Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

@article{Yano2016GenomewideAS,
  title={Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice},
  author={Kenji Yano and Eiji Yamamoto and Koichiro Aya and Hideyuki Takeuchi and Pei-ching Lo and Li Hu and Masanori Yamasaki and Shinya Yoshida and Hidemi Kitano and Ko Hirano and Makoto Matsuoka},
  journal={Nature Genetics},
  year={2016},
  volume={48},
  pages={927-934}
}
A genome-wide association study (GWAS) can be a powerful tool for the identification of genes associated with agronomic traits in crop species, but it is often hindered by population structure and the large extent of linkage disequilibrium. In this study, we identified agronomically important genes in rice using GWAS based on whole-genome sequencing, followed by the screening of candidate genes based on the estimated effect of nucleotide polymorphisms. Using this approach, we identified four… 

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References

SHOWING 1-10 OF 77 REFERENCES

Genome-wide association studies of 14 agronomic traits in rice landraces

This study identifies ∼3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method, demonstrating that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice.

Genome-wide association study of leaf architecture in the maize nested association mapping population

Overall, GWAS results show that variations at the liguleless genes have contributed to more upright leaves, and the use of GWAS with specially designed mapping populations is effective in uncovering the basis of key agronomic traits.

Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

Limited linkage disequilibrium was observed around some SNPs associated with SLB resistance, indicating that the maize NAM population enables high-resolution mapping of some genome regions.

Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels

The genetic architecture of maize oil biosynthesis is extensively examined in a genome-wide association study using 1.03 million SNPs characterized in 368 maize inbred lines, including 'high-oil' lines, to provide insights into the genetic basis ofOil biosynthesis in maize kernels.

Natural variations and genome-wide association studies in crop plants.

The development of sequencing-based genotyping and genome-wide association studies in crops are described and the advent of high-throughput sequencing technology enables rapid and accurate resequencing of a large number of crop genomes to detect the genetic basis of phenotypic variations in crops.
...