Signatures of selection, and environmental suitability mapping of village-based indigenous chickens from certain regions of Limpopo and KwaZulu-Natal provinces of South Africa.
Mogano, R. R.1,2, Rasekgoalo, T.3,4, Mpofu, T. J.2, Mtileni, B.2, Dzomba, E. F.4, Hadebe, K.*1
1 Agricultural Research Council, Biotechnology Platform, Private Bag X5, Ondersterpoort, 0110, South Africa
2 Department of Animal Science, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
3 Limpopo Department of Agriculture & Rural Development, Mara Research Station, Louis Trichardt, South Africa
4 Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, South Africa
The conservation of indigenous chicken has long been recognized in South Africa conservation of indigenous chicken was established in 1994 with the aim of conserving the gene pool of the different native lines and promoting their sustainable use in food production. Climate change, consumer preference, and market demand for high-performing with short turnaround times and established breeds continue to threaten locally adapted chicken populations in various ways. To promote improvement and conservation strategies for these chickens, the study proposed the combination of genetics and landscape genomics approaches as descriptors to be considered. The current study explored signatures of selection in reference to the local adaptation of village-based indigenous chickens from various regions of the two provinces and mapped their environmental suitability across the country. A total of 244 village chickens from rural areas of Capricorn (n=85) and Sekhukhune (n=113) districts of Limpopo Province; Harry Gwala (n=21) and uMzinyathi (n=25) districts of KwaZulu-Natal Province were genotyped using the Illumina 60K BeadChip Single Nucleotide Polymorphisms (SNPs). The Ovambo (OV; n=10), Potchefstroom KoeKoek (PK; n=20), Venda (VD; n=20), and Naked Neck (NN; n=20), New Hampshire (NH; n=10), White Leghorn (WL; n=10) and White Plymouth Rock (WR; n=10) breeds from Agricultural Research Council, Poultry Breeding Unit were used as reference, unravel of breed specific signatures of selection populations and representative of a flock managed under conservation. PC1 and PC2 explained 5.64% of the total variation and resulted in 5 clusters with the Venda, Naked Neck, and White Leghorn being separated from village chickens. Breed specific loci were detected across the chromosome using different approaches. The first three redundancy analysis (RDA) axes capture 46.8% of the total genetic variation used to detect significant outlier SNPs. A total of 386 outlier SNPs associated with all 10 environmental variables were detected. Using ecological niche modelling, chickens from three villages from Limpopo (Dipakakeng, Mgababa, and Podu) had a localised predicted suitability probability, while chickens originating from Nhlonga village, in KwaZulu-Natal, had a broader distribution of predicted suitability habitats with elevation and BIO6 being important variable. The results of this study provide insight into the genetic potential of indigenous chickens as well the contributing environmental factors to the diversity we see today which can be incorporated in conservation and improvement decisions.
Keywords: landscape genomics, environmental suitability, rural chicken production, indigenous chicken conservation
