Estimates of effective population size and inbreeding in South African indigenous chicken populations: implications for the conservation of unique genetic resources

Abstract

Conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. Therefore, the Agricultural Research Council of South Africa initiated a conservation programme for four South African indigenous chicken breeds. The evaluation and monitoring of the genetic constitution of these conservation flocks is important for proper management of the conservation programme. Using molecular genetic analyses, the effective population sizes and relatedness of these conservation flocks were compared to village (field) chicken populations from which they were derived. Genetic diversity within and between these populations are further discussed within the context of population size. The conservation flocks for the respective breeds had relatively small effective population sizes (point estimate range 38.6–78.6) in comparison to the field populations (point estimate range 118.9–580.0). Furthermore, evidence supports a transient heterozygous excess, generally associated with the occurrence of a recent population bottleneck. Genetic diversity, as measured by the number of alleles, heterozygosity and information index, was also significantly reduced in the conservation flocks. The average relatedness amongst the conservation flocks was high, whilst it remained low for the field populations. There was also significant evidence for population differentiation between field and conservation populations. Fst estimates for conservation flocks were moderate to high with a maximum reached between VD_C and VD_F (0.285). However, Fst estimates for field population were excessively low between the NN_C and EC_F (0.007) and between EC_F and OV_F (0.009). The significant population differentiation of the conservation flocks from their geographically correlated field populations of origin is further supported by the analysis of molecular variance (AMOVA), with 10.51 % of genetic diversity ascribed to population differences within groups (FSC = 0.106). The results suggest that significant genetic erosion has occurred within the conservation flocks due to inbreeding, pronounced effects of random drift and selection. It might be necessary to introduce new breeding individuals from the respective field populations in order to increase the effective population sizes of the conservation flocks and counter the effects of genetic erosion.Electronic supplementary materialThe online version of this article (doi:10.1007/s11250-016-1030-9) contains supplementary material, which is available to authorized users.

The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution

“…The local chickens are often kept by villagers under extensive management systems and without controlled breeding programs, but in some cases they are also kept in conservation facilities with the purpose to preserve their genetic architecture [20, 42, 49, 50]. Therefore, the high genetic diversity persists due to the fact that the pool for mating individual is generally larger, and hence a lower rate of inbreeding, and there is some exchange of genetic material by intercrossing of breeds, and little artificial selection is practiced [21, 40, 51]. Although the chicken breeds kept by German fancy breeders cover a wide spectrum of diversity overlapping with local breeds, the management followed by the fancy breeders only preserved the genetic relatedness of these breeds to their ancestral genetic background which, however, caused a drastic reduction in the level of genetic diversity within the breeds.…”

Leveraging Available Resources and Stakeholder Involvement for Improved Productivity of African Livestock in the Era of Genomic Breeding

“…Lower degree of population stratification as well as high within-breed genetic diversity in African chickens are supported by analyses with microsatellite markers (Muchadeyi et al, 2007; Adebambo et al, 2010; Mtileni et al, 2011), mtDNA (Wani et al, 2014; Hassaballah et al, 2015; Eltanany and Hemeda, 2016) and genome-wide SNP chips (Khanyile et al, 2015a,b; Fleming et al, 2016, 2017). Reduced genetic diversity was, however, witnessed with conservation flocks in South Africa which represented a limited sample of the gene pool (Muchadeyi et al, 2007; Mtileni et al, 2016). Increasing expansion of the commercial chicken industry and intermixing of commercial hybrids with local strains in rural backyards are eroding the genetic uniqueness of native breeds and their potential to adapt to local conditions (reviewed by Eltanany et al, 2011).…”

Utilization and Conservation of Landrace Chickens of Nigeria: Physical and Performance Characteristics, Issues and Concerns

“…There is dearth of data on the extinction risk status of NICs but commentators agree that IC genetic resources are the most endangered and under conserved animal genetic resources [6,108,109] with extinction risk of 33% [110] and about 40% of breeds with unknown extinction risk status [111]. Studies have shown the dwindling frequency or apparent loss of rare NIC phenotypes such as the crested head, feathered shank or ptylopody, polydactyl or 5 toed, short flight feathered, and dwarf types, naked neck, frizzle, and silky, and major genes such as naked neck (Na), frizzle (F), dwarf (Dw), ptylopody (Fsh), and polydactyl (Po) believed to enhance survival and performance in tropical environments [6,16,112].…”

“…The concern about loss of IC genetic resources stems from the multifaceted economic, environmental and socio-cultural consequences highlighted by numerous studies [6,7,16,24,109,113]. a.…”

“…Extinction of native strains and loss of overall genetic diversity and heritable variations with co-adapted genes and gene complexes that may be useful to meet breeding goals now and in the long-term [24,105,126]. b. Depletion of adaptive genes and traits, reduced fitness and evolutionary potentials, resulting in reduced flexibility of future breeding options [6,108,109,111].…”