TITLE:
Genetic Diversity and Population Structure of Three Strains of Indigenous Tswana Chickens and Commercial Broiler Using Single Nucleotide Polymormophic (SNP) Markers
AUTHORS:
James Buttie Machete, Patrick Monametsi Kgwatalala, Shalaulani James Nsoso, Nompilo Lucia Hlongwane, John Cassius Moreki
KEYWORDS:
Genetic Distances, Genetic Diversity, Indigenous Tswana Chickens, Population Structure, SNPs
JOURNAL NAME:
Open Journal of Animal Sciences,
Vol.11 No.4,
August
25,
2021
ABSTRACT: The
Tswana chicken is native to Botswana and comprises strains such as the naked
neck, normal, dwarf, frizzled, and
rumples. The origins of the different strains
of Tswana chicken remain unknown and it is not yet clear if the different strains represent distinct breeds within the large Tswana chicken population.
Genetic characterization of different strains of Tswana chickens using SNP
arrays can elucidate their genetic relationships and ascertain if the strains
represent distinct breeds of Tswana chicken population. The aim of this study was therefore to
investigate population structure and diversity and to estimate genetic
distances/identity between the naked neck, normal and dwarf strains of Tswana
chickens. A total of 96 chickens (normal strain (n = 39), naked neck strain (n = 32), dwarf strain (n = 13)
and commercial broiler
(n = 12)) were
used in the study. SNP genotyping was carried out using the Illumina chicken iSelect
SNP 60 Bead chip using the Infinium assay compatible with the Illumina HiScan
SQ genotyping platform. The observed heterozygosity (Ho) values were
0.610 ± 0.012, 0.611 ± 0.014, 0.613 ± 0.0006 for normal, naked neck and dwarf
strains of Tswana chickens respectively and averaged 0.611 ± 0.016 across the
three strains of Tswana chickens compared to Ho of 0.347 ± 0.023 in commercial
broiler chicken. The expected heterozygosity (He) values were 0.613
± 0.00012, 0.614 ± 0.00013, 0.608 ± 0.00021 for normal, naked neck and dwarf
strains of Tswana chickens respectively and averaged 0.612 ± 0.00015 across the
three strains of Tswana chickens compared to He of 0.577 ± 0.00022
in commercial broiler chicken. Principal component analysis (PCA) was used to
get an insight into the population structure of indigenous Tswana chickens. The
first two principal components revealed a set of three clusters. The normal
strain of Tswana chicken and commercial broiler clustered together in one
group. The dwarf strain clustered separately in one group and the naked neck
and normal strains clustered together in the last group. The separate
clustering of the dwarf strain from the rest of Tswana chicken strains suggests
significant genetic uniqueness of the dwarf strain and very close genetic
similarities between the normal and naked neck strains. The
clustering pattern was confirmed by less genetic differentiation and less
genetic distances between the naked neck and normal strains of Tswana chicken
than between the two strains and the dwarf strain of Tswana chicken.