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.

中文翻译：

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鸡F2资源种群不同发育阶段小腿长度和直径的全基因组关联研究。

为了找到影响小腿性状的SNP和基因，我们在五个F型孵化场的八个半同胞家鸡F2种群中进行了GWAS分析，这五个孵化场是从Arian快速生长系和Urmia本地慢速生长鸡之间的相互杂交得到的。使用60K鸡SNP芯片对308只禽进行基因分型。从出生到12周，每周测量一次小腿性状，包括小腿的长度和直径。应用广义线性模型和压缩混合线性模型（CMLM）来实现有效区域。平均基因组膨胀因子（λ统计数据（CMLM）（0.99）表明，在控制人口结构方面，CMLM比广义线性模型更有效。从NCBI，Ensembl和UniProt数据库中鉴定了围绕重要SNP的基因及其生物学功能。结果表明，在12个不同年龄段的12个SNP超过了LD调整的5％Bonferroni显着阈值。2个SNP对刀柄长度有显着影响，9个SNP对刀柄直径有显着影响。重要的SNP位于11个候选基因附近或内部。结果表明，在中世纪，许多重要的SNPs高于其余的。MXRA8基因与第1周的显着SNP有关，该SNP促进生长板软骨细胞的增殖。LOC101747628基因内位于鸡Z染色体上的Gga_rs166​​89511的独特SNP与三种不同年龄的鸟（第8、9和11周）的小腿长度有关。在第4和第7周发现了小腿直径的显着SNP（分别为4和5个SNP）。在这里鉴定SNP和基因可以有助于更好地理解鸡小腿性状的遗传控制。