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The Power of Inbreeding: NGS Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication
Hongru Wang,Xun Xu,Filipe Garrett Vieira,Yunhua Xiao,Zhikang Li,Jun Wang,Rasmus Nielsen,Chengcai Chu
Molecular Plant
Abstract
Low coverage whole genome sequencing is an effective strategy for genome-wide association studies (GWAS) in humans, due to the availability of large reference panels for genotype imputation. However, the utility of this strategy in other species without reference panels is unclear. 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 sequence 203 rice varieties with well-characterized phenotypes from the USDA Rice Minicore 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, we show that our approach leads to direct identification of the previously identified causal SNP in the major-effect loci. For the third trait, pericarp color, an important trait selected for during domestication, we discover a new major-effect locus. While known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica andindica, the new locus we found is unique to another domesticated rice subgroup, aus and together with existing loci 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.
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论文编号: |
DOI:10.1016/j.molp.2016.04.018 |
论文题目: |
The Power of Inbreeding: NGS Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication |
英文论文题目: |
The Power of Inbreeding: NGS Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication |
第一作者: |
Hongru Wang,Xun Xu,Filipe Garrett Vieira,Yunhua Xiao,Zhikang Li,Jun Wang,Rasmus Nielsen,Chengcai Chu |
英文第一作者: |
Hongru Wang,Xun Xu,Filipe Garrett Vieira,Yunhua Xiao,Zhikang Li,Jun Wang,Rasmus Nielsen,Chengcai Chu |
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2016-05-13 |
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摘要: |
Low coverage whole genome sequencing is an effective strategy for genome-wide association studies (GWAS) in humans, due to the availability of large reference panels for genotype imputation. However, the utility of this strategy in other species without reference panels is unclear. 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 sequence 203 rice varieties with well-characterized phenotypes from the USDA Rice Minicore 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, we show that our approach leads to direct identification of the previously identified causal SNP in the major-effect loci. For the third trait, pericarp color, an important trait selected for during domestication, we discover a new major-effect locus. While known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica andindica, the new locus we found is unique to another domesticated rice subgroup, aus and together with existing loci 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. |
英文摘要: |
Low coverage whole genome sequencing is an effective strategy for genome-wide association studies (GWAS) in humans, due to the availability of large reference panels for genotype imputation. However, the utility of this strategy in other species without reference panels is unclear. 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 sequence 203 rice varieties with well-characterized phenotypes from the USDA Rice Minicore 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, we show that our approach leads to direct identification of the previously identified causal SNP in the major-effect loci. For the third trait, pericarp color, an important trait selected for during domestication, we discover a new major-effect locus. While known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica andindica, the new locus we found is unique to another domesticated rice subgroup, aus and together with existing loci 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. |
刊物名称: |
Molecular Plant |
英文刊物名称: |
Molecular Plant |
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其它备注: |
Hongru Wang,Xun Xu,Filipe Garrett Vieira,Yunhua Xiao,Zhikang Li,Jun Wang,Rasmus Nielsen,Chengcai Chu. The Power of Inbreeding: NGS Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication. Molecular Plant. DOI:10.1016/j.molp.2016.04.018 |
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