热带作物学报2026，Vol.47Issue(6)：1449-1463,15.DOI:10.3969/j.issn.1000-2561.2026.06.008
30份莆田地区栽培枇杷种质资源的全基因组重测序分析
Whole-genome Resequencing Analysis of 30 Cultivated Loquat Germplasm Resources in Putian Area
摘要
Abstract
To clarify the genetic background and phylogenetic relationships of currently cultivated loquat cultivars(lines)in Putian,and to provide scientific and theoretical support for regional loquat breeding,a total of 30 loquat germplasm acces-were subjected to whole-genome resequencing in this study.High-quality SNP loci and InDel fragments were obtained for analysis of population genetic diversity.After effective filtering and screening of the sequencing data,158.98 Gb of clean data were generated,with an average sample mapping rate of 97.70%,an average sequencing depth of 6×,and a genome coverage rate of 93.86%.Annotation and analysis of SNP loci,InDel fragments and variant genes revealed that red-fleshed loquats ex-hibited higher values than white-fleshed loquats in multiple indicators,including the total number of genome-wide SNP and InDel,the average number of SNP and InDel in coding regions,the number of non-synonymous mutation genes,the number of frameshift mutation genes,and the population genetic distance.GO enrichment analysis demonstrated that differential genes were mainly involved in cellular processes and metabolic processes.KEGG enrichment analysis indicated that the dif-ferential genes were primarily enriched in biological pathways such as plant-pathogen interaction,MAPK signaling pathway,plant hormone signal transduction,and starch and sucrose metabolism.Population analysis results showed that the phyloge-netic tree constructed based on whole-genome variation data divided the 30 Putian loquat germplasm accessions into five groups.Germplasm accessions with consistent pulp color,those with parent-hybrid progeny relationships,and clonally prop-agated loquat germplasm exhibited obvious aggregation trends in the cluster analysis.Meanwhile,gene flow was detected among different groups,with the genetic differentiation index(Fst)ranging from 0.115 to 0.434 between groups.This study concluded that red-fleshed loquats had higher variation potential at the DNA level and possessed greater genetic diversity than white-fleshed loquats.The classification of Putian loquat germplasm was affected by factors such as pulp color and genetic relationships,and the germplasm accessions still retained moderate to strong genetic differentiation ability.The findings would provide an important basis for the systematic classification,precise evaluation and efficient breeding utilization of Putian loquat germplasm resources.关键词
枇杷/全基因组重测序/SNP/InDel/遗传关系Key words
loquat/whole-genome resequencing/SNP/InDel/genetic relationship分类
农业科技引用本文复制引用
刘小英,吴碧君,曾丽兰,张游南,邓雅婷,许奇志,刘国强..30份莆田地区栽培枇杷种质资源的全基因组重测序分析[J].热带作物学报,2026,47(6):1449-1463,15.基金项目
福建省省属公益类科研院所基本科研专项(No.2023R1083) （No.2023R1083）
福建省农业引导性(重点)项目(No.2024N0066) （重点）
莆田市技术开发与应用项目(No.2023NJJ001). （No.2023NJJ001）
