Phenotypic and genetic characterization of different strains of indigenous Tswana chickens in Kweneng and southern districts of Botswana

Abstract

The aim was to characterise indigenous Tswana chicken populations in Kweneng and Southern districts of Botswana. The qualitative traits involved in the study included tail colour, breast colour, back colour, neck colour, comb type, shank colour, earlobe colour and head shape. Data were subjected to frequency and cross tabulation procedures of descriptive statistics in Statistical Package for Social Sciences (SPSS) to compute frequencies of occurrence of each qualitative trait. The five strains of indigenous Tswana chickens under scavenging management system showed distinct physical variations for most of the qualitative traits. Black was the most predominant tail colour across the strains (51.6%) followed by brown (27.9%). The frequency of brown breast colour and brown back colour were significantly higher in those respective regions. Brown and black were the predominant neck colours across the strains. The single comb type (81.7%), featherless shank (65.4%), red ear lobes (67.6%) and grey shank colour (32.9%) were the most predominant phenotypes across the strains. A total of eight (8) quantitative traits were measured using flexible measuring tape, and live body weight was measured using a Spring-Dial Hoist weighing scale. Data were analysed using mixed model’s procedures of SAS and the model included fixed effects of strain and sex and their interaction. Normal feathered males had significantly higher shank length (9.94±0.23 versus 8.35±0.20), shank circumference (0.99±0.02 versus 0.84±0.02) wing length (20.61±0.51 versus 18.60±0.48), wingspan (41.22±1.03 versus 37.19±0.96), comb length (6.30±0.30 versus 3.48±0.26) and wattle length (3.44±0.16 versus 2.40±0.14) than their female counterparts. Among males, there were no significant strain differences in spur length, wing length, wingspan, comb length, wattle length and live weight. Normal feathered males had the highest live weight and rumpless males had the lowest live weight. Only naked neck and normal-feathered females had significantly higher wingspan and wing length than dwarf females. Finally, it was noted from the study that various strains of Tswana chickens had similar qualitative traits except for shank length and shank circumference which were significantly shorter/smaller in dwarf strain compared to the other four strains. 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 on 96 samples in total for both indigenous Tswana and commercial broiler chickens. Principal component analysis (PCA) was used to obtain insight into the population structure of indigenous Tswana chickens. The first two principal components revealed a set of three clusters such as normal/naked neck, normal/broiler as well as dwarf strain. The dwarf strain clustered separately into one group and the naked neck and normal strains clustered together in the last group. The separate clustering of the dwarf from the rest of Tswana chicken strains suggests significant its genetic uniqueness and very close genetic similarities between the normal and naked neck strains. The clustering pattern was confirmed by less genetic differentiation (0.013) and less genetic distances (0.013) between the naked neck and normal strains of Tswana chicken than between the two strains (0.040, 0.041) and the dwarf strain of Tswana chicken. Further investigations on sequence polymorphisms in the promoter, 5´untranslated regions (UTR) and partial exon regions of chicken HSP-70 gene were carried out in the normal (n= 24), naked neck (n= 22) and dwarf (n=12) strains of indigenous Tswana chickens relative to the commercial broiler chicken (n=20). Genomic DNA extracted from whole blood samples of the three strains of indigenous Tswana chicken and the commercial broiler, were amplified using PCR and sequenced using Big Dye Cycle Sequencing Kit. Multiple sequence alignments of the partial sequences of chicken HSP-70 gene in indigenous Tswana chickens and the commercial broilers revealed two SNPs in the 5´UTR (A303G and G309A) and another two SNPs (G427 and A628G) in the partial exon sequence of chicken HSP-70 gene. The SNP G427A was unique to the normal strain and the other three SNPs were common to all the four ix chicken strains studied. The identified four SNPs associated with individual chickens resulting in a total of seven different haplotypes in the studied chicken populations.