The extent and distribution of linkage disequilibrium in extensive reared chicken populations in southern Africa. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively reared village chicken populations in southern Africa.
INTRODUCTION
The sharing of haplotypes between populations can indicate the transferability of genetic parameters between populations, such as QTL (Megens et al. 2009). 4 revealed the demographic history, the actual population size and the rate of genetic erosion, which facilitates the knowledge of the level of genetic diversity in the studied chicken populations (Qanbari et al. 2010a).
HYPOTHESIS
LD-based Ne scores were calculated to provide an understanding of whether a population of extensively farmed chickens is at risk of extinction or has passed through population bottlenecks, which could result in increased inbreeding and loss of genetic diversity. The aim of the study was to provide additional information on the genetic diversity and population structure of village chickens beyond that provided by previous studies and to provide an understanding of these important animal genetic resources.
GENERAL OBJECTIVES
In this study, the chicken Illumina iSelect 60K SNP chip was used to assess linkage disequilibrium, effective population size, haplo-block structure and haplo-block segregation of widely bred chickens from Zimbabwe, Malawi and South Africa. 5 c) To investigate the structure of LD-linked haplo-blocks, haplo-block partitioning and indications of genetic changes supporting adaptation among widely raised chicken populations of Zimbabwe, South Africa and Malawi.
INTRODUCTION
7 Understanding the genetic architecture of these populations is a vital step for future conservation and genetic improvement programs. An understanding of the evolutionary mechanism that shaped the genetic structures of these populations is also vital.
VILLAGE CHICKEN PRODUCTION SYSTEMS
- Sheltering
- Feeding
- Chicken Health
- Flock sizes, composition and mating systems
The number of haploblocks in Malawi is similar to that reported by Wragg et al. 2012) in traditional and village chicken populations. The level of haplo-block sharing determines the transferability of genetic parameters between populations (Megens et al. 2009).
EFFECTIVE POPULATION SIZE, INBREEDING, SUSTAINABILITY OF A POPULATION
FACTORS INFLUENCING EFFECTIVE POPULATION SIZE OF A POPULATION
- Sex Ratio
- Progeny variation
- Variation in natural factors over time
- Inbreeding
The effective population size of the country chicken population size has not been well studied due to the lack of provenance data including the number of breeding males and females. The number of offspring per parent varies in a population, which may be the result of random, genetic, fertility, environmental and accidental factors that contribute to changing effective population size over time (Falconer & Mackay 1996).
METHODS OF MEASURING EFFECTIVE POPULATION
The decline of LD is influenced by a degree of inbreeding in a finite population (Rao et al. 2008). Normally, assumptions are made about the influence of such factors on LD (Wang 2005; Corbin et al. 2010).
HAPLOTYPE ANALYSIS
In livestock studies, haploblocks have been characterized to understand their diversity within and between breeds and to infer population demography (Qanbari et al. 2010b). Longer haploblocks have been observed in populations that have gone through a bottleneck event and substructuring, indicating genetic drift and inbreeding effects (Qanbari et al. 2010b).
LD ESTIMATION AND HAPLOTYPE ANALYSIS IN THE GENOMICS ERA
Haplotype blocks have been defined by patterns of LD created by hot and cold site recombination (Ardlie et al. Previous studies suggested that the theory that longer haploblocks have low LD and vice versa does not always hold in different populations (Qanbari et al.. 2010b).
CONCLUSION
POTENTIAL OUTPUT
This study will also provide baseline information for further characterization of genes that may be under selection and facilitate inferences about local production pressures acting on the studied populations.
2008) Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. 2001) Linkage disequilibrium in the human genome. 2008) Extent of linkage disequilibrium in North American Holstein cattle. Extent of linkage disequilibrium in a large cattle population in West Africa and its implications for association studies.
Current Opinion in Genetics and Development Extent of linkage disequilibrium and effective population size in Finnish.
INTRODUCTION
The chickens are considered non-descript and have not been bred or selected for commercial traits or for breed development (Ekue et al. 2006). Linkage disequilibrium (LD) is defined as a non-random association of alleles at two or more loci (Hedrick 2004; Qanbari et al. 2010a). LD analysis also helps to understand the biological and demographic processes such as recombination, mutation, selection and founder effects that could have shaped the population structures (Rao et al. 2008).
The breakdown and extent of LD over a pairwise distance can be used to determine the evolutionary history of populations (Andreescu et al.
MATERIALS AND METHODS
- Chickens populations blood collection and SNP genotyping
- SNP genotypes and data preparation
- Minor allele frequency analysis, heterozygosity and deviation from HWE
- Linkage Disequilibrium
- Trends in effective population size
The genotype input file was converted to a PLINK v1.07 (Purcell et al. 2007) input file using a plug-in compatible with the Genome Studio program. The r2 measure was chosen because it is independent of allele frequency and it correlates multiples of SNPs at two independent loci (Lu et al. 2012). The relationship between Ne, recombination frequency and expected LD (r2) was determined using the following equation (Hayes et al. 2003);
The r2 value varies between 0 and 1, with a zero value indicating uncorrelated SNPs, while one value reflects SNPs that are perfectly correlated (Qanbari et al. 2010a).
RESULTS
- SNP marker characteristics
- Minor allele frequency distribution
- LD estimates and the effects of chromosome, SNP intervals and breed
- Effective population size over the past generations
Table 3.3.1: Distribution of markers after SNP quality control and the minor allele frequency, observed and expected heterozygosities of the Malawi, South African and Zimbabwean chicken populations. A population based on chromosome interaction on LD was also observed (Table 3.3.3), with chromosome 8 of Zimbabwe having a highest LD of 0.50 ± 0.25, while chromosome 22 had the highest LD in the SA chicken population. 41 An unexpected trend was observed on chromosome 18, where a very low LD of less than 0.25 was observed at a pairwise distance of 1 kb in Malawi chickens (Figure 3.3.3d).
44 Figure 3.3.3: Average LD decay with an increase in physical distance between SNPs for a) chromosomes 1-28, b) chromosome 22, c) chromosome 8, d) chromosome 18 and e) chromosome 13 for Malawi (Mal) , South Africa (SA) and Zimbabwe (Zim) chicken populations.
DISCUSSION
2010a) but similar to that of the study conducted by Wragg et al. 2012) which also included traditional breeds and country chicken populations from Ethiopia, Kenya and Chile. Although not used in the development of the 60K SNP chip, Wragg et al. 2012) has proven the utility of the 60K chip for non-descript country chicken populations. 47 commercial lines used by Qanbari et al. 2009) and the traditional and country chicken population used by Wragg et al.
It shows that these populations are generally inbred within subpopulations, as suggested in previous research (Muchadeyi et al. 2007a).
CONCLUSION
Reduced levels of actual population size could explain the reduced heterozygosity observed in these populations (Table 3.3.1). These populations are recognized as outbred and diversity studies have shown that these populations are highly diverse. These studies used less dense microsatellite markers that had a lower accuracy power than SNPs (Muchadeyi et al. 2006; van Marle-Köster et al. 2008; Mtileni et al. 2011a).
The population bottleneck may have occurred during the introduction of chickens into South Africa, which according to archaeological findings is thought to have occurred in the year 1600 (van Marle-Köster et al. 2008, Mtileni et al. 2010).
Use of microsatellites and MtDNA to assess genetic diversity within and between Zimbabwean chicken ecotypes. Muchadeyi F., Eding H., Wollny C., Groeneveld E., Makuza S., Shamseldin R., Simianer H. 2007a) Absence of population substructuring in chicken ecotypes in Zimbabwe detected using microsatellite analysis. 2009) Breeding stock selection, preferred production traits and selection criteria for village chickens among the agro-ecological zones of Zimbabwe. 2008) Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation.
2012) Genome-wide analysis of structure, diversity and fine-mapping of Mendelian traits in traditional and village chickens.
INTRODUCTION
Genomic regions with low recombination events have been observed to form a block-like structure that can be shared between individuals within and between populations (Cuc et al. 2006). The boundaries of the haplotype are thought to be structured by recombination hotspots, while recombination cold spots introduce variation within haploblocks (Gabriel et al. 2002;). In the era of next-generation sequencing genomics, the distribution of genome-wide haploblocks reveals the extent of haplotype sharing and diversity within and between breeds (Amaral et al. 2010).
The Illumina chicken iSelect 60K SNP chip has been found useful for studying LD as well as haplo-block partitioning in commercial (Qanbari et al.
MATERIALS AND METHODS
- Animal populations
- SNPs quality control and pruning
- Haplo-blocks partitioning
- Haplotype Diversity and QTLs detection
58 this study that there were differences in the haplo-blocks in chicken populations from different geographical origins due to isolated evolutionary processes. 59 The percentage of SNPs constituting a haplo-block was calculated by dividing the number of SNPs in a block by the total number of SNPs used in the haplo-block partitioning, times one hundred . Unique numbers of haploblocks were defined as those blocks that occurred in one population and were absent in the other.
On chromosome 8 haplo-blocks larger than 50 kb in size and on chromosome 22 haplo-blocks larger than 10 kb in size were selected and for each haplo-block the minimum number of SNPs was set to two.
RESULTS
- Haplo-blocks characteristics per chromosome
- Haplotype distribution per population
- Haplotype sharing between populations
- Haplotype diversity and characteristics
The Zimbabwean and South African populations shared a relatively large number of haploblocks (2689 haploblocks), while the Zimbabwean and Malawian populations shared the least number of 2325 haploblocks (Table 4.3.4). Overall, Zimbabwean and South African chickens shared similar patterns of haploblocks across the genomic regions examined. At least five haploblocks per population were observed in region 1, where South Africa and Zimbabwe appeared to share a similar block pattern.
QTLs on haplo-blocks around the telomeric region did not overlap with QTLs, except for the percentage of spleen QTLs found in Zimbabwean and South African chicken populations.
DISCUSSION
Haploblocks of less than 10 kb were observed in regions of low LD (~0.2) in the putative outbred populations (Megens et al. 2009). A large proportion of haploblocks occurred with a frequency of more than 20% in the total population (Figure 4.3.1). The number of haplo-blocks in South Africa and Zimbabwe are similar to those observed by Qanbari et al. 2010a) in commercial lines (Skyllinger and lag).
Haplotype sharing in this study varied, with a significant number of haploblocks shared between populations.
CONCLUSION
1968) Linkage disequilibrium in finite populations. 2004) Sequence and comparative analysis of the chicken genome provides unique perspectives on vertebrate evolution. 2002). 2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. 2012) Linkage disequilibrium in Angus, Charolais and Crossbred beef cattle. Linkage disequilibrium: what history has to tell us. 2012) Characterization of indigenous chicken production systems in Kenya.
2003) Haplotype blocks and linkage disequilibrium in the human genome. 2005) Estimating effective population sizes from genetic marker data.
In Chapter 4, we sought to assess whether haploblocks on chromosomes that had high LD (chromosomes 8 and 22) could include QTL for traits of economic importance and support the isolated evolution of different populations from different geographic systems and manufacturing. The results showed that the populations shared most haplo-blocks and that most haplo-blocks had a frequency ranging between 0.2-0.5. The observed haploblocks spanning coding regions and no coding regions can be a useful tool in identifying conserved regions of economic importance.
Observed QTL covered by haplo-blocks can be used in conjunction with performance records to extract haplotypes that can be associated with production performance for genetic improvement programs.
