Genome-wide association analysis of neck ring traits in NongHua ma male ducks

ABSTRACT

1. Male NongHua ma ducks have more colourful feathers than females, especially considering that the former have a distinctive neck ring that is different from that of females. This ring development might be influenced by sex selection, the environment, genetics and other elements.

2. Genome-wide association analysis (GWAS) was used to locate candidate genes that affect the neck ring formation of male ducks to investigate the genetic basis of this phenomenon.

3. In this study, the neck ring area and width of 180 male ducks were assessed at ages 80, 90, 100, 110 and 120 d. GWAS was used to identify associated genes. There were 0, 7, 14, 48 and 21 possible candidate genes annotated around the 0, 12, 25, 76 and 40 SNP loci n corresponding regions. A total of 13 candidate genes were identified around 21 SNP sites at the neck ring width of 120 d.

4. These significant genes were annotated and GO and KEGG enrichment analyses were performed. All SNPs that exceeded the significance threshold were annotated and preliminarily screened as candidate genes affecting neck ring formation. From analysis of gene function and enriched KEGG pathways, genes such as THSD1, SLC6A4, DGAT2, PRKDC, B3GAT2, ROR1, GRK7, EXTL3, TXNDC12, COL4A2, PRKG1, ACTR3, were considered important candidate marker sites related to the neck ring. This provided a reference starting point for the genetic mechanism underlying duck feather colour.

KEYWORDS:

• Male duck
• neck ring
• GWAS
• feather colour
• gene
• sexual dimorphism

Acknowledgments

Conceptualisation, Hehe Liu and Huazhen Wang; methodology, Chao Yang and Jianmei Wang; software, Yang Xi; validation, Lili Bai; formal analysis, Chao Yang and Jingjing Qi; investigation, Jiwei Hu; resources, Jiwei Hu; data curation, Hehe Liu; writing-review and editing, Huazhen Wang and Ahsan Mustafa; visualization, Jianmei Wang; supervision, Liang Li; project administration, Hehe Liu and Liang Li; funding acquisition, Hehe Liu and Liang Li. All authors read and agreed to the published version of the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [31872345 and 32072703] and the National Key R&D Program of China [2022YFF1000100].