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Otyama PI, Chamberlin K, Ozias-Akins P, Graham MA, Cannon EKS, Cannon SB, MacDonald GE, Anglin NL. Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). G3 (Bethesda) 2021; 12:6423989. [PMID: 34751378 DOI: 10.1093/g3journal/jkab382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/26/2021] [Indexed: 11/12/2022]
Abstract
The fatty acid composition of seed oil is a major determinant of the flavor, shelf-life, and nutritional quality of peanuts. Major QTLs controlling high oil content, high oleic content, and low linoleic content have been characterized in several seed oil crop species. Here we employ genome-wide association approaches on a recently genotyped collection of 787 plant introduction accessions in the USDA peanut core collection, plus selected improved cultivars, to discover markers associated with the natural variation in fatty acid composition, and to explain the genetic control of fatty acid composition in seed oils. Overall, 251 single nucleotide polymorphisms (SNPs) had significant trait associations with the measured fatty acid components. Twelve SNPs were associated with two or three different traits. Of these loci with apparent pleiotropic effects, 10 were associated with both oleic (C18:1) and linoleic acid (C18:2) content at different positions in the genome. In all 10 cases, the favorable allele had an opposite effect-increasing and lowering the concentration, respectively, of oleic and linoleic acid. The other traits with pleiotropic variant control were palmitic (C16:0), behenic (C22:0), lignoceric (C24:0), gadoleic (C20:1), total saturated, and total unsaturated fatty acid content. One hundred (100) of the significantly associated SNPs were located within 1000 kbp of 55 genes with fatty acid biosynthesis functional annotations. These genes encoded, among others: ACCase carboxyl transferase subunits, and several fatty acid synthase II enzymes. With the exception of gadoleic (C20:1) and lignoceric (C24:0) acid content, which occur at relatively low abundance in cultivated peanut, all traits had significant SNP interactions exceeding a stringent Bonferroni threshold (α = 1%). We detected 7,682 pairwise SNP interactions affecting the relative abundance of fatty acid components in the seed oil. Of these, 627 SNP pairs had at least one SNP within 1000 kbp of a gene with fatty acid biosynthesis functional annotation. We evaluated 168 candidate genes underlying these SNP interactions. Functional enrichment and protein-to-protein interactions supported significant interactions (p-value < 1.0E-16) among the genes evaluated. These results show the complex nature of the biology and genes underlying the variation in seed oil fatty acid composition and contribute to an improved genotype-to-phenotype map for fatty acid variation in peanut seed oil.
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Affiliation(s)
- Paul I Otyama
- Interdepartmental Genetics and Genomics, Iowa State University, Ames, IA 50011, USA.,Agronomy Department, Iowa State University, Ames, IA 50011, USA.,ORISE Postdoctoral Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| | - Kelly Chamberlin
- USDA-Agricultural Research Service, Stillwater, OK 740752714, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics, and Genomics and Department of Horticulture, University of Georgia, Tifton, GA 31793-5766, USA
| | - Michelle A Graham
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Ethalinda K S Cannon
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Steven B Cannon
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | | | - Noelle L Anglin
- USDA-ARS Small Grains and Potato Research Laboratory, Aberdeen, ID 83210, USA
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Valliyodan B, Brown AV, Wang J, Patil G, Liu Y, Otyama PI, Nelson RT, Vuong T, Song Q, Musket TA, Wagner R, Marri P, Reddy S, Sessions A, Wu X, Grant D, Bayer PE, Roorkiwal M, Varshney RK, Liu X, Edwards D, Xu D, Joshi T, Cannon SB, Nguyen HT. Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Sci Data 2021; 8:50. [PMID: 33558550 PMCID: PMC7870887 DOI: 10.1038/s41597-021-00834-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/06/2021] [Indexed: 12/28/2022] Open
Abstract
We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.
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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
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO, 65101, USA
| | - Anne V Brown
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Juexin Wang
- Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Gunvant Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Yang Liu
- MU Institute of Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
| | - Paul I Otyama
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Rex T Nelson
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Tri Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Qijian Song
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, 20705, USA
| | - Theresa A Musket
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Ruth Wagner
- Bayer CropScience, St. Louis, MO, 63141, USA
| | - Pradeep Marri
- Corteva Agriscience, Indianapolis, IN, 46268, USA
- Pairwise Plants LLC, Durham, NC, 27709, USA
| | - Sam Reddy
- Corteva Agriscience, Indianapolis, IN, 46268, USA
| | - Allen Sessions
- Bayer CropScience, Research Triangle Park, NC, 27709, USA
| | - Xiaolei Wu
- Bayer CropScience, Research Triangle Park, NC, 27709, USA
| | - David Grant
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Philipp E Bayer
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Xin Liu
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
- State Key Laboratory of Agricultural Genomics, China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- MU Institute of Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
| | - Trupti Joshi
- Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- MU Institute of Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
- Department of Health Management and Informatics, University of Missouri, Columbia, MO, 65211, USA
| | - Steven B Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, 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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Assefa T, Otyama PI, Brown AV, Kalberer SR, Kulkarni RS, Cannon SB. Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean. BMC Genomics 2019; 20:527. [PMID: 31242867 PMCID: PMC6595607 DOI: 10.1186/s12864-019-5907-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/17/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Breeding programs benefit from information about marker-trait associations for many traits, whether the goal is to place those traits under active selection or to maintain them through background selection. Association studies are also important for identifying accessions bearing potentially useful alleles by characterizing marker-trait associations and allelic states across germplasm collections. This study reports the results of a genome-wide association study and evaluation of epistatic interactions for four agronomic and seed-related traits in soybean. RESULTS Using 419 diverse soybean accessions, together with genotyping data from the SoySNP50K Illumina Infinium BeadChip, we identified marker-trait associations for internode number (IN), plant height (PH), seed weight (SW), and seed yield per plant (SYP). We conducted a genome-wide epistatic study (GWES), identifying candidate genes that show evidence of SNP-SNP interactions. Although these candidate genes will require further experimental validation, several appear to be involved in developmental processes related to the respective traits. For IN and PH, these include the Dt1 determinacy locus (a soybean meristematic transcription factor), as well as a pectinesterase gene and a squamosa promoter binding gene that in other plants are involved in cell elongation and the vegetative-to-reproductive transition, respectively. For SW, candidate genes include an ortholog of the AP2 gene, which in other species is involved in maintaining seed size, embryo size, seed weight and seed yield. Another SW candidate gene is a histidine phosphotransfer protein - orthologs of which are involved in cytokinin-mediated seed weight regulating pathways. The SYP association loci overlap with regions reported in previous QTL studies to be involved in seed yield. CONCLUSIONS This study further confirms the utility of GWAS and GWES approaches for identifying marker-trait associations and interactions within a diverse germplasm collection.
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Affiliation(s)
- Teshale Assefa
- ORISE Fellow, USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
| | - Paul I. Otyama
- Agronomy Department, Iowa State University, Ames, IA USA
| | - Anne V. Brown
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
| | - Scott R. Kalberer
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
| | | | - Steven B. Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
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Otyama PI, Wilkey A, Kulkarni R, Assefa T, Chu Y, Clevenger J, O'Connor DJ, Wright GC, Dezern SW, MacDonald GE, Anglin NL, Cannon EKS, Ozias-Akins P, Cannon SB. Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection. BMC Genomics 2019; 20:481. [PMID: 31185892 PMCID: PMC6558826 DOI: 10.1186/s12864-019-5824-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/21/2019] [Indexed: 12/03/2022] Open
Abstract
Background Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources of variation and to leverage the power of genome-wide association studies (GWAS) to discover markers associated with traits of interest. We report an analysis of linkage disequilibrium (LD), population structure, and genetic diversity, and examine the ability of GWA to infer marker-trait associations in the U.S. peanut mini core collection genotyped with a 58 K SNP array. Results LD persists over long distances in the collection, decaying to r2 = half decay distance at 3.78 Mb. Structure within the collection is best explained when separated into four or five groups (K = 4 and K = 5). At K = 4 and 5, accessions loosely clustered according to market type and subspecies, though with numerous exceptions. Out of 107 accessions, 43 clustered in correspondence to the main market type subgroup whereas 34 did not. The remaining 30 accessions had either missing taxonomic classification or were classified as mixed. Phylogenetic network analysis also clustered accessions into approximately five groups based on their genotypes, with loose correspondence to subspecies and market type. Genome wide association analysis was performed on these lines for 12 seed composition and quality traits. Significant marker associations were identified for arachidic and behenic fatty acid compositions, which despite having low bioavailability in peanut, have been reported to raise cholesterol levels in humans. Other traits such as blanchability showed consistent associations in multiple tests, with plausible candidate genes. Conclusions Based on GWA, population structure as well as additional simulation results, we find that the primary limitations of this collection for GWAS are a small collection size, significant remaining structure/genetic similarity and long LD blocks that limit the resolution of association mapping. These results can be used to improve GWAS in peanut in future studies – for example, by increasing the size and reducing structure in the collections used for GWAS. Electronic supplementary material The online version of this article (10.1186/s12864-019-5824-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul I Otyama
- Agronomy Department, Iowa State University, Ames, IA, USA
| | - Andrew Wilkey
- ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Roshan Kulkarni
- Agronomy Department, Iowa State University, Ames, IA, USA.,ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Teshale Assefa
- Agronomy Department, Iowa State University, Ames, IA, USA.,ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Ye Chu
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Josh Clevenger
- Mars-Wrigley Confectionery, Center for Applied Genetic Technologies, Athens, GA, USA
| | | | | | | | | | | | | | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, USDA - Agricultural Research Service, 1017 Crop Genome Lab 819 Wallace Rd, Ames, IA, 50011-4014, USA.
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