Genome-wide detection of runs of homozygosity and heterozygosity in Tunchang pigs

• Published in: Animal (Cambridge, England) Vol. 18; no. 8; p. 101236
• Main Authors: Liu, S.Q., Xu, Y.J., Chen, Z.T., Li, H., Zhang, Z., Wang, Q.S., Pan, Y.C.
• Format: Journal Article
• Language: English
• Published: England Elsevier B.V 01.08.2024; Elsevier
• Subjects: Animals; Candidate genes; China; Female; Genome; Heterozygote; Homozygote; Inbreeding; Inbreeding coefficient; Male; Runs of heterozygosity; Runs of homozygosity; Sus scrofa - genetics; Swine - genetics; Tunchang pigs; China; Runs of homozygosity; Inbreeding coefficient; Runs of heterozygosity; Tunchang pigs; Candidate genes
• ISSN: 1751-7311; 1751-732X; 1751-732X
• DOI: 10.1016/j.animal.2024.101236

•Tunchang pigs are famous for superior meat quality and heat tolerance.•Research assessed the genetic diversity and identified breed-specific genes.•Inbreeding events have influenced the population’s inbreeding levels.•Selected genes are closely linked to key economic traits of this breed.•Findings contribute to conservation and genetic improvement for this breed. Tunchang pigs, mainly distributed throughout Hainan Province of China, are well-known for their superior meat quality, crude feed tolerance, and adaptability to high temperatures and humidity. Runs of homozygosity (ROH) can provide valuable information about the inbreeding coefficient in individuals and selection signals that may reveal candidate genes associated with key functional traits. Runs of heterozygosity (ROHet) are commonly associated with balance selection, which can help us understand the adaptive evolutionary history of domestic animals. In this study, we investigated ROHs and ROHets in 88 Tunchang pigs. We also compared the estimates of inbreeding coefficients in individuals calculated based on four methods. In summary, we detected a total of 16 ROH islands in our study, and 100 genes were found within ROH regions. These genes were correlated with economically important traits such as reproduction (e.g., SERPIND1, HIRA), meat quality (e.g., PI4KA, TBX1), immunity (e.g., ESS2, RANBP1), adaption to heat stress (TXNRD2 and DGCR8), and crude food tolerance (TRPM6). Moreover, we discovered 18 ROHet islands harbouring genes associated with reproduction (e.g., ARHGEF12, BMPR2), immune system (e.g., BRD4, DNMT3B). These findings may help us design effective breeding and conservation strategies for this unique breed.