Limits...
Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse.

Han H, Zhang Q, Gao K, Yue X, Zhang T, Dang R, Lan X, Chen H, Lei C - Asian-australas. J. Anim. Sci. (2015)

Bottom Line: Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified.Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively.In addition, all the five Y-SNP haplotypes were shared by different breeds.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China .

ABSTRACT
In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five Y-SNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (π = 5.6×10(-4)) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (π = 0.00000) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses.

No MeSH data available.


A Median-joining (MJ) network calculation of Chinese horse Y chromosome. Colored circles represent sequence haplotypes,, the area being proportional to the frequency of the haplotype in total samples. Branch length is proportional to number of mutations. Different colors represent different horse breed. The network clearly revealed that CHT1 was in the center position, which indicated CHT1 maybe an ancestral haplotype. CDM, Chaidamu; CKY, Chakouyi; DT, Datong; YJ, Yanji; BS, Baise; DB, Debao pony; GUZ, Guanzhong; GZ, Guizhou; NQ, Ningqiang; BLK, Balikun; KZK, Kazakh; YS, Yushu; HQ, Hequ.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4478473&req=5

f3-ajas-28-8-1066: A Median-joining (MJ) network calculation of Chinese horse Y chromosome. Colored circles represent sequence haplotypes,, the area being proportional to the frequency of the haplotype in total samples. Branch length is proportional to number of mutations. Different colors represent different horse breed. The network clearly revealed that CHT1 was in the center position, which indicated CHT1 maybe an ancestral haplotype. CDM, Chaidamu; CKY, Chakouyi; DT, Datong; YJ, Yanji; BS, Baise; DB, Debao pony; GUZ, Guanzhong; GZ, Guizhou; NQ, Ningqiang; BLK, Balikun; KZK, Kazakh; YS, Yushu; HQ, Hequ.

Mentions: To further analyze the above three variations of Y chromosome loci, we made a haplotype analysis by combining them together. Hence, a total of five Y-SNP haplotypes (CHT1, CHT2, CHT3, CHT4, and CHT5) were identified (Table 4). And their frequencies among 13 Chinese domestic horse breeds were calculated and presented in Table 5. Among the 13 breeds studied, 12 horse breeds had at least two Y-SNP haplotypes, while Ningqiang breed only had CHT1 haplotype (Table 5). In addition to Guanzhong, Kazakh and Yanji breeds, the CHT1 is a predominant haplotype, consisting of 219 individuals, which accounted for 72.04% of 304 samples. In contrast, the remaining four haplotypes only contained 4, 69, 6 and 6 individuals, respectively (Table 5). The NJ tree based on DA was showed in Figure 2. The dendrogram showed that all five haplotypes could be clustered into two branches. Furthermore, in the first branch haplotype CHT1 and CHT4 gathered together. In the second branch, haplotype CHT2 and haplotype CHT5 gathered firstly, then the haplotype CHT3 was gathered into the branch (Figure 2). All the Y-SNP haplotypes were not restricted to a specific region or breed (Figure 3). The Median-joining (MJ) network showed the relationship among five haplotypes involving relevant breed information. It clearly revealed that CHT1 was in the center position and shared by different breeds, which indicated CHT1 maybe a common and ancestral haplotype (Figure 3). Furthermore, the regional haplotype data clearly demonstrated the increase of genetic variations in a southwest–northwest direction.


Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse.

Han H, Zhang Q, Gao K, Yue X, Zhang T, Dang R, Lan X, Chen H, Lei C - Asian-australas. J. Anim. Sci. (2015)

A Median-joining (MJ) network calculation of Chinese horse Y chromosome. Colored circles represent sequence haplotypes,, the area being proportional to the frequency of the haplotype in total samples. Branch length is proportional to number of mutations. Different colors represent different horse breed. The network clearly revealed that CHT1 was in the center position, which indicated CHT1 maybe an ancestral haplotype. CDM, Chaidamu; CKY, Chakouyi; DT, Datong; YJ, Yanji; BS, Baise; DB, Debao pony; GUZ, Guanzhong; GZ, Guizhou; NQ, Ningqiang; BLK, Balikun; KZK, Kazakh; YS, Yushu; HQ, Hequ.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4478473&req=5

f3-ajas-28-8-1066: A Median-joining (MJ) network calculation of Chinese horse Y chromosome. Colored circles represent sequence haplotypes,, the area being proportional to the frequency of the haplotype in total samples. Branch length is proportional to number of mutations. Different colors represent different horse breed. The network clearly revealed that CHT1 was in the center position, which indicated CHT1 maybe an ancestral haplotype. CDM, Chaidamu; CKY, Chakouyi; DT, Datong; YJ, Yanji; BS, Baise; DB, Debao pony; GUZ, Guanzhong; GZ, Guizhou; NQ, Ningqiang; BLK, Balikun; KZK, Kazakh; YS, Yushu; HQ, Hequ.
Mentions: To further analyze the above three variations of Y chromosome loci, we made a haplotype analysis by combining them together. Hence, a total of five Y-SNP haplotypes (CHT1, CHT2, CHT3, CHT4, and CHT5) were identified (Table 4). And their frequencies among 13 Chinese domestic horse breeds were calculated and presented in Table 5. Among the 13 breeds studied, 12 horse breeds had at least two Y-SNP haplotypes, while Ningqiang breed only had CHT1 haplotype (Table 5). In addition to Guanzhong, Kazakh and Yanji breeds, the CHT1 is a predominant haplotype, consisting of 219 individuals, which accounted for 72.04% of 304 samples. In contrast, the remaining four haplotypes only contained 4, 69, 6 and 6 individuals, respectively (Table 5). The NJ tree based on DA was showed in Figure 2. The dendrogram showed that all five haplotypes could be clustered into two branches. Furthermore, in the first branch haplotype CHT1 and CHT4 gathered together. In the second branch, haplotype CHT2 and haplotype CHT5 gathered firstly, then the haplotype CHT3 was gathered into the branch (Figure 2). All the Y-SNP haplotypes were not restricted to a specific region or breed (Figure 3). The Median-joining (MJ) network showed the relationship among five haplotypes involving relevant breed information. It clearly revealed that CHT1 was in the center position and shared by different breeds, which indicated CHT1 maybe a common and ancestral haplotype (Figure 3). Furthermore, the regional haplotype data clearly demonstrated the increase of genetic variations in a southwest–northwest direction.

Bottom Line: Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified.Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively.In addition, all the five Y-SNP haplotypes were shared by different breeds.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China .

ABSTRACT
In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five Y-SNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (π = 5.6×10(-4)) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (π = 0.00000) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses.

No MeSH data available.