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Assessing the genomic diversity and relatedness in heritage chicken lines using whole-genome sequence (WGS) data

2021 CPRF
In the past 50 years, there has been a steep increase in the demand for poultry products. This demand has been met by increasing production along with genetic selection for improved growth and efficiency. However, selection also tends to reduce the number and type of genetic resources contributing to the majority of production. The University of Alberta maintains 10 heritage chicken lines (Brown Leghorn (BL), Light Sussex (LS), New Hampshire (NH), Saskatchewan Barred Rock (SaskBR), Shaver Barred Rock (ShaverBR), Shaver Rhode Island Red (RIR), White Leghorn (WL) and three commercial crosses called 20s, 30s, and 90s ), that played a large role in the evolution of the poultry industry in Canada. These lines are valuable for genetic research as they have not been subjected to the same intensive selection pressures as commercial counterparts. These birds may contain potential unique genetic variants that may have been lost in commercial lines. Thus, conservation management of these heritage lines requires urgent attention to avoid their extinction. As a first step, it is essential to assess their genetic diversity. To achieve this goal, 71 male samples from across the 10 lines were sequenced and the patterns of genetic diversity and relatedness among these lines were explored using whole-genome sequencing (WGS) including more than 5 million SNPs. Line 30s showed the highest genetic diversity as reflected in observed heterozygosity (0.327), expected heterozygosity (0.250), nucleotide diversity (0.0017), percentage of polymorphic markers (~ 65%), and average recent inbreeding coefficient (-0.039), followed by lines 20 and 90, whereas BL showed the lowest genetic diversity as reflected in observed heterozygosity (0.130), expected heterozygosity (0.116), nucleotide diversity (0.0007), percentage of polymorphic markers (~ 31%), and average recent inbreeding coefficient (0.577), followed by LS, WL, and NH. Moreover, population divergence analyses (FST) showed that BL is the most divergent line (average FST = 0.373), followed by LS (average FST = 0.360) and WL (average FST = 0.340). As expected the least divergent lines were the related lines 20 (average FST = 0.239) and 30 (average FST = 0.240). Population structure evaluations using neighbor-joining tree, principal components analysis, and ADMIXTURE analysis demonstrated that there is no genetic differentiation within lines. Our findings highlight the need for special attention for the populations of BL, WL, LS, and NH, with the largest levels of inbreeding. Our results can be used to develop a breeding strategy (mating system) to optimize and conserve the genetic variation present in the heritage lines.
Tags :
diversity,heritage chicken lines,whole genome sequencing
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University of Alberta

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