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Journal of Integrative Agriculture  2024, Vol. 23 Issue (8): 2541-2556    DOI: 10.1016/j.jia.2023.07.021
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Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice
Xiaogang He1, Zirong Li1, Sicheng Guo1, Xingfei Zheng2, Chunhai Liu1, Zijie Liu1, Yongxin Li1, Zheming Yuan1, Lanzhi Li1#
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
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摘要  

标记辅助选择(MAS)和基因组选择(GS)育种极大地提高了水稻育种效率。由于上位性和基因多效性的影响,如何保证MASGS育种的实际效果仍是一个需要攻克的问题。本研究对113个籼稻品种(V)及565个杂交种(TC)的12个品质性状和9个农艺性状进行了全基因组关联分析,探讨了12个品质性状和9个农艺性状的遗传基础。共检测到381个主效显著相关位点(SAL)和1759个与这些主效SALs发生了上位性互作的微效SALs。筛选出322个位于SALs内或附近的候选基因,其中204个为克隆基因。通过对候选基因的优势单倍型和微效SALs的理想等位基因进行聚合分析,挖掘了39个有利于性状改良的MAS分子模块。通过构建遗传网络,鉴定到91个多效性位点。此外,本研究比较了将主效SALs、微效SALs和上位性SALs作为GS预测模型的协变量的预测精度与不使用SAL作为协变量的预测精度的差异。在TC数据集大多性状4种模型的预测准确性无显著差异但在V数据集中,加入主效SALs、微效SALs和上位性SALs分别显著提高了5(26%)3(16%)11(58%)个性状的预测准确性。这些结果表明,上位性SALs可为亲本品系预测提供相当高的预测能力。这些结果为复杂性状的遗传基础提供了新的见解,为水稻分子育种提供了有价值的信息。



Abstract  

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 mid-parent 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.

Keywords:  rice        genome-wide association study        epistasis        gene pleiotropy        maker-associated selection        genome selection  
Received: 27 March 2023   Accepted: 03 July 2023
Fund: 

This work was 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), and the Key Research and Development Program of Hubei Province, China (2021BBA223). 

About author:  Xiaogang He, E-mail: hexiaogang97@163.com; #Correspondence Lanzhi Li, Tel: +86-731-84618163, E-mail: lancy0829@163.com

Cite this article: 

Xiaogang He, Zirong Li, Sicheng Guo, Xingfei Zheng, Chunhai Liu, Zijie Liu, Yongxin Li, Zheming Yuan, Lanzhi Li. 2024. Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice. Journal of Integrative Agriculture, 23(8): 2541-2556.

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