Modelling environmental suitability and estimating effective population size of South African indigenous chickens implication of conservation.
Mogano, Reneilwe Rose
Mogano, Reneilwe Rose
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Abstract
Indigenous chickens are an important Farm Animal Genetic Resource (AnGR) for poverty alleviation in rural communities across South Africa. Locally adapted populations thrive despite production and climate challenges, as their extensive production system lacks protection from agro-ecological environments, resulting in their diversity. A lack of standardized descriptions, low investment in determining their production potential, and the rise of new markets all contribute to genetic erosion and dilution. Delays in conservation and improvement, limited market access, and low government investments have resulted in only a well-known conservation program for four indigenous chicken breeds in South Africa at the Agricultural Research Council- animal production. This research was therefore carried out to investigate the environmental suitability of indigenous chickens and estimate the risk status in different regions of KwaZulu-Natal and Limpopo provinces, South Africa. A total of 244 village-based indigenous chickens were collected from rural areas in South Africa, including the Harry Gwala (n=21) and uMzinyathi (n=25) districts of KwaZulu-Natal province and Capricorn (n=85), and Sekhukhune (n=113) districts of Limpopo province. A total of 100 conservation flocks: Ovambo (OV; n=10), Potchefstroom Koekoek (PK) (n=20), Naked Neck (NN; n=20), Venda (VD; n =20), White Leghorn (WL; n=10), White Plymouth Rock (WR; n=10), and New Hampshire (NH; n=10) from the Agricultural Research Council-Animal Production (ARC-AP) were used as reference population. All chickens were genotyped using Illumina chicken iSelect SNP60k Bead chip. The raster package in RStudio was used to extract values from 28 environmental variables which included annual trends (e.g., mean annual temperature and annual precipitation), seasonality (e.g., annual range in temperature and precipitation), and extreme or limiting environmental factors (e.g., temperature of the coldest and warmest month, and precipitation of the wet and dry quarters), soil variable, solar radiation and elevation. GQIS software was utilized to align layers, resulting in a 109.47 X 126.24mm layer size, and convert them to ASC files. The GGally r package was used to create a correlation matrix, identifying 10 out of 28 environmental variables as key drivers of environmental adaptation, including minimum temperatures, elevation, soil cation exchange capacity, soil clay content, organic carbon content, soil pH, soil silt content, and solar radiation. ENMeval was used for model tuning and evaluation, which identified linear and quadratic (LQ) features with a regularization-multiple = 0.5 as the best parameter combinations to optimise Maxent and develop suitability maps. Maxent software was used to create suitability maps for chickens in Limpopo and KwaZulu-Natal, with a test gain applied for important variables. Chickens from Dipakakeng, Mgababa, and Podu villages had localized predicted suitability probabilities, while those from Nhlonga had a broader distribution with elevation and BIO6 being important variables. PLINK software was used for genetic diversity calculation. The genetic diversity of indigenous chickens ranged from 0.341 to 0.338 for observed heterozygosity and from 0.381 to 0.387 for expected heterozygosity, whereas the conservation flocks ranged from 0.240 to 0.339 and 0.377 to 1 for both observed and expected heterozygosity. The admixture analysis was conducted using a LEA r package in RStudio, the lowest cross-validation error (0.87) was detected at K = 5. Population structure was done using LEA r package in RStudio, where 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. SNeP software was used to calculate effective population size, both village chickens and conservation flocks showed a steady decrease of effective population size at 12 generations ago. Redundancy analysis (RDA) was done to examine genotype-environment associations using a vegan r package, the first three RDA axes capture 46.8% of total genetic variation, and 386 outlier SNPs associated with all 10 environmental variables were identified. The results of this study provide insight into the risk status, geographic suitability, and contributing environmental factors of indigenous chickens which can be used to influence conservation and improvement decisions
Description
Submitted in partial fulfilment of the requirements for the degree, Master of Agricultural Science in the Department of Animal Sciences, Faculty of Science at the Tshwane University of Technology
Date
2024
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Tshwane University of Technology
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Keywords
Indigenous chickens, Genetic Diversity, Local adaptation, Effective population, Signatures of selection