Limits...
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.

Show MeSH
Phylogenetic tree of Jinchuan population and other 12 domestic yak breeds together with wild population and three sequences from bison, Bos taurue and Bos primigenous respectively, which is the basis of the coding region of complete mitochondrial sequences constructed by neighbor-joining and Bayesian analysis, rooted by a Bos indicus sequence. ● indicate the haplotypes only found in wild population; ■ indicate the haplotypes only found in Jinchuan population; □ indicate the haplotypes shared by Jinchuan population and wild yaks; ★ indicate the haplotypes shared by all yaks including wild and Jinchuan population and 12 other breeds of yak. 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
getmorefigures.php?uid=PMC3472757&req=5

f6-ijms-13-11455: Phylogenetic tree of Jinchuan population and other 12 domestic yak breeds together with wild population and three sequences from bison, Bos taurue and Bos primigenous respectively, which is the basis of the coding region of complete mitochondrial sequences constructed by neighbor-joining and Bayesian analysis, rooted by a Bos indicus sequence. ● indicate the haplotypes only found in wild population; ■ indicate the haplotypes only found in Jinchuan population; □ indicate the haplotypes shared by Jinchuan population and wild yaks; ★ indicate the haplotypes shared by all yaks including wild and Jinchuan population and 12 other breeds of yak. 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 tree was constructed from the coding regions of mitochondrial genomic sequences for all domestic breeds and wild yaks, together with Bos taurus and Bos primigenius, with Bos indicus as the outgroup. All sequences again converged into two distinct lineages (Figure 6), comprising five clades (A–E). The Jinchuan yak haplotypes are in clades A and C, and the Jinchuan-specific haplotype belongs to clade C. One Jinchuan haplotype was located in clade A. This haplotype was also observed in other yaks, including 1 Pali, 1 Huanhu, 2 Tianzhu, 3 Ganlan, 1 Plateau, 1 Jiali, 2 Datong, 2 Maiwa and 1 Jiulong individual, together with 1 wild yak. Another haplotype in clade C was shared only by 1 Jinchuan yak and 1 wild yak. In this study, the Bison was found to be more closely related to yak than to other Bovid species. In addition, Bos taurus and Bos primigenius were clustered into the same clade and indicated the most closely related phylogeny (Figure 6).


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 wild population and three sequences from bison, Bos taurue and Bos primigenous respectively, which is the basis of the coding region of complete mitochondrial sequences constructed by neighbor-joining and Bayesian analysis, rooted by a Bos indicus sequence. ● indicate the haplotypes only found in wild population; ■ indicate the haplotypes only found in Jinchuan population; □ indicate the haplotypes shared by Jinchuan population and wild yaks; ★ indicate the haplotypes shared by all yaks including wild and Jinchuan population and 12 other breeds of yak. 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

f6-ijms-13-11455: Phylogenetic tree of Jinchuan population and other 12 domestic yak breeds together with wild population and three sequences from bison, Bos taurue and Bos primigenous respectively, which is the basis of the coding region of complete mitochondrial sequences constructed by neighbor-joining and Bayesian analysis, rooted by a Bos indicus sequence. ● indicate the haplotypes only found in wild population; ■ indicate the haplotypes only found in Jinchuan population; □ indicate the haplotypes shared by Jinchuan population and wild yaks; ★ indicate the haplotypes shared by all yaks including wild and Jinchuan population and 12 other breeds of yak. 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 tree was constructed from the coding regions of mitochondrial genomic sequences for all domestic breeds and wild yaks, together with Bos taurus and Bos primigenius, with Bos indicus as the outgroup. All sequences again converged into two distinct lineages (Figure 6), comprising five clades (A–E). The Jinchuan yak haplotypes are in clades A and C, and the Jinchuan-specific haplotype belongs to clade C. One Jinchuan haplotype was located in clade A. This haplotype was also observed in other yaks, including 1 Pali, 1 Huanhu, 2 Tianzhu, 3 Ganlan, 1 Plateau, 1 Jiali, 2 Datong, 2 Maiwa and 1 Jiulong individual, together with 1 wild yak. Another haplotype in clade C was shared only by 1 Jinchuan yak and 1 wild yak. In this study, the Bison was found to be more closely related to yak than to other Bovid species. In addition, Bos taurus and Bos primigenius were clustered into the same clade and indicated the most closely related phylogeny (Figure 6).

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