Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers

Xiaoyan Sun; Qunhao Niu; Jing Jiang; Gaofu Wang; Peng Zhou; Jie Li; Cancan Chen; Liangjia Liu; Lingyang Xu; Hangxing Ren

doi:10.3390/genes14061183

Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers

Genes (Basel). 2023 May 29;14(6):1183. doi: 10.3390/genes14061183.

Authors

Xiaoyan Sun¹, Qunhao Niu², Jing Jiang¹, Gaofu Wang¹, Peng Zhou¹, Jie Li¹, Cancan Chen¹, Liangjia Liu¹, Lingyang Xu², Hangxing Ren¹

Affiliations

¹ Chongqing Academy of Animal Sciences, Rongchang 402460, China.
² Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.

Abstract

This study aimed to reveal the potential genetic basis for litter size, coat colour, black middorsal stripe and skin colour by combining genome-wide association analysis (GWAS) and selection signature analysis and ROH detection within the Youzhou dark (YZD) goat population (n = 206) using the Illumina GoatSNP54 BeadChip. In the GWAS, we identified one SNP (snp54094-scaffold824-899720) on chromosome 11 for litter size, two SNPs on chromosome 26 (snp11508-scaffold142-1990450, SORCS3) and chromosome 12 (snp55048-scaffold842-324525, LOC102187779) for coat colour and one SNP on chromosome 18 (snp56013-scaffold873-22716, TCF25) for the black middorsal stripe. In contrast, no SNPs were identified for skin colour. In selection signature analysis, 295 significant iHS genomic regions with a mean |iHS| score > 2.66, containing selection signatures encompassing 232 candidate genes were detected. In particular, 43 GO terms and one KEGG pathway were significantly enriched in the selected genes, which may contribute to the excellent environmental adaptability and characteristic trait formation during the domestication of YZD goats. In ROH detection, we identified 4446 ROH segments and 282 consensus ROH regions, among which nine common genes overlapped with those detected using the iHS method. Some known candidate genes for economic traits such as reproduction (TSHR, ANGPT4, CENPF, PIBF1, DACH1, DIS3, CHST1, COL4A1, PRKD1 and DNMT3B) and development and growth (TNPO2, IFT80, UCP2, UCP3, GHRHR, SIM1, CCM2L, CTNNA3 and CTNNA1) were revealed by iHS and ROH detection. Overall, this study is limited by the small population size, which affects the results of GWAS to a certain extent. Nevertheless, our findings could provide the first overview of the genetic mechanism underlying these important traits and provide novel insights into the future conservation and utilisation of Chinese goat germplasm resources.

Keywords: Youzhou dark goat; genome-wide association study; litter size; morphological traits; runs of homozygosity; selection signature analysis.

Publication types

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

MeSH terms

Animals
Female
Genome
Genome-Wide Association Study*
Goats* / genetics
Homozygote
Litter Size / genetics
Pregnancy

Grants and funding

This work was supported by the National Natural Science Foundation of China (No. 31672393); Chongqing Performance Incentive and Guide Special Projects (No. 21529); the Natural Science Foundation of Chongqing (cstc2019jcyj-msxmX0063); the Key R & D Project in Agriculture and Animal Husbandry of Rongchang (No. 22544C); and the Special key project of technological innovation and application development in Chongqing, China (cstc2021jscx-gksbX0008).