a International Potato Center (CIP), Apartado 1558, Lima 12, Peru.
b Michigan State University, Department of Plant, Soil and Microbial Sciences, 1066 Bogue St., Room 486, East Lansing, MI 48824, USA.
Genome. 2018 Jul;61(7):523-537. doi: 10.1139/gen-2017-0201. Epub 2018 May 24.
Breeders rely on genetic integrity of material from genebanks; however, admixture, mislabeling, and errors in original data can occur and be detrimental. Two hundred and fifty accessions, representing paired samples consisting of original mother plants and their in vitro counterparts from the cultivated potato collection at the International Potato Center (CIP) were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity of the accessions and evaluate genetic diversity of the potato collection. Diploid, triploid, and tetraploid accessions were included, representing seven cultivated potato taxa (based on Hawkes, 1990). Fingerprints between voucher mother plants maintained in the field and in vitro clones of the same accession were used to evaluate identity, relatedness, and ancestry using hierarchal clustering and model-based Bayesian admixture analyses. Generally, in vitro and field clones of the same accession grouped together; however, 11 (4.4%) accessions were mismatches genetically, and in some cases the SNP data revealed the identity of the mixed accession. SNP genotypes were used to assess genetic diversity and to evaluate inter- and intraspecific relationships along with determining population structure and hybrid origins. Phylogenetic analyses suggest that the triploids included in this study are genetically similar. Further, some genetic redundancies among individual accessions were also identified along with some putative misclassified accessions. Accessions generally clustered together based on taxonomic classification and ploidy level with some deviations. STRUCTURE analysis identified six populations with significant gene flow among the populations, as well as revealed hybrid taxa and accessions. Overall, the Infinium 12K V2 Potato Array proved useful in confirming identity and highlighting the diversity in this subset of the CIP collection, providing new insights into the accessions evaluated. This study provides a model for genetic identity of plant genetic resources collections as mistakes in conservation of these collections and in genebanks is a reality. For breeders and other users of these collections, confirmed identity is critical, as well as for quality management programs and to provide insights into the accessions evaluated.
育种者依赖于基因库中材料的遗传完整性；然而，混杂、标记错误和原始数据中的错误可能会发生，并且会造成危害。从国际马铃薯中心（CIP）的栽培马铃薯收集物中选择了 250 个系，这些系由原始母株及其体外对应物组成的成对样本代表，使用 Infinium 12K V2 马铃薯阵列对这些系进行指纹识别，以确认系的遗传同一性并评估马铃薯收集物的遗传多样性。包括二倍体、三倍体和四倍体系，代表七个栽培马铃薯分类群（基于 Hawkes，1990）。使用凭证母株在田间和同一系的体外克隆之间的指纹来评估身份、亲缘关系和祖先，使用层次聚类和基于模型的贝叶斯混合分析。通常，同一系的体外和田间克隆聚集在一起；然而，有 11 个（4.4%）系在遗传上不匹配，在某些情况下，SNP 数据揭示了混合系的身份。SNP 基因型用于评估遗传多样性，并评估种间和种内关系，以及确定种群结构和杂种起源。系统发育分析表明，本研究中包含的三倍体在遗传上相似。此外，还确定了个别系之间的一些遗传冗余以及一些可能被错误分类的系。系通常根据分类学分类和倍性水平聚集在一起，但也存在一些偏差。STRUCTURE 分析确定了六个种群，这些种群之间有显著的基因流，同时还揭示了杂种分类群和系。总体而言，Infinium 12K V2 马铃薯阵列在确认身份和突出 CIP 收集物中这一部分的多样性方面非常有用，为评估的系提供了新的见解。这项研究为植物遗传资源收集物的遗传同一性提供了一个模型，因为这些收集物和基因库中的保存错误是现实存在的。对于育种者和这些收集物的其他使用者来说，确认身份是至关重要的，因为这对于质量管理计划和深入了解评估的系都很重要。
