Unraveling candidate genes related to heat tolerance and immune response traits in some native sheep using whole genome sequencing data

Saadatabadi, L. M. P.; Mohammadabadi, Mohammadreza; Nanaei, Hojjat Asadollahpour; Ghanatsaman, Zeinab Amiri; Stavetska, Ruslana; Kalashnyk, Oleksandr; Kochuk-Yashchenko, O.; Кучер, Д. М.

doi:10.1016/j.smallrumres.2023.107018

Cited by 2 publications

(1 citation statement)

References 94 publications

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“…The adaptation of domestic animals located in tropical regions to hot environmental conditions may have influenced their physical characteristics, such as hair color and skin pigmentation, which are directly associated with heat loss capacity [ 35 ]. For example, it has been reported that indigenous sheep breeds in hot and desert climates have coarse wool coats [ 36 ], while the majority of goat populations in cold geographical regions produce cashmere wool [ 37 ]. Generally, Pakistan has a tropical climate with an extreme annual range of temperature, which ranks it globally among the top ten most prone nations to climate change [ 38 ].…”

Section: Resultsmentioning

confidence: 99%

Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats

Zhang,

Asadollahpour Nanaei,

Jafarpour Negari

et al. 2024

BMC Genomics

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Background Since domestication, both evolutionary forces and human selection have played crucial roles in producing adaptive and economic traits, resulting in animal breeds that have been selected for specific climates and different breeding goals. Pakistani goat breeds have acquired genomic adaptations to their native climate conditions, such as tropical and hot climates. In this study, using next-generation sequencing data, we aimed to assess the signatures of positive selection in three native Pakistani goats, known as milk production breeds, that have been well adapted to their local climate. Results To explore the genomic relationship between studied goat populations and their population structure, whole genome sequence data from native goat populations in Pakistan (n = 26) was merged with available worldwide goat genomic data (n = 184), resulting in a total dataset of 210 individuals. The results showed a high genetic correlation between Pakistani goats and samples from North-East Asia. Across all populations analyzed, a higher linkage disequilibrium (LD) level (– 0.59) was found in the Pakistani goat group at a genomic distance of 1 Kb. Our findings from admixture analysis (K = 5 and K = 6) showed no evidence of shared genomic ancestry between Pakistani goats and other goat populations from Asia. The results from genomic selection analysis revealed several candidate genes related to adaptation to tropical/hot climates (such as; KITLG, HSPB9, HSP70, HSPA12B, and HSPA12B) and milk production related-traits (such as IGFBP3, LPL, LEPR, TSHR, and ACACA) in Pakistani native goat breeds. Conclusions The results from this study shed light on the structural variation in the DNA of the three native Pakistani goat breeds. Several candidate genes were discovered for adaptation to tropical/hot climates, immune responses, and milk production traits. The identified genes could be exploited in goat breeding programs to select efficient breeds for tropical/hot climate regions.

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Section: Resultsmentioning

confidence: 99%

Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats

Zhang,

Asadollahpour Nanaei,

Jafarpour Negari

et al. 2024

BMC Genomics

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Data of whole-genome sequencing of Karakul, Zel, and Kermani sheep breeds

Saadatabadi,

Mohammadabadi,

Ghanatsaman

et al. 2023

BMC Res Notes

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Objective The data provided herein represent the whole-genome sequencing data associated with three sheep breeds of Iranian native breeds. Sheep are the first domesticated animals that, during the long path of the evolution process, have created gene variants with desirable phenotypic effects, so they can be suitable models for biomedical research. In addition, sheep have a vital role in providing protein to a notable part of the human population around the world. Data description Ten blood samples were taken from three Iranian native sheep breeds, the Zel, Karakul, and Kermani kinds. Blood samples genomes were extracted using the salting-out technique. The Illumina NovaSeq 6000 platform was used to carry out sequencing of the whole genome in a laboratory in China. All sequence information is available through the NCBI database in the sequence read archive (SRA) format under the accession number PRJNA904537. The dataset presented here can provide a useful resource for genome analysis of livestock breeds adapted to hot and dry regions.

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Unraveling candidate genes related to heat tolerance and immune response traits in some native sheep using whole genome sequencing data

Cited by 2 publications

References 94 publications

Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats

Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats

Data of whole-genome sequencing of Karakul, Zel, and Kermani sheep breeds

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