Genome‐wide association study of shank length and diameter at different developmental stages in chicken F2 resource population

Abstract

In order to find SNPs and genes affecting shank traits, we performed a GWAS in a chicken F2 population of eight half‐sib families from five hatches derived from reciprocal crosses between an Arian fast‐growing line and an Urmia indigenous slow‐growing chicken. A total of 308 birds were genotyped using a 60K chicken SNP chip. Shank traits including shank length and diameter were measured weekly from birth to 12 weeks of age. A generalized linear model and a compressed mixed linear model (CMLM) were applied to achieve the significant regions. The value of the average genomic inflation factor (λ statistic) of the CMLM model (0.99) indicated that the CMLM was more effective than the generalized linear model in controlling the population structure. The genes surrounding significant SNPs and their biological functions were identified from NCBI, Ensembl and UniProt databases. The results indicated that 12 SNPs at 12 different ages passed the LD‐adjusted 5% Bonferroni significant threshold. Two SNPs were significant for shank length and nine SNPs were significant for shank diameter. The significant SNPs were located near to or inside 11 candidate genes. The results showed that a number of significant SNPs in the middle ages were higher than the rest. The MXRA8 gene was related to the significant SNP at week 1 that promotes proliferation of growth plate chondrocytes. A unique SNP of Gga_rs16689511 located on chicken Z chromosome within the LOC101747628 gene was related to shank length at three different ages of birds (weeks 8, 9 and 11). The significant SNPs for shank diameter were found at weeks 4 and 7 (four and five SNPs respectively). The identifications of SNPs and genes here could contribute to a better understanding of the genetic control of shank traits in chicken.

Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes

“…Thus, we also compared our gene lists (Tables 1, 2 and 3) with gene entries in the ChickenQTLdb (https://www.animalgenome.org/cgi-bin/QTLdb/GG/ index) related to QTL for production traits and only identified a single gene. LPP, noteworthy one of the genes found in common between FPD and pEFP (Table 3), has been reported to be linked to shank length and diameter [21] as well as Bursa of Fabricius weight [22]. The latter finding might correspond the observation of feather pecking being related to the immune system, but this is speculative and needs to be further investigated.…”

Identification of New Genes and Genetic Variant Loci Associated with Breast Muscle Development in the Mini-Cobb F2 Chicken Population Using a Genome-Wide Association Study

“…After the GWAS, we used SNPs with a p-value exceeding the 10% genomic significance level, after the Bonferroni correction, as candidate genes. While in some other GWAS studies in chickens, the SNP significance threshold is usually set to exceed the 5% genomic significance level [ 37 , 38 ]. The Bonferroni correction is very effective for rejecting false positive loci in an association analysis, especially for samples of small sizes.…”

Research progress and applications of genome‐wide association study in farm animals

“…Nevertheless, these methods exhibit the same statistical power as MLM. To improve the statistical power and reduce the increased computation time associated with increasing sample size, Li et al developed a less time-consuming model, CMLM, which was established by reducing the practical sample size through clustering algorithms and was integrated into TASSEL software [47], which has been used to study the genetic mechanism of shank length and diameter in chickens [56]. The algorithm used in Enriched CMLM, FaST-LMM, and SUPER also addresses the limitations of computational time and statistical power [57][58][59].…”