G3 (BETHESDA, MD.) 2017; 7:2345-2352. [PMID: 28592556 PMCID: PMC5499141 DOI: 10.1534/g3.117.039347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/16/2017] [Indexed: 11/18/2022]
Abstract
During ongoing proteomic analysis of the soybean (Glycine max (L.) Merr) germplasm collection, PI 603408 was identified as a landrace whose seeds lack accumulation of one of the major seed storage glycinin protein subunits. Whole genomic resequencing was used to identify a two-base deletion affecting glycinin 5 The newly discovered deletion was confirmed to be causative through immunological, genetic, and proteomic analysis, and no significant differences in total seed protein content were found to be due to the glycinin 5 loss-of-function mutation per se In addition to focused studies on this one specific glycinin subunit-encoding gene, a total of 1,858,185 nucleotide variants were identified, of which 39,344 were predicted to affect protein coding regions. In order to semiautomate analysis of a large number of soybean gene variants, a new SIFT 4G (Sorting Intolerant From Tolerated 4 Genomes) database was designed to predict the impact of nonsynonymous single nucleotide soybean gene variants, potentially enabling more rapid analysis of soybean resequencing data in the future.
Collapse
Affiliation(s)
- Jason D Gillman
- United States Department of Agriculture - Agricultural Research Service Plant Genetics Research Unit, Columbia, Missouri
- Plant Science Division, University of Missouri, Columbia, Missouri 65211
| | - Won-Seok Kim
- Plant Science Division, University of Missouri, Columbia, Missouri 65211
| | - Bo Song
- Key Laboratory of Soybean Biology at the Chinese Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Nathan W Oehrle
- United States Department of Agriculture - Agricultural Research Service Plant Genetics Research Unit, Columbia, Missouri
| | - Nilesh R Tawari
- Computational and Systems Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Shanshan Liu
- Key Laboratory of Soybean Biology at the Chinese Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Hari B Krishnan
- United States Department of Agriculture - Agricultural Research Service Plant Genetics Research Unit, Columbia, Missouri
- Plant Science Division, University of Missouri, Columbia, Missouri 65211
| |
Collapse
|
35
|
Cho YB, Jones SI, Vodkin LO. Mutations in Argonaute5 Illuminate Epistatic Interactions of the K1 and I Loci Leading to Saddle Seed Color Patterns in Glycine max. THE PLANT CELL 2017; 29:708-725. [PMID: 28351993 PMCID: PMC5435447 DOI: 10.1105/tpc.17.00162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 05/18/2023]
Abstract
The soybean (Glycine max) seed coat has distinctive, genetically programmed patterns of pigmentation, and the recessive k1 mutation can epistatically overcome the dominant I and ii alleles, which inhibit seed color by producing small interfering RNAs (siRNAs) targeting chalcone synthase (CHS) mRNAs. Small RNA sequencing of dissected regions of immature seed coats demonstrated that CHS siRNA levels cause the patterns produced by the ii and ik alleles of the I locus, which restrict pigment to the hilum or saddle region of the seed coat, respectively. To identify the K1 locus, we compared RNA-seq data from dissected regions of two Clark isolines having similar saddle phenotypes mediated by CHS siRNAs but different genotypes (homozygous ik K1 versus homozygous ii k1). By examining differentially expressed genes, mapping information, and genome resequencing, we identified a 129-bp deletion in Glyma.11G190900 encoding Argonaute5 (AGO5), a member of the Argonaute family. Amplicon sequencing of several independent saddle pattern mutants from different genetic backgrounds revealed independent lesions affecting AGO5, thus establishing Glyma.11G190900 as the K1 locus. Nonfunctional AGO5 from k1 alleles leads to altered distributions of CHS siRNAs, thus explaining how the k1 mutation reverses the phenotype of the seed coat regions from yellow to pigmented, even in the presence of the normally dominant I or ii alleles.
Collapse
Affiliation(s)
- Young B Cho
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - Sarah I Jones
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - Lila O Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| |
Collapse
|
36
|
Senda M, Yamaguchi N, Hiraoka M, Kawada S, Iiyoshi R, Yamashita K, Sonoki T, Maeda H, Kawasaki M. Accumulation of proanthocyanidins and/or lignin deposition in buff-pigmented soybean seed coats may lead to frequent defective cracking. PLANTA 2017; 245:659-670. [PMID: 27995313 DOI: 10.1007/s00425-016-2638-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
MAIN CONCLUSION Defective cracking frequently occurs in buff-pigmented soybean seed coats, where proanthocyanidins accumulate and lignin is deposited, suggesting that proanthocyanidins and/or lignin may change physical properties and lead to defective cracking. In the seed production of many yellow soybean (Glycine max) cultivars, very low percentages of self-pigmented seeds are commonly found. This phenomenon is derived from a recessive mutation of the I gene inhibiting seed coat pigmentation. In Japan, most of these self-pigmented seeds are buff-colored, and frequently show multiple defective cracks in the seed coat. However, it is not known why cracking occurs specifically in buff seed coats. In this study, quantitative analysis was performed between yellow and buff soybean seed coats. Compared with yellow soybeans, in which defective cracking rarely occurs, contents of proanthocyanidins (PAs) and lignin were significantly higher in buff seed coats. Histochemical data of PAs and lignin in the seed coats strongly supported this result. Measurements of the physical properties of seed coats using a texture analyzer showed that a hardness value was significantly decreased in the buff seed coats. These results suggest that PA accumulation and/or lignin deposition may affect the physical properties of buff seed coats and lead to the defective cracking. This work contributes to understanding of the mechanism of defective cracking, which decreases the seed quality of soybean and related legumes.
Collapse
Affiliation(s)
- Mineo Senda
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan.
| | - Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, 2, Minami 9 sen, Shinsei, Memuro-cho, Kasai-gun, Hokkaido, 082-0081, Japan
| | - Miho Hiraoka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - So Kawada
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Ryota Iiyoshi
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Kazuki Yamashita
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Tomonori Sonoki
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Hayato Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Michio Kawasaki
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| |
Collapse
|
37
|
Song J, Liu Z, Hong H, Ma Y, Tian L, Li X, Li YH, Guan R, Guo Y, Qiu LJ. Identification and Validation of Loci Governing Seed Coat Color by Combining Association Mapping and Bulk Segregation Analysis in Soybean. PLoS One 2016; 11:e0159064. [PMID: 27404272 PMCID: PMC4942065 DOI: 10.1371/journal.pone.0159064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/27/2016] [Indexed: 02/05/2023] Open
Abstract
Soybean seed coat exists in a range of colors from yellow, green, brown, black, to bicolor. Classical genetic analysis suggested that soybean seed color was a moderately complex trait controlled by multi-loci. However, only a couple of loci could be detected using a single biparental segregating population. In this study, a combination of association mapping and bulk segregation analysis was employed to identify genes/loci governing this trait in soybean. A total of 14 loci, including nine novel and five previously reported ones, were identified using 176,065 coding SNPs selected from entire SNP dataset among 56 soybean accessions. Four of these loci were confirmed and further mapped using a biparental population developed from the cross between ZP95-5383 (yellow seed color) and NY279 (brown seed color), in which different seed coat colors were further dissected into simple trait pairs (green/yellow, green/black, green/brown, yellow/black, yellow/brown, and black/brown) by continuously developing residual heterozygous lines. By genotyping entire F2 population using flanking markers located in fine-mapping regions, the genetic basis of seed coat color was fully dissected and these four loci could explain all variations of seed colors in this population. These findings will be useful for map-based cloning of genes as well as marker-assisted breeding in soybean. This work also provides an alternative strategy for systematically isolating genes controlling relative complex trait by association analysis followed by biparental mapping.
Collapse
Affiliation(s)
- Jian Song
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zhangxiong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Huilong Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yansong Ma
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Long Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xinxiu Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Rongxia Guan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| |
Collapse
|
38
|
Cui B, Hu Z, Zhang Y, Hu J, Yin W, Feng Y, Xie Q, Chen G. Anthocyanins and flavonols are responsible for purple color of Lablab purpureus (L.) sweet pods. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 103:183-190. [PMID: 26995313 DOI: 10.1016/j.plaphy.2016.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/08/2016] [Indexed: 06/05/2023]
Abstract
Lablab pods, as dietary vegetable, have high nutritional values similar to most of edible legumes. Moreover, our studies confirmed that purple lablab pods contain the natural pigments of anthocyanins and flavonols. Compared to green pods, five kinds of anthocyanins (malvidin, delphinidin and petunidin derivatives) were found in purple pods by HPLC-ESI-MS/MS and the major contents were delphinidin derivatives. Besides, nine kinds of polyphenol derivatives (quercetin, myricetin, kaempferol and apigenin derivatives) were detected by UPLC-ESI-MS/MS and the major components were quercetin and myricetin derivatives. In order to discover their molecular mechanism, expression patterns of biosynthesis and regulatory gens of anthocyanins and flavonols were investigated. Experimental results showed that LpPAL, LpF3H, LpF3'H, LpDFR, LpANS and LpPAP1 expressions were significantly induced in purple pods compared to green ones. Meanwhile, transcripts of LpFLS were more abundant in purple pods than green or yellow ones, suggestind that co-pigments of anthocyanins and flavonols are accumulated in purple pods. Under continuously dark condition, no anthocyanin accumulation was detected in purple pods and transcripts of LpCHS, LpANS, LpFLS and LpPAP1 were remarkably repressed, indicating that anthocyanins and flavonols biosynthesis in purple pods was regulated in light-dependent manner. These results indicate that co-pigments of anthocyanins and flavonols contribute to purple pigmentations of pods.
Collapse
Affiliation(s)
- Baolu Cui
- Key Laboratory of Biorheological Science and Technology, (Chongqing University), Ministry of Education, Room 515, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing 400044, People's Republic of China
| | - Zongli Hu
- Key Laboratory of Biorheological Science and Technology, (Chongqing University), Ministry of Education, Room 515, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing 400044, People's Republic of China
| | - Yanjie Zhang
- Key Laboratory of Biorheological Science and Technology, (Chongqing University), Ministry of Education, Room 515, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing 400044, People's Republic of China
| | - Jingtao Hu
- Key Laboratory of Biorheological Science and Technology, (Chongqing University), Ministry of Education, Room 515, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing 400044, People's Republic of China
| | - Wencheng Yin
- Key Laboratory of Biorheological Science and Technology, (Chongqing University), Ministry of Education, Room 515, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing 400044, People's Republic of China
| | - Ye Feng
- Key Laboratory of Biorheological Science and Technology, (Chongqing University), Ministry of Education, Room 515, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing 400044, People's Republic of China
| | - Qiaoli Xie
- Key Laboratory of Biorheological Science and Technology, (Chongqing University), Ministry of Education, Room 515, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing 400044, People's Republic of China
| | - Guoping Chen
- Key Laboratory of Biorheological Science and Technology, (Chongqing University), Ministry of Education, Room 515, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing 400044, People's Republic of China.
| |
Collapse
|
39
|
Han Y, Zhao X, Liu D, Li Y, Lightfoot DA, Yang Z, Zhao L, Zhou G, Wang Z, Huang L, Zhang Z, Qiu L, Zheng H, Li W. Domestication footprints anchor genomic regions of agronomic importance in soybeans. THE NEW PHYTOLOGIST 2016; 209:871-84. [PMID: 26479264 DOI: 10.1111/nph.13626] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 07/12/2015] [Indexed: 05/02/2023]
Abstract
Present-day soybeans consist of elite cultivars and landraces (Glycine max, fully domesticated (FD)), annual wild type (Glycine soja, nondomesticated (ND)), and semi-wild type (semi-domesticated (SD)). FD soybean originated in China, although the details of its domestication history remain obscure. More than 500 diverse soybean accessions were sequenced using specific-locus amplified fragment sequencing (SLAF-seq) to address fundamental questions regarding soybean domestication. In total, 64,141 single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAFs) > 0.05 were found among the 512 tested accessions. The results indicated that the SD group is not a hybrid between the FD and ND groups. The initial domestication region was pinpointed to central China (demarcated by the Great Wall to the north and the Qinling Mountains to the south). A total of 800 highly differentiated genetic regions and > 140 selective sweeps were identified, and these were three- and twofold more likely, respectively, to encompass a known quantitative trait locus (QTL) than the rest of the soybean genome. Forty-three potential quantitative trait nucleotides (QTNs; including 15 distinct traits) were identified by genome-wide association mapping. The results of the present study should be beneficial for soybean improvement and provide insight into the genetic architecture of traits of agronomic importance.
Collapse
Affiliation(s)
- Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Dongyuan Liu
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300, China
| | - Yinghui Li
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - David A Lightfoot
- Illinois Soybean Center for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Zhijiang Yang
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Gang Zhou
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300, China
| | - Zhikun Wang
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Long Huang
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300, China
| | - Zhiwu Zhang
- Department of Crop and Soil Science, Washington State University, Pullman, WA, 99164-6420, USA
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| |
Collapse
|
40
|
Yan F, Di S, Takahashi R. CACTA-superfamily transposable element is inserted in MYB transcription factor gene of soybean line producing variegated seeds. Genome 2015; 58:365-74. [PMID: 26360633 DOI: 10.1139/gen-2015-0054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The R gene of soybean, presumably encoding a MYB transcription factor, controls seed coat color. The gene consists of multiple alleles, R (black), r-m (black spots and (or) concentric streaks on brown seed), and r (brown seed). This study was conducted to determine the structure of the MYB transcription factor gene in a near-isogenic line (NIL) having r-m allele. PCR amplification of a fragment of the candidate gene Glyma.09G235100 generated a fragment of about 1 kb in the soybean cultivar Clark, whereas a fragment of about 14 kb in addition to fragments of 1 and 1.4 kb were produced in L72-2040, a Clark 63 NIL with the r-m allele. Clark 63 is a NIL of Clark with the rxp and Rps1 alleles. A DNA fragment of 13 060 bp was inserted in the intron of Glyma.09G235100 in L72-2040. The fragment had the CACTA motif at both ends, imperfect terminal inverted repeats (TIR), inverse repetition of short sequence motifs close to the 5' and 3' ends, and a duplication of three nucleotides at the site of integration, indicating that it belongs to a CACTA-superfamily transposable element. We designated the element as Tgm11. Overall nucleotide sequence, motifs of TIR, and subterminal repeats were similar to those of Tgm1 and Tgs1, suggesting that these elements comprise a family.
Collapse
Affiliation(s)
- Fan Yan
- a Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8518 Japan
| | - Shaokang Di
- a Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8518 Japan
| | - Ryoji Takahashi
- a Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8518 Japan
- b National Institute of Crop Science, Tsukuba, Ibaraki, 305-8518 Japan
| |
Collapse
|
41
|
Sundaramoorthy J, Park GT, Lee JD, Kim JH, Seo HS, Song JT. Genetic and molecular regulation of flower pigmentation in soybean. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13765-015-0077-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
42
|
Sonah H, O'Donoughue L, Cober E, Rajcan I, Belzile F. Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:211-21. [PMID: 25213593 DOI: 10.1111/pbi.12249] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 06/24/2014] [Accepted: 07/29/2014] [Indexed: 05/18/2023]
Abstract
Soya bean is a major source of edible oil and protein for human consumption as well as animal feed. Understanding the genetic basis of different traits in soya bean will provide important insights for improving breeding strategies for this crop. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of agronomic traits in soya bean. A genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>47,000 SNPs) for a panel of 304 short-season soya bean lines. A subset of 139 lines, representative of the diversity among these, was characterized phenotypically for eight traits under six environments (3 sites × 2 years). Marker coverage proved sufficient to ensure highly significant associations between the genes known to control simple traits (flower, hilum and pubescence colour) and flanking SNPs. Between one and eight genomic loci associated with more complex traits (maturity, plant height, seed weight, seed oil and protein) were also identified. Importantly, most of these GWAS loci were located within genomic regions identified by previously reported quantitative trait locus (QTL) for these traits. In some cases, the reported QTLs were also successfully validated by additional QTL mapping in a biparental population. This study demonstrates that integrating GBS and GWAS can be used as a powerful complementary approach to classical biparental mapping for dissecting complex traits in soya bean.
Collapse
Affiliation(s)
- Humira Sonah
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | | | | | | | | |
Collapse
|
43
|
Zabala G, Vodkin LO. Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats. PLoS One 2014; 9:e111959. [PMID: 25369033 PMCID: PMC4219821 DOI: 10.1371/journal.pone.0111959] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/07/2014] [Indexed: 01/26/2023] Open
Abstract
We determined the molecular basis of three soybean lines that vary in seed coat color at the R locus which is thought to encode a MYB transcription factor. RM55-r(m) is homozygous for a mutable allele (r(m)) that specifies black and brown striped seeds; RM30-R* is a stable black revertant isoline derived from the mutable line; and RM38-r has brown seed coats due to a recessive r allele shown to translate a truncated MYB protein. Using long range PCR, 454 sequencing of amplicons, and whole genome re-sequencing, we determined that the variegated RM55-r(m) line had a 13 kb CACTA subfamily transposon insertion (designated TgmR*) at a position 110 bp from the beginning of Intron2 of the R locus, Glyma09g36983. Although the MYB encoded by R was expressed at only very low levels in older seed coats of the black revertant RM30-R* line, it upregulated expression of anthocyanidin synthase genes (ANS2, ANS3) to promote the synthesis of anthocyanins. Surprisingly, the RM30-R* revertant also carried the 13 kb TgmR* insertion in Intron2. Using RNA-Seq, we showed that intron splicing was accurate, albeit at lower levels, despite the presence of the 13 kb TgmR* element. As determined by whole genome methylation sequencing, we demonstrate that the TgmR* sequence was relatively more methylated in RM30-R* than in the mutable RM55-r(m) progenitor line. The stabilized and more methylated RM30-R* revertant line apparently lacks effective binding of a transposae to its subterminal repeats, thus allowing intron splicing to proceed resulting in sufficient MYB protein to stimulate anthocyanin production and thus black seed coats. In this regard, the TgmR* element in soybean resembles McClintock's Spm-suppressible and change-of-state alleles of maize. This comparison explains the opposite effects of the TgmR* element on intron splicing of the MYB gene in which it resides depending on the methylation state of the element.
Collapse
Affiliation(s)
- Gracia Zabala
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Lila O. Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| |
Collapse
|
44
|
Zabala G, Vodkin LO. Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats. PLoS One 2014; 9:e111959. [PMID: 25369033 DOI: 10.1371/journalpone.0111959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/07/2014] [Indexed: 05/28/2023] Open
Abstract
We determined the molecular basis of three soybean lines that vary in seed coat color at the R locus which is thought to encode a MYB transcription factor. RM55-r(m) is homozygous for a mutable allele (r(m)) that specifies black and brown striped seeds; RM30-R* is a stable black revertant isoline derived from the mutable line; and RM38-r has brown seed coats due to a recessive r allele shown to translate a truncated MYB protein. Using long range PCR, 454 sequencing of amplicons, and whole genome re-sequencing, we determined that the variegated RM55-r(m) line had a 13 kb CACTA subfamily transposon insertion (designated TgmR*) at a position 110 bp from the beginning of Intron2 of the R locus, Glyma09g36983. Although the MYB encoded by R was expressed at only very low levels in older seed coats of the black revertant RM30-R* line, it upregulated expression of anthocyanidin synthase genes (ANS2, ANS3) to promote the synthesis of anthocyanins. Surprisingly, the RM30-R* revertant also carried the 13 kb TgmR* insertion in Intron2. Using RNA-Seq, we showed that intron splicing was accurate, albeit at lower levels, despite the presence of the 13 kb TgmR* element. As determined by whole genome methylation sequencing, we demonstrate that the TgmR* sequence was relatively more methylated in RM30-R* than in the mutable RM55-r(m) progenitor line. The stabilized and more methylated RM30-R* revertant line apparently lacks effective binding of a transposae to its subterminal repeats, thus allowing intron splicing to proceed resulting in sufficient MYB protein to stimulate anthocyanin production and thus black seed coats. In this regard, the TgmR* element in soybean resembles McClintock's Spm-suppressible and change-of-state alleles of maize. This comparison explains the opposite effects of the TgmR* element on intron splicing of the MYB gene in which it resides depending on the methylation state of the element.
Collapse
Affiliation(s)
- Gracia Zabala
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Lila O Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| |
Collapse
|
45
|
Kim YH, Park HM, Hwang TY, Lee SK, Choi MS, Jho S, Hwang S, Kim HM, Lee D, Kim BC, Hong CP, Cho YS, Kim H, Jeong KH, Seo MJ, Yun HT, Kim SL, Kwon YU, Kim WH, Chun HK, Lim SJ, Shin YA, Choi IY, Kim YS, Yoon HS, Lee SH, Lee S. Variation block-based genomics method for crop plants. BMC Genomics 2014; 15:477. [PMID: 24929792 PMCID: PMC4229737 DOI: 10.1186/1471-2164-15-477] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/03/2014] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits. RESULTS We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. CONCLUSIONS We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding.
Collapse
Affiliation(s)
- Yul Ho Kim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Hyang Mi Park
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Tae-Young Hwang
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Seuk Ki Lee
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Man Soo Choi
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Seungwoo Hwang
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 306-809, Republic of Korea
| | - Hak-Min Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Dongwoo Lee
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Byoung-Chul Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Chang Pyo Hong
- Theragen Bio Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Yun Sung Cho
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Hyunmin Kim
- Theragen Bio Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Kwang Ho Jeong
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Min Jung Seo
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Hong Tai Yun
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Sun Lim Kim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Young-Up Kwon
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Wook Han Kim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Hye Kyung Chun
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Sang Jong Lim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Young-Ah Shin
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Republic of Korea
| | - Young Sun Kim
- Department of Biology, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Ho-Sung Yoon
- Department of Biology, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Sunghoon Lee
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
- Theragen Bio Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| |
Collapse
|
46
|
Kour A, Boone AM, Vodkin LO. RNA-Seq profiling of a defective seed coat mutation in Glycine max reveals differential expression of proline-rich and other cell wall protein transcripts. PLoS One 2014; 9:e96342. [PMID: 24828743 PMCID: PMC4020777 DOI: 10.1371/journal.pone.0096342] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 04/04/2014] [Indexed: 01/19/2023] Open
Abstract
The plant cell wall performs a number of essential functions including providing shape to many different cell types and serving as a defense against potential pathogens. The net pattern mutation creates breaks in the seed coat of soybean (Glycine max) because of ruptured cell walls. Using RNA-Seq, we examined the seed coat transcriptome from three stages of immature seed development in two pairs of isolines with normal or defective seed coat phenotypes due to the net pattern. The genome-wide comparative study of the transcript profiles of these isolines revealed 364 differentially expressed genes in common between the two varieties that were further divided into different broad functional categories. Genes related to cell wall processes accounted for 19% of the differentially expressed genes in the middle developmental stage of 100-200 mg seed weight. Within this class, the cell wall proline-rich and glycine-rich protein genes were highly differentially expressed in both genetic backgrounds. Other genes that showed significant expression changes in each of the isoline pairs at the 100-200 mg seed weight stage were xylem serine proteinase, fasciclin-related genes, auxin and stress response related genes, TRANSPARENT TESTA 1 (TT1) and other transcription factors. The mutant appears to shift the timing of either the increase or decrease in the levels of some of the transcripts. The analysis of these data sets reveals the physiological changes that the seed coat undergoes during the formation of the breaks in the cell wall.
Collapse
Affiliation(s)
- Anupreet Kour
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Anne M. Boone
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Lila O. Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| |
Collapse
|
47
|
Smýkal P, Vernoud V, Blair MW, Soukup A, Thompson RD. The role of the testa during development and in establishment of dormancy of the legume seed. FRONTIERS IN PLANT SCIENCE 2014; 5:351. [PMID: 25101104 PMCID: PMC4102250 DOI: 10.3389/fpls.2014.00351] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/30/2014] [Indexed: 05/19/2023]
Abstract
Timing of seed germination is one of the key steps in plant life cycles. It determines the beginning of plant growth in natural or agricultural ecosystems. In the wild, many seeds exhibit dormancy and will only germinate after exposure to certain environmental conditions. In contrast, crop seeds germinate as soon as they are imbibed usually at planting time. These domestication-triggered changes represent adaptations to cultivation and human harvesting. Germination is one of the common sets of traits recorded in different crops and termed the "domestication syndrome." Moreover, legume seed imbibition has a crucial role in cooking properties. Different seed dormancy classes exist among plant species. Physical dormancy (often called hardseededness), as found in legumes, involves the development of a water-impermeable seed coat, caused by the presence of phenolics- and suberin-impregnated layers of palisade cells. The dormancy release mechanism primarily involves seed responses to temperature changes in the habitat, resulting in testa permeability to water. The underlying genetic controls in legumes have not been identified yet. However, positive correlation was shown between phenolics content (e.g., pigmentation), the requirement for oxidation and the activity of catechol oxidase in relation to pea seed dormancy, while epicatechin levels showed a significant positive correlation with soybean hardseededness. myeloblastosis family of transcription factors, WD40 proteins and enzymes of the anthocyanin biosynthesis pathway were involved in seed testa color in soybean, pea and Medicago, but were not tested directly in relation to seed dormancy. These phenolic compounds play important roles in defense against pathogens, as well as affecting the nutritional quality of products, and because of their health benefits, they are of industrial and medicinal interest. In this review, we discuss the role of the testa in mediating legume seed germination, with a focus on structural and chemical aspects.
Collapse
Affiliation(s)
- Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacký University in OlomoucOlomouc, Czech Republic
- *Correspondence: Petr Smýkal, Department of Botany, Faculty of Sciences, Palacký University in Olomouc, Šlechtitelů 11, 783 71 Olomouc, Czech Republic e-mail:
| | | | - Matthew W. Blair
- Department of Agricultural and Environmental Sciences, Tennessee State UniversityNashville, TN, USA
| | - Aleš Soukup
- Department of Experimental Plant Biology, Charles UniversityPrague, Czech Republic
| | | |
Collapse
|
48
|
Li XW, Li JW, Zhai Y, Zhao Y, Zhao X, Zhang HJ, Su LT, Wang Y, Wang QY. A R2R3-MYB transcription factor, GmMYB12B2, affects the expression levels of flavonoid biosynthesis genes encoding key enzymes in transgenic Arabidopsis plants. Gene 2013; 532:72-9. [PMID: 24060295 DOI: 10.1016/j.gene.2013.09.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/04/2013] [Indexed: 11/30/2022]
Abstract
Isoflavones play diverse roles in plant-microbe interactions and are potentially important for human nutrition and health. To study the regulation of isoflavonoid synthesis in soybean, the R2R3-MYB transcription factor GmMYB12B2 was isolated and characterized. Yeast expression experiments demonstrated that GmMYB12B2 showed transcriptional activity. GmMYB12B2 was localized in the nucleus when it was transiently expressed in onion epidermal cells. Real-time quantitative PCR analysis revealed that GmMYB12B2 transcription was increased in roots and mature seeds compared with other organs. The gene expression level in immature embryos was consistent with the accumulation of isoflavones. CHS8 is a key enzyme in plant flavonoid biosynthesis. Transient expression experiments in soybean calli demonstrated that CHS8 was regulated by GmMYB12B2 and produced more fluorescence. The expression levels of some key enzymes in flavonoid biosynthesis were examined in transgenic Arabidopsis lines. The results showed that the expression levels of PAL1, CHS and FLS in transgenic plants were significantly higher than those in wild type plants. However, the expression level of DFR was lower, and the expression levels of CHI, F3H and F3'H were the same in all lines. GmMYB12B2 expression caused a constitutive increase in the accumulation of flavonoids in transgenic Arabidopsis lines compared with wild type plants.
Collapse
Affiliation(s)
- Xiao-Wei Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Lenser T, Theißen G. Molecular mechanisms involved in convergent crop domestication. TRENDS IN PLANT SCIENCE 2013; 18:704-14. [PMID: 24035234 DOI: 10.1016/j.tplants.2013.08.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/12/2013] [Accepted: 08/21/2013] [Indexed: 05/21/2023]
Abstract
Domestication has helped to understand evolution. We argue that, vice versa, novel insights into evolutionary principles could provide deeper insights into domestication. Molecular analyses have demonstrated that convergent phenotypic evolution is often based on molecular changes in orthologous genes or pathways. Recent studies have revealed that during plant domestication the causal mutations for convergent changes in key traits are likely to be located in particular genes. These insights may contribute to defining candidate genes for genetic improvement during the domestication of new plant species. Such efforts may help to increase the range of arable crops available, thus increasing crop biodiversity and food security to help meet the predicted demands of the continually growing global population under rapidly changing environmental conditions.
Collapse
Affiliation(s)
- Teresa Lenser
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany
| | | |
Collapse
|
50
|
Reinprecht Y, Yadegari Z, Perry GE, Siddiqua M, Wright LC, McClean PE, Pauls KP. In silico comparison of genomic regions containing genes coding for enzymes and transcription factors for the phenylpropanoid pathway in Phaseolus vulgaris L. and Glycine max L. Merr. FRONTIERS IN PLANT SCIENCE 2013; 4:317. [PMID: 24046770 PMCID: PMC3763686 DOI: 10.3389/fpls.2013.00317] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/29/2013] [Indexed: 05/27/2023]
Abstract
Legumes contain a variety of phytochemicals derived from the phenylpropanoid pathway that have important effects on human health as well as seed coat color, plant disease resistance and nodulation. However, the information about the genes involved in this important pathway is fragmentary in common bean (Phaseolus vulgaris L.). The objectives of this research were to isolate genes that function in and control the phenylpropanoid pathway in common bean, determine their genomic locations in silico in common bean and soybean, and analyze sequences of the 4CL gene family in two common bean genotypes. Sequences of phenylpropanoid pathway genes available for common bean or other plant species were aligned, and the conserved regions were used to design sequence-specific primers. The PCR products were cloned and sequenced and the gene sequences along with common bean gene-based (g) markers were BLASTed against the Glycine max v.1.0 genome and the P. vulgaris v.1.0 (Andean) early release genome. In addition, gene sequences were BLASTed against the OAC Rex (Mesoamerican) genome sequence assembly. In total, fragments of 46 structural and regulatory phenylpropanoid pathway genes were characterized in this way and placed in silico on common bean and soybean sequence maps. The maps contain over 250 common bean g and SSR (simple sequence repeat) markers and identify the positions of more than 60 additional phenylpropanoid pathway gene sequences, plus the putative locations of seed coat color genes. The majority of cloned phenylpropanoid pathway gene sequences were mapped to one location in the common bean genome but had two positions in soybean. The comparison of the genomic maps confirmed previous studies, which show that common bean and soybean share genomic regions, including those containing phenylpropanoid pathway gene sequences, with conserved synteny. Indels identified in the comparison of Andean and Mesoamerican common bean 4CL gene sequences might be used to develop inter-pool phenylpropanoid pathway gene-based markers. We anticipate that the information obtained by this study will simplify and accelerate selections of common bean with specific phenylpropanoid pathway alleles to increase the contents of beneficial phenylpropanoids in common bean and other legumes.
Collapse
Affiliation(s)
| | - Zeinab Yadegari
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
| | - Gregory E. Perry
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
| | - Mahbuba Siddiqua
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
| | - Lori C. Wright
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - K. Peter Pauls
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
| |
Collapse
|