Anglin Noelle L, Chavez Oswaldo, Soto-Torres Julian, Gomez Rene, Panta Ana, Vollmer Rainer, Durand Marisol, Meza Charo, Azevedo Vania, Manrique-Carpintero Norma C, Kauth Philip, Coombs Joesph J, Douches David S, Ellis David
International Potato Center (CIP), Lima, Peru.
Seed Savers - Preservation Department, United States Department of Agriculture Agriculture Research Service (USDA ARS) Small Grains and Potato Germplasm Research, Aberdeen, ID, United States.
Front Plant Sci. 2024 Jul 1;15:1341788. doi: 10.3389/fpls.2024.1341788. eCollection 2024.
A total of 3,860 accessions from the global clonal potato germplasm collection w3ere genotyped with the Illumina Infinium SolCAP V2 12K potato SNP array to evaluate genetic diversity and population structure within the potato germplasm collection. Diploid, triploid, tetraploid, and pentaploid accessions were included representing the cultivated potato taxa. Heterozygosity ranged from 9.7% to 66.6% increasing with ploidy level with an average heterozygosity of 33.5%. Identity, relatedness, and ancestry were evaluated using hierarchal clustering and model-based Bayesian admixture analyses. Errors in genetic identity were revealed in a side-by-side comparison of clonal material with the original mother plants revealing mistakes putatively occurring during decades of processing and handling. A phylogeny was constructed to evaluate inter- and intraspecific relationships which together with a STRUCTURE analysis supported both commonly used treatments of potato taxonomy. Accessions generally clustered based on taxonomic and ploidy classifications with some exceptions but did not consistently cluster by geographic origin. STRUCTURE analysis identified putative hybrids and suggested six genetic clusters in the cultivated potato collection with extensive gene flow occurring among the potato populations, implying most populations readily shared alleles and that introgression is common in potato. (ADG) and (CUR) displayed significant admixture. ADG likely has extensive admixture due to its broad geographic distribution. (PHU), (CHA)/ (STN), and (TBR) populations had less admixture from an accession/population perspective relative to the species evaluated. A core and mini core subset from the genebank material was also constructed. SNP genotyping was also carried out on 745 accessions from the Seed Savers potato collection which confirmed no genetic duplication between the two potato collections, suggesting that the collections hold very different genetic resources of potato. The Infinium SNP Potato Array is a powerful tool that can provide diversity assessments, fingerprint genebank accessions for quality management programs, use in research and breeding, and provide insights into the complex genetic structure and hybrid origin of the diversity present in potato genetic resource collections.
利用Illumina Infinium SolCAP V2 12K马铃薯SNP芯片对全球克隆马铃薯种质资源库中的3860份材料进行基因分型，以评估马铃薯种质资源库中的遗传多样性和群体结构。材料包括代表栽培马铃薯类群的二倍体、三倍体、四倍体和五倍体材料。杂合度范围为9.7%至66.6%，随倍性水平增加，平均杂合度为33.5%。使用层次聚类和基于模型的贝叶斯混合分析评估同一性、亲缘关系和祖先。在将克隆材料与原始母本植物进行并列比较时，发现了遗传同一性方面的错误，揭示了在数十年的处理和操作过程中可能出现的失误。构建了系统发育树以评估种间和种内关系，这与结构分析一起支持了马铃薯分类学中常用的分类方法。材料通常根据分类学和倍性分类进行聚类，但有一些例外，且并非始终按地理起源聚类。结构分析确定了推定的杂种，并在栽培马铃薯群体中发现了六个遗传簇，马铃薯群体之间存在广泛的基因流动，这意味着大多数群体容易共享等位基因，且渐渗在马铃薯中很常见。（ADG）和（CUR）表现出显著的混合。由于其广泛的地理分布，ADG可能有广泛的混合。从种质/群体角度来看，（PHU）、（CHA）/（STN）和（TBR）群体的混合程度相对所评估的物种较少。还从基因库材料中构建了一个核心子集和一个微型核心子集。对种子保存者马铃薯群体中的745份材料也进行了SNP基因分型，证实这两个马铃薯群体之间没有遗传重复，这表明这两个群体拥有非常不同的马铃薯遗传资源。Infinium SNP马铃薯芯片是一种强大的工具，可用于多样性评估、为质量管理计划对基因库种质进行指纹识别、用于研究和育种，并深入了解马铃薯遗传资源库中存在的多样性的复杂遗传结构和杂种起源。
