The development of ideal insertion and deletion (InDel) markers and initial indel map variation in cucumber using re-sequenced data

作者：Jinchang Yang, Pengxu Meng, Huaiyu Mi, Xueying Wang, Jin Yang, Shaohong Fu, Wanzhuo Gong, Ruifan Bao, Wujiao Deng, Haimei Wu, Zhiqin Liu, Sijia Yang, Jixing Ni, Jian Liu, Haoran Shi · 发表于：BMC Genomics · 年份：2025 · DOI：10.1186/s12864-025-11584-z · 被引用次数：6 · 研究领域：Advances in Cucurbitaceae Research、Genetic diversity and population structure、Echinoderm biology and ecology

BACKGROUND: InDels are the most common type of length polymorphism and play a critical role in the genetic traits of many important phenotypes in both plants and animals, making them an ideal source for length polymorphism molecular markers. However, in the process of cucumber breeding, researchers still face deficiencies in the identification of InDel loci and the development of genomic-wide molecular markers. RESULTS: In this study, we conducted InDel identification on 115 cucumber re-sequencing datasets, identifying a total of 7,842,946 InDels, with lengths ranging from 1 to 59 bp and an average density of one InDel every 2.8 kb on the chromosomes. The InDel variations were classified into four main categories, and 81 InDel hotspots were identified, serving as the foundation for constructing a cucumber InDel variation map. Additionally, we utilized an electronic PCR strategy to develop genome-wide InDel markers for cucumber, resulting in the selection of 22,442 InDel primers exhibiting high polymorphism (PIC ≥ 0.5) and major allele differences of ≥ 3 bp. We experimentally validated 50 randomly selected InDel primers, and the results showed that all markers exhibited high polymorphism. CONCLUSIONS: The construction of the cucumber genome InDel variation map aids in understanding the genetic basis of key traits in cucumber derived from InDel variations. The ideal InDel markers developed in this study may enhance the efficiency of cucumber breeding for resistance to both biot...