Abstract Camels play a crucial role in supporting livelihoods and productivity in desert regions. Despite their importance, and our understanding of their genetic composition remains limited. To address this gap, we constructed a telomere-to-telomere (T2T) reference genome for Bactrian camels and carried out a comprehensive genetic analysis concentrating on lactation traits and dwarf defect. The newly assembled genome spans 2.46 Gb in size with a contig N50 of 71.57 Mb and successfully organized into 22 T2T chromosomes with only 7 gaps remaining. Utilizing this comprehensive genome, we detected a total of 33,076,298 genetic variations across the Bactrian camel genome, increasing the effective variant calling rate by 28.14%. A genome-wide association study of 148 lactating Bactrian camels identified 467 significant variations (P − 6) associated with lactation traits, implicating 42 important candidate genes, including ACSL3, COL23A1, ITGA9, PDGFD, CXXC4, FARP1, CACNA2D1. Additionally, utilizing a dwarf Bactrian camel as a disease case, we identified the FBN2 gene as a critical regulator of growth characteristics intrinsic to Bactrian camels. A mutation occurring at the site c.1411C > T, resulting in an amino acid substitution from valine to isoleucine(Val > Ile), was found to underlie the dwarf phenotype. In conclusion, this study provides the most complete and detailed genome sequence assembly for Bactrian camels to date, highlighting significant genes and mutation loci affecting milk production and dwarf defect. These findings offer valuable insights for advancing genetic research on camel biology and enhancing economically important traits through selective breeding.
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