Journal ArticleOpen Access
Prime-InDel version 1: A web tool providing InDel markers for targeted regions narrowing
Authors
Author Affiliations
Guangxi University, Guangxi Academy of Agricultural Science, Chinese Academy of Agricultural Sciences, Institute of Crop Sciences, ...
Published InbioRxiv (Cold Spring Harbor Laboratory)
Year2026
Abstract
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…
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