title: Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse.
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.
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China .
authors.forename: Haoyuan
authors.initials: H
authors.lastname: Han
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China .
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China .
authors.forename: Kexin
authors.initials: K
authors.lastname: Gao
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China .
authors.forename: Xiangpeng
authors.initials: X
authors.lastname: Yue
authors.affiliation: Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China .
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China .
authors.forename: Ruihua
authors.initials: R
authors.lastname: Dang
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China .
authors.forename: Xianyong
authors.initials: X
authors.lastname: Lan
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China .
authors.forename: Hong
authors.initials: H
authors.lastname: Chen
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China .
authors.forename: Chuzhao
authors.initials: C
authors.lastname: Lei
keywords: Chinese Indigenous Horse; Diversity; Single Nucleotide Polymorphisms; Y Chromosome