Prime-InDel version 1: A web tool providing InDel markers for targeted regions narrowing

Abstract While high-density SNP genotyping enables genome-wide assays in rice ( Oryza sativa L.) and other crops, PCR-based markers—particularly those derived from insertion–deletion (InDel) variations—remain crucial for fine-mapping. Currently, readily available primer information for high-density InDel rice markers is still limited. We present the first version of PrimeInDel ( https://rfgb.rmbreeding.cn/search/variation/primeIndel ), an online tool integrating three sets of InDel markers: an 8K-set and a 316K-set from the 3K Rice Genomes (3K-RG) project, and a 22K-set compiled from published literatures. In user cases, primers from PrimeInDel proved highly effective, narrowing a cold-tolerance QTL ( qSR2 ) from 2.7 Mb to 200 kb and a heading-date QTL ( qDeh1 . 1 ) from 239.5 kb to 83.6 kb. Our work provides the community with a robust, PCR-based InDel primer, accessible via an online data set, which will facilitate germplasm genotyping and gene identification in rice breeding.