Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars

Tagliotti et al. BMC Genetics (2018) 19:8 DOI 10.1186/s12863-017-0556-9 RESEARCH ARTICLE Open Access Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars Martin E. Tagliotti1,2*, Sofia I. Deperi1,2, Maria C. Bedogni1, Ruofang Zhang3, Norma C. Manrique Carpintero4, Joseph Coombs4, David Douches4 and Marcelo A. Huarte1 Abstract Background: 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. Results: 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. Conclusions: 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. Keywords: Potato breeding, Phenotypic trait, Genetic diversity, SNP, Population structure * Correspondence: 1 Potato Research Group, Estación Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta 226 km 73.5, Balcarce, Buenos Aires, Argentina 2 Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina Full list of author information is available at the end of the article © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Tagliotti et al. BMC Genetics (2018) 19:8 Background Selection pressure exerted to attain genetic improvement threatens the allelic diversity of crop genomes. Offspring are mainly derived from the elite varieties which generates a narrow genetic base [1, 2]. Genetic diversity analysis reveals the genetic backgrounds and relationships of crop germplasm and provides strategies to establish, utilise, and manage crop core collections [3]. In the same line, understanding taxonomy, phylogenetic relationships and genetic variability in crop varieties is critical for determining genetic relationships, characterising germplasm, controlling genetic erosion, designing sampling strategies or core collections, establishing breeding programs, and the registration of new cultivars. Crop diversity can be assessed through phenotypic and biochemical traits, pedigree analysis or by molecular markers [4–6] and is expected to find some degree of correlation among them taking into account that the molecular approach is the most unbiased. Among these approaches, phenotypic traits, as tuber size or skin colour, are intuitive and practical to assess in the selection process, although they are subject to environmental effects and selection pressure during domestication and breeding. The characterization of the correct population structure within germplasm collections is critical to identify and correctly interpret the associations between functional and molecular diversities [7, 8]. The traditional estimators of population structure will reduce the genetic information of germplasm if pre-defined populations do not accurately match the biological reality [9]. This is a serious problem for correct evaluation of the genetic structure and diversity, especially in a crop cultivated across a large geographical area [10]. Software like STRUCTURE [11] was created to detect genetic relatedness in a collection of genotypes with multilocus molecular markers information (e.g. SNP). Population structure has previously been examined in potatoes within an association mapping context by Simko et al. [12], D’hoop et al. [13] and Hirsch et al. [14]. Despite having many species and subspecies and being distributed in dissimilar environments, potato’s complex genetic nature has hindered the progress of traditional breeding efforts [10, 15]. Different approaches in potato breeding, as linkage and association mapping using genome wide selection or candidate genes, have been described rendering several quantitative trait loci (QTL) important for the regulation of agronomic traits [10, 16–19]. However, association studies need the assessment of phenotypic and genotypic variability [16]. Recently, phenotypic traits with high broad-sense heritability and its QTLs have been described in a potato panel [20]. Usually, high numbers of potato entries with insufficient data are periodically incorporated in breeding centres, either from germplasm collection trips or other Page 2 of 12 from germplasm sources with specific traits of interest. At the beginning of the breeding process, the breeder has several entries to be included in a potato crossing panel with the expectation of having high genetic diversity. This purpose may be hampered by mislabelling, duplications, genetic closeness and environmental covariation, among other factors. Therefore, a preliminary approach with easy measurable phenotypic traits could be a reasonable tool to select genotypes with contrasting traits of interest at the moment of the onset of the potato panel. This is particularly important in develo (...truncated)