[1]王小敏,张春红,胡丽超,等.基于高通量测序的蓝莓果实转录组[J].北方园艺,2022,(13):49-54.[doi:10.11937/bfyy.20214714]
　WANG Xiaomin,ZHANG Chunhong,HU Lichao,et al.SSR Information Analysis of Blueberry Fruit Transcriptome Based on High Throughput Sequencing[J].Northern Horticulture,2022,(13):49-54.[doi:10.11937/bfyy.20214714]
点击复制

基于高通量测序的蓝莓果实转录组

《北方园艺》[ISSN:1001-0009/CN:23-1247/S] 卷: 期数: 2022年13 页码: 49-54 栏目: 出版日期: 2022-07-15
Title:
SSR Information Analysis of Blueberry Fruit Transcriptome Based on High Throughput Sequencing
作者:
王小敏1; 张春红1; 胡丽超2; 吴文龙1; 李维林2
（1.江苏省中国科学院 植物研究所，江苏 南京 210014；2.南京林业大学 林学院，南方现代林业协同创新中心，江苏 南京 210037）
Author(s):
WANG Xiaomin1; ZHANG Chunhong1; HU Lichao2; WU Wenlong1; LI Weilin2
(1．Institute of Botany，Jiangsu Province and Chinese Academy of Sciences，Nanjing，Jiangsu 210014；2．Academy of Forestry，Nanjing Forestry University/Co-Innovation Center for the Sustainable Forestry in Southern China，Nanjing，Jiangsu 210037)
关键词:
蓝莓果实; 转录组; SSR; 引物设计
Keywords:
blueberry fruit; transcriptome; SSR; primer design
DOI:
10.11937/bfyy.20214714
文献标志码:
A
摘要:
以蓝莓品种‘巴尔德温’（Vaccinium Spp.var.Baldwin）的果实为试材，通过转录组高通量测序获得Unigenes数据，分析转录组的SSR信息，开发蓝莓EST-SSR功能性标记引物，以期为开展蓝莓的基因定位及果实品质形成的分子生物学机制等研究提供参考依据。结果表明：转录组测序共获得73 468条Unigenes，其中SSR位点发生频率为20.81%，含有序列的SSR位点3 354条。蓝莓果实转录组SSRs的平均长度为20 bp，平均分布频率为1/3.90 kb。在蓝莓转录组SSR中，2个碱基重复比例最高（41.02%），其次为单碱基重复。单个SSR位点的蓝莓转录组SSR共包含173种重复基元，A/T（36.56%）和AG/CT（41.03%）分别为优势重复基元类型，含有SSR位点的Unigene被富集到3个Ontology类别的57个GO term中，其中涉及生殖、结合、多细胞生物过程的GO term最多。基于蓝莓果实转录组信息分析，最终设计了82对SSR序列引物，开发这些潜在多态性高的SSR在蓝莓遗传育种研究和资源评价上具有较高的应用价值。
Abstract:
Taking the fruit of blueberry variety ‘Baldwin’ as the material，Unigenes was obtained by high-throughput sequencing，SSR information analysis was analyzed，and blueberry EST-SSR functional marker primers were developed，in order to provide reference for the molecular biological mechanism of gene mapping and fruit quality formation of blueberry.The results showed that,a total of 73 468 Unigenes were obtained by transcriptome sequencing，of which the frequency of SSR was 20.81%，and 3 354 SSR sites containing sequences，were obtained.The average length of transcriptome SSRs in blueberry fruit was 20 bp and the average distribution frequency was 1/3.90 kb.In the blueberry transcriptome SSR，the proportion of Dinucleotide was the highest (41.02%)，followed by mononucleotide.The blueberry transcriptome SSR of a single SSR site contains 173 repeat nucleotides，and A/T(36.56%) and AG/CT (41.03%) were the dominant repeat unit types，respectively.Unigene containing SSR sites was enriched into 57 GO terms of three ontology categories，of which the most GO terms involved in reproduction，binding and multicellular biological processes.Based on the transcriptome information analysis of blueberry fruit，82 pairs of SSR sequence primers were finally designed.The development of these potentially polymorphic SSRs might have high application value in blueberry genetic breeding research and resource evaluation.

参考文献/References:

[1]吴林.中国蓝莓35年：科学研究与产业发展[J].吉林农业大学学报，2016，38(1)：1-11.[2]ASLIHAN K，CANAN S G，OZLEM Y C，et al.Investigating anthocyanin contents and in vitro tumor suppression properties of blueberry extracts prepared by various processes[J].European Food Research and Technology，2016，242(5)：693-701.[3]MALLIK A U，HAMILTON J.Harvest date and storage effect on fruit size，phenolic content and antioxidant capacity of wild blueberries of N W Ontario，Canada[J].Journal of Food Science and Technology，2017，54(6)：1545-1554.[4]周继芬，兰武，王军，等.蓝莓营养及独特保健功能研究[J].北方园艺，2020(21)：138-145.[5]李亚东，裴嘉博，陈丽，等.2020中国蓝莓产业年度报告[J].吉林农业大学学报，2021(10)：51-57.[6]SONG G Q，HANCOCK J F.Wild crop relatives：Genomic and breeding resources[M].Berlin：Springer，Springer-Verlag，Heidelberg，2011.[7]徐国辉，张明军，雷蕾，等.2018年美国公布的全球蓝莓新品种及其育种趋势分析[J].分子植物育种，2021，19(11)：3810-3817.[8]乔鑫，李梦，殷豪，等.果树全基因组测序研究进展[J].园艺学报，2014，41(1)：165-177.[9]王云生，聂飞，林顺权.果树高通量测序的最新研究进展[J].基因组学与应用生物学，2015,34(9)：2034-2043.[10]王云生，文光琴，聂飞.矮丛蓝莓品种“美登”叶片转录组测序和生物信息学分析[J].北方园艺,2017(1):101-107.[11]SONG Y，LIU H D，ZHOU Q，et al.High-throughput sequencing of highbush blueberry transcriptome and analysis of Basic helix-loop-helix transcription factors[J].Journal of Integrative Agriculture，2017，76(3)：591-604.[12]燕飞，曲东,周祎炜,等.兔眼蓝莓‘灿烂’果实采后转录组数据组装及基因功能注释[J].分子植物育种，2022，20（7）:2153-5161.[13]CHUNG S W，YU D J，OH H D，et al.Transcriptional regulation of abscisic acid biosynthesis and signal transduction，and anthocyanin biosynthesis in ‘Bluecrop’ highbush blueberry fruit during ripening[J].PLoS One，2019，14(7):e0220015.[14]COLLE M，LEISNER C，WAI C M，et al.Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry[J].Giga Science，2019，8(3):giz012.[15]陈薇薇.分子标记技术及其在果树种质资源上的应用分析[J].南方农业，2018，12(36)：139-140.[16]高雄梅，徐国辉，王贺新,等.基于EST-SSR标记的蓝莓品种指纹图谱构建及遗传多样性[J].贵州农业科学2016,44(4):110-115.[17]LIU Y C，LIU S，LIU D C，et al. Exploiting EST databases for the development and characterization of EST-SSR markers in blueberry (Vaccinium) and their cross-species transferability in Vaccinium spp[J].Scientia Horticulturae，2014，176:319-329.[18]徐国辉，高雄梅，赵丽娜，等.蓝莓优良杂交品系父本鉴定及DNA指纹图谱构建[J].分子植物育种，2018，16(5)：1580-1589.[19]BOCHES P S，BASSIL N V，ROWLAND L J.Microsatellite markers for Vaccinium from EST and genomic libraries[J].Molecular Ecology Notes，2005(5):657-660.[20]DEBNATH S C.Structured diversity using EST-PCR and EST-SSR markers in a set of wild blueberry clones and cultivars[J].Biochemical Systematics and Ecology,2014(54):337-347.[21]张春红，黄正金，樊苏帆，等.不同栽培类型蓝莓遗传多样性的SSR分析[J].中国南方果树，2021，50(2):154-160.[22]CONESA A,GOTZ S,GARCIA-GOMEZ J M，et al. Blast2GO:A universal tool for annotation,visualization and analysis in functional genomics research[J].Bioinfomatics，2005(21)：3674-3676.[23]蒋维昕，梁馨元，兰俊，等.大花序桉顶芽转录组SSR 位点信息分析[J].中南林业科技大学学报，2021，41(4)：148-155.[24]ROZEN S，SKALETSKY H J.Primer 3 on the WWW for general users and for biologist programmers.In：Krawetz S，Misener S (eds) Bioinformatics methods and protocols：Methods in molecular biology[M].Totowa:Humana Press，2000.[25]LIA W L，ZHANG C H，YANG H Y，et al.SSR marker information mining in blackberry from transcriptome sequences[J].Acta Hortic，2016,1133:97-102.[26]SAMIR C D.Structured diversity using EST-PCR and EST-SSR markers in a set of wild blueberry clones and cultivars[J].Biochemical Systematics and Ecology，2014，54：337-347.[27]杨华，陈琪，韦朝领，等.茶树转录组中SSR位点的信息分析[J].安徽农业大学学报，2011，38(6)：882-886.[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 Res，2001，11(8)：1441-1452.[29]DREISIGACKER S，ZHANG P，WARBURTON M L，et al．SSR and pedigree analyses of genetic diversity among CIMMYT wheat lines targeted to different mega environments[J].Crop Science，2004，44(2)：381-388.[30]BASSIL N V.Microsatellite markers：Valuable in Vaccinium L.[J].International Journal of Fruit Science，2012(12)：288-293.

相似文献/References:

[1]黄琼林,何 瑞,詹若挺,等.南药青天葵转录组SSR位点信息分析[J].北方园艺,2015,39(12):76.[doi:10.11937/bfyy.201512021]
　HUANG Qiong-lin,HE Rui,ZHAN Ruo-ting,et al.SSR Loci Information Analysis in Nervilia fordii Transcriptome[J].Northern Horticulture,2015,39(13):76.[doi:10.11937/bfyy.201512021]
[2]苏秀红,李庆磊,陈随清,等.冬凌草转录组SSR位点分析及多态性初步评价[J].北方园艺,2016,40(04):93.[doi:10.11937/bfyy.201604025]
　SU Xiuhong,LI Qinglei,CHEN Suiqing,et al.Analysis of SSR Loci Information in Transcriptome of Rabdosia rubescens (Henmsl.) Hara and Its Polymorphism[J].Northern Horticulture,2016,40(13):93.[doi:10.11937/bfyy.201604025]
[3]刘慧敏,乌云塔娜,杜红岩.杜仲转录组基因密码子使用偏好性分析[J].北方园艺,2016,40(13):85.[doi:10.11937/bfyy.201613023]
　LIU Huimin,WUYUN Tana,DU Hongyan.Analysis of Characteristic of Codon Usage of Eucommia ulmoides Transcriptome[J].Northern Horticulture,2016,40(13):85.[doi:10.11937/bfyy.201613023]
[4]王云生,文光琴,聂飞.矮丛蓝莓品种“美登”叶片转录组测序和生物信息学分析[J].北方园艺,2017,41(01):101.[doi:10.11937/bfyy.201701023]
　WANG Yunsheng,WEN Guangqin,NIE Fei.Leaf Transcriptome Sequencing and Bioinformatics Analysis of Lowbush Blueberry Variety ‘Blomidon’[J].Northern Horticulture,2017,41(13):101.[doi:10.11937/bfyy.201701023]
[5]姚娜,刘秀明,董园园,等.转录组的测序方法及应用研究概述[J].北方园艺,2017,41(12):192.[doi:10.11937/bfyy.201712043]
　YAO Na,LIU Xiuming,DONG Yuanyuan,et al.Advances in Application and Seguencing Methods of Transcriptome[J].Northern Horticulture,2017,41(13):192.[doi:10.11937/bfyy.201712043]
[6]龙月红,宋菊,国红玉,等.刺五加转录因子基因的挖掘[J].北方园艺,2017,41(20):153.[doi:10.11937/bfyy.20170195]
　LONG Yuehong,SONG Ju,GUO Hongyu,et al.Exploring Transcription Factors in Eleutherococcus senticosus[J].Northern Horticulture,2017,41(13):153.[doi:10.11937/bfyy.20170195]
[7]刘洋,卢凯政,卞少杰,等.田间自然温度调控下核桃根系差异表达基因分析[J].北方园艺,2020,44(17):30.[doi:10.11937/bfyy.20194278]
　LIU Yang,LU Kaizheng,BIAN Shaojie,et al.Analysis of Differentially Expressed Gene Profile in the Root of Walnut Under Natural Temperature Regulation in the Field[J].Northern Horticulture,2020,44(13):30.[doi:10.11937/bfyy.20194278]
[8]廖绪红,沙秀芬,廖雪梅,等.藁本属药用植物分子生物学研究进展[J].北方园艺,2021,(12):133.[doi:10.11937/bfyy.20203322]
　LIAO Xuhong,SHA Xiufen,LIAO Xuemei,et al.Research Progress on Molecular Biology of Ligusticum[J].Northern Horticulture,2021,(13):133.[doi:10.11937/bfyy.20203322]
[9]王一清,王安琪,冯钧婷,等.亚洲百合糖代谢相关基因的表达与代谢分析[J].北方园艺,2022,(06):60.[doi:10.11937/bfyy.20213255]
　WANG Yiqing,WANG Anqi,FENG Junting,et al.Analysis of Gene Expression and Metabolism Related to Sugar Metabolism of Lilium Asiatica Hybrida[J].Northern Horticulture,2022,(13):60.[doi:10.11937/bfyy.20213255]
[10]王俊青,张彦辉,易婉莹,等.基于转录组测序红秋葵果实转色期花青素生物合成相关基因研究[J].北方园艺,2022,(14):9.[doi:10.11937/bfyy.20220291]
　WANG Junqing,ZHANG Yanhui,YI Wanying,et al.Study on Genes Related to Anthocyanin Biosynthesis at the Color Turning Stages in Red Okra Fruit Based on Transcriptome Sequencing[J].Northern Horticulture,2022,(13):9.[doi:10.11937/bfyy.20220291]

备注/Memo

第一作者简介：王小敏(1980-)，女，硕士，副研究员，现主要从事果树栽培育种等研究工作。E-mail：xmwang525@163.com.责任作者：吴文龙(1964-)，男，本科，研究员，现主要从事小浆果种质资源利用等研究工作。E-mail：1964wwl@163.com.基金项目：中央财政林业科技示范推广资金资助项目（苏［2021］TG08）。收稿日期：2021-11-21

更新日期/Last Update: 2022-08-31