Genome Diversity and Signatures of Selection for Production and Performance Traits in Dromedary Camels

Abstract

Dromedary camels (Camelus dromedarius) are single-humped animals found throughout the deserts of Africa, the Arabian Peninsula, and the southwest of Asia. This well-adapted species is mainly used for milk and meat production, although some specific types exhibit superior running performance and are used in racing competitions. However, neither performance nor production camels are bred under intensive genomic selection programs with specific aims to improve these traits. In this study, the full genome sequence data of six camels from the Arabian Peninsula and the genotyping-by-sequencing data of 44 camels (29 packing and 15 racing) from Sudan were analyzed to assess their genome diversities, relationships, and candidate signatures of positive selection. Genome ADMIXTURE and principle component analyses indicate clear geographic separation between the Sudanese and the Arabian Peninsula camels, but with no population-specific genetic distinction within populations. Camel samples from the Arabian Peninsula show higher mean heterozygosity (0.560 ± 0.003) than those from Sudan (0.347 ± 0.003). Analyses of signatures of selection, using pooled heterozygosity (Hp) approach, in the Sudanese camels revealed 176, 189, and 308 candidate regions under positive selection in the combined and packing and racing camel populations, respectively. These regions host genes that might be associated with adaptation to arid environment, dairy traits, energy homeostasis, and chondrogenesis. Eight regions show high genetic differentiation, based on Fst analysis, between the Sudanese packing and racing camel types. Genes associated with chondrogenesis, energy balance, and urinary system development were found within these regions. Our results advocate for further detailed investigation of the genome of the dromedary camel to identify and characterize genes and variants associated with their valuable phenotypic traits. The results of which may support the development of breeding programs to improve the production and performance traits of this unique domesticated species.

Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran

“…Principal component analysis suggested that Sudanese camel populations are almost homogeneous [11]. On the contrary, PCA results distinguished the Chinese Bactrian camels from the Mongolian Bactrian camels very well [31].…”

“…Heterozygosity of the Iranian central desert dromedaries was predicted as low (0.25 ± 0.30). Arabian Peninsula and Sudanese dromedaries' H O where 0.560 ± 0.003 and 0.347 ± 0.003, respectively [11]. The camels sampled from the central desert of Iran have higher relationships than dromedaries from Sudan (median A jk = − 0.007 ± 0.018) and lower ones than individuals from the Arabian Peninsula (median A jk = 0.347 ± 0.093) [11].…”

“…The main limitations that camel breeding is facing in Iran are the lack of phenotypic records and pedigrees, small herd size and missing connectedness, and genetic evaluations. Previous investigations about genetic diversity and population structure in dromedaries were confined to microsatellite markers, mitochondrial DNA (mtDNA) [8], geographical regions, e.g., Kenya [9], and Pakistan [10], and candidate gene sequencing [11]. Next-generation sequencing platforms have prepared suitable methods for population genetic analyses in local or regional populations/ breeds to investigate effective population size, breed formation, demographic history, selection and genetic drift (interpreted by linkage disequilibrium (LD)) at the whole-genome level [12].…”

“…Recently, dromedaries' genome sequences have been assembled into chromosomes [14,15] and the whole genomes of two Iranian dromedary camels were analyzed. This genomic information could prompt genome-wide association studies (GWAS) and genomic selection in Iranian camel breeding [16], similar to populations from the Arabian Peninsula and Sudan, which showed signatures of selection in regions associated with adaptation to arid environment, dairy traits, energy homeostasis, and chondrogenesis [11]. To understand the genetic makeup and relatedness of Iranian dromedaries and to create the basis for future breeding programs and genomic selection, we assessed the genomic diversity, linkage disequilibrium and population structure of dromedary camels in different regions of the central desert of Iran.…”

GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds

“…For example, genotyping-by-sequencing (GBS) on livestock has been a sufficient solution that is required for population genetic and genomic studies [15]. This method has been successfully used to identify selection signatures of important economic traits in cattle [16], pigs [17,18], chicken [19], and camels [20]. The goal of this investigation was to perform a pair-wise marker differentiation comparison in a genome-wide scan between Noire de Thibar and Queue fine de l'ouest Tunisian sheep breeds, using genotyping-by-sequencing data to reveal putative regions under strong and recent selection.…”