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Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.).
G3 (Bethesda). 2022 01 04; 12(1)G

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 peanuts, all traits had significant SNP interactions exceeding a stringent Bonferroni threshold (α = 1%). We detected 7682 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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Authors+Show Affiliations

Otyama PI
Interdepartmental Genetics and Genomics, Iowa State University, Ames, IA 50011, USA. Agronomy Department, Iowa State University, Ames, IA 50011, USA.
Chamberlin K
USDA-Agricultural Research Service, Stillwater, OK 740752714, USA.
Ozias-Akins P
Genetics, and Genomics and Department of Horticulture, Institute of Plant Breeding, University of Georgia, Tifton, GA 31793-5766, USA.
Graham MA
Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA 50011, USA.
Cannon EKS
Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA 50011, USA.
Cannon SB
Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA 50011, USA.
MacDonald GE
University of Florida, Gainesville, FL 32611-0500, USA.
Anglin NL
USDA-ARS Small Grains and Potato Research Laboratory, Aberdeen, ID 83210, USA.

MeSH

ArachisFatty AcidsGenome-Wide Association StudyPolymorphism, Single NucleotideQuantitative Trait LociSeeds

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

34751378

Citation

Otyama, Paul I., et al. "Genome-wide Approaches Delineate the Additive, Epistatic, and Pleiotropic Nature of Variants Controlling Fatty Acid Composition in Peanut (Arachis Hypogaea L.)." G3 (Bethesda, Md.), vol. 12, no. 1, 2022.
Otyama PI, Chamberlin K, Ozias-Akins P, et al. Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). G3 (Bethesda). 2022;12(1).
Otyama, P. I., Chamberlin, K., Ozias-Akins, P., Graham, M. A., Cannon, E. K. S., Cannon, S. B., MacDonald, G. E., & Anglin, N. L. (2022). Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). G3 (Bethesda, Md.), 12(1). https://doi.org/10.1093/g3journal/jkab382
Otyama PI, et al. Genome-wide Approaches Delineate the Additive, Epistatic, and Pleiotropic Nature of Variants Controlling Fatty Acid Composition in Peanut (Arachis Hypogaea L.). G3 (Bethesda). 2022 01 4;12(1) PubMed PMID: 34751378.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). AU - Otyama,Paul I, AU - Chamberlin,Kelly, AU - Ozias-Akins,Peggy, AU - Graham,Michelle A, AU - Cannon,Ethalinda K S, AU - Cannon,Steven B, AU - MacDonald,Gregory E, AU - Anglin,Noelle L, PY - 2021/06/22/received PY - 2021/10/26/accepted PY - 2021/11/10/pubmed PY - 2022/3/9/medline PY - 2021/11/9/entrez KW - GWAS of interacting SNPs (GWASi) KW - SNP genotyping KW - genome-wide association study (GWAS) KW - oleic-linoleic acid ratio KW - pleiotropy KW - seed fatty acid composition JF - G3 (Bethesda, Md.) JO - G3 (Bethesda) VL - 12 IS - 1 N2 - 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 peanuts, all traits had significant SNP interactions exceeding a stringent Bonferroni threshold (α = 1%). We detected 7682 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. SN - 2160-1836 UR - https://www.unboundmedicine.com/medline/citation/34751378/Genome_wide_approaches_delineate_the_additive_epistatic_and_pleiotropic_nature_of_variants_controlling_fatty_acid_composition_in_peanut__Arachis_hypogaea_L___ DB - PRIME DP - Unbound Medicine ER -