Development and identification of SSR molecular markers based on whole genomic sequences of <i>Punica granatum</i>

Hong Wenjuan; Hao Zhaoxiang; Liu Kangjia; Luo Hua; Bi Runxia; Yuan Zhaohe; Zong Shixiang; Wang Jun

doi:10.13332/j.1000-1522.20190167

Journal of Beijing Forestry University > 2019 > 41(8): 38-47. > DOI: 10.13332/j.1000-1522.20190167

Hong Wenjuan, Hao Zhaoxiang, Liu Kangjia, Luo Hua, Bi Runxia, Yuan Zhaohe, Zong Shixiang, Wang Jun. Development and identification of SSR molecular markers based on whole genomic sequences of Punica granatum[J]. Journal of Beijing Forestry University, 2019, 41(8): 38-47. DOI: 10.13332/j.1000-1522.20190167

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Development and identification of SSR molecular markers based on whole genomic sequences of Punica granatum

1.
National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing 100083,China
2.
College of Forestry, Beijing Forestry University, Beijing 100083,China
3.
National Germplasm Bank of Pomegranate, Zaozhuang 277300,Shandong, China
4.
College of Forestry, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
5.
College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China

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Received Date: March 27, 2019
Revised Date: May 10, 2019
Available Online: June 11, 2019
Published Date: July 31, 2019

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Abstract

Abstract

Objective The number of polymorphic SSR markers developed through cDNA library is limited. In order to promote studies on genetic diversity, genetic mapping and variety identification, it is necessary to develop molecular marker loci.
Method In this study, SSRs with 1−6 nucleotide repeats were searched from the published whole genome sequences of Punica granatum using MISA and the characterization of SSR sequences and their polymorphisms were analyzed.
Result (1) A total of 146 445 SSR loci were detected in whole genome sequences of Punica granatum. Then content of mono-nucleotide repeat SSRs was the highest, accounting for 51.95%; in contrast, the content of hexa-nucleotide repeat SSRs was the lowest, only 0.38%. In all SSR sequences, most of bases were A/T, showing a bias in SSR sequences. (2) The range of SSR length ranged from 10 to 252 bp, with an average of 15.48 bp. The SSR length among different types of SSRs varied a lot, and the abundance of SSR sequences tended to decrease with the increase of repeat number. (3) In designed 140 pairs of primers including different types of SSRs, valid fragments could be produced with 119 pairs in 12 germplasms of Punica granatum and 41 pairs could produce polymorphic fragments with 0.007−0.566 polymorphic information content (PIC). We further screened 15 pairs of primers with polymorphic and stable fragments, which detected 44 alleles in these germplasms of Punica granatum, with average of 2.933 3 alleles per SSR locus.
Conclusion SSR markers can be developed in large-scale based on whole genome sequences of Punica granatum and a large number of SSR primers also can be identified for genetic diversity analysis, genetic mapping and variety identification. This study provides lots of SSR information and marker resources for researching genetics and breeding of Punica granatum.
- Punica granatum,
- genome,
- SSR,
- marker development,
- polymorphism

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[1]	苑兆和, 吕菲菲. 石榴文化艺术与功能利用[M]. 北京: 中国农业出版社, 2018. Yuan Z H, Lü F F. Culture, art and functional utilization of pomegranate[M]. Beijing: China Agriculture Press, 2018.
[2]	赵丽娜, 侯乐峰, 郝兆祥, 等. 遗传标记在石榴种质资源研究中的应用[J]. 中国农学通报, 2015, 31(4):135−140. Zhao L N, Hou L F, Hao Z X, et al. Application of genetic markers in Punica granatum germplasm research[J]. Chinese Agricultural Science Bulletin, 2015, 31(4): 135−140.
[3]	黄秦军, 苏晓华, 张香华. SSR分子标记与林木遗传育种[J]. 世界林业研究, 2002, 15(3):14−21. doi: 10.3969/j.issn.1001-4241.2002.03.003 Huang Q J, Su X H, Zhang X H. Microsatellite markers and its application in tree genetics and breeding[J]. World Forestry Research, 2002, 15(3): 14−21. doi: 10.3969/j.issn.1001-4241.2002.03.003
[4]	Ebrahimi S, Sayed-Tabatabaei B, Sharifnabi B. Microsatellite isolation and characterization in pomegranate (Punica granatum L.)[J]. Iranian Journal of Biotechnology, 2010, 8(3): 156−163.
[5]	Parvaresh M, Talebi M, Sayed-Tabatabaei B. Molecular diversity and genetic relationship of pomegranate (Punica granatum L.) genotypes using microsatellite markers[J]. Scientia Horticulturae, 2012, 138: 244−252. doi: 10.1016/j.scienta.2012.02.038
[6]	杨健. 基于EST-SSR分子标记的中国石榴遗传多样性研究[D]. 合肥: 安徽农业大学, 2015. Yang J. Genetic analysis of pomegranate in China based on EST-SSR markers[D].Hefei: Anhui Agricultural University, 2015.
[7]	Yuan Z, Fang Y, Zhang T, et al. The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology[J]. Plant Biotechnology Journal, 2018, 6(7): 1363−1374.
[8]	Marshall T C, Slate J, Kruuk L E B, et al. Statistical confidence for likelihood-based paternity inference in natural populations[J]. Molecular Ecology, 1998, 7(5): 639−655. doi: 10.1046/j.1365-294x.1998.00374.x
[9]	Davey J W, Hohenlohe P A, Etter P D, et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J]. Nature Review Genetics, 2011, 12: 499−510. doi: 10.1038/nrg3012
[10]	吴敏, 杜红岩, 乌云塔娜, 等. 杜仲基因组微卫星特征及SSR标记开发[J]. 林业科学研究, 2015, 28(3):387−393. doi: 10.3969/j.issn.1001-1498.2015.03.013 Wu M, Du H Y, Wuyuntana, et al. Characterization of genomic microsatellites and development of SSR markers of Eucommia ulmoides[J]. Forest Research, 2015, 28(3): 387−393. doi: 10.3969/j.issn.1001-1498.2015.03.013
[11]	马秋月, 戴晓港, 陈赢男, 等. 枣基因组的微卫星特征[J]. 林业科学, 2013, 49(12):81−87. Ma Q Y, Dai X G, Chen Y N, et al. Characterization of microsatellites in the genome of Ziziphus jujuba[J]. Scientia Silvae Sinicae, 2013, 49(12): 81−87.
[12]	Karaoglu H, Lee C M Y, Meyer W. Survey of simple sequence repeats in completed fungal genomes[J]. Molecular Biology & Evolution, 2005, 22: 639−649.
[13]	郑燕, 张耿, 吴为人. 禾本科植物微卫星序列的特征分析和比较[J]. 基因组学与应用生物学, 2011, 30(5):513−520. doi: 10.3969/gab.030.000513 Zheng Y, Zhang G, Wu W R. Characterization and comparison of microsatellites in Gramineae[J]. Genomics and Applied Biology, 2011, 30(5): 513−520. doi: 10.3969/gab.030.000513
[14]	Tuskan G A, Gunter L E, Yang Z K, et al. Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa[J]. Canadian Journal of Forest Research, 2004, 34: 85−93. doi: 10.1139/x03-283
[15]	Gur-Arie R, Cohen C J, Eitan Y, et al. Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism[J]. Genome Research, 2000, 10(1): 62−71.
[16]	阎毛毛, 戴晓港, 李淑娴, 等. 松树、杨树及桉树表达基因序列微卫星比对分析[J]. 基因组学与应用生物学, 2011, 30(1):103−109. doi: 10.3969/gab.030.000103 Yan M M, Dai X G, Li S X, et al. Sequence analysis and comparison of EST-SSRs in pine, poplar and Eucalyptus[J]. Genomics and Applied Biology, 2011, 30(1): 103−109. doi: 10.3969/gab.030.000103
[17]	Weber J L. Informativeness of human (dC-dA)n·(dG-dT)n polymorphisms[J]. Genomics, 1990, 7: 524−530. doi: 10.1016/0888-7543(90)90195-Z
[18]	Botsein D, White R L, Skolnick M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. American Journal of Human Genetics, 1980, 32(3): 314−331.
[19]	Luo X, Gao S Y, Hao Z X, et al. Analysis of genetic structure in a large sample of pomegranate (Punica granatum L.) using fluorescent SSR markers[J]. The Journal of Horticultural Science and Biotechnology, 2018, 93(6): 659−665. doi: 10.1080/14620316.2018.1432994
[20]	麻丽颖, 孔德仓, 刘华波, 等. 36份枣品种SSR指纹图谱的构建[J]. 园艺学报, 2012, 39(4):647−654. Ma L Y, Kong D C, Liu H B, et al. Construction of SSR fingerprint on 36 Chinese jujube cultivars[J]. Acta Horticulturae Sinica, 2012, 39(4): 647−654.

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