Zhou Xia, Li Jilong, Chen Lei, Guo Minjie, Liang Renmin, Pan Yinghua
Urban Construction School, Beijing City University, Beijing, 101300, China.
State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
BMC Genomics. 2024 Dec 31;25(1):1263. doi: 10.1186/s12864-024-11178-1.
Rice, 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.
In 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.
Our 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.
水稻作为最重要的主粮作物之一，其遗传改良在农业生产和粮食安全中起着至关重要的作用。尽管广泛的研究已利用单核苷酸多态性（SNP）数据来探索水稻改良中重要农艺性状的遗传基础，但关于其他类型变异（如插入和缺失，INDEL）作用的报道仍然有限。
在本研究中，我们从148个水稻改良品种的重测序数据中提取了INDEL。我们鉴定出938,585个INDEL，并发现随着变异长度的增加，变异数量减少，其中89.0%的INDEL为2 - 10 bp。在第1号染色体上发现的INDEL数量最多，而在第10号染色体上最少。INDEL在基因组中分布不均，共产生33个热点区域。47.0%的INDEL位于基因上下游2 kb范围内。利用来自五个农艺性状（抽穗期、剑叶长度、剑叶宽度、穗数和株高）的表型数据以及INDEL数据进行全基因组关联研究（GWAS），我们鉴定出6331个显著位点，涉及157个已克隆基因。对候选基因的单倍型分析揭示了影响重要功能基因的INDEL，如与抽穗期相关的OsMED25和OsRRMh，以及与株高相关的MOC2。
我们的工作分析了水稻改良中INDEL的变异模式，并鉴定出与农艺性状相关的INDEL。这些结果将为水稻的遗传改良提供有价值的遗传和物质资源。
