Homogeneity of Arabian Peninsula dromedary camel populations with signals of geographic distinction based on whole genome sequence data

Abstract

Dromedary camels in the Arabian Peninsula distribute along different geographical and ecological locations, e.g. desert, mountains and coasts. Here, we are aiming to explore the whole genome sequence data of ten dromedary populations from the Arabian Peninsula to assess their genetic structure, admixture levels, diversity and similarity indices. Upon including reference dromedary and Bactrian camel populations from Iran and Kazakhstan, we characterise inter-species and geographic genetic distinction between the dromedary and the Bactrian camels. Individual-based alpha genetic diversity profiles are found to be generally higher in Bactrian camels than dromedary populations, with the exception of five autosomes (NC_044525.1, NC_044534.1, NC_044540.1, NC_044542.1, NC_044544.1) at diversity orders (q ≥ 2). The Arabian Peninsula camels are generally homogenous, with a small degree of genetic distinction correlating with three geographic groups: North, Central and West; Southwest; and Southeast of the Arabian Peninsula. No significant variation in diversity or similarity indices are observed among the different Arabian Peninsula dromedary populations. This study contributes to our understanding of the genetic diversity of Arabian Peninsula dromedary camels. It will help conserve the genetic stock of this species and support the design of breeding programmes for genetic improvement of favorable traits.

Signatures of purifying selection and site-specific positive selection on the mitochondrial DNA of dromedary camels (Camelus dromedarius)

“…The later divergence between the dromedary and Bactrian camels, about 4.4 Mya, and the different geographical distribution of these two species may explain the mitochondrial genetic distinction observed between them. Such separation has also been observed previously at autosomal level using whole genome sequence data (Ming et al, 2020, Bahbahani andAlmathen, 2022). The genetic distinction between domestic and wild Bactrian camels can likely be attributed to the 1.1 Mya divergence between them (Burger et al, 2019).…”

“…In parallel to transporting goods, dromedaries were used to transfer people from Africa and different parts of the Arabian Peninsula to Makkah during the annual Pilgrimage (Wilson, 1998). All of these practices were associated with high interbreeding and gene flow between the dromedary camels along the region, which have also been observed using whole genome sequence data (Bahbahani and Almathen, 2022). Current breeding practices of local camel owners, which rely on random mating between camels, further enhance gene flow between dromedary populations.…”

“…Whole-genome sequencing data for 102 samples was retrieved from the European Nucleotide Archive. This included: 21 dromedary samples from the Arabian Peninsula (Bioproject accession number: PRJEB47650) (Bahbahani and Almathen, 2022); four dromedaries from Iran, 31 domestic Bactrian camels, and 19 wild Bactrian camels from Central Asia (Bioproject accession number: PRJNA383081) (Ming et al, 2020); and 27 camel samples belong to the Lamini tribe from South America: Llama (n = 7), Vicuna (n = 6), Guanaco (n = 7), and Alpaca (n = 7) (Bioproject accession number: PRJNA612032) (Fan et al, 2020) (Table S2).…”

Assessing genetic diversity and defining signatures of positive selection on the genome of dromedary camels from the southeast of the Arabian Peninsula

“…These groups correspond to three geographical locations: (1) North, Central, and West, (2) Southwest, and (3) Southeast. Similarly, Bahbahani and Almathen ( 14 ) observed the same geographic genetic distinctions based on whole genome sequence analyses.…”

“…Assessing the genetic diversity and relationship of different dromedary camel populations was confined previously to using autosomal microsatellites ( 8 , 11 ) and mitochondrial DNA markers ( 10 , 12 ). Recent efforts have also utilized genotyping-by-sequencing (GBS) ( 13 ) and whole genome sequence data ( 14 ). A recent study by Almathen et al ( 11 ) differentiated dromedary camel populations from the Arabian Peninsula into three groups utilizing 17 microsatellite loci.…”