Data from: Genetic variation and association mapping for 12 agronomic traits in indica rice

Background: Increasing rice (Oryza sativa L.) yield is a crucial challenge
for modern agriculture. The ideal plant architecture is considered to be
critical to enhance rice yield. Elite plant morphological traits should
include compact plant type, short stature, few unproductive tillers, thick
and sturdy stems and erect leaves. To reveal the genetic variations of
important morphological traits, 523 germplasm accessions were genotyped
using the Illumina custom-designed array containing 5,291 single
nucleotide polymorphisms (SNPs) and phenotyped in two independent
environments. Genome-wide association studies were performed to uncover
the genotypic and phenotypic variations using a mixed linear model.
Results: In total, 126 and 172 significant loci were identified and these
loci explained an average of 34.45 % and 39.09 % of the phenotypic
variance in two environments, respectively, and 16 of 298 (~5.37 %) loci
were detected across the two environments. For the 16 loci, 423 candidate
genes were predicted in a 200-kb region (±100 kb of the peak SNP).
Expression-level analyses identified four candidate genes as the most
promising regulators of tiller angle. Known (NAL1 and Rc) and new
significant loci showed pleiotropy and gene linkage. In addition, a long
genome region covering ~1.6 Mb on chromosome 11 was identified, which may
be critical for rice leaf architecture because of a high association with
flag leaf length and the ratio of flag leaf length and width. The pyramid
effect of the elite alleles indicated that these significant loci could be
beneficial for rice plant architecture improvements in the future.
Finally, 37 elite varieties were chosen as breeding donors for further
rice plant architectural modifications. Conclusions: This study detected
multiple novel loci and candidate genes related to rice morphological
traits, and the work demonstrated that genome-wide association studies are
powerful strategies for uncovering the genetic variations of complex
traits and identifying candidate genes in rice, even though the linkage
disequilibrium decayed slowly in self-pollinating species. Future research
will focus on the biological validation of the candidate genes, and elite
varieties will also be of interest in genome selection and breeding by
design.