Browsing by Author "Kyalo, Martina"

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Dataset: SNP genotyping of indigenous goats of Uganda based on the Goat_IGGC_65K_v2 illumina chip
(2024-05-23) Nantongo, Ziwena; Birungi, Josephine; Obol Opiyo, Stephen; Shirima, Gabriel; Mugerwa, Swidiq; Mutai, Collins; Kyalo, Martina; Munishi, Linus; Agaba, Morris; Mrode, Raphael
Uganda's indigenous goats are characterised based on ethnic communities that raise them, average mature weight, and hair coat characteristics. Uganda's indigenous goats have been genotyped based on the Goat_IGGC_65K_v2 illumina chip to study their population structure and genetic characteristics. Information generated from this data is vital for the sustainable utilisation, development, and conservation of Uganda's goat genetic resources.
Dataset: SNP genotyping of indigenous goats of Uganda based on the Goat_IGGC_65K_v2 illumina chip
(Zenodo, 2024) Nantongo, Ziwena; Birungi, Josephine; Obol Opiyo, Stephen; Shirima, Gabriel; Mugerwa, Swidiq; Mutai, Collins; Kyalo, Martina; Munishi, Linus; Agaba, Morris; Mrode, Raphael
Uganda's indigenous goats are characterised based on ethnic communities that raise them, average mature weight, and hair coat characteristics. Uganda's indigenous goats have been genotyped based on the Goat_IGGC_65K_v2 illumina chip to study their population structure and genetic characteristics. Information generated from this data is vital for the sustainable utilisation, development, and conservation of Uganda's goat genetic resources. Methods The data was collected from genomic DNA extracted from ear tissue samples of 1032 indigenous goats from different agro-ecological zones of Uganda. The study aimed to characterise the genetic diversity, population structure and signatures of selection of indigenous goats in different agroecological zones of Uganda. Indigenous goats were identified in their known phenotypic/ ethnic classifications of Mubende, Kigezi and Small East African goats in all the 10 agroecologies. Ear tissue samples were collected from each goat using the allflex tissue sampling system that allows for no cross contamination as each sample self locks in a single use tube after it is collected. Genomic DNA was extracted from each sample using the TANBEAD automated DNA extraction system with the 6T2 total tissue DNA extraction kit. DNA samples were genotyped based on the Goat_IGGC_65K_v2 illumina chip. Data processing After genotyping, 59725 SNPs from 1032 genotypes were received in PLINK format. The data was opened in Tassel Version 5.2 and saved as VCF format for further processing. The near complete goat genome (ARS1) was used as reference to align all the SNPs to the right chromosomes and chromosome positions using R (version 4.3.3) software. The final data set was saved as a VCF file for analysis.
Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations
(Frontiers, 2024-05-30) Nantongo, Ziwena; Birungi, Josephine; Opiyo, Stephen; Shirima, Gabriel; Mungerwa, Swidiq; Mutai, Collins; Kyalo, Martina; Munishi, Linus; Agaba, Morris; Mrode, Raphael
Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda’s indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda’s indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda’s goat genetic resources.