Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru.
Escuela de Formación Profesional de Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Nacional Daniel Alcídes Carrión, Cerro de Pasco 19001, Peru.
Genes (Basel). 2021 Feb 19;12(2):291. doi: 10.3390/genes12020291.
Small farm producers' sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection.
小农场生产者的生计依赖于他们的羊驼群和纤维生产。纤维特性的遗传改良将提高他们的经济效益和生活质量。分子标记技术的应用可以克服当前实施遗传改良计划的限制。因此，本项目的目的是生成羊驼单核苷酸多态性（SNP）微阵列。从普诺和塞罗德帕斯科的四个农场，每个农场各有 2 只，共 150 只华卡约羊驼，用于通过测序（GBS）基因分型发现 SNP。每个动物产生 2 个简化代表性文库，经过 ApeK1 消化和 Pst1-Msp1 双消化后进行 DNA 消化。对 10 只羊驼基因组（测序深度为 12×至 30×）和 VicPac3.1 参考基因组进行读对齐。生物信息学分析发现包含在微阵列中的 76508 个 SNP。还包括用于纤维质量和颜色的候选基因 SNP（302 个）。微阵列 SNP 覆盖基因组长度的 90.5%，DNA 密度约为 39±2.51 SNP/Mb，平均间隔为 26.45±18.57 kbp。通过对 30 个家系三胞胎进行基因分型，并将其与系谱进行比较，以及将微阵列与 GBS 基因型进行比较，评估了该微阵列的性能。观察到用 ApeK1 和 Pst1-Msp1 生成的 SNP 的一致性值分别为 0.93 和 0.94。同样，验证了 290 个纤维质量和颜色候选基因 SNP。该微阵列的可用性将促进全基因组关联研究、标记辅助选择，并最终实现基因组选择。
