Genetic structure of Arabian Peninsula dromedary camels revealed three geographic groups

Long-range linkage disequilibrium events on the genome of dromedary camels as a signal of epistatic and directional positive selection

The genome of dromedary camels has been subjected to various evolutionary forces, such as genetic admixture, natural positive selection, and epistatic selection. These forces are considered as main factors associated with the formation of long-range linkage disequilibrium (LRLD) events. We have analyzed whole-genome data of 56 dromedary camel samples from different geographical regions across the Arabian Peninsula for two main purposes: first, to assess the level of linkage disequilibrium, and second, to identify autosomal LRLD events. The analysis revealed a mean r 2 value of 0.25 (±0.028) over the dromedary autosomes, with a continuous decay until reaching a plateau at inter-variant distances >400 kb. A total of 1847 LRLD events were identified within the dromedary autosomes, which harbor 36 prevalent haplotypes. A level of genetic admixture was observed among the dromedary populations analyzed, which might be a source for the observed LRLD events. Four functional interactions were revealed among the genes found within the LRLD events, with some genes overlapping with prevalent haplotypes, indicative of potential epistatic selection. Genes related to renal function, fertility, thermal regulation, bone structure, and insulin regulation were found among the LRLD genes. These genes, along with the defined prevalent haplotypes, can be considered as hotspots for natural positive selection associated with the LRLD distribution on dromedary genomes. In this study, we have for the first time analyzed the genome of dromedary camels for LRLD events possibly influenced by forces including genetic admixture, epistatic and positive selection. The revealed LRLD elements and prevalent haplotypes should be accounted for when designing breeding programmes to conserve the genetic stock of this well-adapted domestic species.

Review on camel genetic diversity: ecological and economic perspectives

Camels, known as the "Ship of the Desert," play a vital role in the ecosystems and economies of arid and semi-arid regions. They provide meat, milk, transportation, and other essential services, and their resilience to harsh environments makes them invaluable. Despite their similarities, camel breeds exhibit notable differences in size, color, and structure, with over 40 million camels worldwide. This number is projected to increase, underscoring their growing significance. Economically, camels are crucial for food production, tourism, and trade, with camel racing being particularly significant in Arab countries. Their unique physiological traits, such as low disease susceptibility and efficient water conservation, further enhance their value. Camel products, especially meat and milk, offer substantial nutritional and therapeutic benefits, contributing to their high demand. Genetic diversity studies have advanced our understanding of camels' adaptation to extreme environments. Functional genomics and whole-genome sequencing have identified genes responsible for these adaptations, aiding breeding programs and conservation efforts. High-throughput sequencing has revealed genetic markers linked to traits like milk production and disease resistance. The development of SNP chips has revolutionized genetic studies by providing a cost-effective alternative to whole-genome sequencing. These tools facilitate large-scale genotyping, essential for conserving genetic diversity and improving breeding strategies. To prevent the depletion of camel genetic diversity, it is crucial to streamline in situ and ex situ conservation efforts to maintain their ecological and economic value. A comprehensive approach to camel conservation and genetic preservation, involving advanced genomic technologies, reproductive biotechniques, and sustainable management practices, will ensure their continued contribution to human societies.

Positive selection footprints and haplotype distribution in the genome of dromedary camels

Dromedary camels are a domestic species characterized by various adaptive traits. Limited efforts have been employed toward identifying genetic regions and haplotypes under selection that might be related to such adaptations. These genetic elements are considered valuable sources that should be conserved to maintain the dromedaries' adaptability. Here, we have analyzed whole genome sequences of 40 dromedary camels from different Arabian Peninsula populations to assess their genetic relationship and define regions with signatures of selection. Genetic distinction based on geography was observed, classifying the populations into four groups: (1) North and Central, (2) West, (3) Southwest, and (4) Southeast, with substantial levels of genetic admixture. Using the de-correlated composite of multiple signal approach, which combines four intra-population analyses (Tajima's D index, nucleotide diversity, integrated haplotype score, and number of segregating sites by length), a total of 36 candidate regions harboring 87 genes were identified to be under positive selection. These regions overlapped with 185 haplotype blocks encompassing 1 340 haplotypes, of which 30 (∼2%) were found to be approaching fixation. The defined candidate genes are associated with different biological processes related to the dromedaries' adaptive physiologies, including neurological pathways, musculoskeletal development, fertility, fat distribution, immunity, visual development, and kidney physiology. The results of this study highlight opportunities for further investigations at the whole-genome level to enhance our understanding of the evolutionary pressures shaping the dromedary genome.

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

Dromedary camels (Camelus dromedarius) are members of the Camelini tribe within the Camelidae family. They are distributed throughout North Africa, the Arabian Peninsula and Southeast Asia. This domestic species is characterized by its superior adaptability to the harsh desert environment. In this study, whole autosomal data of 29 dromedary samples from the Southeast Arabian Peninsula in Oman; 10 from Muscat, 14 from Al-Batinah, and 5 from Al-Sharqiya, were investigated to assess their genetic relationship and to define candidate signatures of positive selection. A minimal genetic distinction that separates Muscat dromedaries from the other two populations was observed, with a degree of genetic admixture between them. Using the de-correlated composite of multiple signals (DCMS) approach, a total of 47 candidate regions within the autosomes of these dromedary populations were defined with signatures of positive selection. These candidate regions harbor a total of 154 genes that are mainly associated with functional categories related to immune response, lipid metabolism and energy expenditure, optical and auditory functions, and long-term memory. Different functional genomic variants were called on the candidate regions and respective genes that warrant further investigation to find possible association with the different favorable phenotypes in dromedaries. The output of this study paves the way for further research efforts aimed at defining markers for use in genomic breeding programs, with the goal of conserving the genetic diversity of the species and enhancing its productivity.

Identification of local camel populations in Turkiye using morphological, genetic, and breeding info

The aim of this study was to investigate the demographic, morphological, and genetic characteristics of local camel populations reared in the Turkiye provinces of Aydin, Denizli, and Antalya, which have a long history of camel breeding. Although Turkiye has an old history of camel breeding in its historical process, the number of scientific studies aimed at identifying camel populations in Turkiye is almost negligible. In this study, local camel populations in Aydin, Denizli, and Antalya cities of Turkiye were examined in three dimensions as demographic, morphological, and genetic. A face-to-face survey of 117 breeders was used to determine demographic definitions. While the region where local camels were detected the most was determined as Antalya Region with 78.6%, it was determined that 82.6% of the breeders participating in the survey preferred to breed camels due to their docile temperament. Body measurements were made on 45 camels for morphological identification. Moreover, DNA were sampled with oral swabs from 57 camels for phylogenetic analyses using 16 SSR microsatellite loci to identify the genetic structure of local camel populations. The genetic analyses using SSR markers revealed that the camel populations in the Antalya region had a considerably more isolated genetic structure than the Aydin and Denizli populations, and consequently, these populations may be regarded the native camel population.

Domestication of the Dromedary Revisited and Its Consequences for Legislation as to Keeping Livestock or Pet Animals

Being in an advanced stage of domestication is a newly proposed requirement to decide which animals can be safely kept by humans. Dutch legislators were the first to apply it and other European countries may be tempted to adopt a similar approach. Unexpectedly, the Dutch assessors considered the dromedary (Camelus dromedarius) as being insufficiently domesticated and this species will therefore no longer be able to be kept as a production animal from 2024 onwards. In a recent publication on this topic, we showed that the domestication of the dromedary is actually very advanced. In this paper, we apply the same criteria that were used by the Dutch assessors to determine the degree of domestication, taking into account the most recent scientific developments in this area, even though it should be noted that these criteria have neither been peer-reviewed, nor published in an international scientific journal. For the sake of comparison, and in order to validate the procedure, we also applied these criteria to the house cat. The results confirm that the dromedary is highly domesticated, but also that the house cat (Felis silvestris catus) is at most semi-domesticated. Obviously, we agree with the decision of the Dutch legislators to place the house cat on the positive list, but our analysis demonstrates that this was decided on false grounds. Our analysis makes it clear that the requirement of being in an advanced stage of domestication is not suitable. Instead of maintaining this requirement, we recommend implementing evidence-based, peer-reviewed methods to decide which animals can be kept by humans, and to include species specific-guidelines in the legislation on how this can be achieved safely.

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

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.