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The Landscape of Presence/Absence Variations during the Improvement of Rice

文献类型： 外文期刊

作者： Zhou, Xia 1 ; Qiang, Chenggen 2 ; Chen, Lei 3 ; Qing, Dongjin 3 ; Huang, Juan 3 ; Li, Jilong 2 ; Pan, Yinghua 3 ;

作者机构： 1.Beijing City Univ, Urban Construct Sch, Beijing 101300, Peoples R China

2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China

3.Guangxi Acad Agr Sci, Rice Res Inst, Guangxi Key Lab Rice Genet & Breeding, Nanning 530007, Peoples R China

关键词： rice improvement; presence/absence variations; genome-wide association study

期刊名称：GENES （ 影响因子：3.5； 五年影响因子：3.9 ）

ISSN：

年卷期： 2024 年 15 卷 5 期

页码：

收录情况： SCI

摘要： Rice is one of the most important staple crops in the world; therefore, the improvement of rice holds great significance for enhancing agricultural production and addressing food security challenges. Although there have been numerous studies on the role of single-nucleotide polymorphisms (SNPs) in rice improvement with the development of next-generation sequencing technologies, research on the role of presence/absence variations (PAVs) in the improvement of rice is limited. In particular, there is a scarcity of studies exploring the traits and genes that may be affected by PAVs in rice. Here, we extracted PAVs utilizing resequencing data from 148 improved rice varieties distributed in Asia. We detected a total of 33,220 PAVs and found that the number of variations decreased gradually as the length of the PAVs increased. The number of PAVs was the highest on chromosome 1. Furthermore, we identified a 6 Mb hotspot region on chromosome 11 containing 1091 PAVs in which there were 29 genes related to defense responses. By conducting a genome-wide association study (GWAS) using PAV variation data and phenotypic data for five traits (flowering time, plant height, flag leaf length, flag leaf width, and panicle number) across all materials, we identified 186 significantly associated PAVs involving 20 cloned genes. A haplotype analysis and expression analysis of candidate genes revealed that important genes might be affected by PAVs, such as the flowering time gene OsSFL1 and the flag leaf width gene NAL1. Our work investigated the pattern in PAVs and explored important PAV key functional genes associated with agronomic traits. Consequently, these results provide potential and exploitable genetic resources for rice breeding.

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