Genome-Wide Association Study of Copy Number Variation and Early Growth Traits in Inner Mongolian Cashmere Goats
- Posted
- Server
- Preprints.org
- DOI
- 10.20944/preprints202505.2485.v1
In goat breeding programs, early growth traits including birth weight (BW), weaning weight (WW), pre-weaning average daily gain (ADG), and yearling weight (YW) are crucial productivity indicators that directly influence growth rates and economic returns. However, the genetic mechanism of these traits in Inner Mongolia Cashmere goats(IMCGs) has not yet been elucidated. Copy number variation (CNV), as a prevalent form of genomic structural variation and a significant contributor to genetic diversity, has emerged as a valuable molecular marker for complex trait analysis. In this study, we used the genome-wide resequencing data of 461 Inner Mongolia cashmere goats for the first time to detect autosomal CNVs, and performed genome-wide association analysis ( GWAS ) based on CNVs for early growth traits ( BW, WW, ADG, YW ) of IMCGs. Results : We detected 26,003 non-redundant CNVs and 5,014 non-redundant CNVRs, covering a total of 1,015.4 Mb ( 38.97 % ) of the goat autosomal genome. GWAS analysis revealed 11 CNVs significantly associated with early growth traits, including two pleiotropic CNVs simultaneously influencing ADG and WW, suggesting their regulatory roles in growth and fat deposition processes. Through integrated bioinformatics analysis, we identified seven key candidate genes (ZN845, SOX15, FGF11, GPS2, DVL2, SPRY4, and STAT2) associated with early growth traits. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses demonstrated that these genes are primarily involved in biological pathways related to cell proliferation, differentiation, and protein phosphorylation. The identified CNVs were further validated through PCR verification. In addition, t-test was performed on the phenotypes of individuals with significant CNVs and all the IMCGs populations. Among the 11 significant CNVs, 9 were demonstrated to show significant associations with individual phenotypes, indicating the reliability and credibility of the study findings.