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.

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.

As the two main variety groups in improved rice, IND (indica) and JAP (temperate japonica and tropical japonica), extensive studies have utilized (single-nucleotide polymorphisms) SNPs on 233 selected improved rice cultivars to analyze the genetic basis of agronomic traits during their improvement and to compare their similarities and differences. However, the roles of other types of variations, such as insertions and deletions (INDELs) and structural variations (SVs), remain relatively underexplored. Here, using resequencing data from 233 improved rice accessions (IND: 142, JAP: 91), we identified 811,646 INDELs and 16,231 SVs in IND, and 652,793 INDELs and 10,533 SVs in JAP. The abundance of INDELs and SVs decreased as their length increased in both variety groups. INDELs and SVs also showed an uneven distribution across the chromosomes of the two variety groups. In IND, 38.92% of INDELs and 44.1% of SVs were located within the 2 kb upstream and downstream of genes; in JAP, this proportion was 38.49% for INDELs and 43.22% for SVs. By performing genome wide association studies (GWAS) using phenotypic data of six agronomic traits (heading date, flag leaf length, flag leaf width, panicle number, plant height, and thousand grain weight) along with INDELs and SVs, we identified 3,222 significant IND-INDELs, 537 significant IND-SVs, 1,996 significant JAP-INDELs, and 286 significant JAP-SVs. Comparison of significant loci revealed that IND and JAP shared only one INDEL associated with flag leaf length and one SV associated with panicle number, suggesting distinct genetic architectures determined by INDELs and SVs for these traits in the two groups. Furthermore, haplotype analysis of candidate genes demonstrated that INDELs and SVs influence key functional genes, such as the gene TAD1 (IND-INDELs) in flag leaf length, RCN2 (IND-SVs) in heading date, PLS2 (JAP-INDELs) in plant height, and OsYLC2 (JAP-SVs) in leaf development. This study analyzed the variation patterns of INDELs and SVs during the improvement of IND and JAP varieties, and identified INDELs and SVs associated with agronomic traits. These findings will provide valuable genetic and material resources for rice breeding.