Abstract
Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.
Highlights
The choice of chickens by rural small-scale poultry farmers in Sri Lanka is often indigenous chickens for both egg and meat production, owing to numerous advantages they bring, such as disease resistance, high fertility, good maternal quality, longevity, ability to utilize poor-quality feeds, and most, importantly, the ability to manage them under a harsh environment condition with low level of management inputs despite their poor productivity compared with commercial layers and broilers (Silva et al, 2014)
The total number of samples used in the analysis was divided into five populations according to the geographical locations of sampling as DM, LA, OT, TB and TH (Supplementary Table 1), and to eight phenotypic groups; Naked Neck (NN), Long Legged (LL), Crested or Crown (CC), Frizzle Feathered (FF) Giriraj (GR), Commercial Layer (CL), Crossbreds (CR) and non-descript village chicken (VC) (Figure 2, Supplementary Table 2)
Phenotype-Based Populations The highest genetic distance (Reynolds’ genetic distances in Table 7) was observed between GR and CC (0.0914), but the lowest was between the NN and VC (0.0023)
Summary
The choice of chickens by rural small-scale poultry farmers in Sri Lanka is often indigenous chickens for both egg and meat production, owing to numerous advantages they bring, such as disease resistance, high fertility, good maternal quality, longevity, ability to utilize poor-quality feeds, and most, importantly, the ability to manage them under a harsh environment condition with low level of management inputs despite their poor productivity compared with commercial layers and broilers (Silva et al, 2014). The attempts made on phenotypic characterization of indigenous chickens in Sri Lanka identified that the populations consisted of diverse phenotypes (Bett et al, 2014), while Liyanage et al (2015) described seven distinct phenotypic groups, including naked neck, long legged, crest/crown, Giriraj, commercial crosses, frizzle feathered, and the non-descript group of multiple crosses of other groups. The highly polymorphic microsatellite markers are still valid for assessing the genetic diversity of AnGR In this context, this study was conducted to determine the genetic diversity of local chicken populations in two selected areas and among identified phenotypes in Sri Lanka using microsatellite markers
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