Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice  

作　　者：Xiaogang He Zirong Li Sicheng Guo Xingfei Zheng Chunhai Liu Zijie Liu Yongxin Li Zheming Yuan Lanzhi Li 

机构地区：[1]Hunan Engineering&Technology Research Center for Agricultural Big Data Analysis&Decision-making/College of Plant Protection,Hunan Agricultural University,Changsha 410128,China [2]Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement/Food Crop Institute,Hubei Academy of Agricultural Sciences,Wuhan 430064,China

出　　处：《Journal of Integrative Agriculture》2024年第8期2541-2556,共16页农业科学学报（英文版）

基　　金：partially supported by the Science and Technology Innovation Program of Hunan Province,China(2023NK2001);the Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement,China(2022LZJJ08);the Special Funds for Construction of Innovative Provinces in Hunan Province,China(2021NK1011);the Natural Science Foundation of Hunan Province,China(2020JJ4039);the Key Research and Development Program of Hubei Province,China(2021BBA223)。

摘　　要：Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.

关 键 词：rice genome-wide association study EPISTASIS gene pleiotropy maker-associated selection genome selection 

分 类 号：S511[农业科学—作物学]