Genetic diversity of different indigenous chicken ecotypes using highly polymorphic MHC-linked and non-MHC microsatellite markers

Ngeno, Kiplangat; Waaij, E.H. van der; Megens, Hendrik‐Jan; Kahi, A.K.; Arendonk, J.A.M. van; Crooijmans, R.P.M.A.

doi:10.1017/s2078633614000484

Cited by 23 publications

(44 citation statements)

References 27 publications

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“…This is not surprising since these areas border each other geographically. These findings corroborated the observations of a study conducted in Kenya where the Mantel test had uncovered a positive association between hereditary and geographic distances [57]. Our study also confirmed that geographic distances affected the population's genetic structure [57].…”

Section: Phylogenetic Relationship and Population Structuresupporting

confidence: 92%

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Habimana¹,

Okeno²,

Ngeno³

et al. 2020

PLoS ONE

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Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chickens were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. One hundred eighty-six (186) distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant (p<0.05) in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.

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Section: Phylogenetic Relationship and Population Structuresupporting

confidence: 92%

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Habimana¹,

Okeno²,

Ngeno³

et al. 2020

PLoS ONE

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“…Consequently, there is a high influx of genes in these regions This is not surprising since these areas border each other geographically. These findings corroborated the observations of a study conducted in Kenya where the Mantel test had uncovered a positive association between hereditary and geographic distances [43]. Our study also confirmed that geographic distances affected the population’s genetic structure [43].…”

Section: Discussionsupporting

confidence: 92%

“…These findings corroborated the observations of a study conducted in Kenya where the Mantel test had uncovered a positive association between hereditary and geographic distances [43]. Our study also confirmed that geographic distances affected the population’s genetic structure [43]. The portion of SW chicken populations that clustered with the exotic chicken (control) could be attributed to the fact that different crossing programmes between IC and improved chicken breeds have been introduced in that region to improve the genetic potential of IC in Rwanda [44].…”

Section: Discussionsupporting

confidence: 91%

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Habimana

Okeno

Ngeno

et al. 2019

Preprint

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AbstractRwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chicken were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. 186 distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.

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“…1 European Nucleotide Archive (ENA) https://www.ebi.ac.uk/ena/data/view/PRJEB1683; 2 (Bosse et al., ) 3 (Yang et al., ) 4 (Derks et al., ) 5 (Ngeno, ) 6 (Ngeno et al., ) 7 (Derks et al., ), 8 (Derks, Megens et al. (submitted)).…”

Section: Methodsmentioning

confidence: 99%

“…Re‐sequence data from a total of 76 pigs were retrieved from the European Nucleotide Archive (ENA) accession code ERP001813. Re‐sequence data from eight African village chicken were obtained from (Ngeno, and described in Ngeno et al., ). Since Ngeno, is a PhD thesis, the relevant vcf files of the village chicken are deposited into https://www.animalgenome.org/repository/pub/WUR2018.0809/.…”

Section: Data Archiving Statementmentioning

confidence: 99%

Deleterious alleles in the context of domestication, inbreeding, and selection

Bosse

Megens

Derks

et al. 2018

Evolutionary Applications

109

101

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Each individual has a certain number of harmful mutations in its genome. These mutations can lower the fitness of the individual carrying them, dependent on their dominance and selection coefficient. Effective population size, selection, and admixture are known to affect the occurrence of such mutations in a population. The relative roles of demography and selection are a key in understanding the process of adaptation. These are factors that are potentially influenced and confounded in domestic animals. Here, we hypothesize that the series of events of bottlenecks, introgression, and strong artificial selection associated with domestication increased mutational load in domestic species. Yet, mutational load is hard to quantify, so there are very few studies available revealing the relevance of evolutionary processes. The precise role of artificial selection, bottlenecks, and introgression in further increasing the load of deleterious variants in animals in breeding and conservation programmes remains unclear. In this paper, we review the effects of domestication and selection on mutational load in domestic species. Moreover, we test some hypotheses on higher mutational load due to domestication and selective sweeps using sequence data from commercial pig and chicken lines. Overall, we argue that domestication by itself is not a prerequisite for genetic erosion, indicating that fitness potential does not need to decline. Rather, mutational load in domestic species can be influenced by many factors, but consistent or strong trends are not yet clear. However, methods emerging from molecular genetics allow discrimination of hypotheses about the determinants of mutational load, such as effective population size, inbreeding, and selection, in domestic systems. These findings make us rethink the effect of our current breeding schemes on fitness of populations.

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Genetic diversity of different indigenous chicken ecotypes using highly polymorphic MHC-linked and non-MHC microsatellite markers

Cited by 23 publications

References 27 publications

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Deleterious alleles in the context of domestication, inbreeding, and selection

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