文献类型：期刊文献

中文题名：小果甜柿果实转录组的SSR、SNP和InDel特征分析

英文题名：SSR,SNP and InDel analysis based on transcriptome data of Diospyros kaki‘Xiaoguo-tianshi’fruit

作者：王艺儒[1] 索玉静[1] 傅建敏[1]

第一作者：王艺儒

机构：[1]中国林业科学研究院经济林研究所,经济林种质创新与利用国家林业局重点实验室,河南郑州450003

年份：2022

卷号：50

期号：7

起止页码：147-154

中文期刊名：西北农林科技大学学报：自然科学版

外文期刊名：Journal of Northwest A&F University(Natural Science Edition)

收录：CSTPCD;;北大核心:【北大核心2020】；CSCD:【CSCD2021_2022】；

基金：国家重点研发计划项目(2019YFD1001200)。

语种：中文

中文关键词：小果甜柿;果树育种;转录组;SSR;SNP;InDel

外文关键词：‘Xiaoguo-tianshi’;fruit breeding;transcriptome;SSR;SNP;InDel

分类号：S665.201

摘要：【目的】对小果甜柿果实转录组中的SSR、SNP和InDel位点进行分析,为开发中国甜柿特异性分子标记、早期鉴定和遗传多样性分析奠定基础。【方法】以中国甜柿传统小果类型种质为材料,在果实发育的5个时期采样,抽提RNA,采用MISA和GATK3软件对小果甜柿果实转录组进行SSR、SNP和InDel位点特征分析。【结果】在小果甜柿果实转录组中共发现42427个SSR位点,分布于26928条unigenes上,发生频率为31.52%;在重复基元类型中,单碱基重复数量最多,六碱基重复最少,其中出现频率最高的基元为A/T,占总SSR数量的40.91%;各类型重复基元的重复次数集中在5~20次,SSR序列长度介于10~74 bp。共检测到1070614个SNP位点和167924个InDel位点,其中SNP位点平均每kb出现11.46个,InDel位点平均0.556 kb出现1个,且均以含1个位点的unigenes数最多。【结论】小果甜柿转录组中SSR、SNP和InDel位点丰富,具有潜在较高的多态性,有助于后续中国甜柿特异性分子标记的开发。
【Objective】This study analyzed the SSR,SNP and InDel sites of Diospyros kaki‘Xiaoguo-tianshi’fruit to provide the basis for development of specific molecular markers for early identification and genetic diversity analysis of Chinese PCNA persimmon.【Method】C-PCNA type‘Xiaoguo-tianshi’fruits sampled at 5 development stages were used to extract RNA,and MISA and GATK3 software was used to analyze SSR,SNP and InDel sites based on transcriptome data.【Result】A total of 42427 SSR sites were identified on 26928 unigenes in the transcriptome data of‘Xiaoguo-tianshi’fruits,with the incidence ratio of 31.52%.Mononucleotide type had the largest number of repeat motifs,and hexanucleotide type had the least.Among them,the dominant repeating motif was A/T with contribution of 40.91%.The motif repeats of SSR mainly concentrated in 5-20 times and the length of SSR was mainly 10-74 bp.A total of 1070614 SNP sites were detected,with an average of 11.46 SNP sites per kb.A total of 167924 InDel sites were also detected,with an average of 0.556 kb per InDel sites,and most unigenes only contained 1 site.【Conclusion】SSR,SNP and InDel sites were abundant in the transcriptome data of‘Xiaoguo-tianshi’with high potential polymorphism,and were beneficial for the development of C-PCNA specific molecular markers.