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

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.

Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle

“…In a GWAS, CNTNAP5 was speculated to be a candidate gene associated with growth and carcass traits including body weight and body fat deposition in four Beninese indigenous cattle breeds [59], as well as hip cross height in Brahman cattle [11]. CTNNA3 was associated with development and growth by iHS and ROH detection based on genome-wide SNP markers in Youzhou dark goats [60] and in Hu sheep [61], as well as skeletal muscle during chicken embryonic development [62]. A large body of published studies may provide evidence for certain genes involved in the regulation of body conformation traits.…”

A Multibreed Genome-Wide Association Study for Cattle Leukocyte Telomere Length

“…A GWAS in Holstein–Friesian cattle identified 14 candidate genes for TL at birth and 9 at first lactation [ 36 ]. However, the genomic architecture of many quantitative traits in livestock differs substantially across various breeds [ 46 , 47 ]. Therefore, the GWAS of TL in non-Holstein breeds may help to gain a complete view of the genetic basis of TL variation in cattle.…”

Functional Characterization of the Almstn2 Gene and Its Association with Growth Traits in the Yellowfin Seabream Acanthopagrus latus (Hottuyn, 1782)

“…A single-nucleotide polymorphism (SNP) is a genetic marker that has many excellent characteristics. Firstly, there are a large number and wide distribution in the genome; secondly, some SNPs are located in the internal coding region of genes, and can be used as molecular selection sites for target traits; thirdly, the detection method is simple, and the large-scale experiment and detection automation requirements are low, which can greatly shorten the working time; and, lastly, an SNP is a single-nucleotide mutation with a low mutation rate, and has a higher genetic stability compared with repeat sequence markers such as microsatellites [2,[5][6][7][8][9]. Therefore, they have been widely used in the research of growth traits related to aquatic animals.…”