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Joint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids

文献类型： 外文期刊

作者： Li, Lanzhi 1 ; Zheng, Xingfei 2 ; Wang, Jiabo 4 ; Zhang, Xueli 1 ; He, Xiaogang 1 ; Xiong, Liwen 1 ; Song, Shufeng 5 ; Su, Jing 1 ; Diao, Ying 6 ; Yuan, Zheming 1 ; Zhang, Zhiwu 7 ; Hu, Zhongli 3 ;

作者机构： 1.Hunan Agr Univ, Coll Plant Protect, Hunan Engn & Technol Res Ctr Agr Big Data Anal & D, Changsha 410128, Hunan, Peoples R China

2.Hubei Acad Agr Sci, Food Crop Inst, Hubei Key Lab Food Crop Germplasm & Genet Improvem, Wuhan 430064, Hubei, Peoples R China

3.Wuhan Univ, Coll Life Sci, State Key Lab Hybrid Rice, Wuhan 430072, Hubei, Peoples R China

4.Southwest Minzu Univ, Minist Educ & Sichuan Prov, Key Lab Qinghai Tibetan Plateau Anim Genet Resourc, Chengdu 610041, Sichuan, Peoples R China

5.Hunan Acad Agr Sci, Hunan Hybrid Rice Res Ctr, State Key Lab Hybrid Rice, Changsha 410125, Hunan, Peoples R China

6.Wuhan Polytech Univ, Sch Life Sci & Technol, Wuhan 430023, Hubei, Peoples R China

7.Washington State Univ, Dept Crop & Soil Sci, Pullman, WA 99164 USA

期刊名称：NATURE COMMUNICATIONS （ 影响因子：16.6； 五年影响因子：17.0 ）

ISSN：

年卷期： 2023 年 14 卷 1 期

页码：

收录情况： SCI

摘要： Genetic improvement of grain quality is more challenging in hybrid rice than in inbred rice due to additional nonadditive effects such as dominance. Here, we describe a pipeline developed for joint analysis of phenotypes, effects, and generations (JPEG). As a demonstration, we analyze 12 grain quality traits of 113 inbred lines (male parents), five tester lines (female parents), and 565 (113x5) of their hybrids. We sequence the parents for single nucleotide polymorphisms calling and infer the genotypes of the hybrids. Genome-wide association studies with JPEG identify 128 loci associated with at least one of the 12 traits, including 44, 97, and 13 loci with additive effects, dominant effects, and both additive and dominant effects, respectively. These loci together explain more than 30% of the genetic variation in hybrid performance for each of the traits. The JEPG statistical pipeline can help to identify superior crosses for breeding rice hybrids with improved grain quality. Genetic dissection of hybrids is more difficult than inbreds as nonadditive effects are involved. Here, the authors report a pipeline for joint analysis of phenotypes, effects, and generations and demonstrate its usefulness in identification of loci associated with quality traits and improving predict accuracy in genomic selection of hybrid rice.

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