Genetic diversity of Y-short tandem repeats in chinese native cattle breeds

Yp, Xin; Ls, Zan; Yf, Liu; Wq, Tian; Hb, Wang; Chen, Gong; An, Li; Yang, Wei‐Jun

doi:10.4238/2014.november.14.1

Cited by 2 publications

(2 citation statements)

References 13 publications

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“…Yanbian cattle is a taurine breed that living in northeast China (Xin et al, 2010) and belongs to the "yellow" class of Chinese cattle (Ji et al, 2014). Unlike majority of Chinese indigenous breeds, Yanbian cattle have had no ancestral to breed with indicine cattle (Xin et al, 2014). They are mainly used as herbivores, especially in the rice fields but are also increasingly used for the beef purpose.…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle

et al. 2020

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Yanbian cattle is inhabitant of North of China, exhibiting many phenotypic features, such as long, dense body hair, and abundant intramuscular fat, designed to combat the extreme cold climate adaption. In the current study, we studied the cold tolerance of nine Yanbian cattle by whole genome resequencing and compared with African tropical cattle, N'Dama, as a control group. Yanbian cattle was aligned to the Bos taurus reference genome (ARS-UCD1.2) yielding an average of 10.8 fold coverage. The positive selective sweep analysis for the cold adaption in Yanbian cattle were analyzed using composite likelihood ratio (CLR) and nucleotide diversity (qp), resulting in 292 overlapped genes. The strongest selective signal was found on BTA16 with potential mutation in CORT gene, a regulatory gene of primary hormone in the hypothalamic-pituitary-adrenal (HPA) axis, is reported to be associated with the cold stress, representedfour missense mutations (c.269C > T, p.Lys90Ile; c.251A > G, p.Glu84Gly; c.112C > T, p.Pro38Ser; c.86G > A, p.Pro29His). Meanwhile another gene on BTA6, showed significantly higher selective sweep signals for a cold adapted trait for hair follicle and length development, FGF5 (fibroblast growth factor 5) with a missense mutation (c.191C > T, p.Ser64Phe). Moreover, cold adapted Yanbian cattle was statistically compared with the hot adapted N'Dama cattle, a taurine cattle reported to show superior heat tolerance than zebu cattle, making them better adapted to the hot regions of Africa. XP-CLR, Fst, and qp ratio were used to compare both breeds, yielding 487, 924, and 346 genes respectively. Among the 12 overlapped genes, (CD36) (c.638A > G, p.Lys 213Arg) involved in fat digestion and absorption plays an important role in membrane transport of long-chain fatty acid and its expression could increase in cold exposure. Henceforth, our study provides a novel genetic insights into the cold climate adaptation of Yanbian cattle and identified three candidate genes (CORT, FGF5, and CD36), which can add to an understanding of the cold climate adaptation of Yanbian cattle.

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Section: Introductionmentioning

confidence: 99%

Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle

et al. 2020

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“…Various molecular genetic markers have been used to determine genetic diversity, molecular evolution and genetic relationship within and among cattle breeds ( Horsburgh et al, 2013 ; Ludwig et al, 2013 ; San et al, 2014 ; Tu et al, 2014 ; Xin et al, 2014 ; Hristov et al, 2015 ). Of these, mitochondrial DNA (mtDNA) contains a maternal genetic pattern, and is a very useful marker for evaluating the origin and gene flow of modern cattle breeds.…”

Section: Introductionmentioning

confidence: 99%

Haplogroup Classification of Korean Cattle Breeds Based on Sequence Variations of mtDNA Control Region

Kim¹,

Seongsu²,

Kim³

et al. 2016

Asian Australas. J. Anim. Sci

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Many studies have reported the frequency and distribution of haplogroups among various cattle breeds for verification of their origins and genetic diversity. In this study, 318 complete sequences of the mtDNA control region from four Korean cattle breeds were used for haplogroup classification. 71 polymorphic sites and 66 haplotypes were found in these sequences. Consistent with the genetic patterns in previous reports, four haplogroups (T1, T2, T3, and T4) were identified in Korean cattle breeds. In addition, T1a, T3a, and T3b sub-haplogroups were classified. In the phylogenetic tree, each haplogroup formed an independent cluster. The frequencies of T3, T4, T1 (containing T1a), and T2 were 66%, 16%, 10%, and 8%, respectively. Especially, the T1 haplogroup contained only one haplotype and a sample. All four haplogroups were found in Chikso, Jeju black and Hanwoo. However, only the T3 and T4 haplogroups appeared in Heugu, and most Chikso populations showed a partial of four haplogroups. These results will be useful for stable conservation and efficient management of Korean cattle breeds.

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Genetic diversity of Y-short tandem repeats in chinese native cattle breeds

Cited by 2 publications

References 13 publications

Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle

Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle

Haplogroup Classification of Korean Cattle Breeds Based on Sequence Variations of mtDNA Control Region

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