Skip to main content
Springer Nature Link
Log in

Genome-wide characterization of perfect microsatellites in yak (Bos grunniens)

  • Published:
Genetica Aims and scope Submit manuscript

Abstract

Microsatellites or simple sequence repeats (SSRs) constitute a significant portion of genomes and play an important role in gene function and genome organization. The availability of a complete genome sequence for yak (Bos grunniens) has made it possible to carry out genome-wide analysis of microsatellites in this species. We analyzed the abundance and density of perfect SSRs in the yak genome. We found a total of 723,172 SSRs with 1–6 bp nucleotide motifs, indicating that about 0.47 % of the yak whole genome sequence (2.66 Gb) comprises perfect SSRs, the average length of which was 17.34 bp/Mb. The average frequency and density of perfect SSRs was 272.18 loci/Mb and 4719.25 bp/Mb, respectively. The proportion of the six classes of perfect SSRs was not evenly distributed in the yak genome. Mononucleotide repeats (44.04 %) with a total number of 318,435 and a average length of 14.71 bp appeared to be the most abundant SSRs class, while the percentages of dinucleotide, trinucleotide, pentanucleotide, tetranucleotide and hexanucleotide repeats was 24.11 %, 15.80 %, 9.50 %, 6.40 % and 0.15 %, respectively. Different repeat classes of SSRs varied in their repeat number with the highest being 1206. Our results suggest that 15 motifs comprised the predominant categories with a frequency above 1 loci/Mb: A, AC, AT, AG, AGC, AAC, AAT, ACC, ATTT, GTTT, AATG, CTTT, ATGG, AACTG and ATCTG.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+
from $39.99 /Month
  • Starting from 10 chapters or articles per month
  • Access and download chapters and articles from more than 300k books and 2,500 journals
  • Cancel anytime
View plans

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

Explore related subjects

Discover the latest articles and news from researchers in related subjects, suggested using machine learning.

References

  • Cai X, Mipam T, Zhao FF, Sun L (2014) Isolation and characterization of polymorphic microsatellites in the genome of Yak (Bos grunniens). Mol Biol Rep 41:3829–3837

    Article  CAS  PubMed  Google Scholar 

  • Campregher C, Scharl T, Nemeth M, Honeder C, Jascur T, Boland CR, Gasche C (2010) The nucleotide composition of microsatellites impacts both replication fidelity and mismatch repair in human colorectal cells. Hum Mol Genet 19:2648–2657

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Du L, Li Y, Zhang X, Yue B (2013) MSDB: a user-friendly program for reporting Distribution and building databases of microsatellites from genome sequences. J Hered 104:154–157

    Article  PubMed  Google Scholar 

  • Guichoux E, Lagache L, Wagner S, Chaumeil P, Léger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ (2011) Current trends in microsatellite genotyping. Mol Ecol Resour 11:591–611

    Article  CAS  PubMed  Google Scholar 

  • Hefferon TW, Groman JD, Yurk CE, Cutting GR (2004) A variable dinucleotide repeat in the CFTR gene contributes to phenotype diversity by forming RNA secondary structures that alter splicing. Proc Natl Acad Sci USA 101:3504–3509

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hu QJ, Ma T, Wang K, Xu T, Liu JQ, Qiu Q (2012) The yak genome database: an integrative database for studying yak biology and high-altitude adaption. BMC Genomics 13:600

    Article  PubMed Central  PubMed  Google Scholar 

  • Huang J, Du LM, Li YZ, Li WJ, Zhang XY, Yue BS (2012) Distribution regularities of microsatellites in the Gallus gallus genome. Sichuan J Zool 31:358–363 (in chinese with english abstract)

    CAS  Google Scholar 

  • Katti MV, Ranjekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18:1161–1167

    Article  CAS  PubMed  Google Scholar 

  • Li B, Xia QY, Lu C, Zhou ZY, Xiang ZH (2004) Analysis on frequency and density of microsatellites in coding sequence of several eukaryotic genomes. Genomics, Proteomics Bioinform 2:24–31

    CAS  Google Scholar 

  • Luo XL, Song HF, Guan JQ (2014) Investigation on mechanism of sterility of male hybrids between yak and cattle. J Appl Anim Res 42:395–399

    Article  Google Scholar 

  • Nguyen TT, Genini S, Ménétrey F, Malek M, Vögeli P, Goe MR, Stranzinger G (2005) Application of bovine microsatellite markers for genetic diversity analysis of Swiss yak (Poephagus grunniens). Anim Genet 36:484–489

    Article  CAS  PubMed  Google Scholar 

  • Qi XB, Han JL, Lkhagva B, Chekarova I, Badamdorj D, Rege JE, Hanotte O (2005) Genetic diversity and differentiation of Mongolian and Russian yak populations. J Anim Breed Genet 122:117–126

    Article  Google Scholar 

  • Qi XB, Han JL, Wang G, Rege JEO, Hanotte O (2010) Assessment of cattle genetic introgression into domestic yak populations using mitochondrial and microsatellite DNA markers. Anim Genet 41:242–252

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Qi WH, Jiang XM, Xiao GS, Huang XY, Du LM (2013) Seeking and bioinformatics analysis of microsatellite sequence in the genomes of cow and sheep. Acta Veterinaria et Zootechnica Sinica 44:1724–1733 (in chinese with english abstract)

    CAS  Google Scholar 

  • Qiu Q, Zhang GJ, Ma T, Qian W, Wang J, Ye Z, Cao C, Hu Q, Kim J, Larkin DM, Auvil L, Capitanu B, Ma J, Lewin HA, Qian X, Lang Y, Zhou R, Wang L, Wang K, Xia J, Liao S, Pan S, Lu X, Hou H, Wang Y, Zang X, Yin Y, Ma H, Zhang J, Wang Z, Zhang Y, Zhang D, Yonezawa T, Hasegawa M, Zhong Y, Liu W, Zhang Y, Huang Z, Zhang S, Long R, Yang H, Wang J, Lenstra JA, Cooper DN, Wu Y, Wang J, Shi P, Wang J, Liu JQ (2012) The yak genome and adaptation to life at high altitude. Nat Genet 44:946–949

    Article  CAS  PubMed  Google Scholar 

  • Ramesha KP, Biswas TK, Jayakumar S, Das S, Gupta N, Kataktalware MA, Gupta SC (2012) Application of cattle microsatellite markers to assess genetic diversity of Indian yaks. Indian J Anim Sci 82:770–772

    Google Scholar 

  • Ritz LR, Glowatzki-Mullis ML, MacHugh DE, Gaillard C (2000) Phylogenetic analysis of the tribe Bovini using microsatellites. Anim Genet 31:178–185

    Article  CAS  PubMed  Google Scholar 

  • Schlotterer C (1998) Genome evolution: are microsatellites really simple sequences? Curr Biol 8:132–134

    Article  Google Scholar 

  • Subramanian S, Mishra RK, Singh L (2003) Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol 4:R13

    Article  PubMed Central  PubMed  Google Scholar 

  • Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tong XL, Dai FY, Li B, Yu QY, Xia QY, Lu C (2006) Microsatellite repeats in mouse: abundance, distribution and density. Curr Zool 52:138–152

    CAS  Google Scholar 

  • Wang MQ, Weigend S, Barre-Dirie A, Carnwath JW, Lu ZL, Niemann H (2003) Analysis of two Chinese yak (Bos grunniens) populations using bovine microsatellite primers. J Anim Breed Genet 120:237–244

    Article  CAS  Google Scholar 

  • Wiener G, Han JL, Long RJ (2003) The yak. Regional Office for Asia and the Pacific of the Food and Agriculture Organization of the United Nations, Bangkok, Thailand

  • Yu QY, Li B, Li GR, Fang SM, Yan H, Tong XL, Qian JF, Xia QY, Lu C (2005) Abundance and distribution of microsatellite in the entire mosquito. Prog Biochem Biophys 32:435–441

    CAS  Google Scholar 

  • Zhang GX, Chen WS, Xue M, Wang ZG, Chang H, Han X, Liao XJ, Wang DL (2008) Analysis of genetic diversity and population structure of Chinese yak breeds (Bos grunniens) using microsatellite markers. J Genet Genomics 35:233–238

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The author thank Prof. Michael W. Bruford, Dr. Penny C. Gardner and Dr. David Stanton (Cardiff university, UK) for their assistance in improving English on the manuscript. This study was supported by the National Natural Science Foundation of China (No. 31360267), the 123 high-level personnel training project of Qinghai university, the scientific and technological innovation platform of bovine (milk, meat, wool) industry of Qinghai Province and the Technology Foundation for Selected Overseas Chinese Scholar, Department of Human Resources and Social Security of Qinghai Province.

Author information

Authors and Affiliations

  1. Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, No. 1 Weier Road, Bio-Science Industrial District, Xining, 810016, Qinghai, People’s Republic of China

    Zhijie Ma

Authors
  1. Zhijie Ma
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to Zhijie Ma.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ma, Z. Genome-wide characterization of perfect microsatellites in yak (Bos grunniens). Genetica 143, 515–520 (2015). https://doi.org/10.1007/s10709-015-9849-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10709-015-9849-y

Keywords