title: The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication.
abstract: Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in humans, 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 SNPs 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.
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Hongru
authors.initials: H
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.
authors.forename: Filipe Garrett
authors.initials: FG
authors.lastname: Vieira
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yunhua
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: Institute of Crop Sciences/National Key Facilities for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China.
authors.forename: Zhikang
authors.initials: Z
authors.lastname: Li
authors.affiliation: College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China. Electronic address: wangj@genomics.org.cn.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, CA 94720 USA. Electronic address: rasmus_nielsen@berkeley.edu.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: ccchu@genetics.ac.cn.
authors.forename: Chengcai
authors.initials: C
authors.lastname: Chu
mesh_terms: D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D006239:Haplotypes / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics
chemical_list: D010940:Plant Proteins
keywords: GWAS; inbreeding; pericarp color; rice