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The genomic pattern of insertion/deletion variations during rice improvement

文献类型： 外文期刊

作者： Zhou, Xia 1 ; Li, Jilong 2 ; Chen, Lei 4 ; Guo, Minjie 5 ; Liang, Renmin 6 ; Pan, Yinghua 4 ;

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 Plant Divers & Specialty Crops, Beijing 100093, Peoples R China

3.China Natl Bot Garden, Beijing 100093, Peoples R China

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

5.Kaifeng Acad Agr & Forestry Sci, Peanut Inst, Kaifeng 475004, Peoples R China

6.Guangxi Acad Agr Sci, Hechi Agr Sci Res Inst, Hechi 546306, Peoples R China

关键词： Insertion and deletions; Genomic pattern; Improvement of rice

期刊名称：BMC GENOMICS （ 影响因子：3.7； 五年影响因子：4.2 ）

ISSN： 1471-2164

年卷期： 2024 年 25 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundRice, as one of the most important staple crops, its genetic improvement plays a crucial role in agricultural production and food security. Although extensive research has utilized single nucleotide polymorphisms (SNPs) data to explore the genetic basis of important agronomic traits in rice improvement, reports on the role of other types of variations, such as insertions and deletions (INDELs), are still limited.ResultsIn this study, we extracted INDELs from resequencing data of 148 rice improved varieties. We identified 938,585 INDELs and found that as the length of the variation increases, the number of variations decreases, with 89.0% of INDELs being 2-10 bp. The highest number of INDELs was found on chromosome 1, while the least was on chromosome 10. INDELs were unevenly distributed across the genome, generating a total of 33 hotspot regions. 47.0% of INDELs were located within 2 kb upstream and downstream of genes. Using phenotypic data from five agronomic traits (heading date, flag leaf length, flag leaf width, panicle number, and plant height) along with INDEL data to perform genome-wide association study (GWAS), we identified 6,331 significant loci involving 157 cloned genes. Haplotype analysis of candidate genes revealed INDELs affecting important functional genes, such as OsMED25 and OsRRMh related to heading date, and MOC2 related to plant height.ConclusionsOur work analyzed the variation patterns of INDELs in rice improvement and identified INDELs associated with agronomic traits. These results will provide valuable genetic and material resources for the genetic improvement of rice.

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