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Genetic architecture of bone quality variation in layer chickens revealed by a genome-wide association study

View Article: PubMed Central - PubMed

ABSTRACT

Skeletal problems in layer chickens are gaining attention due to animal welfare and economic losses in the egg industry. The genetic improvement of bone traits has been proposed as a potential solution to these issues; however, genetic architecture is not well understood. We conducted a genome-wide association study (GWAS) on bone quality using a sample of 1534 hens genotyped with a 600 K Chicken Genotyping Array. Using a linear mixed model approach, a novel locus close to GSG1L, associated with femur bone mineral density (BMD), was uncovered in this study. In addition, nine SNPs in genes were associated with bone quality. Three of these genes, RANKL, ADAMTS and SOST, were known to be associated with osteoporosis in humans, which makes them good candidate genes for osteoporosis in chickens. Genomic partitioning analysis supports the fact that common variants contribute to the variations of bone quality. We have identified several strong candidate genes and genomic regions associated with bone traits measured in end-of-lay cage layers, which accounted for 1.3–7.7% of the phenotypic variance. These SNPs could provide the relevant information to help elucidate which genes affect bone quality in chicken.

No MeSH data available.


Heritability of femoral BMD by chromosome.Estimates of chromosome-wise heritability on BMD are drawn against the chromosome length (x-axis). The blue line represents heritability regressed on chromosome length. Grey area around the blue line is the 95% confidence level interval for prediction from the linear model. Chromosomes 7, 14, and 20 fell outside of the 95% confidence interval, indicating that these chromosomes could explain more heritability than expected according to chromosome length.
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f4: Heritability of femoral BMD by chromosome.Estimates of chromosome-wise heritability on BMD are drawn against the chromosome length (x-axis). The blue line represents heritability regressed on chromosome length. Grey area around the blue line is the 95% confidence level interval for prediction from the linear model. Chromosomes 7, 14, and 20 fell outside of the 95% confidence interval, indicating that these chromosomes could explain more heritability than expected according to chromosome length.

Mentions: The phenotypic variance explained by each chromosome is shown in Figs 4 and 5. Heritability obtained from the joint analysis of variance explained by each chromosome were linearly related with the chromosome lengths for BMD and breaking strength (Adjusted R2 = 0.64 and 0.57, respectively). These results agreed with the infinitesimal model theory, that is, common variants throughout the genome dissected the total variances. In total, 28 autosomes and two linkage groups account for 37.73% of BMD variance and 28.47% of breaking strength variance. These results were not different than the univariate heritability estimates (Table 3). The contribution of particular chromosomes differed from each other. Three chromosomes, GGA1, GGA2 and GGA14, explained more than 5.00% of BMD variance, indicating more genetic contributions than other chromosome segments. The contribution of GGA2 accounted for a large fraction of BMD variance, although association analysis with a mixed model did not identify significantly associated SNPs on this chromosome.


Genetic architecture of bone quality variation in layer chickens revealed by a genome-wide association study
Heritability of femoral BMD by chromosome.Estimates of chromosome-wise heritability on BMD are drawn against the chromosome length (x-axis). The blue line represents heritability regressed on chromosome length. Grey area around the blue line is the 95% confidence level interval for prediction from the linear model. Chromosomes 7, 14, and 20 fell outside of the 95% confidence interval, indicating that these chromosomes could explain more heritability than expected according to chromosome length.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5382839&req=5

f4: Heritability of femoral BMD by chromosome.Estimates of chromosome-wise heritability on BMD are drawn against the chromosome length (x-axis). The blue line represents heritability regressed on chromosome length. Grey area around the blue line is the 95% confidence level interval for prediction from the linear model. Chromosomes 7, 14, and 20 fell outside of the 95% confidence interval, indicating that these chromosomes could explain more heritability than expected according to chromosome length.
Mentions: The phenotypic variance explained by each chromosome is shown in Figs 4 and 5. Heritability obtained from the joint analysis of variance explained by each chromosome were linearly related with the chromosome lengths for BMD and breaking strength (Adjusted R2 = 0.64 and 0.57, respectively). These results agreed with the infinitesimal model theory, that is, common variants throughout the genome dissected the total variances. In total, 28 autosomes and two linkage groups account for 37.73% of BMD variance and 28.47% of breaking strength variance. These results were not different than the univariate heritability estimates (Table 3). The contribution of particular chromosomes differed from each other. Three chromosomes, GGA1, GGA2 and GGA14, explained more than 5.00% of BMD variance, indicating more genetic contributions than other chromosome segments. The contribution of GGA2 accounted for a large fraction of BMD variance, although association analysis with a mixed model did not identify significantly associated SNPs on this chromosome.

View Article: PubMed Central - PubMed

ABSTRACT

Skeletal problems in layer chickens are gaining attention due to animal welfare and economic losses in the egg industry. The genetic improvement of bone traits has been proposed as a potential solution to these issues; however, genetic architecture is not well understood. We conducted a genome-wide association study (GWAS) on bone quality using a sample of 1534 hens genotyped with a 600 K Chicken Genotyping Array. Using a linear mixed model approach, a novel locus close to GSG1L, associated with femur bone mineral density (BMD), was uncovered in this study. In addition, nine SNPs in genes were associated with bone quality. Three of these genes, RANKL, ADAMTS and SOST, were known to be associated with osteoporosis in humans, which makes them good candidate genes for osteoporosis in chickens. Genomic partitioning analysis supports the fact that common variants contribute to the variations of bone quality. We have identified several strong candidate genes and genomic regions associated with bone traits measured in end-of-lay cage layers, which accounted for 1.3–7.7% of the phenotypic variance. These SNPs could provide the relevant information to help elucidate which genes affect bone quality in chicken.

No MeSH data available.