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 cons...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-03-01
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| Series: | Animal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1751731124000296 |
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| author | H. Bahbahani A. Alfoudari A. Al-Ateeqi M. Al Abri F. Almathen |
| author_facet | H. Bahbahani A. Alfoudari A. Al-Ateeqi M. Al Abri F. Almathen |
| author_sort | H. Bahbahani |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-24T22:21:35Z |
| format | Article |
| id | doaj.art-951942e282c2455099830d60a46e7ff3 |
| institution | Directory Open Access Journal |
| issn | 1751-7311 |
| language | English |
| last_indexed | 2024-04-24T22:21:35Z |
| publishDate | 2024-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Animal |
| spelling | doaj.art-951942e282c2455099830d60a46e7ff32024-03-20T06:08:59ZengElsevierAnimal1751-73112024-03-01183101098Positive selection footprints and haplotype distribution in the genome of dromedary camelsH. Bahbahani0A. Alfoudari1A. Al-Ateeqi2M. Al Abri3F. Almathen4Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait; Corresponding author.Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, KuwaitEnvironment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, KuwaitDepartment of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, OmanDepartment of Public Health, King Faisal University, 400 Al-Ahsa, Kingdom of Saudi Arabia; Camel Research Center, King Faisal University, 400 Al-Ahsa, Saudi ArabiaDromedary 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.http://www.sciencedirect.com/science/article/pii/S1751731124000296Adaptive traitsCandidate regionsGenome-wide analysisHaplotype blocksSignatures of selection |
| spellingShingle | H. Bahbahani A. Alfoudari A. Al-Ateeqi M. Al Abri F. Almathen Positive selection footprints and haplotype distribution in the genome of dromedary camels Animal Adaptive traits Candidate regions Genome-wide analysis Haplotype blocks Signatures of selection |
| title | Positive selection footprints and haplotype distribution in the genome of dromedary camels |
| title_full | Positive selection footprints and haplotype distribution in the genome of dromedary camels |
| title_fullStr | Positive selection footprints and haplotype distribution in the genome of dromedary camels |
| title_full_unstemmed | Positive selection footprints and haplotype distribution in the genome of dromedary camels |
| title_short | Positive selection footprints and haplotype distribution in the genome of dromedary camels |
| title_sort | positive selection footprints and haplotype distribution in the genome of dromedary camels |
| topic | Adaptive traits Candidate regions Genome-wide analysis Haplotype blocks Signatures of selection |
| url | http://www.sciencedirect.com/science/article/pii/S1751731124000296 |
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