Skip to main content
Log in

Genetic diversity and differentiation of four goat lineages based on analysis of complete mtDNA d-loop

  • Research Article
  • Published:
Frontiers of Agriculture in China

Abstract

The complete sequences of mtDNA D-loops from 362 individuals were analyzed in order to investigate the genetic diversity and differentiation of their lineages. The results indicated that all of the analyzed sequences were differentiated into four clear lineages (A, B, C, and D). Lineages C and D might originate from Lineages B and A, respectively. The genetic diversity of complete mtDNA D-loop of four lineages was very abundant. The 76 bp insertion and the 17 bp deletion were detected in the longest and the shortest sequences, respectively. The 76 bp insertion was a repeat like motif found in many other animals. Lineages C and D were differentiated into two subclades (C1 and C2) and (D1 and D2), respectively. Lineage C might originate from Asia, and Lineage D might originate from Fertile Crescent.

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

Access this article

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

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Arnason U, Gullberg A, Johnsson E, Ledje C (1993). The nucleotide sequence of the mitochondrial DNA molecule of the grey seal, Halichoerus grypus, and a comparison with mitochondrial sequences of other true seals. J Mol Evol, 37(4): 323–330

    PubMed  CAS  Google Scholar 

  • Arnason U, Gullberg A, Widegren B (1991). The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus. J Mol Evol, 33(6): 556–568

    Article  PubMed  CAS  Google Scholar 

  • Azor P J, Monteagudo L V, Luque M, Tejedor M T, Rodero E, Sierra I, Herrera M, Rodero A, Arruga M V (2005). Phylogenetic relationships among Spanish goats breeds. Anim Genet, 36(5): 423–425

    Article  PubMed  CAS  Google Scholar 

  • Bibb M J, Van Etten R A, Wright C T, Walberg M W, Clayton D A (1981). Sequence and gene organization of mouse mitochondrial DNA. Cell, 26(2): 167–180

    Article  PubMed  CAS  Google Scholar 

  • Bruford M W, Bradley D G, Luikart G (2003). DNA markers reveal the complexity of livestock domestication. Nat Rev Genet, 4(11): 900–910

    Article  PubMed  CAS  Google Scholar 

  • Fan B, Chen S L, Kijas J H, Liu B, Yu M, Zhao S H, Zhu M J, Xiong T A, Li K (2007). Phylogenetic relationships among Chinese indigenous goat breeds inferred from mitochondrial control region sequence. Small Rumin Res, 73(1–3): 262–266

    Article  Google Scholar 

  • Chen S Y, Su Y H, Wu S F, Sha T, Zhang Y P (2005). Mitochondrial diversity and phylogeographic structure of Chinese domestic goats. Mol Phylogenet Evol, 37(3): 804–814

    Article  PubMed  CAS  Google Scholar 

  • Clayton D A (1992). Transcription and replication of animal mitochondrial DNAs. Int Rev Cytol, 141: 217–232

    Article  PubMed  CAS  Google Scholar 

  • Doda J N, Wright C T, Clayton D A (1981). Elongation of displacementloop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc Natl Acad Sci USA, 78(10): 6116–6120

    Article  PubMed  CAS  Google Scholar 

  • Foran D R, Hixson J E, Brown W M (1988). Comparisons of ape and human sequences that regulate mitochondrial DNA transcription and D-loop DNA synthesis. Nucleic Acids Res, 16(13): 5841–5861

    Article  PubMed  CAS  Google Scholar 

  • Ghivizzani S C, Mackay S L, Madsen C S, Laipis P J, Hauswirth W W (1993). Transcribed heteroplasmic repeated sequences in the porcine mitochondrial DNA D-loop region. J Mol Evol, 37(1): 36–37

    Article  PubMed  CAS  Google Scholar 

  • Hiendleder S, Lewalski H, Wassmuth R, Janke A (1998). The complete mitochondrial DNA sequence of the domestic sheep (Ovis aries) and comparison with the other major ovine haplotype. J Mol Evol, 47(4): 441–448

    Article  PubMed  CAS  Google Scholar 

  • Joshi M B, Rout P K, Mandal A K, Tyler-Smith C, Singh L, Thangaraj K (2003). Phylogeography and origin of Indian domestic goats. Mol Biol Evol, 21(3): 454–462

    Article  PubMed  Google Scholar 

  • Kumar S, Tamura K, Nei M (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Bioinformmatics, 5(2): 150–163

    CAS  Google Scholar 

  • Li Q F, Li Y X, Zhao X B, Pan Z X (2008). SequencingD-loop region of mitochondrial DNA in yak and study on its taxonomic status in bovinae. Acta Veterinaria et Zootechnica Sinica, 39(1): 1–6

    Google Scholar 

  • Li X L, Gong Y F, Liu Z Z, Zheng G R, Zhou R Y, Jin X M, Li L H, Wang H L (2006). Study on tandem repeat sequence variation in sheep mtDNA D-loop region. Yi Chuan Xue Bao, 33(12): 1087–1095

    PubMed  Google Scholar 

  • Liu R Y, Yang G S, Lei C Z (2006). The genetic diversity of mtDNA Dloop and the origin of Chinese goats. Yi Chuan Xue Bao, 33(5): 420–428

    PubMed  Google Scholar 

  • Lopez J V, Cevario S, O’Brien S J (1996). Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics, 33(2): 229–246

    Article  PubMed  CAS  Google Scholar 

  • Luikart G, Gielly L, Excoffier L, Vigne J D, Bouvet J, Taberlet P (2001). Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc Natl Acad Sci USA, 98(10): 5927–5932

    Article  PubMed  CAS  Google Scholar 

  • Lynch M, Crease T J (1990). The analysis of population survey data on DNA sequence variation. Mol Biol Evol, 7(4): 377–394

    PubMed  CAS  Google Scholar 

  • Mignotte F M, Gueride M, Champagne A M, Mounolou J C (1990). Direct repeats in the non-coding region of rabbit mitochondrial DNA. Involvement in the generation of intra- and inter-individual heterogeneity. Eur J Biochem, 194(2): 561–571

    CAS  Google Scholar 

  • Morin G B, Cech T R (1986). The telomeres of the linear mitochondrial DNA of Tetrahymena thermophila consist of 53 bp tandem repeats. Cell, 46(6): 873–883

    Article  PubMed  CAS  Google Scholar 

  • Naderi S, Rezaei H R, Taberlet P, Zundel S, Rafat S A, Naghash H R, el-Barody M A, Ertugrul O, Pompanon F, Harpending H, Econogene Consortium (2007). Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS ONE, 2(10): e1012

    Article  PubMed  Google Scholar 

  • Saccone C, Pesole G, Sbisá E (1991). The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J Mol Evol, 33(1): 83–91

    Article  PubMed  CAS  Google Scholar 

  • Sardina M T, Ballester M, Marmi J, Finocchiaro R, Kaam J B, Portolano B, Folch J M (2006). Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage. Anim Genet Aug, 37(4): 376–378

    Article  CAS  Google Scholar 

  • Savolainen P, Zhang Y P, Luo J, Lundeberg J, Leitner T (2002). Genetic evidence for an East Asian origin of domestic dogs. Science, 298(5598): 1610–1613

    Article  PubMed  CAS  Google Scholar 

  • Sultana S, Mannen H, Tsuji S (2003). Mitochondrial DNA diversity of Pakistani goats. Anim Genet, 34(6): 417–421

    Article  PubMed  CAS  Google Scholar 

  • Tajima F (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(3): 585–595

    PubMed  CAS  Google Scholar 

  • Takada T, Kikkawa Y, Yonekawa H, Kawakami S, Amano T (1997). Bezor (Capra aegagrus) is a matriarchal candidate for ancestor of domestic goat (Capra hircus): evidence from the mitochondrial DNA diversity. Biochem Genet, 35(9–10): 315–326

    Article  PubMed  CAS  Google Scholar 

  • Troy C S, MacHugh D E, Bailey J F, Magee D A, Loftus R T, Cunningham P, Chamberlain A T, Sykes B C, Bradley D G (2001). Genetic evidence for Near-Eastern origins of European cattle. Nature, 410(6832): 1088–1091

    Article  PubMed  CAS  Google Scholar 

  • Wilkinson G S, Chapman A M (1991). Length and sequence variation in evening bat D-loop mtDNA. Genetics, 128(3): 607–617

    PubMed  CAS  Google Scholar 

  • Wilkinson G S, Mayer F, Kerth G, Petri B (1997). Evolution of repeated sequence arrays in the D-loop region of bat mitochondrial DNA. Genetics, 146(3): 1035–1048

    PubMed  CAS  Google Scholar 

  • Xiufeng X, Arnason U (1994). The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region. Gene, 148(2): 357–362

    Article  Google Scholar 

  • Xu X, Gullberg A, Arnason U (1996). The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs. J Mol Evol, 43(5): 438–446

    Article  PubMed  CAS  Google Scholar 

  • Yang Y J, Lin Y S, Wu J L, Hui C F (1994). Variation in mitochondrial DNA and population structure of the Taipei treefrog Rhacophorus taipeianus in Taiwan. Mol Ecol, 3(3): 219–228

    Article  PubMed  CAS  Google Scholar 

  • Zeder M A, Hesse B (2000). The initial domestication of goats (Capra hircus) in the Zagros mountains 10000 years ago. Science, 287(5461): 2254–2257

    Article  PubMed  CAS  Google Scholar 

  • Zhao Q J, Guan W J, Guo J, Qiao H Y, He X H, Pu Y B (2008). Origin and Phylogenetics of Seven Chinese Sheep Breeds Based on D-loop Sequence. Acta Veteri naria et Zootechnica Sinica 39(4): 417–422

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Xianglong Li.

About this article

Cite this article

Kang, J., Li, X., Zhou, R. et al. Genetic diversity and differentiation of four goat lineages based on analysis of complete mtDNA d-loop. Front. Agric. China 5, 87–93 (2011). https://doi.org/10.1007/s11703-010-1061-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11703-010-1061-3

Keywords

Navigation