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Maternal phylogeny of a newly-found yak population in china.

Mipam TD, Wen Y, Fu C, Li S, Zhao H, Ai Y, Li L, Zhang L, Zou D - Int J Mol Sci (2012)

Bottom Line: This population has a special anatomical characteristic: an additional pair of ribs compared with other yak breeds.The Jinquan yaks were found to carry clades A and B from lineage I and clade C of lineage II, respectively.The special anatomic characteristic that we found in the Jinchuan population needs further studies based on nuclear data.

View Article: PubMed Central - PubMed

Affiliation: Ecological Conservation and Animal Husbandry Research and Development Base of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu 610041, China; E-Mail: tdmipam@163.com ; College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, China; E-Mails: swun-zhw@163.com (H.Z.); neoacnew@gmail.com (Y.A.); lulu860620@yahoo.com.cn (L.L.); shitouji27@yahoo.com.cn (L.Z.); swunzdq@yahoo.com.cn (D.Z.).

ABSTRACT
The Jinchuan yak is a new yak population identified in Sichuan, China. This population has a special anatomical characteristic: an additional pair of ribs compared with other yak breeds. The genetic structure of this population is unknown. In the present study, we investigated the maternal phylogeny of this special yak population using the mitochondrial DNA variation. A total of 23 Jinchuan yaks were sequenced for a 823-bp fragment of D-loop control region and three individuals were sequenced for the whole mtDNA genome with a length of 16,371-bp. To compare with the data from other yaks, we extracted sequence data from Genebank, including D-loop of 398 yaks (from 12 breeds) and 55 wild yaks, and whole mitochondrial genomes of 53 yaks (from 12 breeds) and 21 wild yaks. A total of 127 haplotypes were defined, based on the D-loop data. Thirteen haplotypes were defined from 23 mtDNA D-loop sequences of Jinchuan yaks, six of which were shared only by Jinchuan, and one was shared by Jinchuan and wild yaks. The Jinquan yaks were found to carry clades A and B from lineage I and clade C of lineage II, respectively. It was also suggested that the Jinchuan population has no distinct different phylogenetic relationship in maternal inheritance with other breeds of yak. The highly haplotype diversity of the Pali breed, Jinchuan population, Maiwa breed and Jiulong breed suggested that the yak was first domesticated from wild yaks in the middle Himalayan region and the northern Hengduan Mountains. The special anatomic characteristic that we found in the Jinchuan population needs further studies based on nuclear data.

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Nucleotide variations of 127 haplotypes in 476 Bos grunniens individuals based on mtDNA control regions. N in the right column listed the number of individuals sharing the same haplotype. Mutations are scored relative to the reference sequence of Bison bison (abbreviated as 1, Accession No. U12936). Numbers at the top of the figure indicate the nucleotide sequence position. Dots denote identity with the reference sequence.
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f3-ijms-13-11455: Nucleotide variations of 127 haplotypes in 476 Bos grunniens individuals based on mtDNA control regions. N in the right column listed the number of individuals sharing the same haplotype. Mutations are scored relative to the reference sequence of Bison bison (abbreviated as 1, Accession No. U12936). Numbers at the top of the figure indicate the nucleotide sequence position. Dots denote identity with the reference sequence.

Mentions: For the mtDNA control region, we also downloaded data of 398 yaks (from 12 breeds) and 55 wild yaks from Genebank. Together with the control region sequence data from the 23 Jinchuan yak individuals, a total of 476 sequences were obtained with 638 bp available on each sequence. Substitution analyses of these 476 sequences revealed 97 variable sites (Figure 3) and the global nucleotide diversity (Pi) was 0.01614 ± 0.00069. In total, 127 haplotypes were identified with a haplotype diversity (Hd) of 0.9280 ± 0.0083 (Table 1). In the 23 Jinchuan yak individuals, 33 nucleotide variants were observed and 13 haplotypes were identified. Thirty-two haplotypes were identified in the 55 wild individuals and only one haplotype was shared between Jinchuan and wild yaks. The Jinchuan yaks showed higher genetic diversity (Pi = 0.02035 ± 0.00225, Hd = 0.925 ± 0.035) than most other breeds including Tianzhu, Gannan, Datong, Huanhu, Plateau, Jali, Sibu, Pali, Maiwa, Jiulong and Bazhou, but a somewhat smaller genetic diversity than the Zhongdian yak (Pi = 0.02210 ± 0.00385, Hd = 0.917 ± 0.092) (Table 1).


Maternal phylogeny of a newly-found yak population in china.

Mipam TD, Wen Y, Fu C, Li S, Zhao H, Ai Y, Li L, Zhang L, Zou D - Int J Mol Sci (2012)

Nucleotide variations of 127 haplotypes in 476 Bos grunniens individuals based on mtDNA control regions. N in the right column listed the number of individuals sharing the same haplotype. Mutations are scored relative to the reference sequence of Bison bison (abbreviated as 1, Accession No. U12936). Numbers at the top of the figure indicate the nucleotide sequence position. Dots denote identity with the reference sequence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3472757&req=5

f3-ijms-13-11455: Nucleotide variations of 127 haplotypes in 476 Bos grunniens individuals based on mtDNA control regions. N in the right column listed the number of individuals sharing the same haplotype. Mutations are scored relative to the reference sequence of Bison bison (abbreviated as 1, Accession No. U12936). Numbers at the top of the figure indicate the nucleotide sequence position. Dots denote identity with the reference sequence.
Mentions: For the mtDNA control region, we also downloaded data of 398 yaks (from 12 breeds) and 55 wild yaks from Genebank. Together with the control region sequence data from the 23 Jinchuan yak individuals, a total of 476 sequences were obtained with 638 bp available on each sequence. Substitution analyses of these 476 sequences revealed 97 variable sites (Figure 3) and the global nucleotide diversity (Pi) was 0.01614 ± 0.00069. In total, 127 haplotypes were identified with a haplotype diversity (Hd) of 0.9280 ± 0.0083 (Table 1). In the 23 Jinchuan yak individuals, 33 nucleotide variants were observed and 13 haplotypes were identified. Thirty-two haplotypes were identified in the 55 wild individuals and only one haplotype was shared between Jinchuan and wild yaks. The Jinchuan yaks showed higher genetic diversity (Pi = 0.02035 ± 0.00225, Hd = 0.925 ± 0.035) than most other breeds including Tianzhu, Gannan, Datong, Huanhu, Plateau, Jali, Sibu, Pali, Maiwa, Jiulong and Bazhou, but a somewhat smaller genetic diversity than the Zhongdian yak (Pi = 0.02210 ± 0.00385, Hd = 0.917 ± 0.092) (Table 1).

Bottom Line: This population has a special anatomical characteristic: an additional pair of ribs compared with other yak breeds.The Jinquan yaks were found to carry clades A and B from lineage I and clade C of lineage II, respectively.The special anatomic characteristic that we found in the Jinchuan population needs further studies based on nuclear data.

View Article: PubMed Central - PubMed

Affiliation: Ecological Conservation and Animal Husbandry Research and Development Base of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu 610041, China; E-Mail: tdmipam@163.com ; College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, China; E-Mails: swun-zhw@163.com (H.Z.); neoacnew@gmail.com (Y.A.); lulu860620@yahoo.com.cn (L.L.); shitouji27@yahoo.com.cn (L.Z.); swunzdq@yahoo.com.cn (D.Z.).

ABSTRACT
The Jinchuan yak is a new yak population identified in Sichuan, China. This population has a special anatomical characteristic: an additional pair of ribs compared with other yak breeds. The genetic structure of this population is unknown. In the present study, we investigated the maternal phylogeny of this special yak population using the mitochondrial DNA variation. A total of 23 Jinchuan yaks were sequenced for a 823-bp fragment of D-loop control region and three individuals were sequenced for the whole mtDNA genome with a length of 16,371-bp. To compare with the data from other yaks, we extracted sequence data from Genebank, including D-loop of 398 yaks (from 12 breeds) and 55 wild yaks, and whole mitochondrial genomes of 53 yaks (from 12 breeds) and 21 wild yaks. A total of 127 haplotypes were defined, based on the D-loop data. Thirteen haplotypes were defined from 23 mtDNA D-loop sequences of Jinchuan yaks, six of which were shared only by Jinchuan, and one was shared by Jinchuan and wild yaks. The Jinquan yaks were found to carry clades A and B from lineage I and clade C of lineage II, respectively. It was also suggested that the Jinchuan population has no distinct different phylogenetic relationship in maternal inheritance with other breeds of yak. The highly haplotype diversity of the Pali breed, Jinchuan population, Maiwa breed and Jiulong breed suggested that the yak was first domesticated from wild yaks in the middle Himalayan region and the northern Hengduan Mountains. The special anatomic characteristic that we found in the Jinchuan population needs further studies based on nuclear data.

Show MeSH