Tarsani Eirini, Matika Oswald, McIntosh Kiah, Desire Suzanne, Dunn Ian C, Talenti Andrea, Rae Anne M, Kranis Andreas, Watson Kellie A
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
Department of Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Easter Bush, Midlothian, EH25 9RG, UK.
Sci Rep. 2025 Jul 2;15(1):23625. doi: 10.1038/s41598-025-08852-z.
Average daily gain (ADG), body weight (BW), primary feather length (PRF) and breast depth (BD) are economically important traits in duck production, and understanding the genetic architecture of these traits remains limited. Genome-wide association studies (GWAS) can provide insight into the genetic mechanism underlying these traits. Increasing the power of GWAS by applying approaches such as genotype imputation can improve the ability to detect quantitative trait loci associations with polygenic traits. To increase the power of detecting marker-trait associations in this study, we also exploited imputed data and on a larger sample size. The objective of this study was to investigate marker-trait associations for ADG, BW, PRF and BD in ducks. First, we conducted univariate GWA analyses using chip data (hence medium density data) using 45 K autosomal SNPs and 1445 ducks from single breeding line. Second, we exploited imputed data with a larger sample size (13020) from the same line and performed univariate analyses. Comparison of SNP signals between the medium density and imputed data identified 63 common SNPs that were co-localized on chromosome 4. Several functional candidate genes such as PPARGC1A, LDB2 and LCORL were found within or close to the identified region. Indeed, the LCORL-NCAPG region has been reported in many mammalian species to be related to growth. Considering results from both analyses, current findings propose novel putative pleiotropic candidate quantitative trait loci (QTL) with the associated genes for the traits we analysed while identifying the most promising QTL region on chromosome 4.
平均日增重（ADG）、体重（BW）、主羽长度（PRF）和胸深（BD）是鸭生产中具有重要经济意义的性状，而对这些性状遗传结构的了解仍然有限。全基因组关联研究（GWAS）可以深入了解这些性状背后的遗传机制。通过应用基因型填充等方法提高GWAS的效能，可以增强检测多基因性状数量性状位点关联的能力。为了在本研究中提高检测标记-性状关联的效能，我们还利用了填充数据并扩大了样本量。本研究的目的是调查鸭的ADG、BW、PRF和BD的标记-性状关联。首先，我们使用芯片数据（即中等密度数据），利用45K常染色体单核苷酸多态性（SNP）和来自单一育种系的1445只鸭进行单变量GWAS分析。其次，我们利用来自同一品系的更大样本量（13020）的填充数据并进行单变量分析。中等密度数据和填充数据之间SNP信号的比较确定了63个共定位在4号染色体上的常见SNP。在确定的区域内或附近发现了几个功能候选基因，如PPARGC1A、LDB2和LCORL。事实上，在许多哺乳动物物种中都报道过LCORL-NCAPG区域与生长有关。综合两项分析的结果，当前研究结果提出了新的假定多效性候选数量性状位点（QTL）以及我们分析的性状的相关基因，同时确定了4号染色体上最有前景的QTL区域。
