551
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Valliyodan B, Ye H, Song L, Murphy M, Shannon JG, Nguyen HT. Genetic diversity and genomic strategies for improving drought and waterlogging tolerance in soybeans. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1835-1849. [PMID: 27927997 DOI: 10.1093/jxb/erw433] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Drought and its interaction with high temperature are the major abiotic stress factors affecting soybean yield and production stability. Ongoing climate changes are anticipated to intensify drought events, which will further impact crop production and food security. However, excessive water also limits soybean production. The success of soybean breeding programmes for crop improvement is dependent on the extent of genetic variation present in the germplasm base. Screening for natural genetic variation in drought- and flooding tolerance-related traits, including root system architecture, water and nitrogen-fixation efficiency, and yield performance indices, has helped to identify the best resources for genetic studies in soybean. Genomic resources, including whole-genome sequences of diverse germplasms, millions of single-nucleotide polymorphisms, and high-throughput marker genotyping platforms, have expedited gene and marker discovery for translational genomics in soybean. This review highlights the current knowledge of the genetic diversity and quantitative trait loci associated with root system architecture, canopy wilting, nitrogen-fixation ability, and flooding tolerance that contributes to the understanding of drought- and flooding-tolerance mechanisms in soybean. Next-generation mapping approaches and high-throughput phenotyping will facilitate a better understanding of phenotype-genotype associations and help to formulate genomic-assisted breeding strategies, including genomic selection, in soybean for tolerance to drought and flooding stress.
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Affiliation(s)
- Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - Heng Ye
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - Li Song
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - MacKensie Murphy
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - J Grover Shannon
- Division of Plant Sciences, University of Missouri-Fisher Delta Research Center, Portageville, MO 63873, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
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552
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Gao L, Zhao G, Huang D, Jia J. Candidate loci involved in domestication and improvement detected by a published 90K wheat SNP array. Sci Rep 2017; 7:44530. [PMID: 28327671 PMCID: PMC5361097 DOI: 10.1038/srep44530] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/10/2017] [Indexed: 11/12/2022] Open
Abstract
Selection is one of the most important forces in crop evolution. Common wheat is a major world food crop and a typical allopolyploid with a huge and complex genome. We applied four approaches to detect loci selected in wheat during domestication and improvement. A total of 7,984 candidate loci were detected, accounting for 23.3% of all 34,317 SNPs analysed, a much higher proportion than estimated in previous reports. We constructed a first generation wheat selection map which revealed the following new insights on genome-wide selection: (1) diversifying selection acted by increasing, decreasing or not affecting gene frequencies; (2) the number of loci under selection during domestication was much higher than that during improvement; (3) the contribution to wheat improvement by the D sub-genome was relatively small due to the bottleneck of hexaploidisation and diversity can be expanded by using synthetic wheat and introgression lines; and (4) clustered selection regions occur throughout the wheat genome, including the centromere regions. This study will not only help future wheat breeding and evolutionary studies, but will also accelerate study of other crops, especially polyploids.
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Affiliation(s)
- Lifeng Gao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
| | - Guangyao Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
| | - Dawei Huang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
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553
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Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L, Zhou X, Nie X, Li Z, Guo K, Ma Y, Huang C, Jin S, Zhu L, Yang X, Min L, Yuan D, Zhang Q, Lindsey K, Zhang X. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet 2017; 49:579-587. [PMID: 28263319 DOI: 10.1038/ng.3807] [Citation(s) in RCA: 260] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/10/2017] [Indexed: 12/16/2022]
Abstract
Comparative population genomics offers an excellent opportunity for unraveling the genetic history of crop domestication. Upland cotton (Gossypium hirsutum) has long been an important economic crop, but a genome-wide and evolutionary understanding of the effects of human selection is lacking. Here, we describe a variation map for 352 wild and domesticated cotton accessions. We scanned 93 domestication sweeps occupying 74 Mb of the A subgenome and 104 Mb of the D subgenome, and identified 19 candidate loci for fiber-quality-related traits through a genome-wide association study. We provide evidence showing asymmetric subgenome domestication for directional selection of long fibers. Global analyses of DNase I-hypersensitive sites and 3D genome architecture, linking functional variants to gene transcription, demonstrate the effects of domestication on cis-regulatory divergence. This study provides new insights into the evolution of gene organization, regulation and adaptation in a major crop, and should serve as a rich resource for genome-based cotton improvement.
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Affiliation(s)
- Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Min Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Zhengxiu Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaolin Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xinhui Nie
- Key Laboratory of Oasis Eco-agriculture of the Xinjiang Production and Construction Corps, College of Agronomy, Shihezi University, Shihezi, China
| | - Zhonghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Kai Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Cong Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiyan Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ling Min
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Daojun Yuan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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554
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Zong Y, Yao S, Crawford GW, Fang H, Lang J, Fan J, Sun Z, Liu Y, Zhang J, Duan X, Zhou G, Xiao T, Luan F, Wang Q, Chen X, Jiang H. Selection for Oil Content During Soybean Domestication Revealed by X-Ray Tomography of Ancient Beans. Sci Rep 2017; 7:43595. [PMID: 28240321 PMCID: PMC5327410 DOI: 10.1038/srep43595] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/24/2017] [Indexed: 11/24/2022] Open
Abstract
When and under what circumstances domestication related traits evolved in soybean (Glycine max) is not well understood. Seed size has been a focus of archaeological attention because increased soybean seed weight/size is a trait that distinguishes most modern soybeans from their ancestors; however, archaeological seed size analysis has had limited success. Modern domesticated soybean has a significantly higher oil content than its wild counterpart so oil content is potentially a source of new insight into soybean domestication. We investigated soybean oil content using X-ray computed tomography (CT; specifically, synchrotron radiation X-ray CT or SRX-CT) of charred, archaeological soybean seeds. CT identified holes in the specimens that are associated with oil content. A high oil content facilitates the development of small holes, whereas a high protein content results in larger holes. The volume of small holes increased slowly from 7,500 to 4,000 cal B.P. We infer that human selection for higher oil content began as early as 7,500 cal B.P. and that high oil content cultivars were well established by 4,000 cal B.P.
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Affiliation(s)
- Yunbing Zong
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
| | - Shengkun Yao
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Gary W. Crawford
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Hui Fang
- Department of Archaeology, Shandong University, Jinan, Shandong 250100, China
| | - Jianfeng Lang
- Department of Archaeology, Shandong University, Jinan, Shandong 250100, China
| | - Jiadong Fan
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhibin Sun
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
| | - Yang Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
| | - Jianhua Zhang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
| | - Xiulan Duan
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
| | - Guangzhao Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Tiqiao Xiao
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Fengshi Luan
- Department of Archaeology, Shandong University, Jinan, Shandong 250100, China
| | - Qing Wang
- Department of Archaeology, Shandong University, Jinan, Shandong 250100, China
| | - Xuexiang Chen
- Department of Archaeology, Shandong University, Jinan, Shandong 250100, China
| | - Huaidong Jiang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
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555
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Muñoz N, Liu A, Kan L, Li MW, Lam HM. Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement. Int J Mol Sci 2017; 18:E328. [PMID: 28165413 PMCID: PMC5343864 DOI: 10.3390/ijms18020328] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 01/14/2023] Open
Abstract
Challenged by population increase, climatic change, and soil deterioration, crop improvement is always a priority in securing food supplies. Although the production of grain legumes is in general lower than that of cereals, the nutritional value of grain legumes make them important components of food security. Nevertheless, limited by severe genetic bottlenecks during domestication and human selection, grain legumes, like other crops, have suffered from a loss of genetic diversity which is essential for providing genetic materials for crop improvement programs. Illustrated by whole-genome-sequencing, wild relatives of crops adapted to various environments were shown to maintain high genetic diversity. In this review, we focused on nine important grain legumes (soybean, peanut, pea, chickpea, common bean, lentil, cowpea, lupin, and pigeonpea) to discuss the potential uses of their wild relatives as genetic resources for crop breeding and improvement, and summarized the various genetic/genomic approaches adopted for these purposes.
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Affiliation(s)
- Nacira Muñoz
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Centro de Investigaciones Agropecuarias-INTA, Instituto de Fisiología y Recursos Genéticos Vegetales, Córdoba X5000, Argentina.
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba X5000, Argentina.
| | - Ailin Liu
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Leo Kan
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Man-Wah Li
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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556
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Jubery TZ, Shook J, Parmley K, Zhang J, Naik HS, Higgins R, Sarkar S, Singh A, Singh AK, Ganapathysubramanian B. Deploying Fourier Coefficients to Unravel Soybean Canopy Diversity. FRONTIERS IN PLANT SCIENCE 2017; 7:2066. [PMID: 28154570 PMCID: PMC5243820 DOI: 10.3389/fpls.2016.02066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/26/2016] [Indexed: 05/28/2023]
Abstract
Soybean canopy outline is an important trait used to understand light interception ability, canopy closure rates, row spacing response, which in turn affects crop growth and yield, and directly impacts weed species germination and emergence. In this manuscript, we utilize a methodology that constructs geometric measures of the soybean canopy outline from digital images of canopies, allowing visualization of the genetic diversity as well as a rigorous quantification of shape parameters. Our choice of data analysis approach is partially dictated by the need to efficiently store and analyze large datasets, especially in the context of planned high-throughput phenotyping experiments to capture time evolution of canopy outline which will produce very large datasets. Using the Elliptical Fourier Transformation (EFT) and Fourier Descriptors (EFD), canopy outlines of 446 soybean plant introduction (PI) lines from 25 different countries exhibiting a wide variety of maturity, seed weight, and stem termination were investigated in a field experiment planted as a randomized complete block design with up to four replications. Canopy outlines were extracted from digital images, and subsequently chain coded, and expanded into a shape spectrum by obtaining the Fourier coefficients/descriptors. These coefficients successfully reconstruct the canopy outline, and were used to measure traditional morphometric traits. Highest phenotypic diversity was observed for roundness, while solidity showed the lowest diversity across all countries. Some PI lines had extraordinary shape diversity in solidity. For interpretation and visualization of the complexity in shape, Principal Component Analysis (PCA) was performed on the EFD. PI lines were grouped in terms of origins, maturity index, seed weight, and stem termination index. No significant pattern or similarity was observed among the groups; although interestingly when genetic marker data was used for the PCA, patterns similar to canopy outline traits was observed for origins, and maturity indexes. These results indicate the usefulness of EFT method for reconstruction and study of canopy morphometric traits, and provides opportunities for data reduction of large images for ease in future use.
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Affiliation(s)
- Talukder Z. Jubery
- Department of Mechanical Engineering, Iowa State UniversityAmes, IA, USA
| | | | - Kyle Parmley
- Department of Agronomy, Iowa State UniversityAmes, IA, USA
| | - Jiaoping Zhang
- Department of Agronomy, Iowa State UniversityAmes, IA, USA
| | - Hsiang S. Naik
- Department of Mechanical Engineering, Iowa State UniversityAmes, IA, USA
| | - Race Higgins
- Department of Agronomy, Iowa State UniversityAmes, IA, USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State UniversityAmes, IA, USA
| | - Arti Singh
- Department of Agronomy, Iowa State UniversityAmes, IA, USA
| | | | - Baskar Ganapathysubramanian
- Department of Mechanical Engineering, Iowa State UniversityAmes, IA, USA
- Department of Electrical and Computer Engineering, Iowa State UniversityAmes, IA, USA
- Plant Sciences Institute, Iowa State UniversityAmes, IA, USA
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557
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Leamy LJ, Zhang H, Li C, Chen CY, Song BH. A genome-wide association study of seed composition traits in wild soybean (Glycine soja). BMC Genomics 2017; 18:18. [PMID: 28056769 PMCID: PMC5217241 DOI: 10.1186/s12864-016-3397-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 12/07/2016] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Cultivated soybean (Glycine max) is a major agricultural crop that provides a crucial source of edible protein and oil. Decreased amounts of saturated palmitic acid and increased amounts of unsaturated oleic acid in soybean oil are considered optimal for human cardiovascular health and therefore there has considerable interest by breeders in discovering genes affecting the relative concentrations of these fatty acids. Using a genome-wide association (GWA) approach with nearly 30,000 single nucleotide polymorphisms (SNPs), we investigated the genetic basis of protein, oil and all five fatty acid levels in seeds from a sample of 570 wild soybeans (Glycine soja), the progenitor of domesticated soybean, to identify quantitative trait loci (QTLs) affecting these seed composition traits. RESULTS We discovered 29 SNPs located on ten different chromosomes that are significantly associated with the seven seed composition traits in our wild soybean sample. Eight SNPs co-localized with QTLs previously uncovered in linkage or association mapping studies conducted with cultivated soybean samples, while the remaining SNPs appeared to be in novel locations. Twenty-four of the SNPs significantly associated with fatty acid variation, with the majority located on chromosomes 14 (6 SNPs) and seven (8 SNPs). Two SNPs were common for two or more fatty acids, suggesting loci with pleiotropic effects. We also identified some candidate genes that are involved in fatty acid metabolism and regulation. For each of the seven traits, most of the SNPs produced differences between the average phenotypic values of the two homozygotes of about one-half standard deviation and contributed over 3% of their total variability. CONCLUSIONS This is the first GWA study conducted on seed composition traits solely in wild soybean populations, and a number of QTLs were found that have not been previously discovered. Some of these may be useful to breeders who select for increased protein/oil content or altered fatty acid ratios in the seeds. The results also provide additional insight into the genetic architecture of these traits in a large sample of wild soybean, and suggest some new candidate genes whose molecular effects on these traits need to be further studied.
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Affiliation(s)
- Larry J Leamy
- Department of Biological Sciences, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Hengyou Zhang
- Department of Biological Sciences, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Changbao Li
- Double Haploid Optimization Group, Monsanto Company, Chesterfield, MO, 63017, USA
| | - Charles Y Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Bao-Hua Song
- Department of Biological Sciences, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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558
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Liu Z, Li H, Wen Z, Fan X, Li Y, Guan R, Guo Y, Wang S, Wang D, Qiu L. Comparison of Genetic Diversity between Chinese and American Soybean ( Glycine max (L.)) Accessions Revealed by High-Density SNPs. FRONTIERS IN PLANT SCIENCE 2017; 8:2014. [PMID: 29250088 PMCID: PMC5715234 DOI: 10.3389/fpls.2017.02014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/13/2017] [Indexed: 05/20/2023]
Abstract
Soybean is one of the most important economic crops for both China and the United States (US). The exchange of germplasm between these two countries has long been active. In order to investigate genetic relationships between Chinese and US soybean germplasm, 277 Chinese soybean accessions and 300 US soybean accessions from geographically diverse regions were analyzed using 5,361 SNP markers. The genetic diversity and the polymorphism information content (PIC) of the Chinese accessions was higher than that of the US accessions. Population structure analysis, principal component analysis, and cluster analysis all showed that the genetic basis of Chinese soybeans is distinct from that of the USA. The groupings observed in clustering analysis reflected the geographical origins of the accessions; this conclusion was validated with both genetic distance analysis and relative kinship analysis. FST-based and EigenGWAS statistical analysis revealed high genetic variation between the two subpopulations. Analysis of the 10 loci with the strongest selection signals showed that many loci were located in chromosome regions that have previously been identified as quantitative trait loci (QTL) associated with environmental-adaptation-related and yield-related traits. The pattern of diversity among the American and Chinese accessions should help breeders to select appropriate parental accessions to enhance the performance of future soybean cultivars.
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Affiliation(s)
- Zhangxiong Liu
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Huihui Li
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Xuhong Fan
- Institute of Soybean Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yinghui Li
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Rongxia Guan
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Yong Guo
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Shuming Wang
- Institute of Soybean Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- *Correspondence: Dechun Wang
| | - Lijuan Qiu
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
- Lijuan Qiu
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559
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Cui C, Mei H, Liu Y, Zhang H, Zheng Y. Genetic Diversity, Population Structure, and Linkage Disequilibrium of an Association-Mapping Panel Revealed by Genome-Wide SNP Markers in Sesame. FRONTIERS IN PLANT SCIENCE 2017; 8:1189. [PMID: 28729877 PMCID: PMC5498554 DOI: 10.3389/fpls.2017.01189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 06/22/2017] [Indexed: 05/11/2023]
Abstract
The characterization of genetic diversity and population structure can be used in tandem to detect reliable phenotype-genotype associations. In the present study, we genotyped a set of 366 sesame germplasm accessions by using 89,924 single-nucleotide polymorphisms (SNPs). The number of SNPs on each chromosome was consistent with the physical length of the respective chromosome, and the average marker density was approximately 2.67 kb/SNP. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1.1 × 10-3, with averages of 1.0 × 10-4, 2.7 × 10-4, and 3.6 × 10-4 obtained, respectively for three identified subgroups of the panel: Pop 1, Pop 2, and the Mixed. The genetic structure analysis revealed that these sesame germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in the panel. The genome-wide linkage disequilibrium (LD) analysis showed that an average LD extended up to ∼99 kb. The genetic diversity and population structure revealed in this study should provide guidance to the future design of association studies and the systematic utilization of the genetic variation characterizing the sesame panel.
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Affiliation(s)
- Chengqi Cui
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural UniversityNanjing, China
| | - Hongxian Mei
- Henan Sesame Research Center, Henan Academy of Agricultural SciencesZhengzhou, China
- Key Laboratory of Oil Crops in Huanghuaihai Plain, Ministry of AgricultureZhengzhou, China
- Henan Provincial Key Laboratory for Oil Crops ImprovementZhengzhou, China
| | - Yanyang Liu
- Henan Sesame Research Center, Henan Academy of Agricultural SciencesZhengzhou, China
- Key Laboratory of Oil Crops in Huanghuaihai Plain, Ministry of AgricultureZhengzhou, China
- Henan Provincial Key Laboratory for Oil Crops ImprovementZhengzhou, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural SciencesZhengzhou, China
- Key Laboratory of Oil Crops in Huanghuaihai Plain, Ministry of AgricultureZhengzhou, China
- Henan Provincial Key Laboratory for Oil Crops ImprovementZhengzhou, China
- *Correspondence: Haiyang Zhang, Yongzhan Zheng,
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural SciencesZhengzhou, China
- Key Laboratory of Oil Crops in Huanghuaihai Plain, Ministry of AgricultureZhengzhou, China
- Henan Provincial Key Laboratory for Oil Crops ImprovementZhengzhou, China
- *Correspondence: Haiyang Zhang, Yongzhan Zheng,
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560
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Lu K, Peng L, Zhang C, Lu J, Yang B, Xiao Z, Liang Y, Xu X, Qu C, Zhang K, Liu L, Zhu Q, Fu M, Yuan X, Li J. Genome-Wide Association and Transcriptome Analyses Reveal Candidate Genes Underlying Yield-determining Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2017; 8:206. [PMID: 28261256 PMCID: PMC5309214 DOI: 10.3389/fpls.2017.00206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/03/2017] [Indexed: 05/19/2023]
Abstract
Yield is one of the most important yet complex crop traits. To improve our understanding of the genetic basis of yield establishment, and to identify candidate genes responsible for yield improvement in Brassica napus, we performed genome-wide association studies (GWAS) for seven yield-determining traits [main inflorescence pod number (MIPN), branch pod number (BPN), pod number per plant (PNP), seed number per pod (SPP), thousand seed weight, main inflorescence yield (MIY), and branch yield], using data from 520 diverse B. napus accessions from two different yield environments. In total, we detected 128 significant single nucleotide polymorphisms (SNPs), 93 of which were revealed as novel by integrative analysis. A combination of GWAS and transcriptome sequencing on 21 haplotype blocks from samples pooled by four extremely high-yielding or low-yielding accessions revealed the differential expression of 14 crucial candiate genes (such as Bna.MYB83, Bna.SPL5, and Bna.ROP3) associated with multiple traits or containing multiple SNPs associated with the same trait. Functional annotation and expression pattern analyses further demonstrated that these 14 candiate genes might be important in developmental processes and biomass accumulation, thus affecting the yield establishment of B. napus. These results provide valuable information for understanding the genetic mechanisms underlying the establishment of high yield in B. napus, and lay the foundation for developing high-yielding B. napus varieties.
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Affiliation(s)
- Kun Lu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- *Correspondence: Kun Lu
| | - Liu Peng
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- School of Management, Xihua UniversityChengdu, China
| | - Chao Zhang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural SciencesGuiyang, China
| | - Junhua Lu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Bo Yang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Zhongchun Xiao
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Ying Liang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Xingfu Xu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Qinlong Zhu
- College of Life Sciences, South China Agricultural UniversityGuangzhou, China
| | - Minglian Fu
- Industrial Crops Institute, Yunnan Academy of Agricultural SciencesKunming, China
| | - Xiaoyan Yuan
- Industrial Crops Institute, Yunnan Academy of Agricultural SciencesKunming, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Jiana Li
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Hradilová I, Trněný O, Válková M, Cechová M, Janská A, Prokešová L, Aamir K, Krezdorn N, Rotter B, Winter P, Varshney RK, Soukup A, Bednář P, Hanáček P, Smýkal P. A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea ( Pisum sp.). FRONTIERS IN PLANT SCIENCE 2017; 8:542. [PMID: 28487704 PMCID: PMC5404241 DOI: 10.3389/fpls.2017.00542] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/27/2017] [Indexed: 05/19/2023]
Abstract
The origin of the agriculture was one of the turning points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. Seed dispersal and germination are two key traits which have been selected to facilitate cultivation and harvesting of crops. The objective of this study was to analyze anatomical structure of seed coat and pod, identify metabolic compounds associated with water-impermeable seed coat and differentially expressed genes involved in pea seed dormancy and pod dehiscence. Comparative anatomical, metabolomics, and transcriptomic analyses were carried out on wild dormant, dehiscent Pisum elatius (JI64, VIR320) and cultivated, indehiscent Pisum sativum non-dormant (JI92, Cameor) and recombinant inbred lines (RILs). Considerable differences were found in texture of testa surface, length of macrosclereids, and seed coat thickness. Histochemical and biochemical analyses indicated genotype related variation in composition and heterogeneity of seed coat cell walls within macrosclereids. Liquid chromatography-electrospray ionization/mass spectrometry and Laser desorption/ionization-mass spectrometry of separated seed coats revealed significantly higher contents of proanthocyanidins (dimer and trimer of gallocatechin), quercetin, and myricetin rhamnosides and hydroxylated fatty acids in dormant compared to non-dormant genotypes. Bulk Segregant Analysis coupled to high throughput RNA sequencing resulted in identification of 770 and 148 differentially expressed genes between dormant and non-dormant seeds or dehiscent and indehiscent pods, respectively. The expression of 14 selected dormancy-related genes was studied by qRT-PCR. Of these, expression pattern of four genes: porin (MACE-S082), peroxisomal membrane PEX14-like protein (MACE-S108), 4-coumarate CoA ligase (MACE-S131), and UDP-glucosyl transferase (MACE-S139) was in agreement in all four genotypes with Massive analysis of cDNA Ends (MACE) data. In case of pod dehiscence, the analysis of two candidate genes (SHATTERING and SHATTERPROOF) and three out of 20 MACE identified genes (MACE-P004, MACE-P013, MACE-P015) showed down-expression in dorsal and ventral pod suture of indehiscent genotypes. Moreover, MACE-P015, the homolog of peptidoglycan-binding domain or proline-rich extensin-like protein mapped correctly to predicted Dpo1 locus on PsLGIII. This integrated analysis of the seed coat in wild and cultivated pea provides new insight as well as raises new questions associated with domestication and seed dormancy and pod dehiscence.
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Affiliation(s)
- Iveta Hradilová
- Department of Botany, Palacký University in OlomoucOlomouc, Czechia
| | - Oldřich Trněný
- Department of Plant Biology, Mendel University in BrnoBrno, Czechia
- Agricultural Research, Ltd.Troubsko, Czechia
| | - Markéta Válková
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Monika Cechová
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Anna Janská
- Department of Experimental Plant Biology, Charles UniversityPrague, Czechia
| | - Lenka Prokešová
- Department of Crop Science, Breeding and Plant Medicine, Mendel University in BrnoBrno, Czechia
| | - Khan Aamir
- Research Program-Genetic Gains, ICRISATHyderabad, India
| | | | | | | | | | - Aleš Soukup
- Department of Experimental Plant Biology, Charles UniversityPrague, Czechia
| | - Petr Bednář
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Pavel Hanáček
- Department of Plant Biology, Mendel University in BrnoBrno, Czechia
| | - Petr Smýkal
- Department of Botany, Palacký University in OlomoucOlomouc, Czechia
- *Correspondence: Petr Smýkal
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562
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Chang HX, Hartman GL. Characterization of Insect Resistance Loci in the USDA Soybean Germplasm Collection Using Genome-Wide Association Studies. FRONTIERS IN PLANT SCIENCE 2017; 8:670. [PMID: 28555141 PMCID: PMC5430066 DOI: 10.3389/fpls.2017.00670] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/12/2017] [Indexed: 05/18/2023]
Abstract
Management of insects that cause economic damage to yields of soybean mainly rely on insecticide applications. Sources of resistance in soybean plant introductions (PIs) to different insect pests have been reported, and some of these sources, like for the soybean aphid (SBA), have been used to develop resistant soybean cultivars. With the availability of SoySNP50K and the statistical power of genome-wide association studies, we integrated phenotypic data for beet armyworm, Mexican bean beetle (MBB), potato leafhopper (PLH), SBA, soybean looper (SBL), velvetbean caterpillar (VBC), and chewing damage caused by unspecified insects for a comprehensive understanding of insect resistance in the United States Department of Agriculture Soybean Germplasm Collection. We identified significant single nucleotide (SNP) polymorphic markers for MBB, PLH, SBL, and VBC, and we highlighted several leucine-rich repeat-containing genes and myeloblastosis transcription factors within the high linkage disequilibrium region surrounding significant SNP markers. Specifically for soybean resistance to PLH, we found the PLH locus is close but distinct to a locus for soybean pubescence density on chromosome 12. The results provide genetic support that pubescence density may not directly link to PLH resistance. This study offers a novel insight of soybean resistance to four insect pests and reviews resistance mapping studies for major soybean insects.
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Affiliation(s)
- Hao-Xun Chang
- Department of Plant, Soil, and Microbial Sciences, Michigan State UniversityEast Lansing, MI, USA
| | - Glen L. Hartman
- United States Department of Agriculture - Agricultural Research Service, University of IllinoisUrbana, IL, USA
- *Correspondence: Glen L. Hartman ;
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563
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Zhou Y, Tang H, Cheng MP, Dankwa KO, Chen ZX, Li ZY, Gao S, Liu YX, Jiang QT, Lan XJ, Pu ZE, Wei YM, Zheng YL, Hickey LT, Wang JR. Genome-Wide Association Study for Pre-harvest Sprouting Resistance in a Large Germplasm Collection of Chinese Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2017; 8:401. [PMID: 28428791 PMCID: PMC5382224 DOI: 10.3389/fpls.2017.00401] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/09/2017] [Indexed: 05/06/2023]
Abstract
Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments. A large number of landraces (194) displayed high levels of PHS resistance (i.e., mean GR < 0.20), which included nine white-grained accessions. Overall, white-grained accessions displayed a significantly higher mean GR (42.7-79.6%) compared to red-grained accessions (19.1-56.0%) across the six environments. Landraces from mesic growing zones in southern China showed higher levels of PHS resistance than those sourced from xeric areas in northern and north-western China. Three main quantitative trait loci (QTL) were detected by GWAS: one on 5D that appeared to be novel and two co-located with the grain color transcription factor Tamyb10 on 3A and 3D. An additional 32 grain color related QTL (GCR-QTL) were detected when the set of red-grained landraces were analyzed separately. GCR-QTL occurred at high frequencies in the red-grained accessions and a strong correlation was observed between the number of GCR-QTL and GR (R2 = 0.62). These additional factors could be critical for maintaining high levels of PHS resistance and represent targets for introgression into white-grained wheat cultivars. Further, investigation of the origin of haplotypes associated with the three main QTL revealed that favorable haplotypes for PHS resistance were more common in accessions from higher rainfall zones in China. Thus, a combination of natural and artificial selection likely resulted in landraces incorporating PHS resistance in China.
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Affiliation(s)
- Yong Zhou
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Hao Tang
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Meng-Ping Cheng
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Kwame O. Dankwa
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Zhong-Xu Chen
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Zhan-Yi Li
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Shang Gao
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Ya-Xi Liu
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Xiu-Jin Lan
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Zhi-En Pu
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural UniversityYa’an, China
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, BrisbaneQLD, Australia
| | - Ji-Rui Wang
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
- *Correspondence: Ji-Rui Wang,
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564
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Li Z, Jiang L, Ma Y, Wei Z, Hong H, Liu Z, Lei J, Liu Y, Guan R, Guo Y, Jin L, Zhang L, Li Y, Ren Y, He W, Liu M, Htwe NMPS, Liu L, Guo B, Song J, Tan B, Liu G, Li M, Zhang X, Liu B, Shi X, Han S, Hua S, Zhou F, Yu L, Li Y, Wang S, Wang J, Chang R, Qiu L. Development and utilization of a new chemically-induced soybean library with a high mutation density . JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:60-74. [PMID: 27774740 PMCID: PMC5248594 DOI: 10.1111/jipb.12505] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/20/2016] [Indexed: 05/20/2023]
Abstract
Mutagenized populations have provided important materials for introducing variation and identifying gene function in plants. In this study, an ethyl methanesulfonate (EMS)-induced soybean (Glycine max) population, consisting of 21,600 independent M2 lines, was developed. Over 1,000 M4 (5) families, with diverse abnormal phenotypes for seed composition, seed shape, plant morphology and maturity that are stably expressed across different environments and generations were identified. Phenotypic analysis of the population led to the identification of a yellow pigmentation mutant, gyl, that displayed significantly decreased chlorophyll (Chl) content and abnormal chloroplast development. Sequence analysis showed that gyl is allelic to MinnGold, where a different single nucleotide polymorphism variation in the Mg-chelatase subunit gene (ChlI1a) results in golden yellow leaves. A cleaved amplified polymorphic sequence marker was developed and may be applied to marker-assisted selection for the golden yellow phenotype in soybean breeding. We show that the newly developed soybean EMS mutant population has potential for functional genomics research and genetic improvement in soybean.
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565
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Du Y, Luo S, Li X, Yang J, Cui T, Li W, Yu L, Feng H, Chen Y, Mu J, Chen X, Shu Q, Guo T, Luo W, Zhou L. Identification of Substitutions and Small Insertion-Deletions Induced by Carbon-Ion Beam Irradiation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:1851. [PMID: 29163581 PMCID: PMC5665000 DOI: 10.3389/fpls.2017.01851] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/11/2017] [Indexed: 05/06/2023]
Abstract
Heavy-ion beam irradiation is one of the principal methods used to create mutants in plants. Research on mutagenic effects and molecular mechanisms of radiation is an important subject that is multi-disciplinary. Here, we re-sequenced 11 mutagenesis progeny (M3) Arabidopsis thaliana lines derived from carbon-ion beam (CIB) irradiation, and subsequently focused on substitutions and small insertion-deletion (INDELs). We found that CIB induced more substitutions (320) than INDELs (124). Meanwhile, the single base INDELs were more prevalent than those in large size (≥2 bp). In details, the detected substitutions showed an obvious bias of C > T transitions, by activating the formation of covalent linkages between neighboring pyrimidine residues in the DNA sequence. An A and T bias was observed among the single base INDELs, in which most of these were induced by replication slippage at either the homopolymer or polynucleotide repeat regions. The mutation rate of 200-Gy CIB irradiation was estimated as 3.37 × 10-7 per site. Different from previous researches which mainly focused on the phenotype, chromosome aberration, genetic polymorphism, or sequencing analysis of specific genes only, our study revealed genome-wide molecular profile and rate of mutations induced by CIB irradiation. We hope our data could provide valuable clues for explaining the potential mechanism of plant mutation breeding by CIB irradiation.
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Affiliation(s)
- Yan Du
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Shanwei Luo
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Li
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Jiangyan Yang
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Tao Cui
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenjian Li
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Lixia Yu
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Hui Feng
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuze Chen
- College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jinhu Mu
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xia Chen
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qingyao Shu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Wenlong Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Libin Zhou
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- *Correspondence: Libin Zhou
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566
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Zhang H, Mittal N, Leamy LJ, Barazani O, Song B. Back into the wild-Apply untapped genetic diversity of wild relatives for crop improvement. Evol Appl 2017; 10:5-24. [PMID: 28035232 PMCID: PMC5192947 DOI: 10.1111/eva.12434] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/07/2016] [Indexed: 12/18/2022] Open
Abstract
Deleterious effects of climate change and human activities, as well as diverse environmental stresses, present critical challenges to food production and the maintenance of natural diversity. These challenges may be met by the development of novel crop varieties with increased biotic or abiotic resistance that enables them to thrive in marginal lands. However, considering the diverse interactions between crops and environmental factors, it is surprising that evolutionary principles have been underexploited in addressing these food and environmental challenges. Compared with domesticated cultivars, crop wild relatives (CWRs) have been challenged in natural environments for thousands of years and maintain a much higher level of genetic diversity. In this review, we highlight the significance of CWRs for crop improvement by providing examples of CWRs that have been used to increase biotic and abiotic stress resistance/tolerance and overall yield in various crop species. We also discuss the surge of advanced biotechnologies, such as next-generation sequencing technologies and omics, with particular emphasis on how they have facilitated gene discovery in CWRs. We end the review by discussing the available resources and conservation of CWRs, including the urgent need for CWR prioritization and collection to ensure continuous crop improvement for food sustainability.
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Affiliation(s)
- Hengyou Zhang
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Neha Mittal
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Larry J. Leamy
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Oz Barazani
- The Institute for Plant SciencesIsrael Plant Gene BankAgricultural Research OrganizationBet DaganIsrael
| | - Bao‐Hua Song
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
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567
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Thudi M, Chitikineni A, Liu X, He W, Roorkiwal M, Yang W, Jian J, Doddamani D, Gaur PM, Rathore A, Samineni S, Saxena RK, Xu D, Singh NP, Chaturvedi SK, Zhang G, Wang J, Datta SK, Xu X, Varshney RK. Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.). Sci Rep 2016; 6:38636. [PMID: 27982107 PMCID: PMC5159902 DOI: 10.1038/srep38636] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/10/2016] [Indexed: 12/18/2022] Open
Abstract
In order to understand the impact of breeding on genetic diversity and gain insights into temporal trends in diversity in chickpea, a set of 100 chickpea varieties released in 14 countries between 1948 and 2012 were re-sequenced. For analysis, the re-sequencing data for 29 varieties available from an earlier study was also included. Copy number variations and presence absence variations identified in the present study have potential to drive phenotypic variations for trait improvement. Re-sequencing of a large number of varieties has provided opportunities to inspect the genetic and genomic changes reflecting the history of breeding, which we consider as breeding signatures and the selected loci may provide targets for crop improvement. Our study also reports enhanced diversity in both desi and kabuli varieties as a result of recent chickpea breeding efforts. The current study will aid the explicit efforts to breed for local adaptation in the context of anticipated climate changes.
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Affiliation(s)
- Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Xin Liu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Dadakhalandar Doddamani
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Srinivasan Samineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Narendra P. Singh
- All India Coordinated Research Project (AICRP) on Chickpea, Indian Council of Agricultural Research (ICAR), New Delhi, India
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, India
| | - Sushil K. Chaturvedi
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, India
| | | | | | | | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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568
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Zhang J, Wang J, Jiang W, Liu J, Yang S, Gai J, Li Y. Identification and Analysis of NaHCO 3 Stress Responsive Genes in Wild Soybean ( Glycine soja) Roots by RNA-seq. FRONTIERS IN PLANT SCIENCE 2016; 7:1842. [PMID: 28018382 PMCID: PMC5161042 DOI: 10.3389/fpls.2016.01842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 11/22/2016] [Indexed: 05/25/2023]
Abstract
Soil alkalinity is a major abiotic constraint to crop productivity and quality. Wild soybean (Glycine soja) is considered to be more stress-tolerant than cultivated soybean (G. max), and has considerable genetic variation for increasing alkalinity tolerance of soybean. In this study, we analyzed the transcriptome profile in the roots of an alkalinity tolerant wild soybean variety N24852 at 12 and 24 h after 90 mM NaHCO3 stress by RNA-sequencing. Compared with the controls, a total of 449 differentially expressed genes (DEGs) were identified, including 95 and 140 up-regulated genes, and 108 and 135 down-regulated genes at 12 and 24 h after NaHCO3 treatment, respectively. Quantitative RT-PCR analysis of 14 DEGs showed a high consistency with their expression profiles by RNA-sequencing. Gene Ontology (GO) terms related to transcription factors and transporters were significantly enriched in the up-regulated genes at 12 and 24 h after NaHCO3 stress, respectively. Nuclear factor Y subunit A transcription factors were enriched at 12 h after NaHCO3 stress, and high percentages of basic helix-loop-helix, ethylene-responsive factor, Trihelix, and zinc finger (C2H2, C3H) transcription factors were found at both 12 and 24 h after NaHCO3 stress. Genes related to ion transporters such as ABC transporter, aluminum activated malate transporter, glutamate receptor, nitrate transporter/proton dependent oligopeptide family, and S-type anion channel were enriched in up-regulated DEGs at 24 h after NaHCO3 treatment, implying their roles in maintaining ion homeostasis in soybean roots under alkalinity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed "phenylpropanoid biosynthesis" and "phenylalanine metabolism" pathways might participate in soybean response to alkalinity. This study provides a foundation to further investigate the functions of NaHCO3 stress-responsive genes and the molecular basis of soybean tolerance to alkalinity.
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569
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Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection. Sci Rep 2016; 6:38496. [PMID: 27924947 PMCID: PMC5141495 DOI: 10.1038/srep38496] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/11/2016] [Indexed: 01/28/2023] Open
Abstract
Fiber quality is one of the most important agronomic traits of cotton, and understanding the genetic basis of its target traits will accelerate improvements to cotton fiber quality. In this study, a panel comprising 355 upland cotton accessions was used to perform genome-wide association studies (GWASs) of five fiber quality traits in four environments. A total of 16, 10 and 7 SNPs were associated with fiber length (FL), fiber strength (FS) and fiber uniformity (FU), respectively, based on the mixed linear model (MLM). Most importantly, two major genomic regions (MGR1 and MGR2) on chromosome Dt7 and four potential candidate genes for FL were identified. Analyzing the geographical distribution of favorable haplotypes (FHs) among these lines revealed that two favorable haplotype frequencies (FHFs) were higher in accessions from low-latitude regions than in accessions from high-latitude regions. However, the genetic diversity of lines from the low-latitude regions was lower than the diversity of lines from the high-latitude regions in China. Furthermore, the FHFs differed among cultivars developed during different breeding periods. These results indicate that FHs have undergone artificial selection during upland cotton breeding in recent decades in China and provide a foundation for the further improvement of fiber quality traits.
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570
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Kim KS, Vuong TD, Qiu D, Robbins RT, Grover Shannon J, Li Z, Nguyen HT. Advancements in breeding, genetics, and genomics for resistance to three nematode species in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2295-2311. [PMID: 27796432 DOI: 10.1007/s00122-016-2816-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 10/18/2016] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE Integration of genetic analysis, molecular biology, and genomic approaches drastically enhanced our understanding of genetic control of nematode resistance and provided effective breeding strategies in soybeans. Three nematode species, including soybean cyst (SCN, Heterodera glycine), root-knot (RKN, Meloidogyne incognita), and reniform (RN, Rotylenchulus reniformis), are the most destructive pests and have spread to soybean growing areas worldwide. Host plant resistance has played an important role in their control. This review focuses on genetic, genomic studies, and breeding efforts over the past two decades to identify and improve host resistance to these three nematode species. Advancements in genetics, genomics, and bioinformatics have improved our understanding of the molecular and genetic mechanisms of nematode resistance and enabled researchers to generate large-scale genomic resources and marker-trait associations. Whole-genome resequencing, genotyping-by-sequencing, genome-wide association studies, and haplotype analyses have been employed to map and dissect genomic locations for nematode resistance. Recently, two major SCN-resistant loci, Rhg1 and Rhg4, were cloned and other novel resistance quantitative trait loci (QTL) have been discovered. Based on these discoveries, gene-specific DNA markers have been developed for both Rhg1 and Rhg4 loci, which were useful for marker-assisted selection. With RKN resistance QTL being mapped, candidate genes responsible for RKN resistance were identified, leading to the development of functional single nucleotide polymorphism markers. So far, three resistances QTL have been genetically mapped for RN resistance. With nematode species overcoming the host plant resistance, continuous efforts in the identification and deployment of new resistance genes are required to support the development of soybean cultivars with multiple and durable resistance to these pests.
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Affiliation(s)
- Ki-Seung Kim
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
- KSK's Current Address: LG Chem-FarmHannong, Ltd., Daejeon, 34115, Korea.
| | - Tri D Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Dan Qiu
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Robert T Robbins
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, 72701, USA
| | - J Grover Shannon
- Division of Plant Sciences, University of Missouri-Fisher Delta Research Center, Portageville, MO, 63873, USA
| | - Zenglu Li
- Center for Applied Genetic Technologies and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
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571
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Badenes ML, Fernández I Martí A, Ríos G, Rubio-Cabetas MJ. Application of Genomic Technologies to the Breeding of Trees. Front Genet 2016; 7:198. [PMID: 27895664 PMCID: PMC5109026 DOI: 10.3389/fgene.2016.00198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/31/2016] [Indexed: 12/22/2022] Open
Abstract
The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.
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Affiliation(s)
- Maria L Badenes
- Instituto Valenciano de Investigaciones Agrarias Valencia, Spain
| | - Angel Fernández I Martí
- Hortofruticulture Department, Agrifood Research and Technology Centre of AragonZaragoza, Spain; Genome Center, University of California, Davis, Davis, CAUSA
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias Valencia, Spain
| | - María J Rubio-Cabetas
- Hortofruticulture Department, Agrifood Research and Technology Centre of Aragon Zaragoza, Spain
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572
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Genome-wide association study of 12 agronomic traits in peach. Nat Commun 2016; 7:13246. [PMID: 27824331 PMCID: PMC5105138 DOI: 10.1038/ncomms13246] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 09/15/2016] [Indexed: 12/31/2022] Open
Abstract
Peach (Prunus persica L.) is a highly valuable crop species and is recognized by molecular researchers as a model fruit for the Rosaceae family. Using whole-genome sequencing data generated from 129 peach accessions, here we perform a comprehensive genome-wide association study for 12 key agronomic traits. We show that among the 10 qualitative traits investigated, nine exhibit consistent and more precise association signals than previously identified by linkage analysis. For two of the qualitative traits, we describe candidate genes, one potentially involved in cell death and another predicted to encode an auxin-efflux carrier, that are highly associated with fruit shape and non-acidity, respectively. Furthermore, we find that several genomic regions harbouring association signals for fruit weight and soluble solid content overlapped with predicted selective sweeps that occurred during peach domestication and improvement. Our findings contribute to the large-scale characterization of genes controlling agronomic traits in peach. Peach is both an economically important crop species and a model for Rosaceae fruit development research. Here, the authors perform genome-wide association analysis in peach and find candidate genes associated with variation in agronomically important fruit phenotypes.
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573
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Li Q, Fang C, Duan Z, Liu Y, Qin H, Zhang J, Sun P, Li W, Wang G, Tian Z. Functional conservation and divergence of GmCHLI genes in polyploid soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:584-596. [PMID: 27459730 DOI: 10.1111/tpj.13282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/17/2016] [Accepted: 07/21/2016] [Indexed: 05/15/2023]
Abstract
Polyploidy is prevalent in nature. As the fate of duplicated genes becomes more complicated when the encoded proteins function as oligomers, functional investigations into duplicated oligomer-encoding genes in polyploid genomes will facilitate our understanding of how traits are expressed. In this study, we identified GmCHLI1, a gene encoding the I subunit of magnesium (Mg)-chelatase, which functions in hexamers as responsible for the semi-dominant etiolation phenotype in soybean. Four GmCHLI copies derived from two polyploidy events were identified in the soybean genome. Further investigation with regard to expression patterns indicated that these four copies have diverged into two pairs; mutation in the other copy of the pair that includes GmCHLI1 also resulted in a chlorophyll-deficient phenotype. Protein interaction assays showed that these four GmCHLIs can interact with each other, but stronger interactions were found with mutated subunits. The results indicate that, in polyploidy, deficiency in each copy of duplicated oligomer-encoding genes could result in a mutant phenotype due to hetero-oligomer formation, which is different from the model of allelic dosage or functional redundancy. In addition, we interestingly found an increase in isoflavonoids in the heterozygous etiolated plants, which might be useful for improving soybean seed quality.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chao Fang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Hao Qin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jixiang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Peng Sun
- Affiliated Hospital of Hebei University, Baoding, 071000, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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574
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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575
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Liu Y, Khan SM, Wang J, Rynge M, Zhang Y, Zeng S, Chen S, Maldonado dos Santos JV, Valliyodan B, Calyam PP, Merchant N, Nguyen HT, Xu D, Joshi T. PGen: large-scale genomic variations analysis workflow and browser in SoyKB. BMC Bioinformatics 2016; 17:337. [PMID: 27766951 PMCID: PMC5074001 DOI: 10.1186/s12859-016-1227-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed "PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS). The workflow allows users to identify single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), perform SNP annotations and conduct copy number variation analyses on multiple resequencing datasets in a user-friendly and seamless way. RESULTS We have developed both a Linux version in GitHub ( https://github.com/pegasus-isi/PGen-GenomicVariations-Workflow ) and a web-based implementation of the PGen workflow integrated within the Soybean Knowledge Base (SoyKB), ( http://soykb.org/Pegasus/index.php ). Using PGen, we identified 10,218,140 single-nucleotide polymorphisms (SNPs) and 1,398,982 indels from analysis of 106 soybean lines sequenced at 15X coverage. 297,245 non-synonymous SNPs and 3330 copy number variation (CNV) regions were identified from this analysis. SNPs identified using PGen from additional soybean resequencing projects adding to 500+ soybean germplasm lines in total have been integrated. These SNPs are being utilized for trait improvement using genotype to phenotype prediction approaches developed in-house. In order to browse and access NGS data easily, we have also developed an NGS resequencing data browser ( http://soykb.org/NGS_Resequence/NGS_index.php ) within SoyKB to provide easy access to SNP and downstream analysis results for soybean researchers. CONCLUSION PGen workflow has been optimized for the most efficient analysis of soybean data using thorough testing and validation. This research serves as an example of best practices for development of genomics data analysis workflows by integrating remote HPC resources and efficient data management with ease of use for biological users. PGen workflow can also be easily customized for analysis of data in other species.
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Affiliation(s)
- Yang Liu
- Informatics Institute, University of Missouri, Columbia, MO USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
| | - Saad M. Khan
- Informatics Institute, University of Missouri, Columbia, MO USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
| | - Juexin Wang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
- Department of Computer Science, University of Missouri, Columbia, MO USA
| | - Mats Rynge
- Information Sciences Institute, University of Southern California, Los Angeles, CA USA
| | - Yuanxun Zhang
- Department of Computer Science, University of Missouri, Columbia, MO USA
| | - Shuai Zeng
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
- Department of Computer Science, University of Missouri, Columbia, MO USA
| | - Shiyuan Chen
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
- Department of Computer Science, University of Missouri, Columbia, MO USA
| | | | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO USA
- National Center of Soybean Biotechnology, Columbia, MO USA
| | - Prasad P. Calyam
- Department of Computer Science, University of Missouri, Columbia, MO USA
| | - Nirav Merchant
- iPlant Collaborative, University of Arizona, Tucson, AZ USA
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO USA
- National Center of Soybean Biotechnology, Columbia, MO USA
| | - Dong Xu
- Informatics Institute, University of Missouri, Columbia, MO USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
- Department of Computer Science, University of Missouri, Columbia, MO USA
| | - Trupti Joshi
- Informatics Institute, University of Missouri, Columbia, MO USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
- Department of Computer Science, University of Missouri, Columbia, MO USA
- Department of Molecular Microbiology and Immunology and Office of Research, School of Medicine, University of Missouri, Columbia, MO USA
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576
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Zhang YQ, Lu X, Zhao FY, Li QT, Niu SL, Wei W, Zhang WK, Ma B, Chen SY, Zhang JS. Soybean GmDREBL Increases Lipid Content in Seeds of Transgenic Arabidopsis. Sci Rep 2016; 6:34307. [PMID: 27694917 PMCID: PMC5046110 DOI: 10.1038/srep34307] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 09/12/2016] [Indexed: 01/08/2023] Open
Abstract
A DREB-type transcription factor gene GmDREBL has been characterized for its functions in oil accumulation in seeds. The gene is specifically expressed in soybean seeds. The GmDREBL is localized in nucleus and has transcriptional activation ability. Overexpression of GmDREBL increased the fatty acid content in the seeds of transgenic Arabidopsis plants. GmDREBL can bind to the promoter region of WRI1 to activate its expression. Several other genes in the fatty acid biosynthesis pathway were also enhanced in the GmDREBL-transgenic plants. The GmDREBL can be up-regulated by GmABI3 and GmABI5. Additionally, overexpression of GmDREBL significantly promoted seed size in transgenic plants compared to that of WT plants. Expression of the DREBL is at higher level on the average in cultivated soybeans than that in wild soybeans. The promoter of the DREBL may have been subjected to selection during soybean domestication. Our results demonstrate that GmDREBL participates in the regulation of fatty acid accumulation by controlling the expression of WRI1 and its downstream genes, and manipulation of the gene may increase the oil contents in soybean plants. Our study provides novel insights into the function of DREB-type transcription factors in oil accumulation in addition to their roles in stress response.
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Affiliation(s)
- Yu-Qin Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beichen West Road, Campus #1, No. 2, Beijing 100101, China
| | - Xiang Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beichen West Road, Campus #1, No. 2, Beijing 100101, China
| | - Fei-Yi Zhao
- School of Bioengineering & Biotechnology, Tianshui Normal University, Tianshui, Gansu 741000, China
| | - Qing-Tian Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beichen West Road, Campus #1, No. 2, Beijing 100101, China
| | - Su-Ling Niu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beichen West Road, Campus #1, No. 2, Beijing 100101, China
| | - Wei Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beichen West Road, Campus #1, No. 2, Beijing 100101, China
| | - Wan-Ke Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beichen West Road, Campus #1, No. 2, Beijing 100101, China
| | - Biao Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beichen West Road, Campus #1, No. 2, Beijing 100101, China
| | - Shou-Yi Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beichen West Road, Campus #1, No. 2, Beijing 100101, China
| | - Jin-Song Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beichen West Road, Campus #1, No. 2, Beijing 100101, China
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577
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Tripathi N, Khare D. Molecular approaches for genetic improvement of seed quality and characterization of genetic diversity in soybean: a critical review. Biotechnol Lett 2016; 38:1645-54. [PMID: 27334709 DOI: 10.1007/s10529-016-2154-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
Soybean is an economically important leguminous crop. Genetic improvements of soybeans have focused on enhancement of seed and oil yield, development of varieties suited to different cropping systems, and breeding resistant/tolerant varieties for various biotic and abiotic stresses. Plant breeders have used conventional breeding techniques for the improvement of these traits in soybean. The conventional breeding process can be greatly accelerated through the application of molecular and genomic approaches. Molecular markers have proved to be a new tool in soybean breeding by enhancing selection efficiency in a rapid and time-bound manner. An overview of molecular approaches for the genetic improvement of soybean seed quality parameters, considering recent applications of marker-assisted selection and 'omics' research, is provided in this article.
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Affiliation(s)
- Niraj Tripathi
- Biotechnology Centre, Jawaharlal Nehru Agricultural University, Jabalpur, 482004, India.
| | - Dhirendra Khare
- Department of Plant Breeding and Genetics, Jawaharlal Nehru Agricultural University, Jabalpur, 482004, India
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578
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Wang F, Sun X, Shi X, Zhai H, Tian C, Kong F, Liu B, Yuan X. A Global Analysis of the Polygalacturonase Gene Family in Soybean (Glycine max). PLoS One 2016; 11:e0163012. [PMID: 27657691 PMCID: PMC5033254 DOI: 10.1371/journal.pone.0163012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/01/2016] [Indexed: 01/27/2023] Open
Abstract
Polygalacturonase is one of the pectin hydrolytic enzymes involved in various developmental and physiological processes such as seed germination, organ abscission, pod and anther dehiscence, and xylem cell formation. To date, no systematic analysis of polygalacturonase incorporating genome organization, gene structure, and expression profiling has been conducted in soybean (Glycine max var. Williams 82). In this study, we identified 112 GmPG genes from the soybean Wm82.a2v1 genome. These genes were classified into three groups, group I (105 genes), group II (5 genes), and group III (2 genes). Fifty-four pairs of duplicate paralogous genes were preferentially identified from duplicated regions of the soybean genome, which implied that long segmental duplications significantly contributed to the expansion of the GmPG gene family. Moreover, GmPG transcripts were analyzed in various tissues using RNA-seq data. The results showed the differential expression of 64 GmPGs in the tissue and partially redundant expression of some duplicate genes, while others showed functional diversity. These findings suggested that the GmPGs were retained by substantial subfunctionalization during the soybean evolutionary processes. Finally, evolutionary analysis based on single nucleotide polymorphisms (SNPs) in wild and cultivated soybeans revealed that 107 GmPGs had selected site(s), which indicated that these genes may have undergone strong selection during soybean domestication. Among them, one non-synonymous SNP of GmPG031 affected floral development during selection, which was consistent with the results of RNA-seq and evolutionary analyses. Thus, our results contribute to the functional characterization of GmPG genes in soybean.
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Affiliation(s)
- Feifei Wang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia Sun
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
| | - Xinyi Shi
- School of Computer Science and Technology, Heilongjiang University, Harbin, 150080, China
| | - Hong Zhai
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
| | - Changen Tian
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Fanjiang Kong
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
| | - Baohui Liu
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
- * E-mail: (XY); (BL)
| | - Xiaohui Yuan
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
- * E-mail: (XY); (BL)
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Vaughn JN, Li Z. Genomic Signatures of North American Soybean Improvement Inform Diversity Enrichment Strategies and Clarify the Impact of Hybridization. G3 (BETHESDA, MD.) 2016; 6:2693-705. [PMID: 27402364 PMCID: PMC5015928 DOI: 10.1534/g3.116.029215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/14/2016] [Indexed: 11/18/2022]
Abstract
Crop improvement represents a long-running experiment in artificial selection on a complex trait, namely yield. How such selection relates to natural populations is unclear, but the analysis of domesticated populations could offer insights into the relative role of selection, drift, and recombination in all species facing major shifts in selective regimes. Because of the extreme autogamy exhibited by soybean (Glycine max), many "immortalized" genotypes of elite varieties spanning the last century have been preserved and characterized using ∼50,000 single nucleotide polymorphic (SNP) markers. Also due to autogamy, the history of North American soybean breeding can be roughly divided into pre- and posthybridization eras, allowing for direct interrogation of the role of recombination in improvement and selection. Here, we report on genome-wide characterization of the structure and history of North American soybean populations and the signature of selection in these populations. Supporting previous work, we find that maturity defines population structure. Though the diversity of North American ancestors is comparable to available landraces, prehybridization line selections resulted in a clonal structure that dominated early breeding and explains many of the reductions in diversity found in the initial generations of soybean hybridization. The rate of allele frequency change does not deviate sharply from neutral expectation, yet some regions bare hallmarks of strong selection, suggesting a highly variable range of selection strengths biased toward weak effects. We also discuss the importance of haplotypes as units of analysis when complex traits fall under novel selection regimes.
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Affiliation(s)
- Justin N Vaughn
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 Department of Crop and Soil Science, University of Georgia, Athens, Georgia 30602
| | - Zenglu Li
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 Department of Crop and Soil Science, University of Georgia, Athens, Georgia 30602
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580
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Takeshima R, Hayashi T, Zhu J, Zhao C, Xu M, Yamaguchi N, Sayama T, Ishimoto M, Kong L, Shi X, Liu B, Tian Z, Yamada T, Kong F, Abe J. A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5247-58. [PMID: 27422993 PMCID: PMC5014162 DOI: 10.1093/jxb/erw283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
FLOWERING LOCUS T (FT) is an important floral integrator whose functions are conserved across plant species. In soybean, two orthologs, FT2a and FT5a, play a major role in initiating flowering. Their expression in response to different photoperiods is controlled by allelic combinations at the maturity loci E1 to E4, generating variation in flowering time among cultivars. We determined the molecular basis of a quantitative trait locus (QTL) for flowering time in linkage group J (Chromosome 16). Fine-mapping delimited the QTL to a genomic region of 107kb that harbors FT5a We detected 15 DNA polymorphisms between parents with the early-flowering (ef) and late-flowering (lf) alleles in the promoter region, an intron, and the 3' untranslated region of FT5a, although the FT5a coding regions were identical. Transcript abundance of FT5a was higher in near-isogenic lines for ef than in those for lf, suggesting that different transcriptional activities or mRNA stability caused the flowering time difference. Single-nucleotide polymorphism (SNP) calling from re-sequencing data for 439 cultivated and wild soybean accessions indicated that ef is a rare haplotype that is distinct from common haplotypes including lf The ef allele at FT5a may play an adaptive role at latitudes where early flowering is desirable.
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Affiliation(s)
- Ryoma Takeshima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Takafumi Hayashi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Jianghui Zhu
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Chen Zhao
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Meilan Xu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, Memuro, Hokkaido 082-0081, Japan
| | - Takashi Sayama
- National Institute of Agrobiological Sciences, Kannondai, Ibaraki 305-8602, Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Sciences, Kannondai, Ibaraki 305-8602, Japan
| | - Lingping Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xinyi Shi
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 1001014, China
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
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581
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Kim N, Jeong YM, Jeong S, Kim GB, Baek S, Kwon YE, Cho A, Choi SB, Kim J, Lim WJ, Kim KH, Park W, Kim JY, Kim JH, Yim B, Lee YJ, Chun BM, Lee YP, Park BS, Yu HJ, Mun JH. Identification of candidate domestication regions in the radish genome based on high-depth resequencing analysis of 17 genotypes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1797-814. [PMID: 27377547 DOI: 10.1007/s00122-016-2741-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 06/04/2016] [Indexed: 05/20/2023]
Abstract
This study provides high-quality variation data of diverse radish genotypes. Genome-wide SNP comparison along with RNA-seq analysis identified candidate genes related to domestication that have potential as trait-related markers for genetics and breeding of radish. Radish (Raphanus sativus L.) is an annual root vegetable crop that also encompasses diverse wild species. Radish has a long history of domestication, but the origins and selective sweep of cultivated radishes remain controversial. Here, we present comprehensive whole-genome resequencing analysis of radish to explore genomic variation between the radish genotypes and to identify genetic bottlenecks due to domestication in Asian cultivars. High-depth resequencing and multi-sample genotyping analysis of ten cultivated and seven wild accessions obtained 4.0 million high-quality homozygous single-nucleotide polymorphisms (SNPs)/insertions or deletions. Variation analysis revealed that Asian cultivated radish types are closely related to wild Asian accessions, but are distinct from European/American cultivated radishes, supporting the notion that Asian cultivars were domesticated from wild Asian genotypes. SNP comparison between Asian genotypes identified 153 candidate domestication regions (CDRs) containing 512 genes. Network analysis of the genes in CDRs functioning in plant signaling pathways and biochemical processes identified group of genes related to root architecture, cell wall, sugar metabolism, and glucosinolate biosynthesis. Expression profiling of the genes during root development suggested that domestication-related selective advantages included a main taproot with few branched lateral roots, reduced cell wall rigidity and favorable taste. Overall, this study provides evolutionary insights into domestication-related genetic selection in radish as well as identification of gene candidates with the potential to act as trait-related markers for background selection of elite lines in molecular breeding.
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Affiliation(s)
- Namshin Kim
- Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, 34141, Korea
| | - Young-Min Jeong
- Department of Life Science, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Seongmun Jeong
- Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea
| | - Goon-Bo Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea
| | - Seunghoon Baek
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea
| | - Young-Eun Kwon
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea
| | - Ara Cho
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea
| | - Sang-Bong Choi
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea
| | - Jiwoong Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Won-Jun Lim
- Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, 34141, Korea
| | - Kyoung Hyoun Kim
- Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, 34141, Korea
| | - Won Park
- Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, 34141, Korea
| | - Jae-Yoon Kim
- Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, 34141, Korea
| | - Jin-Hyun Kim
- Department of Genetic Engineering, Dong-A University, Busan, 49315, Korea
| | - Bomi Yim
- Department of Life Science, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Young Joon Lee
- Department of Life Science, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Byung-Moon Chun
- Breeding Research Institute, Dongbu Farm Hannong Co. Ltd., Ansung, 17503, Korea
| | - Young-Pyo Lee
- Breeding Research Institute, Dongbu Farm Hannong Co. Ltd., Ansung, 17503, Korea
| | - Beom-Seok Park
- Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 54874, Korea
| | - Hee-Ju Yu
- Department of Life Science, The Catholic University of Korea, Bucheon, 14662, Korea.
| | - Jeong-Hwan Mun
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea.
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582
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Leamy LJ, Lee CR, Song Q, Mujacic I, Luo Y, Chen CY, Li C, Kjemtrup S, Song BH. Environmental versus geographical effects on genomic variation in wild soybean (Glycine soja) across its native range in northeast Asia. Ecol Evol 2016. [PMID: 27648247 DOI: 10.1022/ece3.2351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
A fundamental goal in evolutionary biology is to understand how various evolutionary factors interact to affect the population structure of diverse species, especially those of ecological and/or agricultural importance such as wild soybean (Glycine soja). G. soja, from which domesticated soybeans (Glycine max) were derived, is widely distributed throughout diverse habitats in East Asia (Russia, Japan, Korea, and China). Here, we utilize over 39,000 single nucleotide polymorphisms genotyped in 99 ecotypes of wild soybean sampled across their native geographic range in northeast Asia, to understand population structure and the relative contribution of environment versus geography to population differentiation in this species. A STRUCTURE analysis identified four genetic groups that largely corresponded to the geographic regions of central China, northern China, Korea, and Japan, with high levels of admixture between genetic groups. A canonical correlation and redundancy analysis showed that environmental factors contributed 23.6% to population differentiation, much more than that for geographic factors (6.6%). Precipitation variables largely explained divergence of the groups along longitudinal axes, whereas temperature variables contributed more to latitudinal divergence. This study provides a foundation for further understanding of the genetic basis of climatic adaptation in this ecologically and agriculturally important species.
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Affiliation(s)
- Larry J Leamy
- Department of Biological Sciences University of North Carolina at Charlotte Charlotte North Carolina 28223
| | - Cheng-Ruei Lee
- Gregor Mendel Institute of Molecular Plant Biology Vienna A-1030 Austria
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory Department of Agriculture USDA-Agricultural Research Service Beltsville Maryland 20705
| | - Ibro Mujacic
- Department of Bioinformatics and Genomics University of North Carolina at Charlotte Charlotte North Carolina 28223
| | - Yan Luo
- Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Yunnan 666303 China
| | - Charles Y Chen
- Department of Crop, Soil and Environmental Sciences Auburn University Auburn Alabama 36849
| | - Changbao Li
- Biotechnology Assay and Phenotyping Group Monsanto Company Durham North Carolina 27709
| | - Susanne Kjemtrup
- Biotechnology Assay and Phenotyping Group Monsanto Company Durham North Carolina 27709
| | - Bao-Hua Song
- Department of Biological Sciences University of North Carolina at Charlotte Charlotte North Carolina 28223
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583
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Zhang H, Li C, Davis EL, Wang J, Griffin JD, Kofsky J, Song BH. Genome-Wide Association Study of Resistance to Soybean Cyst Nematode (Heterodera glycines) HG Type 2.5.7 in Wild Soybean (Glycine soja). FRONTIERS IN PLANT SCIENCE 2016; 7:1214. [PMID: 27582748 PMCID: PMC4987380 DOI: 10.3389/fpls.2016.01214] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/02/2016] [Indexed: 05/07/2023]
Abstract
Soybean cyst nematode (SCN) is the most destructive soybean pest worldwide. Host plant resistance is the most environmentally friendly and cost-effective way of mitigating SCN damage to soybeans. However, overuse of the resistant soybean [Glycine max (L.) Merr.] cultivars from limited genetic resources has resulted in SCN race shifts in many soybean-growing areas. Thus, exploration of novel sources of SCN resistance and dissection of the genetic basis are urgently needed. In this study, we screened 235 wild soybean (Glycine soja Sieb. & Zucc.) accessions to identify genotypes resistant to SCN HG Type 2.5.7 (race 5), a less investigated type but is prevalent in the southeastern US. We also dissected the genetic basis of SCN resistance using a genome-wide association study with SNPs genotyped by SoySNP50k iSelect BeadChip. In total, 43 resistant accessions (female index < 30) were identified, with 10 SNPs being significantly associated with SCN HG 2.5.7 resistance in this wild species. Furthermore, four significant SNPs were localized to linked regions of the known quantitative trait locus (QTL) rhg1 on chromosome 18. The other four SNPs on chromosome 18 and two SNPs on chromosome 19 are novel. Genes encoding disease resistance-related proteins with a leucine-rich region, a mitogen-activated protein kinase (MAPK) on chromosome 18, and a MYB transcription factor on chromosome 19 were identified as promising candidate genes. The identified SNPs and candidate genes will benefit future marker-assisted breeding and dissection of the molecular mechanisms underlying the soybean-SCN interaction.
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Affiliation(s)
- Hengyou Zhang
- Bao-Hua Song Lab, Department of Biological Sciences, University of North Carolina at CharlotteCharlotte, NC, USA
| | - Chunying Li
- Eric Davis Lab, Department of Plant Pathology, North Carolina State UniversityRaleigh, NC, USA
| | - Eric L. Davis
- Eric Davis Lab, Department of Plant Pathology, North Carolina State UniversityRaleigh, NC, USA
| | - Jinshe Wang
- Institute of Industrial Crops, Henan Academy of Agricultural Sciences, National Subcenter for Soybean Improvement/Key Laboratory of Oil CropsZhengzhou, China
| | | | - Janice Kofsky
- Bao-Hua Song Lab, Department of Biological Sciences, University of North Carolina at CharlotteCharlotte, NC, USA
| | - Bao-Hua Song
- Bao-Hua Song Lab, Department of Biological Sciences, University of North Carolina at CharlotteCharlotte, NC, USA
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584
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Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y, Fang C, Shen Y, Liu T, Li C, Li Q, Wu M, Wang M, Wu Y, Dong Y, Wan W, Wang X, Ding Z, Gao Y, Xiang H, Zhu B, Lee SH, Wang W, Tian Z. Erratum: Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol 2016; 34:441. [PMID: 27054996 DOI: 10.1038/nbt0416-441c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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585
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Leamy LJ, Lee CR, Song Q, Mujacic I, Luo Y, Chen CY, Li C, Kjemtrup S, Song BH. Environmental versus geographical effects on genomic variation in wild soybean (Glycine soja) across its native range in northeast Asia. Ecol Evol 2016; 6:6332-44. [PMID: 27648247 PMCID: PMC5016653 DOI: 10.1002/ece3.2351] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 02/05/2023] Open
Abstract
A fundamental goal in evolutionary biology is to understand how various evolutionary factors interact to affect the population structure of diverse species, especially those of ecological and/or agricultural importance such as wild soybean (Glycine soja). G. soja, from which domesticated soybeans (Glycine max) were derived, is widely distributed throughout diverse habitats in East Asia (Russia, Japan, Korea, and China). Here, we utilize over 39,000 single nucleotide polymorphisms genotyped in 99 ecotypes of wild soybean sampled across their native geographic range in northeast Asia, to understand population structure and the relative contribution of environment versus geography to population differentiation in this species. A STRUCTURE analysis identified four genetic groups that largely corresponded to the geographic regions of central China, northern China, Korea, and Japan, with high levels of admixture between genetic groups. A canonical correlation and redundancy analysis showed that environmental factors contributed 23.6% to population differentiation, much more than that for geographic factors (6.6%). Precipitation variables largely explained divergence of the groups along longitudinal axes, whereas temperature variables contributed more to latitudinal divergence. This study provides a foundation for further understanding of the genetic basis of climatic adaptation in this ecologically and agriculturally important species.
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Affiliation(s)
- Larry J Leamy
- Department of Biological Sciences University of North Carolina at Charlotte Charlotte North Carolina 28223
| | - Cheng-Ruei Lee
- Gregor Mendel Institute of Molecular Plant Biology Vienna A-1030 Austria
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory Department of Agriculture USDA-Agricultural Research Service Beltsville Maryland 20705
| | - Ibro Mujacic
- Department of Bioinformatics and Genomics University of North Carolina at Charlotte Charlotte North Carolina 28223
| | - Yan Luo
- Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Yunnan 666303 China
| | - Charles Y Chen
- Department of Crop, Soil and Environmental Sciences Auburn University Auburn Alabama 36849
| | - Changbao Li
- Biotechnology Assay and Phenotyping Group Monsanto Company Durham North Carolina 27709
| | - Susanne Kjemtrup
- Biotechnology Assay and Phenotyping Group Monsanto Company Durham North Carolina 27709
| | - Bao-Hua Song
- Department of Biological Sciences University of North Carolina at Charlotte Charlotte North Carolina 28223
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586
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Muñoz N, Qi X, Li MW, Xie M, Gao Y, Cheung MY, Wong FL, Lam HM. Improvement in nitrogen fixation capacity could be part of the domestication process in soybean. Heredity (Edinb) 2016; 117:84-93. [PMID: 27118154 PMCID: PMC4949726 DOI: 10.1038/hdy.2016.27] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 02/14/2016] [Accepted: 03/16/2016] [Indexed: 01/21/2023] Open
Abstract
Biological nitrogen fixation (BNF) in soybeans is a complex process involving the interplay between the plant host and the symbiotic rhizobia. As nitrogen supply has a crucial role in growth and development, higher nitrogen fixation capacity would be important to achieve bigger plants and larger seeds, which were important selection criteria during plant domestication by humans. To test this hypothesis, we monitored the nitrogen fixation-related performance in 31 cultivated and 17 wild soybeans after inoculation with the slow-growing Bradyrhizobium diazoefficiens sp. nov. USDA110 and the fast-growing Sinorhizobium (Ensifer) fredii CCBAU45436. Our results showed that, in general, cultivated soybeans gave better performance in BNF. Electron microscopic studies indicated that there was an exceptionally high accumulation of poly-β-hydroxybutyrate bodies in bacteroids in the nodules of all wild soybeans tested, suggesting that the C/N balance in wild soybeans may not be optimized for nitrogen fixation. Furthermore, we identified new quantitative trait loci (QTLs) for total ureides and total nodule fresh weight by employing a recombinant inbred population composed of descendants from a cross between a cultivated and a wild parent. Using nucleotide diversity (θπ), divergence index (Fst) and distribution of fixed single-nucleotide polymorphisms as parameters, we found that some regions in the total ureides QTL on chromosome 17 and the total nodule fresh weight QTL on chromosome 12 exhibited very low diversity among cultivated soybeans, suggesting that these were traits specially selected during the domestication and breeding process.
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Affiliation(s)
- N Muñoz
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
- Centro de Investigaciones
Agropecuarias-INTA, Instituto de Fisiología y Recursos
Genéticos Vegetales, Córdoba,
Argentina
- Cátedra de Fisiología
Vegetal, Facultad de Ciencias Exactas Físicas y Naturales,
Universidad Nacional de Córdoba, Córdoba,
Argentina
| | - X Qi
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - M-W Li
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - M Xie
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - Y Gao
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - M-Y Cheung
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - F-L Wong
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - H-M Lam
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
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587
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Kwong QB, Teh CK, Ong AL, Heng HY, Lee HL, Mohamed M, Low JZB, Apparow S, Chew FT, Mayes S, Kulaveerasingam H, Tammi M, Appleton DR. Development and Validation of a High-Density SNP Genotyping Array for African Oil Palm. MOLECULAR PLANT 2016; 9:1132-1141. [PMID: 27112659 DOI: 10.1016/j.molp.2016.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/21/2016] [Accepted: 04/17/2016] [Indexed: 05/18/2023]
Abstract
High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineensis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of >3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations (ranging from 120 kb at r(2) = 0.43 to 146 kb at r(2) = 0.50) when compared with the semi-wild populations (19.5 kb at r(2) = 0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on chromosome 2 associated with the polygenic component of the shell thickness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy (r = 0.65) with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.
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Affiliation(s)
- Qi Bin Kwong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
| | - Chee Keng Teh
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Ai Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Huey Ying Heng
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Heng Leng Lee
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Mohaimi Mohamed
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Joel Zi-Bin Low
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Sukganah Apparow
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Sean Mayes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough LE12 5RD, UK
| | | | - Martti Tammi
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - David Ross Appleton
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
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588
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Kumar V, Khan AW, Saxena RK, Garg V, Varshney RK. First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1673-81. [PMID: 26821983 PMCID: PMC5066660 DOI: 10.1111/pbi.12528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/06/2015] [Accepted: 12/10/2015] [Indexed: 05/02/2023]
Abstract
Whole genome re-sequencing (WGRS) was conducted on a panel of 20 Cajanus spp. accessions (crossing parentals of recombinant inbred lines, introgression lines, multiparent advanced generation intercross and nested association mapping population) comprising of two wild species and 18 cultivated species accessions. A total of 791.77 million paired-end reads were generated with an effective mapping depth of ~12X per accession. Analysis of WGRS data provided 5 465 676 genome-wide variations including 4 686 422 SNPs and 779 254 InDels across the accessions. Large structural variations in the form of copy number variations (2598) and presence and absence variations (970) were also identified. Additionally, 2 630 904 accession-specific variations comprising of 2 278 571 SNPs (86.6%), 166 243 deletions (6.3%) and 186 090 insertions (7.1%) were also reported. Identified polymorphic sites in this study provide the first-generation HapMap in Cajanus spp. which will be useful in mapping the genomic regions responsible for important traits.
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Affiliation(s)
- Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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589
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Alonso-Blanco C, Andrade J, Becker C, Bemm F, Bergelson J, Borgwardt KM, Cao J, Chae E, Dezwaan TM, Ding W, Ecker JR, Exposito-Alonso M, Farlow A, Fitz J, Gan X, Grimm DG, Hancock AM, Henz SR, Holm S, Horton M, Jarsulic M, Kerstetter RA, Korte A, Korte P, Lanz C, Lee CR, Meng D, Michael TP, Mott R, Muliyati NW, Nägele T, Nagler M, Nizhynska V, Nordborg M, Novikova PY, Picó FX, Platzer A, Rabanal FA, Rodriguez A, Rowan BA, Salomé PA, Schmid KJ, Schmitz RJ, Seren Ü, Sperone FG, Sudkamp M, Svardal H, Tanzer MM, Todd D, Volchenboum SL, Wang C, Wang G, Wang X, Weckwerth W, Weigel D, Zhou X. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 2016; 166:481-491. [PMID: 27293186 PMCID: PMC4949382 DOI: 10.1016/j.cell.2016.05.063] [Citation(s) in RCA: 710] [Impact Index Per Article: 88.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/20/2016] [Accepted: 05/17/2016] [Indexed: 12/30/2022]
Abstract
Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.
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590
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Wang H, Xu X, Vieira FG, Xiao Y, Li Z, Wang J, Nielsen R, Chu C. The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication. MOLECULAR PLANT 2016; 9:975-85. [PMID: 27179918 DOI: 10.1016/j.molp.2016.04.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/16/2016] [Accepted: 04/27/2016] [Indexed: 05/22/2023]
Abstract
Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in humans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice (Oryza sativa L.), which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5× and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SNPs in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.
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Affiliation(s)
- Hongru Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Yunhua Xiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facilities for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Jun Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720 USA.
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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591
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Zhou L, Luo L, Zuo JF, Yang L, Zhang L, Guang X, Niu Y, Jian J, Geng QC, Liang L, Song Q, Dunwell JM, Wu Z, Wen J, Liu YQ, Zhang YM. Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean. THE PLANT GENOME 2016; 9. [PMID: 27898807 DOI: 10.3835/plantgenome2015.09.0090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 01/23/2016] [Indexed: 05/08/2023]
Abstract
Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 trait-associated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene (). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.
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592
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Nogué F, Mara K, Collonnier C, Casacuberta JM. Genome engineering and plant breeding: impact on trait discovery and development. PLANT CELL REPORTS 2016; 35:1475-86. [PMID: 27193593 PMCID: PMC4903109 DOI: 10.1007/s00299-016-1993-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/11/2016] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE New tools for the precise modification of crops genes are now available for the engineering of new ideotypes. A future challenge in this emerging field of genome engineering is to develop efficient methods for allele mining. Genome engineering tools are now available in plants, including major crops, to modify in a predictable manner a given gene. These new techniques have a tremendous potential for a spectacular acceleration of the plant breeding process. Here, we discuss how genetic diversity has always been the raw material for breeders and how they have always taken advantage of the best available science to use, and when possible, increase, this genetic diversity. We will present why the advent of these new techniques gives to the breeders extremely powerful tools for crop breeding, but also why this will require the breeders and researchers to characterize the genes underlying this genetic diversity more precisely. Tackling these challenges should permit the engineering of optimized alleles assortments in an unprecedented and controlled way.
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Affiliation(s)
- Fabien Nogué
- INRA AgroParisTech, IJPB, UMR 1318, INRA Centre de Versailles, Route de Saint Cyr, 78026, Versailles Cedex, France.
| | - Kostlend Mara
- INRA AgroParisTech, IJPB, UMR 1318, INRA Centre de Versailles, Route de Saint Cyr, 78026, Versailles Cedex, France
| | - Cécile Collonnier
- INRA AgroParisTech, IJPB, UMR 1318, INRA Centre de Versailles, Route de Saint Cyr, 78026, Versailles Cedex, France
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193, Barcelona, Spain
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593
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Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nat Genet 2016; 48:927-34. [PMID: 27322545 DOI: 10.1038/ng.3596] [Citation(s) in RCA: 360] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/26/2016] [Indexed: 02/07/2023]
Abstract
A genome-wide association study (GWAS) can be a powerful tool for the identification of genes associated with agronomic traits in crop species, but it is often hindered by population structure and the large extent of linkage disequilibrium. In this study, we identified agronomically important genes in rice using GWAS based on whole-genome sequencing, followed by the screening of candidate genes based on the estimated effect of nucleotide polymorphisms. Using this approach, we identified four new genes associated with agronomic traits. Some genes were undetectable by standard SNP analysis, but we detected them using gene-based association analysis. This study provides fundamental insights relevant to the rapid identification of genes associated with agronomic traits using GWAS and will accelerate future efforts aimed at crop improvement.
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594
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Campbell BW, Stupar RM. Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects. ACTA ACUST UNITED AC 2016; 1:307-327. [PMID: 30775866 DOI: 10.1002/cppb.20015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic bottlenecks during domestication and modern breeding limited the genetic diversity of soybean (Glycine max (L.) Merr.). Therefore, expanding and diversifying soybean genetic resources is a major priority for the research community. These resources, consisting of natural and induced genetic variants, are valuable tools for improving soybean and furthering soybean biological knowledge. During the twentieth century, researchers gathered a wealth of genetic variation in the forms of landraces, Glycine soja accessions, Glycine tertiary germplasm, and the U.S. Department of Agriculture (USDA) Type and Isoline Collections. During the twenty-first century, soybean researchers have added several new genetic and genomic resources. These include the reference genome sequence, genotype data for the USDA soybean germplasm collection, next-generation mapping populations, new irradiation and transposon-based mutagenesis populations, and designer nuclease platforms for genome engineering. This paper briefly surveys the publicly accessible soybean genetic resources currently available or in development and provides recommendations for developing such genetic resources in the future. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
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595
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Lu X, Li QT, Xiong Q, Li W, Bi YD, Lai YC, Liu XL, Man WQ, Zhang WK, Ma B, Chen SY, Zhang JS. The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:530-44. [PMID: 27062090 DOI: 10.1111/tpj.13181] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/21/2016] [Accepted: 03/30/2016] [Indexed: 05/22/2023]
Abstract
Cultivated soybean has undergone many transformations during domestication. In this paper we report a comprehensive assessment of the evolution of gene co-expression networks based on the analysis of 40 transcriptomes from developing soybean seeds in cultivated and wild soybean accessions. We identified 2680 genes that are differentially expressed during seed maturation and established two cultivar-specific gene co-expression networks. Through analysis of the two networks and integration with quantitative trait locus data we identified two potential key drivers for seed trait formation, GA20OX and NFYA. GA20OX encodes an enzyme in a rate-limiting step of gibberellin biosynthesis, and NFYA encodes a transcription factor. Overexpression of GA20OX and NFYA enhanced seed size/weight and oil content, respectively, in seeds of transgenic plants. The two genes showed significantly higher expression in cultivated than in wild soybean, and the increases in expression were associated with genetic variations in the promoter region of each gene. Moreover, the expression of GA20OX and NFYA in seeds of soybean accessions correlated with seed weight and oil content, respectively. Our study reveals transcriptional adaptation during soybean domestication and may identify a mechanism of selection by expression for seed trait formation, providing strategies for future breeding practice.
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Affiliation(s)
- Xiang Lu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing-Tian Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Xiong
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Li
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ying-Dong Bi
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yong-Cai Lai
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xin-Lei Liu
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wei-Qun Man
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wan-Ke Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Biao Ma
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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596
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Anderson JE, Michno JM, Kono TJY, Stec AO, Campbell BW, Curtin SJ, Stupar RM. Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants. BMC Biotechnol 2016; 16:41. [PMID: 27176220 PMCID: PMC4866027 DOI: 10.1186/s12896-016-0271-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/04/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. RESULTS On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. CONCLUSIONS Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods.
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Affiliation(s)
- Justin E Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Jean-Michel Michno
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Adrian O Stec
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Benjamin W Campbell
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Robert M Stupar
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA.
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597
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Page JT, Liechty ZS, Alexander RH, Clemons K, Hulse-Kemp AM, Ashrafi H, Van Deynze A, Stelly DM, Udall JA. DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton. PLoS Genet 2016; 12:e1006012. [PMID: 27168520 PMCID: PMC4864293 DOI: 10.1371/journal.pgen.1006012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/06/2016] [Indexed: 01/08/2023] Open
Abstract
Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved resolution of 34 deeply re-sequenced genomes. We also explore the evolution of homoeologous regions in the AT- and DT-genomes and especially the phenomenon of conversion between genomes. We did not find any compelling evidence for homoeologous conversion between genomes. These findings are very different from other recent reports of frequent conversion events between genomes. We also identified several distinct regions of the genome that have been introgressed between G. hirsutum and G. barbadense, which presumably resulted from breeding efforts targeting associated beneficial alleles. Finally, the genotypic data resulting from this study provides access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars.
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Affiliation(s)
- Justin T. Page
- Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Zach S. Liechty
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Rich H. Alexander
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Kimberly Clemons
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Amanda M. Hulse-Kemp
- Department of Soil & Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California-Davis, Davis, California, United States of America
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California-Davis, Davis, California, United States of America
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
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598
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Fang C, Ma Y, Yuan L, Wang Z, Yang R, Zhou Z, Liu T, Tian Z. Chloroplast DNA Underwent Independent Selection from Nuclear Genes during Soybean Domestication and Improvement. J Genet Genomics 2016; 43:217-21. [PMID: 27090605 DOI: 10.1016/j.jgg.2016.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 11/22/2022]
Affiliation(s)
- Chao Fang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanming Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Beijing University of Agriculture, Beijing 102206, China
| | - Lichai Yuan
- The Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengkui Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tengfei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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599
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Wang Y, Gu Y, Gao H, Qiu L, Chang R, Chen S, He C. Molecular and geographic evolutionary support for the essential role of GIGANTEAa in soybean domestication of flowering time. BMC Evol Biol 2016; 16:79. [PMID: 27072125 PMCID: PMC4830004 DOI: 10.1186/s12862-016-0653-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/06/2016] [Indexed: 12/16/2023] Open
Abstract
BACKGROUND Flowering time is a domestication trait of Glycine max and varies in soybeans, yet, a gene for flowering time variation has not been associated with soybean domestication. GIGANTEA (GI) is a major gene involved in the control of flowering time in Arabidopsis, although three GI homologs complicate this model in the soybean genome. RESULTS In the present work, we revealed that the geographic evolution of the GIGANTEAa (GIa) haplotypes in G. max (GmGIa) and Glycine soja (GsGIa). Three GIa haplotypes (H1, H2, and H3) were found among cultivated soybeans and their wild relatives, yet an additional 44 diverse haplotypes were observed in wild soybeans. H1 had a premature stop codon in the 10(th) exon, whereas the other haplotypes encoded full-length GIa protein isoforms. In both wild-type and cultivated soybeans, H2 was present in the Southern region of China, and H3 was restricted to areas near the Northeast region of China. H1 was genetically derived from H2, and it was dominant and widely distributed among cultivated soybeans, whereas in wild populations, the ortholog of this domesticated haplotype H1 was only found in Yellow River basin with a low frequency. Moreover, this mutated GIa haplotype significantly correlated with early flowering. We further determined that the differences in gene expression of the three GmGIa haplotypes were not correlated to flowering time variations in cultivated soybeans. However, only the truncated GmGIa H1 could partially rescue gi-2 Arabidopsis from delayed flowering in transgenic plants, whereas both GmGIa H2 and H3 haplotypes could significantly repress flowering in transgenic Arabidopsis with a wild-type background. CONCLUSIONS Thus, GmGIa haplotype diversification may have contributed to flowering time adaptation that facilitated the radiation of domesticated soybeans. In light of the evolution of the GIa gene, soybean domestication history for an early flowering phenotype is discussed.
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Affiliation(s)
- Yan Wang
- />State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan 100093 Beijing, China
| | - Yongzhe Gu
- />State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan 100093 Beijing, China
- />Graduate University, Chinese Academy of Sciences, Yuquan Road 19, 100049 Beijing, China
| | - Huihui Gao
- />State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan 100093 Beijing, China
- />Graduate University, Chinese Academy of Sciences, Yuquan Road 19, 100049 Beijing, China
| | - Lijuan Qiu
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Ruzhen Chang
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Shouyi Chen
- />National Key Laboratory of Plant Genomic, Institute of Genetics and Developmental Biology, Chinese Academy of sciences, 100101 Beijing, China
| | - Chaoying He
- />State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan 100093 Beijing, China
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600
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Anderson JE, Kono TJY, Stupar RM, Kantar MB, Morrell PL. Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans. G3 (BETHESDA, MD.) 2016; 6:835-43. [PMID: 26818076 PMCID: PMC4825654 DOI: 10.1534/g3.116.026914] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/22/2016] [Indexed: 01/04/2023]
Abstract
Natural populations across a species range demonstrate population structure owing to neutral processes such as localized origins of mutations and migration limitations. Selection also acts on a subset of loci, contributing to local adaptation. An understanding of the genetic basis of adaptation to local environmental conditions is a fundamental goal in basic biological research. When applied to crop wild relatives, this same research provides the opportunity to identify adaptive genetic variation that may be used to breed for crops better adapted to novel or changing environments. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses. The identification of potentially adaptive variants in this ex situ collection may permit a more targeted use of germplasm collections.
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Affiliation(s)
- Justin E Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Michael B Kantar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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