The Power of Inbreeding： NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication

• Published in: Molecular plant Vol. 9; no. 7; pp. 975 - 985
• Main Authors: Wang, Hongru, Xu, Xun, Vieira, Filipe Garrett, Xiao, Yunhua, Li, Zhikang, Wang, Jun, Nielsen, Rasmus, Chu, Chengcai
• Format: Journal Article
• Language: English
• Published: England Elsevier Inc 06.07.2016
• Subjects: Evolution, Molecular; Genome, Plant - genetics; Genome-Wide Association Study - methods; GWAS; Haplotypes - genetics; inbreeding; Oryza - genetics; pericarp color; Plant Proteins - genetics; Polymorphism, Single Nucleotide - genetics; rice; 全基因组测序; 权力; 水稻品种; 澳大利亚; 直链淀粉含量; 趋同进化; 近亲繁殖; 驯化过程; pericarp color; GWAS; inbreeding; rice
• ISSN: 1674-2052; 1752-9867
• DOI: 10.1016/j.molp.2016.04.018

Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in hu- mans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice （Oryza sativa L.）, which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5~ and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SN Ps in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice,japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.