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

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.

Key words： goat; mtDNA D-loop; lineages; origin; differentiation

Acknowledgments

This work was funded by the subproject of Breeding System Establishment Production in Scale of Dairy Cow with High Performance: Breeding System Establishment of Dairy Goat (No. 2006BAD04A10–06).

References

1 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

2 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

3 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

4 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

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

6 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

7 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

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

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

10 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

11 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

12 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

13 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

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

15 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

16 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

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

18 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

19 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

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

21 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

22 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

23 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

24 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

25 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

26 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

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

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

29 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

30 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

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

32 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

33 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

34 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

35 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

36 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

37 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