Genetic diversity and population structure among indigenous and imported goat breeds in Kenya

Waineina, R.W.; Ngeno, Kiplangat; Okeno, T.O.; Ilatsia, E. D.

doi:10.46265/genresj.eqfq1540

Cited by 6 publications

(7 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The iHS and XP-EHH analyses intersect detected candidate regions mostly in Saanen and Galla breeds on chromosomes 3 (46.0–53.0 Mb). The reasons might be Saanen and Galla breed alleles have almost reached the point of fixation, which is in agreement with Waineina et al (2021 ) findings that the two breeds were less admixed than the other breeds and are managed in seclusion from other breeds in this study. Additionally, random genetic drift and natural selection for adaptation to their environment might have contributed to the detection of strong signals in candidate selection signatures.…”

Section: Discussionsupporting

confidence: 92%

“…Although the history of the selected goats in this study has witnessed founding events and introgression, demographic events most likely have influenced the pattern of the selected goats’ genome diversity ( Waineina et al, 2021 ). It is challenging to differentiate between the effects of natural selection and demographic events.…”

Section: Discussionmentioning

confidence: 99%

“…It is very possible that some key genome regions might not have been detected because the genome coverage and ascertainment bias of the tool was toward pure dairy goats, Saanen and Alpine, among others, which were included in the panel discovery ( Tosser-Klopp et al, 2014 ). Worth noting, according to Waineina et al (2021) , the breeds in this study were admixed at different levels. Therefore, further research is recommended using whole-genome deep sequencing to build up the findings from this study.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya

et al. 2022

Self Cite

View full text Add to dashboard Cite

Artificial and natural selection in livestock is expected to leave unique footprints on their genomes. Goat breeds in Kenya have evolved for survival, breeding, and production in various harsh ecological areas, and their genomes are likely to have acquired unique alleles for adaptation to such diverse production environments and other traits of economic importance. To investigate signals of selection for some selected goat breeds in Kenya, Alpine (n = 29), Galla (n = 12), Saanen (n = 24), and Toggenburg (n = 31) were considered. A total of 53,347 single-nucleotide polymorphisms (SNPs) generated using the Illumina GoatSNP50 BeadChip were analyzed. After quality control, 47,663 autosomal single-nucleotide polymorphisms remained for downstream analyses. Several complementary approaches were applied for the following analyses: integrated Haplotype Score (iHS), cross-population-extended haplotype homozygosity (XP-EHH), hapFLK, and FLK. A total of 404 top genomic regions were identified across all the four breeds, based on the four complementary analyses. Out of the 16 identified putative selection signature regions by the intersection of multiple-selective signal analyses, most of the putative regions were found to overlap significantly with the iHS and XP-EHH analyses on chromosomes 3, 4, 10, 15, 22, and 26. These regions were enriched with some genes involved in pathways associated directly or indirectly with environmental adaptation regulating immune responses (e.g., HYAL1 and HYAL3), milk production (e.g., LEPR and PDE4B), and adaptability (e.g., MST1 and PCK). The results revealed few intersect between breeds in genomic selection signature regions. In general, this did not present the typical classic selection signatures as predicted due to the complex nature of the traits. The results support that some various selection pressures (e.g., environmental challenges, artificial selection, and genome admixture challenges) have molded the genome of goat breeds in Kenya. Therefore, the research provides new knowledge on the conservation and utilization of these goat genetic resources in Kenya. In-depth research is needed to detect precise genes connected with adaptation and production in goat breeds in Kenya.

show abstract

Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…Similarly, AB, CH and BG goat breeds displayed higher Ne at 983 generations ago, suggesting that these animals could have been influenced by artificial selection and probably due to the upward selection intensity, the higher sample size and the high inbreeding coefficient, whereas a decreasing recent Ne was observed for the MR and AF breeds, signifying that these animals were subjected to genetic drift that resulted in decreased population size. This result is consistent with that reported by [42] for the Kenya Tankwa ecotype and commercial goat breeds across generations, which detected higher effective population sizes. Our results revealed the highest and lowest number of variants detected on chromosomes 1 and 25, respectively.…”

Section: Genetic Diversity Characteristicssupporting

confidence: 93%

Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing

Gebreselase,

Nigussie,

Wang

et al. 2024

Animals

View full text Add to dashboard Cite

Goats belong to a group of animals called small ruminants and are critical sources of livelihood for rural people. Genomic sequencing can provide information ranging from basic knowledge about goat diversity and evolutionary processes that shape genomes to functional information about genes/genomic regions. In this study, we exploited a whole-genome sequencing data set to analyze the genetic diversity, population structure and selection signatures of 44 individuals belonging to 5 Ethiopian goat populations: 12 Aberegalle (AB), 5 Afar (AF), 11 Begait (BG), 12 Central highlands (CH) and 5 Meafure (MR) goats. Our results revealed the highest genetic diversity in the BG goat population compared to the other goat populations. The pairwise genetic differentiation (FST) among the populations varied and ranged from 0.011 to 0.182, with the closest pairwise value (0.003) observed between the AB and CH goats and a distant correlation (FST = 0.182) between the BG and AB goats, indicating low to moderate genetic differentiation. Phylogenetic tree, ADMIXTURE and principal component analyses revealed a classification of the five Ethiopian goat breeds in accordance with their geographic distribution. We also found three top genomic regions that were detected under selection on chromosomes 2, 5 and 13. Moreover, this study identified different candidate genes related to milk characteristics (GLYCAM1 and SRC), carcass (ZNF385B, BMP-7, PDE1B, PPP1R1A, FTO and MYOT) and adaptive and immune response genes (MAPK13, MAPK14, SCN7A, IL12A, EST1 DEFB116 and DEFB119). In conclusion, this information could be helpful for understanding the genetic diversity and population structure and selection scanning of these important indigenous goats for future genetic improvement and/or as an intervention mechanism.

show abstract

“…Kenya is home to native goat populations widely distributed across diverse agroecological regions 13 . These goats play a vital role in supporting rural household economies by providing food and nutritional security through milk and meat supply, generating income from surplus livestock sales, and serving as insurance against unforeseen risks 1 .…”

Section: Introductionmentioning

confidence: 99%

Assessing the population structure and genetic variability of Kenyan native goats under extensive production system

Kichamu,

Wanjala,

Cziszter

et al. 2024

Sci Rep

View full text Add to dashboard Cite

Indigenous goats are important to many livelihoods. Despite this, they are subjected to indiscriminate crossbreeding. This affects their genetic variability which is needed to survive in current regime of climate change. The study assessed population structure and genetic diversity of Galla and Small East African goats (SEA) using pedigree information. A total of 7384 animals, 5222 of the Galla and 2162 of the SEA breeds, born between the years 1983 and 2022, were utilized. Individuals with known parents were defined as reference population. From the results, the maximum generation traced for Galla and SEA populations was 14.6 and 14.5, respectively. However, only 6 and 5 generations for Galla and SEA were complete. Pedigree completeness increased with the increasing number of generations. The average generation interval (GI) for Galla and SEA was 3.84 ± 0.04 and 4.4 ± 0.13 years. The average increase in the rate of inbreeding per generation for Galla and SEA was 0.04 and 0.05, with the effective ancestors and founders (fa/fe) ratio being same (1.00) for both breeds. Fifty percent (50%) of the genetic variability in the populations was contributed by 3 and 1 ancestor for Galla SEA, respectively. The effective population size (Ne) was 5.19 and 4.77 for Galla and SEA. Therefore, the current breeding programs should be changed to avoid future genetic bottlenecks in this population. These findings offer an opportunity to enhance the current genetic status and management of Kenyan native goats and other regions with similar production systems.

show abstract

Genetic diversity and population structure among indigenous and imported goat breeds in Kenya

Cited by 6 publications

References 30 publications

Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya

Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya

Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing

Assessing the population structure and genetic variability of Kenyan native goats under extensive production system

Contact Info

Product

Resources

About