‘玉环柚’与‘早玉文旦’果实转录组测序SSR、SNP和Indel标记分析  

SSR,SNP and Indel Analysis Based on Transcriptome Data of‘Yuhuanyou’and‘Zaoyuwendan’Fruits

作　　者：王罗云 孙立方 徐建国[1] 聂振朋 黄秀 崔长江 柯甫志[1] WANG Luoyun;SUN Lifang;XU Jianguo;NIE Zhenpeng;HUANG Xiu;CUI Changjiang;KE Fuzhi(Institute of Citrus Research,Zhejiang Academy of Agricultural Sciences/National Center for Citrus Variety Improvement,Huangyan,Taizhou Zhejiang 318026,China)

机构地区：[1]浙江省农业科学院,浙江省柑橘研究所/国家柑橘品种改良中心,浙江台州318026

出　　处：《西北农业学报》2025年第4期667-675,共9页Acta Agriculturae Boreali-occidentalis Sinica

基　　金：浙江省农业新品种选育重大专项—柑橘新品种选育项目(2021C02066-1);浙江省“三农九方”科技协作计划项目(2024SNJF023);台州市科技计划项目(22nya06、23nya16);黄岩院地合作项目。

摘　　要：为分析‘玉环柚’和‘早玉文旦’转录组中SSR、SNP和Indel位点的分布特征和差异,以期开发出更多鉴定‘玉环柚’和‘早玉文旦’遗传差异的分子标记,丰富柚类植物的特异DNA分子标记库。本研究以‘玉环柚’和‘早玉文旦’为材料,在果实发育的6个不同时期进行取样,获取RNA,进一步测序建库,并利用MI-SA和Samtools软件对两个品种果实转录组数据进行SSR、SNP和Indel位点特征分析。结果表明,基于转录组数据共发现了12697个SSR位点分布于9401个基因序列,发生频率为29.61%;重复基元以单碱基重复数量最多,其次为三碱基重复,五碱基重复最少。出现频率最高的基元为A/T(6859个,占比54.02%)。共检测到742606个SNP位点和77132个Indel位点,两个品种果实在不同发育时期的SNP和Indel位点个数均有不同。分别对SNP和Indel位点出现频率最高的基因进行分析发现,均包含独属于‘玉环柚’或‘早玉文旦’的SNP和Indel位点,基因功能多与抗病性、细胞核结构或者细胞质组成相关。综上认为,柚类转录组中SSR、SNP和Indel位点丰富,‘玉环柚’和‘早玉文旦’的SNP和Indel位点存在差异。Thevariety‘Yuhuanyou’and the newly developed early maturing variety‘Zaoyuwendan’derived from a bud mutation,are recognized for their local significance in China.However,current literature is limited regarding the molecular mechanism and related markers linked to fruit traits of these two varieties,and it is still difficult to distinguish‘Yuhuanyou’and‘Zaoyuwendan’.This study aims to analyze the distribution characteristics and differences of SSR,SNP and Indel loci in the transcriptome of‘Yuhuanyou’and‘Zaoyuwendan’to facilitate the development of additional molecular markers that can effectively distinguish the genetic variations between these two varieties,thereby enriching the specific DNA molecular marker library for pomelo.In this study,‘Yuhuanyou’and‘Zaoyuwendan’were used as materials,samples were collected at 6 different stages of fruit development to extract RNA,which was subsequently sequenced to construct a comprehensive database.The characteristics of SSR,SNP,and Indel loci were analyzed utilizing MISA and Samtools software.Based on transcriptome data,a total of 12697 SSR loci were identified within 9401 gene sequences,with a frequency of 29.61%.The most prevalent,followed by Trinucleotide,and Pentanucleotide repeats.The most frequent type was identified as A/T(6859,accounting for 54.02%).A total of 742606 SNP loci and 77132 Indel loci were detected.The number of SNP and Indel loci varied across different developmental stages of the fruits from the two varieties.The analysis of the unigenes with the highest frequency of SNP and Indel loci respectively found that all of them contained SNP and Indel loci belonging only to‘Yuhuanyou’and‘Zaoyuwendan’,and the gene functions were mostly related to disease resistance,nuclear structure or cytoplasmic composition.The findings of this study indicate that SSR,SNP and Indel loci are abundant in the transcriptome of pomelo,and significant differences exist in the SNP and Indel loci between‘Yuhuanyou’and‘Zaoyuwendan’.

关 键 词：‘玉环柚’ ‘早玉文旦’ 转录组 SSR SNP INDEL 

分 类 号：S666.3[农业科学—果树学]