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

Chenxi Zhang; Hojjat Asadollahpour Nanaei; Niloufar Jafarpour Negari; Mahmoud Amiri Roudbar; Zeinab Amiri Ghanatsaman; Zhannur Niyazbekova; Xiaojun Yang

doi:10.1186/s12864-024-10387-y

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

BMC Genomics. 2024 May 14;25(1):477. doi: 10.1186/s12864-024-10387-y.

Authors

Chenxi Zhang¹, Hojjat Asadollahpour Nanaei^{2

3

4}, Niloufar Jafarpour Negari⁵, Mahmoud Amiri Roudbar⁶, Zeinab Amiri Ghanatsaman⁷, Zhannur Niyazbekova⁸, Xiaojun Yang⁹

Affiliations

¹ College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
² College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China. h.asadollahpour@agr.uk.ac.ir.
³ College of Life Sciences, Northwest A&F University, Yangling, 712100, China. h.asadollahpour@agr.uk.ac.ir.
⁴ Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran. h.asadollahpour@agr.uk.ac.ir.
⁵ Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran.
⁶ Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful 333, Iran.
⁷ Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.
⁸ Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
⁹ College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China. yangxj@nwafu.edu.cn.

Abstract

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.

Keywords: Adaptation; Candidate genes; Pakistan indigenous goats; Population genomics; Whole-genome sequence.

MeSH terms

Adaptation, Physiological / genetics
Animals
Breeding
Genomics* / methods
Goats* / genetics
Linkage Disequilibrium*
Milk* / metabolism
Pakistan
Phenotype
Polymorphism, Single Nucleotide
Selection, Genetic
Tropical Climate*

Abstract

MeSH terms

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