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Multivariate Genome-Wide Association Analyses Reveal the Genetic Basis of Seed Fatty Acid Composition in Oat (Avena sativa L.).

ABSTRACT: Oat (Avena sativa L.) has a high concentration of oils, comprised primarily of healthful unsaturated oleic and linoleic fatty acids. To accelerate oat plant breeding efforts, we sought to identify loci associated with variation in fatty acid composition, defined as the types and quantities of fatty acids. We genotyped a panel of 500 oat cultivars with genotyping-by-sequencing and measured the concentrations of ten fatty acids in these oat cultivars grown in two environments. Measurements of individual fatty acids were highly correlated across samples, consistent with fatty acids participating in shared biosynthetic pathways. We leveraged these phenotypic correlations in two multivariate genome-wide association study (GWAS) approaches. In the first analysis, we fitted a multivariate linear mixed model for all ten fatty acids simultaneously while accounting for population structure and relatedness among cultivars. In the second, we performed a univariate association test for each principal component (PC) derived from a singular value decomposition of the phenotypic data matrix. To aid interpretation of results from the multivariate analyses, we also conducted univariate association tests for each trait. The multivariate mixed model approach yielded 148 genome-wide significant single-nucleotide polymorphisms (SNPs) at a 10% false-discovery rate, compared to 129 and 73 significant SNPs in the PC and univariate analyses, respectively. Thus, explicit modeling of the correlation structure between fatty acids in a multivariate framework enabled identification of loci associated with variation in seed fatty acid concentration that were not detected in the univariate analyses. Ultimately, a detailed characterization of the loci underlying fatty acid variation can be used to enhance the nutritional profile of oats through breeding.

SUBMITTER: Carlson MO

PROVIDER: S-EPMC6723141 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Multivariate Genome-Wide Association Analyses Reveal the Genetic Basis of Seed Fatty Acid Composition in Oat (<i>Avena sativa</i> L.).

Carlson Maryn O MO Montilla-Bascon Gracia G Hoekenga Owen A OA Tinker Nicholas A NA Poland Jesse J Baseggio Matheus M Sorrells Mark E ME Jannink Jean-Luc JL Gore Michael A MA Yeats Trevor H TH

G3 (Bethesda, Md.) 20190904 9

Oat (<i>Avena sativa</i> L.) has a high concentration of oils, comprised primarily of healthful unsaturated oleic and linoleic fatty acids. To accelerate oat plant breeding efforts, we sought to identify loci associated with variation in fatty acid composition, defined as the types and quantities of fatty acids. We genotyped a panel of 500 oat cultivars with genotyping-by-sequencing and measured the concentrations of ten fatty acids in these oat cultivars grown in two environments. Measurements ...[more]

PMID: 31296616

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Project description:The observable phenotype is the manifestation of information that is passed along different organization levels (transcriptional, translational, and metabolic) of a biological system. The widespread use of various omic technologies (RNA-sequencing, metabolomics, etc.) has provided plant genetics and breeders with a wealth of information on pertinent intermediate molecular processes that may help explain variation in conventional traits such as yield, seed quality, and fitness, among others. A major challenge is effectively using these data to help predict the genetic merit of new, unobserved individuals for conventional agronomic traits. Trait-specific genomic relationship matrices (TGRMs) model the relationships between individuals using genome-wide markers (SNPs) and place greater emphasis on markers that most relevant to the trait compared to conventional genomic relationship matrices. Given that these approaches define relationships based on putative causal loci, it is expected that these approaches should improve predictions for related traits. In this study we evaluated the use of TGRMs to accommodate information on intermediate molecular phenotypes (referred to as endophenotypes) and to predict an agronomic trait, total lipid content, in oat seed. Nine fatty acids were quantified in a panel of 336 oat lines. Marker effects were estimated for each endophenotype, and were used to construct TGRMs. A multikernel TRGM model (MK-TRGM-BLUP) was used to predict total seed lipid content in an independent panel of 210 oat lines. The MK-TRGM-BLUP approach significantly improved predictions for total lipid content when compared to a conventional genomic BLUP (gBLUP) approach. Given that the MK-TGRM-BLUP approach leverages information on the nine fatty acids to predict genetic values for total lipid content in unobserved individuals, we compared the MK-TGRM-BLUP approach to a multi-trait gBLUP (MT-gBLUP) approach that jointly fits phenotypes for fatty acids and total lipid content. The MK-TGRM-BLUP approach significantly outperformed MT-gBLUP. Collectively, these results highlight the utility of using TGRM to accommodate information on endophenotypes and improve genomic prediction for a conventional agronomic trait.

Project description:In the present study, 30 potential germplasm of oat (Avena sativa L.) were subjected to proximate, elemental, and HPLC analysis to provide a scientific basis to genetic diversity present among them. The extracts of the selected germplasms were also evaluated for their antioxidant potentials through DPPH and ABTS assays. Proximate analysis showed protein contents to be in the range 8.35-17.72% with the highest protein contents in the accession line 22,365 (17.72 ± 0.38%). The genotype-725 showed the highest carbohydrate, and dry matter (53.35 ± 0.01 and 93.50 ± 0.07% respectively) contents whereas, the germplasm-830 contained the highest fat (7.88 ± 0.12%) contents while the highest moisture contents were there in germplasm-22348 (11.95 ± 0.06%). The crude fiber contents (19.67 ± 0.19%) were found high in germplasm-832. The mentioned contents were also correlated to each other where a negative (-0.431*) correlation was noted for crude protein and carbohydrate while ash content to crude protein has a positive (0.38*) correlation. A positive and a negative correlation were there in Crude fats/crude protein (0.30*) and crude fats/moisture contents (-0.39*) respectively. Principal component analysis showed an Eigenvalue of 0.76 with a total variation of 85.01% when applied to proximate components. Based on cluster analysis to proximate composition all the oat germplasms were divided into 5 sub-clusters, where accession numbers 769 and 817 were found to be the most diverse genotypes. The elemental analysis confirmed the presence of magnesium (2.89-7.62 mg/L), sodium (3.71-8.03 mg/L), manganese (0.93-3.71 mg/L), copper (0.35-3.36 mg/L), iron (2.15-6.82 mg/L), zinc (1.30-3.37 mg/L), chromium (0.37-3.34 mg/L), and potassium (50.70-59.60 mg/L) in the selected germplasms. Principal component analysis for elemental composition showed the total variation of 73.75% with the Eigenvalue of 0.97. Cluster analysis on an elemental basis divided all the oat germplasms into 7 sub-clusters where accession numbers 769 and 22,350 were found to be the most diverse germplasm. Phytochemical analysis performed through HPLC resulted in the identification of nine possible compounds (malic acid, epigallocatechin gallate, quercetin, morin, ellagic acid, catechin hydrate, rutin, pyrogallol, and mandelic acid) in various germplasm of oat. A concentration-dependent antioxidant response was recorded when extracts were tested as an inhibitor of DPPH and ABTS free radicals. The results revealed that oat grains are a good source of nutrients, minerals, and phytochemicals that can be used as nutraceuticals and as food. The genetic differences revealed that this plant can be grown under varied environmental conditions.

Project description:BackgroundDeficiency of available forms of phosphorus is common in most soils and causes reduction of crop plants growth and yield. Recently, model plants responses to phosphate (Pi) deficiency have been intensively studied. However, acclimation mechanisms of cereals like oat (Avena sativa L.), to low Pi stress remains not fully understood. Oat plants have been usually cultured on poor soils, with a low nutrient content, but their responses to such conditions are not well known, therefore the main goal of the study was to investigate the mechanisms that enable oat plants to grow under low Pi conditions.MethodsFour oat cultivars (A. sativa, cv. Arab, Krezus, Rajtar and Szakal) were grown for three weeks in a nutrient media with various P sources: inorganic-KH2PO4 (control), organic-phytate (PA) and with no phosphate (-P). The effects of Pi deficiency on the level of P, oat growth parameters, intensity of photosynthesis, plant productivity, root exudation ability, localization, activity and isoforms of acid phosphatases, enzymes involved in Pi mobilization, were estimated. In addition, the effect of mycorrhization on plant growth was also observed.ResultsAll studied oat cultivars grown on Pi-deficient media had significantly decreased Pi content in the tissues. Pi deficiency caused inhibition of shoot growth, but generally it did not affect root elongation; root diameter was decreased, root/shoot ratios increased, whereas PA plants showed a similar growth to control. Photosynthesis rate and productivity parameters decreased under low Pi nutrition, however, sugar content generally increased. Studied oat cultivars did not respond to low Pi via increased exudation of carboxylates from the roots, as pH changes in the growth media were not observed. Pi starvation significantly increased the activity of extracellular and intracellular acid phosphatases (APases) in comparison to the control plants. Three major APase isoforms were detected in oat tissues and the isoform pattern was similar in all studied conditions, usually with a higher level of one of the isoforms under Pi starvation. Generally no significant effects of mycorrhizal colonization on growth of oat cultivars were observed.DiscussionWe postulated that acid phosphatases played the most important role in oat cultivars acclimation to Pi deficiency, especially extracellular enzymes involved in Pi acquisition from soil organic P esters. These APases are mainly located in the epidermis of young roots, and may be released to the rhizosphere. On the other hand, intracellular APases could be involved in fast Pi remobilization from internal sources. Our study showed that oat, in contrast to other plants, can use phytates as the sole source of P. The studied oat cultivars demonstrated similar acclimation mechanisms to Pi deficiency, however, depending on stress level, they can use different pools of acid phosphatases.

Dataset Information

Multivariate Genome-Wide Association Analyses Reveal the Genetic Basis of Seed Fatty Acid Composition in Oat (Avena sativa L.).

Publications

Multivariate Genome-Wide Association Analyses Reveal the Genetic Basis of Seed Fatty Acid Composition in Oat (<i>Avena sativa</i> L.).

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