Genome-Wide Association Study of the Reproductive Traits of the Dazu Black Goat (Capra hircus) Using Whole-Genome Resequencing

Xingqiang Fang; Bowen Gu; Meixi Chen; Ruifan Sun; Jipan Zhang; Le Zhao; Yongju Zhao

doi:10.3390/genes14101960

Genome-Wide Association Study of the Reproductive Traits of the Dazu Black Goat (Capra hircus) Using Whole-Genome Resequencing

Genes (Basel). 2023 Oct 19;14(10):1960. doi: 10.3390/genes14101960.

Authors

Xingqiang Fang^{1

2

3}, Bowen Gu^{1

2

3}, Meixi Chen^{1

2

3}, Ruifan Sun^{1

2

3}, Jipan Zhang^{1

2

3}, Le Zhao^{1

2

3}, Yongju Zhao^{1

2

3}

Affiliations

¹ College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
² Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China.
³ Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China.

Abstract

Reproductive traits are the basic economic traits of goats and important indicators in goat breeding. In this study, Dazu black goats (DBGs; n = 150), an important Chinese local goat breed with excellent reproductive performance, were used to screen for important variation loci and genes of reproductive traits. Through genome-wide association studies (GWAS), 18 SNPs were found to be associated with kidding traits (average litter size, average litter size in the first three parity, and average litter size in the first six parity), and 10 SNPs were associated with udder traits (udder depth, teat diameter, teat length, and supernumerary teat). After gene annotation of the associated SNPs and in combination with relevant references, the candidate genes, namely ATP1A1, LRRC4C, SPCS2, XRRA1, CELF4, NTM, TMEM45B, ATE1, and FGFR2, were associated with udder traits, while the ENSCHIG00000017110, SLC9A8, GLRB, GRIA2, GASK1B, and ENSCHIG00000026285 genes were associated with litter size. These SNPs and candidate genes can provide useful biological information for improvement of the reproductive traits of goats.

Keywords: GWAS; goat; reproductive traits; udder traits; whole-genome resequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Female
Genome / genetics
Genome-Wide Association Study*
Goats* / genetics
Phenotype
Pregnancy
Sequence Analysis, DNA

Grants and funding

This work was financially supported by the Key Project of Chongqing Natural Science Foundation (cstc2020jcyj-zdxmX0015); Chongqing Modern Agricultural Industry Technology System (CQMAITS202313); Collection, Utilization, and Innovation of Germplasm Resources by Research Institutes and Enterprise of Chongqing (Cqnyncw-kqlhtxm).