Screening of genes related to milk production traits in Bactrian camels in eastern and northern Xinjiang region based on whole genome resequencing technology

The eastern and northern parts of Xinjiang are the main camel breeding areas in the region. Currently, there is a lack of systematic comparative genetic studies of local populations with significant phenotypic differences at the whole-genome level. Previous research has shown significant differences in milk production traits between Bactrian camels in the eastern and northern regions of Xinjiang. To further elucidate the genetic differences between the Bactrian camel populations in these two areas and the molecular basis of their lactation traits, this study selected 106 Bactrian camels—55 from three camel farms in the northern region and 51 from one farm in the eastern region—for whole-genome resequencing. Through variant detection, genetic diversity analysis, population structure, and selection signal analysis, a total of 6,451,453 SNPs were identified. The genetic diversity of the northern Bactrian camel population was slightly higher than that of the eastern population, with minimal overall difference. Principal component analysis and phylogenetic tree analysis indicated that the Bactrian camel populations in the eastern and northern regions could be clearly distinguished. GO and KEGG enrichment analyses showed that, compared with the northern population, candidate genes in the eastern population were mainly enriched in the cell membrane and thyroid hormone synthesis pathways. Based on three inter-population selection signal analysis methods (Fst, $$\pi $$, and XP-EHH), 459 intersecting genes were identified, among which eight were candidate genes related to lactation traits: DUOX1, DUOX2, CPQ, CGA, PLCG1, FYN, GNRHR, and TRHR. These genes can serve as potential marker sites for future molecular breeding.