Genome-wide Simple Sequence Repeat Markers in Potato: Abundance, Distribution, Composition, and Polymorphism

Overview

Journal DNA Res

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2021 Oct 5

PMID 34609514

Citations 5

Authors

Yinqiao Jian

Wenyuan Yan

Jianfei Xu

Shaoguang Duan

Guangcun Li

Liping Jin

Affiliations

Soon will be listed here.

Abstract

Simple sequence repeats (SSRs) are important sources of genetic diversity and are widely used as markers in genetics and molecular breeding. In this study, we examined four potato genomes of DM1-3 516 R44 (DM) from Solanum phureja, RH89039-16 (RH) from Solanum tuberosum, M6 from Solanum chacoense and Solanum commersonii to determine SSR abundance and distribution and develop a larger list of polymorphic markers for a potentially wide range of uses for the potato community. A total of 1,734,619 SSRs were identified across the four genomes with an average of 433,655 SSRs per genome and 2.31kb per SSR. The most abundant repeat units for mono-, di-, tri-, and tetra-nucleotide SSRs were (A/T)n, (AT/AT)n, (AAT/ATT)n, and (ATAT/ATAT)n, respectively. The SSRs were most abundant (78.79%) in intergenic regions and least abundant (3.68%) in untranslated regions. On average, 168,069 SSRs with unique flanking sequences were identified in the four genomes. Further, we identified 16,245 polymorphic SSR markers among the four genomes. Experimental validation confirmed 99.69% of tested markers could generate target bands. The high-density potato SSR markers developed in this study will undoubtedly facilitate the application of SSR markers for genetic research and marker-pyramiding in potato breeding.

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References

Aversano R, Contaldi F, Ercolano M, Grosso V, Iorizzo M, Tatino F . The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives. Plant Cell. 2015; 27(4):954-68. PMC: 4558694. DOI: 10.1105/tpc.114.135954. View

Ghislain M, Spooner D, Rodriguez F, VILLAMON F, Nunez J, Vasquez C . Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Genet. 2003; 108(5):881-90. DOI: 10.1007/s00122-003-1494-7. View

Beier S, Thiel T, Munch T, Scholz U, Mascher M . MISA-web: a web server for microsatellite prediction. Bioinformatics. 2017; 33(16):2583-2585. PMC: 5870701. DOI: 10.1093/bioinformatics/btx198. View

Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P . Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet. 2004; 109(4):800-5. DOI: 10.1007/s00122-004-1685-x. View

Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth B, Remm M . Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012; 40(15):e115. PMC: 3424584. DOI: 10.1093/nar/gks596. View

Li Y, Colleoni C, Zhang J, Liang Q, Hu Y, Ruess H . Genomic Analyses Yield Markers for Identifying Agronomically Important Genes in Potato. Mol Plant. 2018; 11(3):473-484. DOI: 10.1016/j.molp.2018.01.009. View

Xu J, Liu L, Xu Y, Chen C, Rong T, Ali F . Development and characterization of simple sequence repeat markers providing genome-wide coverage and high resolution in maize. DNA Res. 2013; 20(5):497-509. PMC: 3789560. DOI: 10.1093/dnares/dst026. View

Feingold S, Lloyd J, Norero N, Bonierbale M, Lorenzen J . Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theor Appl Genet. 2005; 111(3):456-66. DOI: 10.1007/s00122-005-2028-2. View

Koressaar T, Remm M . Enhancements and modifications of primer design program Primer3. Bioinformatics. 2007; 23(10):1289-91. DOI: 10.1093/bioinformatics/btm091. View

10.

Spooner D, Nunez J, Trujillo G, Del Rosario Herrera M, Guzman F, Ghislain M . Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Proc Natl Acad Sci U S A. 2007; 104(49):19398-403. PMC: 2148301. DOI: 10.1073/pnas.0709796104. View

11.

Morgante M, Hanafey M, Powell W . Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet. 2002; 30(2):194-200. DOI: 10.1038/ng822. View

12.

Toth G, Gaspari Z, Jurka J . Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 2000; 10(7):967-81. PMC: 310925. DOI: 10.1101/gr.10.7.967. View

13.

McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M . Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 2003; 9(6):199-207. DOI: 10.1093/dnares/9.6.199. View

14.

Lawson M, Zhang L . Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol. 2006; 7(2):R14. PMC: 1431726. DOI: 10.1186/gb-2006-7-2-r14. View

15.

Xia E, Yao Q, Zhang H, Jiang J, Zhang L, Gao L . CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences. Front Plant Sci. 2016; 6:1171. PMC: 4703815. DOI: 10.3389/fpls.2015.01171. View

16.

Yang S, Wang L, Huang J, Zhang X, Yuan Y, Chen J . Parent-progeny sequencing indicates higher mutation rates in heterozygotes. Nature. 2015; 523(7561):463-7. DOI: 10.1038/nature14649. View

17.

Zhou Q, Tang D, Huang W, Yang Z, Zhang Y, Hamilton J . Haplotype-resolved genome analyses of a heterozygous diploid potato. Nat Genet. 2020; 52(10):1018-1023. PMC: 7527274. DOI: 10.1038/s41588-020-0699-x. View

18.

Deng P, Wang M, Feng K, Cui L, Tong W, Song W . Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution. Sci Rep. 2016; 6:32224. PMC: 4999822. DOI: 10.1038/srep32224. View

19.

Zhang Z, Deng Y, Tan J, Hu S, Yu J, Xue Q . A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Res. 2007; 14(1):37-45. PMC: 2779893. DOI: 10.1093/dnares/dsm005. View

20.

Asadi A, Rashidi Monfared S . Characterization of EST-SSR markers in durum wheat EST library and functional analysis of SSR-containing EST fragments. Mol Genet Genomics. 2014; 289(4):625-40. DOI: 10.1007/s00438-014-0839-z. View