More Manuel, Veli Eudosio, Cruz Alan, Gutiérrez Juan Pablo, Gutiérrez Gustavo, Ponce de León F Abel
Facultad de Agronomía y Zootecnia, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, Peru.
Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru.
Animals (Basel). 2023 Oct 25;13(21):3316. doi: 10.3390/ani13213316.
The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (-log(-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray.
本研究的目的是鉴定与羊驼纤维直径相关的候选基因组区域。从秘鲁安第斯地区两个地理区域（帕斯科和普诺）的1011只雌性华卡亚羊驼以及每个区域内的三个羊驼养殖场采集了DNA样本。使用包含76,508个单核苷酸多态性（SNP）的Affymetrix定制羊驼基因分型阵列对样本进行基因分型。经过质量控制后，保留了960个样本和51,742个SNP。进行了三种关联研究方法。基于线性模型的全基因组关联研究（GWAS）分别利用所有羊驼和纤维直径极值羊驼的信息，使我们能够鉴定出11个和35个SNP（-log（P值）> 4）。单倍型和标记分析方法使我们能够鉴定出9种标准化单倍型遗传力高于6个标准差的单倍型。基于跨群体扩展单倍型纯合性（XP-EHH）的选择特征使我们能够鉴定出180个XP-EHH值大于|3|的SNP。通过两种关联分析方法鉴定出的四个相邻SNP的候选区域位于VPA6、VPA9、VPA29和一个染色体未分配支架上。本研究代表了首次使用最近组装的羊驼SNP微阵列对羊驼全基因组与纤维直径进行的分析。
