Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle

Jinghang Zhou; Liyuan Liu; Chunpeng James Chen; Menghua Zhang; Xin Lu; Zhiwu Zhang; Xixia Huang; Yuangang Shi

doi:10.1186/s12864-019-6224-x

Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle

BMC Genomics. 2019 Nov 8;20(1):827. doi: 10.1186/s12864-019-6224-x.

Authors

Jinghang Zhou^{1

2}, Liyuan Liu^{1

2}, Chunpeng James Chen², Menghua Zhang³, Xin Lu¹, Zhiwu Zhang⁴, Xixia Huang⁵, Yuangang Shi⁶

Affiliations

¹ School of Agriculture, Ningxia University, Yinchuan, China.
² Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA.
³ College of Animal Science, Xinjiang Agricultural University, Urumqi, China.
⁴ Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA. Zhiwu.Zhang@WSU.Edu.
⁵ College of Animal Science, Xinjiang Agricultural University, Urumqi, China. xjau-huangxixia@xjau.edu.cn.
⁶ School of Agriculture, Ningxia University, Yinchuan, China. shi_yg@nxu.edu.cn.

Abstract

Background: Dual-purpose cattle are more adaptive to environmental challenges than single-purpose dairy or beef cattle. Balance among milk, reproductive, and mastitis resistance traits in breeding programs is therefore more critical for dual-purpose cattle to increase net income and maintain well-being. With dual-purpose Xinjiang Brown cattle adapted to the Xinjiang Region in northwestern China, we conducted genome-wide association studies (GWAS) to dissect the genetic architecture related to milk, reproductive, and mastitis resistance traits. Phenotypic data were collected for 2410 individuals measured during 1995-2017. By adding another 445 ancestors, a total of 2855 related individuals were used to derive estimated breeding values for all individuals, including the 2410 individuals with phenotypes. Among phenotyped individuals, we genotyped 403 cows with the Illumina 150 K Bovine BeadChip.

Results: GWAS were conducted with the FarmCPU (Fixed and random model circulating probability unification) method. We identified 12 markers significantly associated with six of the 10 traits under the threshold of 5% after a Bonferroni multiple test correction. Seven of these SNPs were in QTL regions previously identified to be associated with related traits. One identified SNP, BovineHD1600006691, was significantly associated with both age at first service and age at first calving. This SNP directly overlapped a QTL previously reported to be associated with calving ease. Within 160 Kb upstream and downstream of each significant SNP identified, we speculated candidate genes based on functionality. Four of the SNPs were located within four candidate genes, including CDH2, which is linked to milk fat percentage, and GABRG2, which is associated with milk protein yield.

Conclusions: These findings are beneficial not only for breeding through marker-assisted selection, but also for genome editing underlying the related traits to enhance the overall performance of dual-purpose cattle.

Keywords: Cattle; Dual-purpose; GWAS; Milk; Reproduction; SCS.

MeSH terms

Animals
Cattle / genetics*
Cattle / metabolism
Cattle / physiology*
Disease Resistance / genetics
Female
Genome-Wide Association Study*
Mastitis / genetics
Milk / metabolism*
Phenotype
Reproduction / genetics*

Abstract

MeSH terms

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