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Combination of favorable gene haplotypes plays an important role in rice hybrid grain quality traits based on genome-wide association analysis

By Lanzhi Li, Xingfei Zheng, Xueli Zhang, Kai Xu, Shufeng Song, Jing Su, Chao Wu, Zirong Li, Wenbang Tang, Ying Diao, Zhonghai Tang, Zheming Yuan, Zhongli Hu

Posted 04 Jun 2020
bioRxiv DOI: 10.1101/2020.06.04.134023

Yield level and grain quality determine the commercial potential of rice ( Oryza sativa L.) varieties. Mining and using genes that control important rice grain quality characteristics are major tasks for plant breeders. Here, a genome-wide association study was conducted to determine the genetic bases of 12 rice grain quality traits in 113 varieties and 565 testcross hybrids. A total of 56 significant SNPs were associated with 9 of the traits in variety phenotypic, general combining ability, testcross hybrid phenotypic and mid-parental heterotic datasets, from which 45 novel loci were identified. The cumulative effects of superior alleles or favorable haplotypes of genes closest to significant quality trait-associated loci were found in the four datasets. Additionally, the favorable gene haplotypes performed better than those of superior alleles in the variety and testcross hybrid datasets. Pyramiding the favorable haplotypes of five cloned rice grain quality genes resulted in a very low amylose content and high yield in the latter. These testcross hybrids had rice grain qualities similar to their parental lines but with much higher yields. The amylose content, grain width and grain length predictions for potential hybrids among the 113 varieties using genomic selection based on the BayesB method revealed a performance trend similar to those the testcross hybrids in our study. Thus, the selection of combination of favorable rice quality-related gene haplotypes is recommended to breed hybrids with high yields and elite grain qualities.

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