Genetic basis investigation of wattle phenotype in goat using genome‐wide sequence data

Abstract

In domestic goats, wattles often appear in even numbers, mostly on the neck and a few under the ear. Goat wattle is composed of ectopic cartilage tissue covered by skin and was reported as a dominant inheritance. Thirty‐eight goats from two Southwest Chinese breeds were studied to elucidate the genetic basis of wattle phenotype in goat. Their genomes were sequenced for wide‐genome selective sweep analysis (WGSA) and a genome‐wide association study (GWAS). The WGSA results revealed 500 candidate genes identified by fixation index and π ratio and 261 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched with 195 genes and 38 significantly enriched KEGG items. In particular, three chondrogenesis‐related pathways (Wnt, Hippo and MAPK signaling pathways) were found. Among the 500 genes, 474 were enriched to 2855 Gene Ontology items, and four (BMP2, BMP4, RARA and MSX1) were annotated in the regulation and development of chondrogenesis. Four chondrogenesis‐related genes (GREM1, NEDD4, ATG7 and ITGA1) were identified from 519 single‐nucleotide polymorphisms (SNPs) with a GWAS above the threshold. Six and 11 SNPs on chromosome 10 are located on GREM1 and NEDD4 respectively, and the highest numbers of SNPs on chromosomes 20 and 22 are located on ITGA1 and ATG7 respectively. All of these genes are related to cartilage development. This study identified a series of genes related to chondroplasia by GWAS and WGSA and presented the possibility that wattle inheritance may be influenced by multiple genes. This work provides a new theoretical understanding of the hereditary basis of wattle phenotype.

Phenotypic and Genomic Characterization of the Comune di Sicilia Goat: Towards the Conservation of an Endangered Local Breed

“…FAN1 and TRPM1 genes were retained in both methods. Among the identified genes, SLC9A9 and NEDD4 genes were previously accounted as a potential candidate gene for wattle presence in goat [42]. Interestingly, our analyses identified both the NEDD4 gene (included in ROH of animals with wattles) and its binding protein N4BP1 (through F ST ), further supporting their potential roles in the development of wattles in goats.…”

Novel Heredity Basis of the Four-Horn Phenotype in Sheep Using Genome-Wide Sequence Data

“…Indeed, a private population's genetic background can severely influence the identification of target-trait-associated markers when a single breed represents the target trait in a GWAS. Accordingly, different associated candidate genomic regions of goat wattle traits were identified from previous reports with various breeds [48,49]. Furthermore, several GWASs on sheep ear size have shown an inconsistently associated candidate genomic region because of the genetic composition of the testing animals [50,51].…”

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

“…First, two genes, namely ATG7 and MAP1LC3A , were found to be associated with the ferroptosis pathway in the LN versus NJ comparison group. Studies have demonstrated that ATG7 is activated by SIRT1 , enhancing chondrocyte autophagy by deacetylating lysine residues to ensure cartilage integrity (Zhang et al., 2022). Additionally, it has been shown that knockdown of ULK1 in goat support cells reduces autophagy activation, as evidenced by reduced expression of the autophagy‐related marker ATG7 (Pang et al., 2019).…”