Molecular Genetics and Genomics

, Volume 292, Issue 1, pp 117–131 | Cite as

Evolutionary dynamics of meiotic recombination hotspots regulator PRDM9 in bovids

  • Sonika AhlawatEmail author
  • Sachinandan De
  • Priyanka Sharma
  • Rekha Sharma
  • Reena Arora
  • R. S. Kataria
  • T. K. Datta
  • R. K. Singh
Original Article


Hybrid sterility or reproductive isolation in mammals has been attributed to allelic incompatibilities in a DNA-binding protein PRDM9. Not only is PRDM9 exceptional in being the only known ‘speciation gene’ in vertebrates, but it is also considered to be the fastest evolving gene in the genome. The terminal zinc finger (ZF) domain of PRDM9 specifies genome-wide meiotic recombination hotspot locations in mammals. Intriguingly, PRDM9 ZF domain is highly variable between as well as within species, possibly activating different recombination hotspots. The present study characterized the full-length coding sequence of PRDM9 in cattle and buffalo and explored the diversity of the ZF array in 514 samples from different bovids (cattle, yak, mithun, and buffalo). Substantial numerical and sequence variability were observed in the ZFs, with the number of repeats ranging from 6 to 9 in different bovines. Sequence analysis revealed the presence of 37 different ZFs in cattle, 3 in mithun, 4 in yak, and 13 in buffaloes producing 41 unique PRDM9 alleles in these species. The posterior mean of dN/dS or omega values calculated using Codeml tool of PAMLX identified sites −5, −1, +2, +3, +4, +5, and +6 in the ZF domain to be evolving positively in the studied species. Concerted evolution which typifies the evolution of this gene was consistently evident in all bovines. Our results demonstrate the extraordinary diversity of PRDM9 ZF array across bovines, reinforcing similar observations in other metazoans. The high variability is suggestive of unique repertoire of meiotic recombination hotspots in each species.


Meiosis Recombination Speciation Positive selection Concerted evolution 



This study was supported by the Indian Council of Agricultural Research, New Delhi, India.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Ethical approval

This article does not contain any studies with animals performed by any of the authors.

Supplementary material

438_2016_1260_MOESM1_ESM.docx (22 kb)
Supplementary material 1 (DOCX 22 kb)


  1. Ahlawat S, Sharma P, Sharma R, Arora R, Verma NK, Brahma B, Mishra P, De S (2016a) Evidence of positive selection and concerted evolution in the rapidly evolving PRDM9 zinc finger domain in goats and sheep. Anim Genet. doi: 10.1111/age.12487 PubMedGoogle Scholar
  2. Ahlawat S, Sharma P, Sharma R, Arora R, De S (2016b) Zinc finger domain of the PRDM9 gene on chromosome 1 exhibits high diversity in ruminants but its paralog PRDM7 contains multiple disruptive mutations. PLoS One 11(5):e0156159CrossRefPubMedPubMedCentralGoogle Scholar
  3. Auton A, Fledel-Alon A, Pfeifer S, Venn O, Ségurel L, Street T, Leffler EM, Bowden R, Aneas I, Broxholme J, Humburg P, Iqbal Z, Lunter G, Maller J, Hernandez RD, Melton C, Venkat A, Nobrega MA, Bontrop R, Myers S, Donnelly P, Przeworski M, McVean G (2012) A fine-scale chimpanzee genetic map from population sequencing. Science 336:193–198CrossRefPubMedPubMedCentralGoogle Scholar
  4. Baker CL, Kajita S, Walker M, Petkov PM, Paigen K (2014) PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration. Genome Res 24:724–732CrossRefPubMedPubMedCentralGoogle Scholar
  5. Baker CL, Petkova P, Walker M, Flachs P, Mihola O, Trachtulec Z, Petkov PM, Paigen K (2015) Multimer formation explains allelic suppression of PRDM9 recombination hotspots. PLoS Genet 11:e1005512CrossRefPubMedPubMedCentralGoogle Scholar
  6. Barton NH, Charlesworth B (1998) Why sex and recombination? Science 281:1986–1990CrossRefPubMedGoogle Scholar
  7. Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, Przeworski M, Coop G, de Massy B (2010) PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327:836–840CrossRefPubMedGoogle Scholar
  8. Berg IL, Neumann R, Lam KW, Sarbajna S, Odenthal-Hesse L, May CA, Jeffreys AJ (2010) PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans. Nat Genet 42:859–863CrossRefPubMedPubMedCentralGoogle Scholar
  9. Berg IL, Neumann R, Sarbajna S, Odenthal-Hesse L, Butler NJ, Jeffreys AJ (2011) Variants of the protein PRDM9 differentially regulate a set of human meiotic recombination hotspots highly active in African populations. Proc Natl Acad Sci USA 108:12378–12383CrossRefPubMedPubMedCentralGoogle Scholar
  10. Borel C, Cheung F, Stewart H, Koolen DA, Phillips C, Thomas NS, Jacobs PA, Eliez S, Sharp AJ (2012) Evaluation of PRDM9 variation as a risk factor for recurrent genomic disorders and chromosomal non-disjunction. Human Genet 131:1519–1524CrossRefGoogle Scholar
  11. Brick K, Smagulova F, Khil P, Camerini-Otero RD, Petukhova GV (2012) Genetic recombination is directed away from functional genomic elements in mice. Nature 485:642–645CrossRefPubMedPubMedCentralGoogle Scholar
  12. Buard J, Rivals E, Dunoyer de Segonzac D, Garres C, Caminade P, de Massy B, Boursot P (2014) Diversity of PRDM9 zinc finger array in wild mice unravels new facets of the evolutionary turnover of this coding minisatellite. PLoS One 9:e85021CrossRefPubMedPubMedCentralGoogle Scholar
  13. Coop G, Przeworski M (2007) An evolutionary view of human recombination. Nat Rev Genet 8:23–34CrossRefPubMedGoogle Scholar
  14. Dobzhansky T (1951) Genetics and the origin of species. Columbia University, New YorkGoogle Scholar
  15. Francino MP, Ochman H (1997) Strand asymmetries in DNA evolution. Trends Genet 13:240–245CrossRefPubMedGoogle Scholar
  16. Graffelman J, Balding DJ, Gonzalez-Neira A, Bertranpetit J (2007) Variation in estimated recombination rates across human populations. Human Genet 122:301–310CrossRefGoogle Scholar
  17. Gray MM, Granka JM, Bustamante CD, Sutter NB, Bokyo AR, Zhu L, Ostrander EA, Wayne RK (2009) Linkage disequilibrium and demographic history of wild and domestic canids. Genetics 181:1493–1505CrossRefPubMedPubMedCentralGoogle Scholar
  18. Groeneveld LF, Atencia R, Garriga RM, Vigilant L (2012) High diversity at PRDM9 in chimpanzees and bonobos. PLoS One 7:e39064CrossRefPubMedPubMedCentralGoogle Scholar
  19. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium series 41:95–98Google Scholar
  20. Hayashi K, Yoshida K, Matsui Y (2005) A histone H3 methyltransferase controls epigenetic events required for meiotic prophase. Nature 438:374–378CrossRefPubMedGoogle Scholar
  21. Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, Palmer CD, Chen GK, Wang K, Buxbaum SG, Akylbekova EL, Aldrich MC, Ambrosone CB, Amos C, Bandera EV, Berndt SI, Bernstein L, Blot WJ, Bock CH, Boerwinkle E, Cai Q, Caporaso N, Casey G, Cupples LA, Deming SL, Diver WR, Divers J, Fornage M, Gillanders EM, Glessner J, Harris CC, Hu JJ, Ingles SA, Isaacs W, John EM, Kao WH, Keating B, Kittles RA, Kolonel LN, Larkin E, Le Marchand L, McNeill LH, Millikan RC, Murphy A, Musani S, Neslund-Dudas C, Nyante S, Papanicolaou GJ, Press MF, Psaty BM, Reiner AP, Rich SS, Rodriguez-Gil JL, Rotter JI, Rybicki BA, Schwartz AG, Signorello LB, Spitz M, Strom SS, Thun MJ, Tucker MA, Wang Z, Wiencke JK, Witte JS, Wrensch M, Wu X, Yamamura Y, Zanetti KA, Zheng W, Ziegler RG, Zhu X, Redline S, Hirschhorn JN, Henderson BE, Taylor HA Jr, Price AL, Hakonarson H, Chanock SJ, Haiman CA, Wilson JG, Reich D, Myers SR (2011) The landscape of recombination in African Americans. Nature 476:170–175CrossRefPubMedPubMedCentralGoogle Scholar
  22. Hussin J, Sinnett D, Casals F, Idaghdour Y, Bruat V, Saillour V, Healy J, Grenier JC, de Malliard T, Busche S, Spinella JF, Larivière M, Gibson G, Andersson A, Holmfeldt L, Ma J, Wei L, Zhang J, Andelfinger G, Downing JR, Mullighan CG, Awadalla P (2013) Rare allelic forms of PRDM9 associated with childhood leukemogenesis. Genome Res 23:419–430CrossRefPubMedPubMedCentralGoogle Scholar
  23. Irie S, Tsujimura A, Miyagawa Y, Ueda T, Matsuoka Y, Matsui Y, Okuyama A, Nishimune Y, Tanaka H (2009) Single-nucleotide polymorphisms of the PRDM9 (MEISETZ) gene in patients with nonobstructive azoospermia. J Androl 30:426–431CrossRefPubMedGoogle Scholar
  24. Jeffreys AJ, Cotton VE, Neumann R, Lam KW (2013) Recombination regulator PRDM9 influences the instability of its own coding sequence in humans. Proc Natl Acad Sci USA 110:600–605CrossRefPubMedGoogle Scholar
  25. Kauppi L, Jeffreys AJ, Keeney S (2004) Where the crossovers are: recombination distributions in mammals. Nat Rev Genet 5:413–424CrossRefPubMedGoogle Scholar
  26. Khatun M, Kaur S, Kanchan Mukhopadhyay CS (2013) Subfertility problems leading to disposal of breeding bulls. Asian-Australas J Anim Sci 26:303–308CrossRefPubMedPubMedCentralGoogle Scholar
  27. Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, Jonasdottir A, Walters GB, Jonasdottir A, Gylfason A, Kristinsson KT, Gudjonsson SA, Frigge ML, Helgason A, Thorteinsdottir U, Stefansson K (2010) Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467:1099–1103CrossRefPubMedGoogle Scholar
  28. Kono H, Tamura M, Osada N, Suzuki H, Abe K, Moriwaki K, Ohta K, Shiroishi T (2014) PRDM9 polymorphism unveils mouse evolutionary tracks. DNA Res. doi: 10.1093/dnares/dst059 PubMedPubMedCentralGoogle Scholar
  29. Lou YN, Liu WJ, Wang CL, Huang L, Jin SY, Lin YQ, Zheng YC (2014) Histological evaluation and PRDM9 expression level in the testis of sterile male cattle-yaks. Livestock Sci 160:208–213CrossRefGoogle Scholar
  30. Ma L, O’Connell JR, VanRaden PM, Shen B, Padhi A, Sun C, Bickhart DM, Cole JB, Null DJ, Liu GE, Da Y, Wiggans GR (2015) Cattle sex-specific recombination and genetic control from a large pedigree analysis. PLoS Genet 11:e1005387CrossRefPubMedPubMedCentralGoogle Scholar
  31. Mandal DK, Tyagi S (2004) Pre-copulatory behaviour of Sahiwal bulls during semen collection and effects of age and season on their sexual performance. Indian J Dairy Sci 57:334–338Google Scholar
  32. Masly J, Jones C, Noor M, Locke J, Orr H (2006) Gene transposition as a cause of hybrid sterility in Drosophila. Science 313:1448–1450CrossRefPubMedGoogle Scholar
  33. Mihola O, Trachtulec Z, Vlcek C, Schimenti JC, Forejt J (2009) A mouse speciation gene encodes a meiotic histone H3 methyltransferase. Science 323:373–375CrossRefPubMedGoogle Scholar
  34. Miyamoto T, Koh E, Sakugawa N, Sato H, Hayashi H, Namiki M, Sengoku K (2008) Two single nucleotide polymorphisms in PRDM9 (MEISETZ) gene may be a genetic risk factor for Japanese patients with azoospermia by meiotic arrest. J Assist Reprod Genet 25:553–557CrossRefPubMedPubMedCentralGoogle Scholar
  35. Mukhopadhyay CS, Gupta AK, Yadav BR, Khate K, Raina VS, Mohanty TK, Dubey PP (2012) Subfertility in males: an important cause of bull disposal in bovines. Asian-Australas J Anim Sci 23:450–455CrossRefGoogle Scholar
  36. Muller H (1942) Isolating mechanisms, evolution, and temperature. In: T D (ed.) Biological Symposia. Jaques Cattell Press, Lancaster, p 71–125Google Scholar
  37. Myers S, Bowden R, Tumian A, Bontrop RE, Freeman C, MacFie TS, McVean G, Donnelly P (2010) Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327:876–879CrossRefPubMedGoogle Scholar
  38. Neale MJ (2010) PRDM9 points the zinc finger at meiotic recombination hotspots. Genome Biol 11:104–106CrossRefPubMedPubMedCentralGoogle Scholar
  39. Oliver PL, Goodstadt L, Bayes JJ, Birtle Z, Roach KC, Phadnis N, Beatson SA, Lunter G, Malik HS, Ponting CP (2009) Accelerated evolution of the PRDM9 speciation gene across diverse metazoan taxa. PLoS Genet 5:e1000753CrossRefPubMedPubMedCentralGoogle Scholar
  40. Parvanov ED, Petkov PM, Paigen K (2010) PRDM9 controls activation of mammalian recombination hotspots. Science 327:835–837CrossRefPubMedGoogle Scholar
  41. Perez D, Wu C (1995) Further characterization of the Odysseus locus of hybrid sterility in Drosophila: one gene is not enough. Genetics 140:201–206PubMedPubMedCentralGoogle Scholar
  42. Phadnis N, Orr H (2009) A single gene causes both male sterility and segregation distortion in Drosophila hybrids. Science 323:376–379CrossRefPubMedGoogle Scholar
  43. Pratto F, Brick K, Khil P, Smagulova F, Petukhova GV, Camerini-Otero RD (2014) Recombination initiation maps of individual human genomes. Science 346:1256442CrossRefPubMedGoogle Scholar
  44. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542CrossRefPubMedPubMedCentralGoogle Scholar
  45. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbour Laboratory, New YorkGoogle Scholar
  46. Sandor C, Li W, Coppieters W, Druet T, Charlier C, Georges M (2012) Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle. PLoS Genet 8:e1002854CrossRefPubMedPubMedCentralGoogle Scholar
  47. Schwartz JJ, Roach DJ, Thomas JH, Shendure J (2014) Primate evolution of the recombination regulator PRDM9. Nat Commun 5:4370–4376CrossRefPubMedPubMedCentralGoogle Scholar
  48. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539–544CrossRefPubMedPubMedCentralGoogle Scholar
  49. Singh A (2005) Crossbreeding of cattle for increasing milk production in India: a review. Indian J Anim Sci 75:383–390Google Scholar
  50. Steiner CC, Ryder OA (2013) Characterization of PRDM9 in equids and sterility in mules. PLoS One 8:e61746CrossRefPubMedPubMedCentralGoogle Scholar
  51. Stothard P (2000) The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 8:1102–1104Google Scholar
  52. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526PubMedGoogle Scholar
  53. Thomas JH, Emerson RO, Shendure J (2009) Extraordinary molecular evolution in the PRDM9 fertility gene. PLoS One 4:e8505CrossRefPubMedPubMedCentralGoogle Scholar
  54. Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, Bontrop RE, McVean GA, Gabriel SB, Reich D, Donnelly P, Altshuler D (2005) Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308:107–111CrossRefPubMedGoogle Scholar
  55. Xu B, Yang Z (2013) PAMLX: a graphical user interface for PAML. Mol Biol Evol 30:723–2724CrossRefGoogle Scholar
  56. Yang Z, Wong WSW, Nielsen R (2005) Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107–1118CrossRefPubMedGoogle Scholar
  57. Zhang QB, Li QF, Li JH, Li XF, Liu ZS, Song D, Xie Z (2008) b-DAZL: a novel gene in bovine spermatogenesis. Prog Nat Sci 18:1209–1218CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Sonika Ahlawat
    • 1
    • 4
    Email author
  • Sachinandan De
    • 2
  • Priyanka Sharma
    • 1
  • Rekha Sharma
    • 1
  • Reena Arora
    • 1
  • R. S. Kataria
    • 1
  • T. K. Datta
    • 2
  • R. K. Singh
    • 3
  1. 1.National Bureau of Animal Genetic ResourcesKarnalIndia
  2. 2.National Dairy Research InstituteKarnalIndia
  3. 3.National Research Center on MithunNagalandIndia
  4. 4.Animal Biotechnology DivisionNBAGRKarnalIndia

Personalised recommendations