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

doi:10.1007/s11703-010-1061-3

Front Agric Chin

2011, Vol. 5

Issue (1) : 87-93 https://doi.org/10.1007/s11703-010-1061-3

RESEARCH ARTICLE

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

Jingfen KANG, Xianglong LI(

), Rongyan ZHOU, Lanhui LI, Guiru ZHENG, Hongyuan ZHAO

College of Animal Science, Agricultural University of Hebei, Baoding 071001, China

Download: PDF(146 KB) HTML
Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks

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.

Keywords goat mtDNA D-loop lineages origin differentiation

Corresponding Author(s): LI Xianglong,Email:lixianglongcn@yahoo.com

Issue Date: 05 March 2011

Cite this article:

Xianglong LI,Rongyan ZHOU,Jingfen KANG, et al. Genetic diversity and differentiation of four goat lineages based on analysis of complete mtDNA d-loop[J]. Front Agric Chin, 2011, 5(1): 87-93.

URL:

https://academic.hep.com.cn/fag/EN/10.1007/s11703-010-1061-3
https://academic.hep.com.cn/fag/EN/Y2011/V5/I1/87

Tab.1 The mtDNA D-loop sequences of different goat breeds from GenBank

Fig.1 Neighbor-joining tree constructed with 255 haplotypes of goat mtDNA D-loop

Tab.2 Genetic variability of goat mtDNAD-loop of different lineages

Fig.2 Network analysis of mtDNA HVR lineage C in world goat breeds

Fig.3 Network analysis of mtDNA HVR lineage D in world goat breeds

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 doi: 10.1007/BF00178862
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 doi: 10.1007/BF02102808
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 doi: 10.1111/j.1365-2052.2005.01327.x
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 doi: 10.1038/nrg1203
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 doi: 10.1016/j.smallrumres.2006.12.007
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 doi: 10.1016/j.ympev.2005.06.014
8	Clayton D A (1992). Transcription and replication of animal mitochondrial DNAs. Int Rev Cytol , 141: 217–232 doi: 10.1016/S0074-7696(08)62067-7
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 doi: 10.1073/pnas.78.10.6116
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 doi: 10.1093/nar/16.13.5841
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 doi: 10.1007/BF00170460
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 doi: 10.1007/PL00006401
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 doi: 10.1093/molbev/msh038
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 doi: 10.1006/geno.1996.0188
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 doi: 10.1073/pnas.091591198
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 doi: 10.1111/j.1432-1033.1990.tb15653.x
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 doi: 10.1007/BF02100199
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 doi: 10.1126/science.1073906
27	Sultana S, Mannen H, Tsuji S (2003). Mitochondrial DNA diversity of Pakistani goats. Anim Genet , 34(6): 417–421 doi: 10.1046/j.0268-9146.2003.01040.x
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 doi: 10.1023/A:1021869704889
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 doi: 10.1038/35074088
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 doi: 10.1007/BF02337515
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 doi: 10.1111/j.1365-294X.1994.tb00055.x
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 doi: 10.1126/science.287.5461.2254
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

[1]	Jun ZHANG, Jinmao WANG, Haiyong LIANG, Minsheng YANG, . A poplar chimera with stable differentiation regulation[J]. Front. Agric. China, 2009, 3(4): 486-492.
[2]	Xianglong LI, Hailiang WANG, Rongyan ZHOU, Guiru ZHENG, Lanhui LI, Zunan SHEN. Variation of 184C→T of goat callipyge gene in different populations and its effect on body weight[J]. Front Agric Chin, 2009, 3(3): 319-324.
[3]	YIN Jun, ZHANG Yanjun, LI Changqing, LI Jinquan. Sequence of a Cashmere goat type I hair keratin gene and its expression in skin[J]. Front. Agric. China, 2008, 2(4): 502-507.
[4]	GENG Yan, YANG Zhangping, CHANG Hong, MAO Yongjiang, SUN Wei, GUO Xiaoya, QU Dongyan. Genetic differentiation and gene flow among six sheep breeds of Mongolian group in China[J]. Front. Agric. China, 2008, 2(3): 338-342.
[5]	GU Youfang, WANG Bingyun, ZHANG Hongying, MAO Xinzhi, SHEN Yonglin. Cytokines level changes in goats infected with [J]. Front. Agric. China, 2008, 2(2): 242-244.
[6]	LI Xianglong, ZHOU Rongyan, ZHENG Guiru, LI Lanhui, LIU Zhengzhu, GONG Yuanfang. Deletion of TTTTA in 5′UTR of goat gene and its distribution in different population groups and genetic effect on bodyweight at different ages[J]. Front. Agric. China, 2008, 2(1): 103-109.
[7]	QU Dongyan, YANG Zhangping, GUO Xiaoya, MAO Yongjiang, SUN Wei, GEN Rongqing, REN Xianglian, CHANG Guobing, HUANG Danli, CHANG Hong, MA Yuehui. Study on polymorphisms of microsatellite DNA of six Chinese indigenous sheep and goat breeds[J]. Front. Agric. China, 2007, 1(4): 472-477.
[8]	WANG Zhiguo, YANG Zhangping, WANG Qinghua, MAO Yongjiang, CHANG Hong, ZHOU Qunlan, XU Ming, MA Yuehui. Analysis of genetic diversity among seven goat populations in the middle and lower valley of Yangtse River and southeast coastal regions in China[J]. Front. Agric. China, 2007, 1(3): 324-328.
[9]	LI Qifa, LI Yinxia, LIU Zhenshan, XU Yefen, SONG Dawei, QU Xuguang, XIE Zhuang, ZHAO Xingbo, LI Ning. Study on the origin and taxonomic status of yak (Poephagus) using cytochrome b gene of mitochondrial DNA[J]. Front. Agric. China, 2007, 1(3): 329-333.
[10]	WANG Linfeng, YANG Gaiqing, FANG Liyun, LU Dexun, SUN Haizhou, ZHAO Xiuying, SHAN Dan. Effects of photoperiod and melatonin on nitrogen partitioning and production performance of Inner Mongolia White Cashmere Goats[J]. Front. Agric. China, 2007, 1(2): 229-236.

Viewed

Full text

Abstract

Cited

Shared

Discussed