title: Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study.
abstract: Cattle and water buffalo belong to the same subfamily Bovinae and share chromosome banding and gene order homology. In this study, we used genome-wide Illumina BovineSNP50 BeadChip to analyze 91 DNA samples from three breeds of water buffalo (Nili-Ravi, Murrah and their crossbred with local GuangXi buffalos in China), to demonstrate the genetic divergence between cattle and water buffalo through a large single nucleotide polymorphism (SNP) transferability study at the whole genome level, and performed association analysis of functional traits in water buffalo as well. A total of 40,766 (75.5 %) bovine SNPs were found in the water buffalo genome, but 49,936 (92.5 %) were with only one allele, and finally 935 were identified to be polymorphic and useful for association analysis in water buffalo. Therefore, the genome sequences of water buffalo and cattle shared a high level of homology but the polymorphic status of the bovine SNPs varied between these two species. The different patterns of mutations between species may associate with their phenotypic divergence due to genome evolution. Among 935 bovine SNPs, we identified a total of 9 and 7 SNPs significantly associated to fertility and milk production traits in water buffalo, respectively. However, more works in larger sample size are needed in future to verify these candidate SNPs for water buffalo.
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
authors.forename: Jun Jing
authors.initials: JJ
authors.lastname: Wu
authors.forename: Li Jun
authors.initials: LJ
authors.lastname: Song
authors.forename: Fang Jie
authors.initials: FJ
authors.lastname: Wu
authors.forename: Xian Wei
authors.initials: XW
authors.lastname: Liang
authors.forename: Bing Zhuang
authors.initials: BZ
authors.lastname: Yang
authors.forename: D Claire
authors.initials: DC
authors.lastname: Wathes
authors.forename: Geoff E
authors.initials: GE
authors.lastname: Pollott
authors.forename: Zhangrui
authors.initials: Z
authors.lastname: Cheng
authors.forename: De Shun
authors.initials: de S
authors.lastname: Shi
authors.forename: Qing You
authors.initials: QY
authors.lastname: Liu
authors.forename: Li Guo
authors.initials: LG
authors.lastname: Yang
authors.forename: Shu Jun
authors.initials: SJ
authors.lastname: Zhang
mesh_terms: D000818:Animals; D002020:Buffaloes / Q000235:genetics*; D002417:Cattle / Q000235:genetics*; D033481:Chromosomes, Mammalian / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D005298:Fertility / Q000235:genetics; D005787:Gene Frequency; D055106:Genome-Wide Association Study; D060005:Genotyping Techniques; D006579:Heterozygote; D007774:Lactation / Q000235:genetics; D008892:Milk / Q000378:metabolism; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid