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Dissecting Adaptive Traits with Nested Association Mapping: Genetic Architecture of Inflorescence Morphology in Sorghum.

ABSTRACT: In the cereal crop sorghum (Sorghum bicolor) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. We characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter). Trait correlations suggest that lower and upper branch length are under somewhat independent control, while lower branch length and rachis diameter are highly pleiotropic. Joint linkage and genome-wide association mapping revealed an oligogenic architecture with 1-22 QTL per trait, each explaining 0.1-5.0% of variation across the entire NAM population. There is a significant enrichment (2.twofold) of QTL colocalizing with grass inflorescence gene homologs, notably with orthologs of maize Ramosa2 and rice Aberrant Panicle Organization1 and TAWAWA1 Still, many QTL do not colocalize with inflorescence gene homologs. In global georeferenced germplasm, allelic variation at the major inflorescence QTL is geographically patterned but only weakly associated with the gradient of annual precipitation. Comparison of NAM with diversity panel association suggests that naive association models may capture some true associations not identified by mixed linear models. Overall, the findings suggest that global inflorescence diversity in sorghum is largely controlled by oligogenic, epistatic, and pleiotropic variation in ancestral regulatory networks. The findings also provide a basis for genomics-enabled breeding of locally-adapted inflorescence morphology.

SUBMITTER: Olatoye MO

PROVIDER: S-EPMC7202033 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Dissecting Adaptive Traits with Nested Association Mapping: Genetic Architecture of Inflorescence Morphology in Sorghum.

Olatoye Marcus O MO Marla Sandeep R SR Hu Zhenbin Z Bouchet Sophie S Perumal Ramasamy R Morris Geoffrey P GP

G3 (Bethesda, Md.) 20200504 5

In the cereal crop sorghum (<i>Sorghum bicolor</i>) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. We characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branc ...[more]

PMID: 32217633

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Project description:BACKGROUND: Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs. RESULTS: Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1) showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel. CONCLUSIONS: This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition.

Dataset Information

Dissecting Adaptive Traits with Nested Association Mapping: Genetic Architecture of Inflorescence Morphology in Sorghum.

Publications

Dissecting Adaptive Traits with Nested Association Mapping: Genetic Architecture of Inflorescence Morphology in Sorghum.

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