Genome Wide Association Study on Development and Evolution of Glutinous Rice

Abstract Background: As a globally known staple food, rice is well domesticated in the world. Various regions have different food preferences, which lead to design the goals for breeding programs. Glutinous rice as a special endosperm type is also consumed as a staple food in East Asian countries by consumers’ preference. Genetic studies on glutinous rice could be conducive to improve rice quality and understand its development and evolution. Genome-wide association study was performed to explore the associated loci/genes underlying glutinous rice by using 2108 rice accessions. Results: A total of 399, 262 and 156 annotated genes with significant loci were identified to be associated with endosperm type. By combining the expression patterns analysis, 127, 81, and 48 candidate genes were screened in whole rice panel, indica , and japonica sub-populations with moderate expression in seeds. There were 32 genes, including three starch synthesis-related genes Wx , SSG6 , and OsSSIIa, detected simultaneously in the whole rice panel and subpopulations, playing important role in determining glutinous rice. The main waxy haplotypes of three starch synthesis-related genes were identified by haplotype analysis, while the combined haplotype analyses, revealed that the waxy combined haplotype mainly distributed in Southeast Asia (SEA), SEA islands (SER) and East Asia islands (EAR). Through population structure and genetic differentiation, we proposed the evolutionary model of waxy haplotypes of the three genes from wild rice to japonica , and then to indica . Conclusion: It was concluded that the waxy haplotypes of the three genes firstly generated (or were directly inherited from wild rice) in japonica , and then flowed into indica in SER, SEA and EAR . These results provide valuable information for further gene discovery and understanding the development and evolution for glutinous rice.