Pan-Genome Analysis Reveals the Abundant Gene Presence/Absence Variations Among Different Varieties of Melon and Their Influence on Traits
文献类型： 外文期刊
第一作者： Sun, Yang
作者： Sun, Yang;Wang, Jing;Li, Yan;Jiang, Bin;Wang, Xu;Xu, Wen-Hui;Wang, Yu-Qing;Zhang, Pei-Tao;Li, Yan;Zhang, Yong-Jun;Kong, Xiang-Dong
作者机构：
关键词： domestication; improvement; pan-genome; presence; absence variation (PAV); resistance gene analogs (RGAs); GWAS; melon
期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：6.627； 五年影响因子：7.255 ）
ISSN： 1664-462X
年卷期： 2022 年 13 卷
页码：
收录情况： SCI
摘要： Melon (Cucumismelo L.) is an important vegetable crop that has been subjected to domestication and improvement. Several varieties of melons with diverse phenotypes have been produced. In this study, we constructed a melon pan-genome based on 297 accessions comprising 168 Mb novel sequences and 4,325 novel genes. Based on the results, there were abundant genetic variations among different melon groups, including 364 unfavorable genes in the IMP_A vs. LDR_A group, 46 favorable genes, and 295 unfavorable genes in the IMP_M vs. LDR_M group. The distribution of 709 resistance gene analogs (RGAs) was also characterized across 297 melon lines, of which 603 were core genes. Further, 106 genes were found to be variable, 55 of which were absent in the reference melon genome. Using gene presence/absence variation (PAV)-based genome-wide association analysis (GWAS), 13 gene PAVs associated with fruit length, fruit shape, and fruit width were identified, four of which were located in pan-genome additional contigs.
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