[1]尹玉环,于心怡,李冰,等.基于梨转录组的SSR分子标记的开发与应用[J].北方园艺,2026,(2):19-26.[doi:10.11937/bfyy.20252200]
　YIN Yuhuan,YU Xinyi,LI Bing,et al.Development and Application of SSR Molecular Markers Based on the Transcriptome of Pear[J].Northern Horticulture,2026,(2):19-26.[doi:10.11937/bfyy.20252200]
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基于梨转录组的SSR分子标记的开发与应用

《北方园艺》[ISSN:1001-0009/CN:23-1247/S] 卷: 期数: 2026年2 页码: 19-26 栏目: 出版日期: 2026-01-30
Title:
Development and Application of SSR Molecular Markers Based on the Transcriptome of Pear
文章编号:
1001-0009(2026)02-0019-08
作者:
尹玉环1; 2; 于心怡1; 2; 李冰1; 2; 刘建龙1; 2; 杨英杰1; 2; 李鼎立1; 2
（1.青岛农业大学 园艺学院，青岛市园艺植物遗传改良与育种重点实验室,山东 青岛 266109;2.青岛农业大学 梨工程技术研究所，山东 青岛 266109）
Author(s):
YIN Yuhuan1; 2; YU Xinyi1; 2; LI Bing1; 2; LIU Jianlong1; 2; YANG Yingjie1; 2; LI Dingli1; 2
(1.College of Horticulture，Qingdao Agricultural University/Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants,Qingdao，Shandong 266109;2.Pear Engineering and Technology Research Institute,Qingdao Agricultural University，Qingdao，Shandong 266109)
关键词:
梨; 转录组; EST-SSR; 引物开发
Keywords:
pear; transcriptome; EST-SSR; primer development
分类号:
S685.12
DOI:
10.11937/bfyy.20252200
文献标志码:
A
摘要:
以“QAUP-1/青砧D1”嫁接组合的嫁接口为试材，采用转录组测序、Trinity无参组装、Hisat2序列比对及MISA位点搜索与Primer3引物设计的方法，研究了该嫁接组合嫁接口的EST-SSR位点特征及引物开发，以期为梨嫁接相关的分子标记应用与遗传研究提供参考依据。结果表明：“QAUP-1/青砧D1”嫁接组合嫁接口转录组共有71 544个Unigenes，使用最长转录本（编码基因数量）进行EST-SSR位点预测，共搜索到2 433个SSR位点，在“QAUP-1/青砧D1”嫁接组合嫁接口转录组中的出现频率为5.47%（检出的SSR位点个数与总unigene数目之比）。重复次数最多的基序为AG/CT和TC/GA，分别占19.40%和13.93%。EST-SSR基序的重复次数主要分布在6~10次，该范围内有1 557个EST-SSR位点，占总EST-SSR位点的63.99%。“QAUP-1/青砧D1”嫁接组合嫁接口转录组SSR位点多态性较好，长度在10~12 bp的SSR有217条，占总SSR位点的8.92%，13~20 bp的SSR有1 127条，占总SSR位点的46.32%，而长度在20 bp以上的SSR有1 089条，占总SSR位点数的44.76%。随机选取12对EST-SSR引物，在5个梨组织样本中共扩增出59个条带，平均每条EST-SSR有4.9个等位位点，多样性条带有4个。
Abstract:
Taking the graft union of the ‘QAUP-1/Qingzhen D1’ grafting combination as the test material，methods included transcriptome sequencing，Trinity de novo assembly，Hisat2 sequence alignment，MISA locus searching，and Primer3 primer design were used to investigate the characteristics of EST-SSR loci and primer development at the graft union of this combination,in order to provide reference for the application of molecular markers and genetic research related to pear grafting.The results showed that the grafting interface transcriptome of the ‘QAUP-1/Qingzhen D1’ grafting combination contained 71 544 unigenes.Taking the longest transcript (number of coding genes) for EST-SSR locus prediction，a total of 2 433 SSR loci were identified，with a frequency of 5.47% in the grafting interface transcriptome of the ‘QAUP-1/Qingzhen D1’ grafting combination (the ratio of the number of detected SSR loci to the total number of unigenes).The most frequently repeated motifs were AG/CT and TC/GA，accounting for 19.40% and 13.93%，respectively.The repeat times of EST-SSR motifs were mainly distributed between 6 and 10，with 1 557 EST-SSR loci in this range，accounting for 63.99% of the total EST-SSR loci.The SSR (simple sequence repeat) loci in the transcriptome at the graft union of the ‘QAUP-1/Qingzhen D1’ grafting combination exhibited good polymorphism.There were 217 SSRs with a length of 10-12 bp，accounting for 8.92% of the total SSR loci.Additionally，there were 1 127 SSRs with lengths ranging from 13-20 bp，representing 46.32% of the total SSR loci.Furthermore，1 089 SSRs with lengths exceeding 20 bp made up 44.76% of the total SSR loci.Twelve pairs of EST-SSR primers were randomly selected，and a total of 59 bands were amplified across five pear tissue samples，with an average of 4.9 allelic loci per EST-SSR and 4 diverse bands.

参考文献/References:

［1］王文辉,王国平,田路明,等.新中国果树科学研究70年:梨［J］.果树学报，2019，36(10)：1273-1282.［2］马文尧,范文琦,王晓祥,等.梨×苹果远缘杂交不同组合果实生长发育动态［J］.北方园艺，2024(22)：8-14.［3］PEI D,SONG S Y,KANG J,et al.Characterization of simple sequence repeat (SSR) markers mined in whole grape genomes［J］.Genes，2023，14(3)：663.［4］SAHU J,SARMAH R,DEHURY B,et al.Mining for SSRs and FDMs from expressed sequence tags of Camellia sinensis［J］.Bioinformation，2012，8(6)：260-266.［5］EUJAYL I,SORRELLS M E,BAUM M,et al.Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat［J］.Theoretical and Applied Genetics，2002，104(2)：399-407.［6］NICOLA M,PISANI C,BOUCHET J P,et al.Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)［J］.Genetics and Molecular Research，2012，11(3)：2295-2300.［7］KAUR S,PEMBLETON L W,COGAN N O I,et al.Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers［J］.BMC Genomics，2012(13)：104.［8］TAHERI S,LEE ABDULLAH T,YUSOP M R,et al.Mining and development of novel SSR markers using next generation sequencing (NGS) data in plants［J］.Molecules，2018，23(2)：399.［9］XIE H,SUI Y,CHANG F Q,et al.SSR allelic variation in almond (Prunus dulcis Mill.)［J］.Theoretical and Applied Genetics，2006，112(2)：366-372.［10］ROSSETTO M,MCNALLY J,HENRY R J.Evaluating the potential of SSR flanking regions for examining taxonomic relationships in the Vitaceae［J］.Theoretical and Applied Genetics，2002，104(1)：61-66.［11］PARK H,HEO T H,CHO J,et al.Evaluation and characteristic analysis of SSRs from the transcriptomic sequences of Perilla crop (Perilla frutescens L.)［J］.Gene，2025，933：148938.［12］JIAO L,HAN C,ZHU J,et al.Transcriptome analysis and development of EST-SSR markers in the mushroom Auricularia heimuer［J］.Scientific Reports，2024，14(1)：12340.［13］XIANG N,LU B,YUAN T,et al.De novo transcriptome assembly and EST-SSR marker development and application in Chrysosplenium macrophyllum［J］.Genes，2023，14(2)：279.［14］CHEN M,NIE G,LI X,et al.Development of EST-SSR markers based on transcriptome sequencing for germplasm evaluation of 65 lilies (Lilium)［J］.Molecular Biology Reports，2023，50(4)：3259-3269.［15］ZHOU Q,ZHOU P Y,ZOU W T,et al.EST-SSR marker development based on transcriptome sequencing and genetic analyses of Phoebe bournei (Lauraceae)［J］.Molecular Biology Reports，2021，48(3)：2201-2208.［16］王西成,姜淑苓,上官凌飞,等.梨EST-SSR标记的开发及其在梨品种遗传多样性分析中的应用评价［J］.中国农业科学，2010，43(24)：5079-5087.［17］宋尚伟,张恒涛,张芳明,等.苹果EST-SSR引物的开发及部分品种亲缘关系分析［J］.果树学报，2013，30(4)：509-515.［18］BRINI W,MARS M,HORMAZA J I.Genetic diversity in local Tunisian pears (Pyrus communis L.) studied with SSR markers［J］.Scientia Horticulturae，2008，115(4)：337-341.［19］GRABHERR M G,HAAS B J,YASSOUR M,et al.Full-length transcriptome assembly from RNA-Seq data without a reference genome［J］.Nature Biotechnology，2011，29(7)：644-652.［20］THIEL T,MICHALEK W,VARSHNEY R,et al.Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)［J］.Theoretical and Applied Genetics，2003，106(3)：411-422.［21］贾琼,石茂竹,薛贤滨,等.金荞麦转录组SSR位点分析及分子标记开发［J］.西北农业学报，2024，33(11)：2028-2037.［22］杨仕美,乔光,毛永亚,等.基于火龙果转录组测序的SSR标记开发及种质亲缘关系分析［J］.分子植物育种，2018，16(24)：8096-8110.［23］唐美琼,林杨,李刚,等.基于RNA-Seq高通量测序的五指毛桃叶片转录组特征分析［J/OL］.分子植物育种，(2023-09-07)［2025-06-12］.https://link.cnki.net/urlid/46.1068.S.20230906.1949.008.［24］尹航,李冰,张明智,等.野大麦转录组SSR序列特征分析［J］.分子植物育种，2024，22(19)：6352-6358.［25］杨芩,付燕,邓洁,等.蓝莓自花和异花授粉花柱转录组SSR位点分析［J］.安徽农学通报，2024，30(11)：33-41.［26］王永行,武悦,杨钦方,等.基于高通量测序的地笋叶片转录组分析［J］.分子植物育种，2022，20(9)：2885-2890.［27］彭劲谕,朱泽莉,李恩良,等.基于高通量转录组测序的云南栘(木衣)微卫星位点特征分析［J］.分子植物育种，2020，18(16)：5419-5427.［28］TEMNYKH S,DECLERCK G,LUKASHOVA A,et al.Computational and experimental analysis of microsatellites in rice (Oryza sativa L.):Frequency,length variation,transposon associations,and genetic marker potential［J］.Genome Research，2001，11(8)：1441-1452.

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备注/Memo

第一作者简介：尹玉环（2000-），女，硕士研究生，研究方向为果树分子育种。E-mail：15066233938@163.com.责任作者：李鼎立（1979-），男，博士，教授，现主要从事梨遗传改良与栽培技术等研究工作。E-mail：lidingli@qau.edu.cn.基金项目：山东省农业良种工程资助项目（2022LZGC011）；国家现代农业产业技术体系建设专项资金资助项目（CARS-29-07）；国家自然科学基金青年基金资助项目（31401832）。收稿日期：2025-06-16

更新日期/Last Update: 2026-02-03