Analysis of simple sequence repeats in transcriptome of garlic (Allium sativum L.) and development of molecular markers

doi:10.3969/j.issn.1004-1524.2020.09.10

›› 2020, Vol. 32 ›› Issue (9): 1615-1625.DOI: 10.3969/j.issn.1004-1524.2020.09.10

• Horticultural Science • Previous Articles Next Articles

Analysis of simple sequence repeats in transcriptome of garlic (Allium sativum L.) and development of molecular markers

LIU Xinyu¹, TIAN Jie^1,2,*

1. Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China;
2. State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China

Received:2020-04-09 Online:2020-09-25 Published:2020-10-10

Abstract

Abstract: In order to investigate features of SSR sequence and develop SSR primers of Allium sativum for garlic breeding, MISA software was used to detect the SSR loci and analyse the SSR information of the garlic transcriptome sequence in this study. The effectiveness and polymorphism of primers were determined by PCR amplification. The results showed that 444 865 unigenes were obtained from garlic transcriptome sequencing. A total of 141 132 SSR loci were identified, the occurrence frequency was 31.72%, the average distribution distance was 3.45 kb. The major repeat motifs were mononucleotide and dinucleotide, which accounted for 68.02% and 24.12%, respectively. 82 repeat motifs of SSR loci were identified, and the most abundant motifs were A/T and AT/AT,which accounted for 65.02% and 12.37%, respectively. A total of 125 616 pairs of SSR primers were designed by Primer 3.0, and 14 pairs of primers were randomly selected and amplified. There were 12 pairs of primers that were clearly amplified. Among them, 6 pairs showed rich polymorphism in 35 garlic germplasm. 26 polymorphic bands were obtained by using 6 pairs polymorphic primers, and the average polymorphic amplification band of each SSR primer was 4.33. According to the UPGMA analysis, 35 garlic germplasm resources were divided into 5 groups at the genetic similarity coefficient of 0.756 9. In conclusion, abundant SSR loci were obtained by development of SSR molecular markers in garlic transcriptome and SSR markers could be widely used.

Key words: Allium sativum L., transcriptome, simple sequence repeats, polymorphism

CLC Number:

S682.32

LIU Xinyu, TIAN Jie. Analysis of simple sequence repeats in transcriptome of garlic (Allium sativum L.) and development of molecular markers[J]. , 2020, 32(9): 1615-1625.

References

[1] 都真真, 李锡香, 宋江萍, 等. 228份引进大蒜资源的表型多样性分析及适应性初步评价[J]. 植物遗传资源学报, 2019, 20(5): 1186-1196.
DU Z Z, LI X X, SONG J P, et al.Phenotypic diversity and adaptability analysis of 228 accessions of introduced garlic genetic resources[J]. Journal of Plant Genetic Resources, 2019, 20(5): 1186-1196.(in Chinese with English abstract)
[2] 王薇薇, 郭军, 梅燚, 等. 大蒜种质资源的综合评价与聚类分析[J]. 江苏农业学报, 2017, 33(2): 397-403.
WANG W W, GUO J, MEI Y, et al.Comprehensive evaluation and clustering analysis of garlic germplasm resources[J]. Jiangsu Journal of Agricultural Sciences, 2017, 33(2): 397-403.(in Chinese with English abstract)
[3] 冯翠, 衣政伟, 杜静, 等. 大蒜种质资源农艺性状综合评价与适应性鉴定[J]. 江苏农业科学, 2019, 47(6): 119-123.
FENG C, YI Z W, DU J, et al.Adaptive identification and agronomic evaluation of garlic germplasm resources[J]. Jiangsu Agricultural Sciences, 2019, 47(6): 119-123.(in Chinese)
[4] 张芬. 大蒜种质资源的形态学评价、愈伤诱导再生和原生质体培养[D]. 杭州: 浙江大学, 2008.
ZHANG F.Evaluation of garlic germplasms based on morphological characters, induction and regeneration of calluses and culture of protoplasts of garlic[D]. Hangzhou: Zhejiang University, 2008.(in Chinese with English abstract)
[5] 陈昕, 周涵韬, 杨志伟, 等. 大蒜种质资源遗传多样性的分子标记研究[J]. 厦门大学学报(自然科学版), 2005, 44(增刊1): 144-149.
CHEN X, ZHOU H T, YANG Z W, et al.Assessment of genetic diversity of garlic (Allium sativum L.) by the technique of molecular marker[J]. Journal of Xiamen University (Natural Science), 2005, 44(Suppl.1): 144-149.(in Chinese with English abstract)
[6] 王海平, SIMON P W, 李锡香, 等. 中国大蒜种质资源遗传多样性和群体遗传结构分析[J]. 中国农业科学, 2012, 45(16): 3318-3329.
WANG H P, SIMON P W, LI X X, et al.Diversity and genetic structure of garlic(Allium sativum L.) germplasm resource in China[J]. Scientia Agricultura Sinica, 2012, 45(16): 3318-3329.(in Chinese with English abstract)
[7] FAVILLE M J, VECCHIES A C, SCHREIBER M, et al.Functionally associated molecular genetic marker map construction in perennial ryegrass (Lolium perenne L.)[J]. Theoretical and Applied Genetics, 2004, 110(1): 12-32.
[8] 高天翔, 蔡宇良, 冯瑛, 等. 中国樱桃14个自然居群遗传多样性和遗传结构的SSR评价[J]. 园艺学报, 2016, 43(6): 1148-1156.
GAO T X, CAI Y L, FENG Y, et al.Genetic diversity and genetic structure of Prunus pseudocerasus populations from China as revealed by SSR markers[J]. Acta Horticulturae Sinica, 2016, 43(6): 1148-1156.(in Chinese with English abstract)
[9] BORDES J, GOUDEMAND E, DUCHALAIS L, et al.Genome-wide association mapping of three important traits using bread wheat elite breeding populations[J]. Molecular Breeding, 2014, 33(4): 755-768.
[10] 陈彪, 陈铭, 李洋洋, 等. 烟草糖酯SSR分子标记筛选及辅助育种应用[J]. 中国烟草科学, 2019, 40(3): 8-15.
CHEN B, CHEN M, LI Y Y, et al.Screening and assisted breeding applications of SSR molecular markers of sugar esters in tobacco[J]. Chinese Tobacco Science, 2019, 40(3): 8-15.(in Chinese with English abstract)
[11] FEYISSA T, NYBOM H, BARTISH I V, et al.Analysis of genetic diversity in the endangered tropical tree species Hagenia abyssinica using ISSR markers[J]. Genetic Resources and Crop Evolution, 2007, 54(5): 947-958.
[12] PANG Q Q, SUI Z H, KANG K H, et al.Application of SSR and AFLP to the analysis of genetic diversity in Gracilariopsis lemaneiformis (Rhodophyta)[J]. Journal of Applied Phycology, 2010, 22(5): 607-612.
[13] 刘宏久, 温艳斌, 刘晓雪, 等. 大蒜分子生物学研究进展[J]. 园艺学报, 2018, 45(9): 1778-1790.
LIU H J, WEN Y B, LIU X X, et al.A review for molecular biology of Allium sativum[J]. Acta Horticulturae Sinica, 2018, 45(9): 1778-1790.(in Chinese with English abstract)
[14] 周静. 大蒜种质亲缘关系的形态学和分子标记研究[D]. 杨凌: 西北农林科技大学, 2011.
ZHOU J.Study on genetic relationship of garlic (Allium sativum L.) germpalsm resources by morphological and molecular techniques[D]. Yangling: Northwest A & F University, 2011.(in Chinese with English abstract)
[15] 孙亚丽, 史庆华, 刘世琦, 等. 基于SSR分子标记的大蒜种质资源遗传多样性研究[J]. 山东农业大学学报(自然科学版), 2017, 48(3): 384-389.
SUN Y L, SHI Q H, LIU S Q, et al.The study on the genetic diversity of garlic germplasm based on SSR molecular marker[J]. Journal of Shandong Agricultural University (Natural Science Edition), 2017, 48(3): 384-389.(in Chinese with English abstract)
[16] IPEK M, IPEK A, ALMQUIST S G, et al.Demonstration of linkage and development of the first low-density genetic map of garlic, based on AFLP markers[J]. Theoretical and Applied Genetics, 2005, 110(2): 228-236.
[17] 韩曙, 丁玉梅, 王世华, 等. 18份大蒜种质资源遗传多样性的RAPD分析[J]. 云南农业大学学报, 2010, 25(1): 84-89.
HAN S, DING Y M, WANG S H, et al.Genetic diversity analysis of 18 samplers of Allium sativum L. germplasm resources using RAPD markers[J]. Journal of Yunnan Agricultural University, 2010, 25(1): 84-89.(in Chinese with English abstract)
[18] 杜晓华, 杨雅萍, 朱小佩, 等. 三色堇转录组SSR分析及分子标记开发[J]. 园艺学报, 2019, 46(4): 797-806.
DU X H, YANG Y P, ZHU X P, et al.Development of genic-SSR markers by transcriptome sequencing in Viola×Wittrockiana[J]. Acta Horticulturae Sinica, 2019, 46(4): 797-806.(in Chinese with English abstract)
[19] 杨旭, 杨志玲, 谭美, 等. 厚朴转录组特征分析及EST-SSR标记的开发[J]. 核农学报, 2019, 33(7): 1318-1329.
YANG X, YANG Z L, TAN M, et al.Characteristics analysis of Houpoëa officinalis transcription and development of EST-SSR markers[J]. Journal of Nuclear Agricultural Sciences, 2019, 33(7): 1318-1329.(in Chinese with English abstract)
[20] 林珲, 李永平, 薛珠政, 等. 花椰菜转录组SSR位点分析及其分子标记开发[J]. 西北农林科技大学学报(自然科学版), 2019, 47(3): 85-93.
LIN H, LI Y P, XUE Z Z, et al.Analysis of SSR loci in transcriptome and development of molecular markers in Brassica oleracea L.var.botrytis L[J]. Journal of Northwest A & F University (Natural Science Edition), 2019, 47(3): 85-93.(in Chinese with English abstract)
[21] 杨彬, 许蔷薇, 牛明月, 等. 云锦杜鹃转录组SSR分析及其分子标记开发[J]. 核农学报, 2018, 32(12): 2335-2345.
YANG B, XU Q W, NIU M Y, et al.Analysis of SSR information in transcriptome and development of SSR molecular markers in Rhododendron fortunei[J]. Acta Agriculturae Nucleatae Sinica, 2018, 32(12): 2335-2345.(in Chinese with English abstract)
[22] 陈欣, 余懋群, 龙海, 等. 大麦EST-SSR分子标记开发及特征分析[J]. 应用与环境生物学报, 2018, 24(1): 102-106.
CHEN X, YU M Q, LONG H, et al.Data mining and analysis for simple sequence repeats in expressed sequence tags from barley[J]. Chinese Journal of Applied and Environmental Biology, 2018, 24(1): 102-106.(in Chinese with English abstract)
[23] 张海平, 陈妍, 王志, 等. 基于SSR标记的山西野生大豆种质资源遗传多样性分析[J]. 大豆科学, 2019, 38(2): 189-197.
ZHANG H P, CHEN Y, WANG Z, et al.Genetic diversity analysis of wild soybean (Glycine soja) in Shanxi Province based on SSR analysis[J]. Soybean Science, 2019, 38(2): 189-197.(in Chinese with English abstract)
[24] 赵彤, 常圣鑫, 冷青云, 等. 基于三角梅转录组测序的SSR分子标记的开发[J]. 分子植物育种, 2019, 17(13): 4331-4341.
ZHAO T, CHANG S X, LENG Q Y, et al.Development of SSR molecular markers based on transcriptome sequencing of Bougainvillea[J]. Molecular Plant Breeding, 2019, 17(13): 4331-4341.(in Chinese with English abstract)
[25] MA K H, KWAG J G, ZHAO W G, et al.Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (Allium sativum L.)[J]. Scientia Horticulturae, 2009, 122(3): 355-361.
[26] CUNHA C P, HOOGERHEIDE E S S, ZUCCHI M I, et al. New microsatellite markers for garlic, Allium sativum(Alliaceae)[J]. American Journal of Botany, 2012, 99(1): e17-e19.
[27] 陈书霞, 常燕霞, 周静, 等. 大蒜种质遗传多样性的SSR分析[J]. 农业生物技术学报, 2012, 20(4): 372-381.
CHEN S X, CHANG Y X, ZHOU J, et al.Genetic diversity of garlic (Allium sativum L.) germplasm by simple sequence repeats[J]. Journal of Agricultural Biotechnology, 2012, 20(4): 372-381.(in Chinese with English abstract)
[28] 石艳, 童再康, 高燕会. 换锦花EST-SSR标记开发及遗传多样性分析[J]. 核农学报, 2018, 32(6): 1089-1096.
SHI Y, TONG Z K, GAO Y H.Development of EST-SSR markers and genetic diversity analysis in Lycoris sprengeri[J]. Journal of Nuclear Agricultural Sciences, 2018, 32(6): 1089-1096.(in Chinese with English abstract)
[29] 李延龙, 张华敏, 崔蕴刚, 等. 韭菜全长转录组SSR信息分析及分子标记开发[J]. 园艺学报, 2020, 47(4):759-768.
LI Y L, ZHANG H M, CUI Y G, et al.Analysis on SSR information in full-length transcriptome and development of molecular markers in Allium tuberosum[J]. Acta Horticulturae Sinica, 2020, 47(4):759-768. (in Chinese with English abstract)
[30] 王晖, 谢岩, 孙志超, 等. 基于桑葚转录组测序的SSR位点分析[J/OL]. 分子植物育种, 2020, 18(1):28. (2020-02-17)[2020-04-09]. http://kns.cnki.netkcmsdetail/46. 1068. S. 20190319. 0857. 004. html.
WANG H, XIE Y, SUN Z C, et al. Analysis on SSR locis in mulberry fruit transcriptome[J/OL]. Molecular Plant Breeding: 2020, 18(1):28. (2020-02-17)[2020-04-09]. http://kns.cnki.netkcmsdetail/46. 1068. S. 20190319. 0857. 004. html.(in Chinese with English abstract)
[31] 贺润丽, 韩毅丽, 段静静, 等. 款冬转录组SSR标记开发及其多态性研究[J]. 中草药, 2019, 50(20): 5026-5032.
HE R L, HAN Y L, DUAN J J, et al.Development and polymorphism analysis of SSR molecular markers in Tussilago farfara transcriptome[J]. Chinese Traditional and Herbal Drugs, 2019, 50(20): 5026-5032.(in Chinese with English abstract)
[32] 潘丽芹, 李纪元, 李绍翠, 等. 基于山茶转录组的SSR标记开发及亲缘关系分析[J]. 北京林业大学学报, 2019, 41(7): 111-120.
PAN L Q, LI J Y, LI S C, et al.Development of SSR markers based on transcriptome of Camellia japonica and analysis of genetic relationship[J]. Journal of Beijing Forestry University, 2019, 41(7): 111-120.(in Chinese with English abstract)
[33] 刘冬梅, 娄喜艳, 吴狄, 等. 基于棉花转录组测序的SSR分子标记的开发[J]. 江苏农业科学, 2019, 47(7): 32-35.
LIU D M, LOU X Y, WU D, et al.Excavation of SSR molecular markers based on transcriptome sequencing of cotton[J]. Jiangsu Agricultural Sciences, 2019, 47(7): 32-35.(in Chinese with English abstract)
[34] 贺丹, 吴芳芳, 张佼蕊, 等. 牡丹转录组SSR信息分析及其分子标记开发[J]. 江苏农业学报, 2019, 35(6): 1428-1433.
HE D, WU F F, ZHANG J R, et al.Analysis of SSR information in transcriptome and development of molecular markers in Paeonia suffruticosa[J]. Jiangsu Journal of Agricultural Sciences, 2019, 35(6): 1428-1433.(in Chinese with English abstract)
[35] 魏秀清, 许玲, 章希娟, 等. 莲雾转录组SSR信息分析及其分子标记开发[J]. 园艺学报, 2018, 45(3): 541-551.
WEI X Q, XU L, ZHANG X J, et al.Analysis on SSR information in transcriptome and development of molecular markers in wax apple[J]. Acta Horticulturae Sinica, 2018, 45(3): 541-551.(in Chinese with English abstract)
[36] 张庆田, 李晓艳, 杨义明, 等. 蓝靛果忍冬转录组SSR信息分析及其分子标记开发[J]. 园艺学报, 2016, 43(3): 557-563.
ZHANG Q T, LI X Y, YANG Y M, et al.Analysis on SSR information in transcriptome and development of molecular markers in Lonicera caerulea[J]. Acta Horticulturae Sinica, 2016, 43(3): 557-563.(in Chinese with English abstract)
[37] 鄢秀芹, 鲁敏, 安华明. 刺梨转录组SSR信息分析及其分子标记开发[J]. 园艺学报, 2015, 42(2): 341-349.
YAN X Q, LU M, AN H M.Analysis on SSR information in transcriptome and development of molecular markers in Rosa roxburghii[J]. Acta Horticulturae Sinica, 2015, 42(2): 341-349.(in Chinese with English abstract)
[38] 王兴春, 谭河林, 陈钊, 等. 基于RNA-Seq技术的连翘转录组组装与分析及SSR分子标记的开发[J]. 中国科学: 生命科学, 2015, 45(3): 301-310.
WANG X C, TAN H L, CHEN Z, et al.Assembly and characterization of the transcriptome and development of SSR markers in Forsythia suspensa based on RNA-seq technology[J]. Scientia Sinica Vitae, 2015, 45(3): 301-310.(in Chinese with English abstract)
[39] 方智振, 叶新福, 周丹蓉, 等. ‘芙蓉李’转录组SSR信息分析与分子标记开发[J]. 果树学报, 2016, 33(4): 416-424.
FANG Z Z, YE X F, ZHOU D R, et al.Analysis on SSR information in‘Furongli’ plum transcriptome and development of molecular markers in Prunus salicina Lindl[J]. Journal of Fruit Science, 2016, 33(4): 416-424.(in Chinese with English abstract)
[40] 杨世鹏, 孙雪梅, 王丽慧, 等. 基于菊芋转录组的SSR分子标记开发及鉴定[J]. 分子植物育种, 2018, 16(2): 484-492.
YANG S P, SUN X M, WANG L H, et al.Development and identification of SSR markers based on transcriptome of Helianthus tuberosus L[J]. Molecular Plant Breeding, 2018, 16(2): 484-492.(in Chinese with English abstract)
[41] 应东山, 唐浩, 韩瑞玺, 等. 基于转录组测序的油梨EST-SSR引物开发[J]. 热带作物学报, 2018, 39(12): 2446-2451.
YING D S, TANG H, HAN R X, et al.Development EST-SSR markers based on transcriptome sequences in avocado[J]. Chinese Journal of Tropical Crops, 2018, 39(12): 2446-2451.(in Chinese with English abstract)

Analysis of simple sequence repeats in transcriptome of garlic (Allium sativum L.) and development of molecular markers

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