Tagliotti Martin E, Deperi Sofia I, Bedogni Maria C, Zhang Ruofang, Manrique Carpintero Norma C, Coombs Joseph, Douches David, Huarte Marcelo A
Potato Research Group, Estación Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta 226 km 73.5, Balcarce, Buenos Aires, Argentina.
Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Saavedra 15, C1083ACA, Ciudad Autónoma de Buenos Aires, Argentina.
BMC Genet. 2018 Jan 16;19(1):8. doi: 10.1186/s12863-017-0556-9.
Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study. A characterization of population structure using easy measurable phenotypic traits could be a preliminary and low-cost approach to elucidate the genetic structure of a population. A potato population of 183 genotypes was evaluated using 4859 high-quality SNPs and 19 phenotypic traits commonly recorded in potato breeding programs. A Bayesian approach, Minimum Spanning Tree (MST) and diversity estimator, as well as multivariate analysis based on phenotypic traits, were adopted to assess the population structure.
Analysis based on molecular markers showed groups linked to the phylogenetic relationship among the germplasm as well as the link with the breeding program that provided the material. Diversity estimators consistently structured the population according to a priori group estimation. The phenotypic traits only discriminated main groups with contrasting characteristics, as different subspecies, ploidy level or membership in a breeding program, but were not able to discriminate within groups. A joint molecular and phenotypic characterization analysis discriminated groups based on phenotypic classification, taxonomic category, provenance source of genotypes and genetic background.
This paper shows the significant level of diversity existing in a parental population of potato as well as the putative phylogenetic relationships among the genotypes. The use of easily measurable phenotypic traits among highly contrasting genotypes could be a reasonable approach to estimate population structure in the initial phases of a potato breeding program.
作物多样性是植物育种工作的基础。使用单核苷酸多态性（SNP）等分子标记对遗传多样性进行准确评估，必须能够揭示所研究群体的结构。利用易于测量的表型性状对群体结构进行表征，可能是阐明群体遗传结构的一种初步且低成本的方法。使用4859个高质量SNP和19个马铃薯育种计划中常用记录的表型性状，对一个包含183个基因型的马铃薯群体进行了评估。采用贝叶斯方法、最小生成树（MST）和多样性估计器，以及基于表型性状的多变量分析来评估群体结构。
基于分子标记的分析显示，群体分组与种质间的系统发育关系以及提供材料的育种计划有关。多样性估计器根据先验群体估计一致地构建了群体结构。表型性状仅区分了具有不同特征的主要群体，如不同的亚种、倍性水平或育种计划中的成员，但无法在群体内部进行区分。联合分子和表型特征分析根据表型分类、分类类别、基因型的来源和遗传背景对群体进行了区分。
本文展示了马铃薯亲本群体中存在的显著多样性水平以及基因型之间可能的系统发育关系。在高度不同的基因型中使用易于测量的表型性状，可能是在马铃薯育种计划初始阶段估计群体结构的一种合理方法。
