Genome-wide association study for traits related to plant and grain morphology, and root architecture in temperate rice accessions

These are the data (phenotypes and genotypes) used for the genome-wide association study described below. The data are linked to the paper "Genome-wide association study for traits related to plant and grain morphology, and root architecture in temperate rice accessions", to be published on Plos ONE.

Phenotypes: two ASCII files (root phenotypes, plant&grain phenotypes), space/tab separated. Each row is a rice sample record, the columns are the phenotypes. Full explanation can be found in the paper.

Genotypes: tar.gz archive with imputed GBS (genotyping by sequencing) imputed rice genotypes. Genotypes are in Plink format: a .map file with information on the SNP markers (chromosome and position), and a .ped file whose rows are SNP genotypes per each rice samples. 

Abstract

In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate rice. A set of 391 rice accessions were GBS-genotyped yielding —after data editing— 57 000 polymorphic and informative SNPS, among which 54% were in genic regions. In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10^−7 to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (F DR = 3 · 10^-7 ) and for plant height on chromosome 6 (F DR = 0.011).
We demonstrate the effectiveness and resolution of the developed platform for
high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for
relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio.
Our findings pave the way to successfully exploit the narrow genetic pool of
European temperate rice and to pinpoint the most relevant genetic components
contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.