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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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Phylogenetic tree of Jinchuan population and other 12 domestic yak breeds, together with a wild population basis of mtDNA control region constructed by neighbor-joining and Bayesian analysis, rooted by a bison sequence. ● indicates the haplotypes only found in the wild population; ○ indicates the haplotype shared by wild and yaks excluding the Jinchuan population; ■ indicates the haplotypes only found in the Jinchuan population; □ indicate the haplotypes shared by the Jinchuan population and wild yaks; ▼ indicates the haplotypes shared by the Jinchuan population and other 12 breeds; ★ indicate the haplotypes shared by all yaks, including wild, the Jinchuan population and other 12 breeds of yaks. The numbers at the nodes before the split means Bayesian posterior probabilities and after the sprit indicate the bootstrap values for 1000 Kimura two-parameter distance replications.
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f4-ijms-13-11455: Phylogenetic tree of Jinchuan population and other 12 domestic yak breeds, together with a wild population basis of mtDNA control region constructed by neighbor-joining and Bayesian analysis, rooted by a bison sequence. ● indicates the haplotypes only found in the wild population; ○ indicates the haplotype shared by wild and yaks excluding the Jinchuan population; ■ indicates the haplotypes only found in the Jinchuan population; □ indicate the haplotypes shared by the Jinchuan population and wild yaks; ▼ indicates the haplotypes shared by the Jinchuan population and other 12 breeds; ★ indicate the haplotypes shared by all yaks, including wild, the Jinchuan population and other 12 breeds of yaks. The numbers at the nodes before the split means Bayesian posterior probabilities and after the sprit indicate the bootstrap values for 1000 Kimura two-parameter distance replications.

Mentions: A neighbor-joining (NJ) tree based on the control region sequences showed that all the haplotypes fell into two distinct lineages (Figure 4). Lineage I diverged into clade A, B, E and Lineage II into clade C, D, F, G. Both lineages included the haplotypes of wild yak. The yak haplotypes were distributed randomly in the six clades (Figure 4). The Jinchuan yaks were found in the clade of A, B and C. Six Jinchuan haplotypes belonged to the clades of A and C. One haplotype in the clade of A was shared between Jinchuan, wild and domestic yaks. Five haplotypes (three in clade A, one in clade B and the other one in clade C) were shared between Jinchuan and other breeds of yak in the clade of A, B and C. Another haplotype in the clade C was only shared between Jinchuan and wild yaks (Table 2 and Figure 4).


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)

Phylogenetic tree of Jinchuan population and other 12 domestic yak breeds, together with a wild population basis of mtDNA control region constructed by neighbor-joining and Bayesian analysis, rooted by a bison sequence. ● indicates the haplotypes only found in the wild population; ○ indicates the haplotype shared by wild and yaks excluding the Jinchuan population; ■ indicates the haplotypes only found in the Jinchuan population; □ indicate the haplotypes shared by the Jinchuan population and wild yaks; ▼ indicates the haplotypes shared by the Jinchuan population and other 12 breeds; ★ indicate the haplotypes shared by all yaks, including wild, the Jinchuan population and other 12 breeds of yaks. The numbers at the nodes before the split means Bayesian posterior probabilities and after the sprit indicate the bootstrap values for 1000 Kimura two-parameter distance replications.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4-ijms-13-11455: Phylogenetic tree of Jinchuan population and other 12 domestic yak breeds, together with a wild population basis of mtDNA control region constructed by neighbor-joining and Bayesian analysis, rooted by a bison sequence. ● indicates the haplotypes only found in the wild population; ○ indicates the haplotype shared by wild and yaks excluding the Jinchuan population; ■ indicates the haplotypes only found in the Jinchuan population; □ indicate the haplotypes shared by the Jinchuan population and wild yaks; ▼ indicates the haplotypes shared by the Jinchuan population and other 12 breeds; ★ indicate the haplotypes shared by all yaks, including wild, the Jinchuan population and other 12 breeds of yaks. The numbers at the nodes before the split means Bayesian posterior probabilities and after the sprit indicate the bootstrap values for 1000 Kimura two-parameter distance replications.
Mentions: A neighbor-joining (NJ) tree based on the control region sequences showed that all the haplotypes fell into two distinct lineages (Figure 4). Lineage I diverged into clade A, B, E and Lineage II into clade C, D, F, G. Both lineages included the haplotypes of wild yak. The yak haplotypes were distributed randomly in the six clades (Figure 4). The Jinchuan yaks were found in the clade of A, B and C. Six Jinchuan haplotypes belonged to the clades of A and C. One haplotype in the clade of A was shared between Jinchuan, wild and domestic yaks. Five haplotypes (three in clade A, one in clade B and the other one in clade C) were shared between Jinchuan and other breeds of yak in the clade of A, B and C. Another haplotype in the clade C was only shared between Jinchuan and wild yaks (Table 2 and Figure 4).

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