Genome wide association study on development and evolution of glutinous rice

BMC Genomic Data

Muhammad Abdul Rehman Rashid¹  Yanhong Zhang²  Yinghua Pan³  Conghui Jiang⁴  Yan Zhao⁵ 

[1] Department of Bioinformatics and Biotechnology, Government College University;Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences;Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding;Shandong Rice Engineering Technology Research Center, Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences;State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University;

关键词: Glutinous rice;    Genome-wide association study;    Oryza Sativa L.;    Haplotype analysis;    Evolution;   

DOI  :  10.1186/s12863-022-01033-1

来源: DOAJ

【 摘 要 】

Abstract Background Glutinous rice as a special endosperm type is 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. Therefor, we sought to explore more genes related to glutinous by genome wide association study and research the formation history for glutinous. Results Here, genome-wide association study was performed to explore the associated loci/genes underlying glutinous rice by using 2108 rice accessions. Combining the expression patterns analysis, 127, 81, and 48 candidate genes were identified to be associated with endosperm type in whole rice panel, indica, and japonica sub-populations. 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 combined haplotype analyses revealed that the waxy haplotypes combination of three genes mainly distributed in Southeast Asia (SEA), SEA islands (SER) and East Asia islands (EAR). Through population structure and genetic differentiation, we suggest that waxy haplotypes of the three genes firstly evolved or were directly inherited from wild rice in japonica, and then introgressed into indica in SER, SEA and EAR. Conclusions The cloning and natural variation analysis of waxy-related genes are of great significance for the genetic improvement of quality breeding and comprehend the history in glutinous rice. This work provides valuable information for further gene discovery and understanding the evolution and formation for glutinous rice in SEA, SER and EAR.

【 授权许可】

Unknown