Taxonomy and Genetic Differentiation among Wild and Cultivated Germplasm of Solanum sect. Petota

Because of their adaptation to a diverse set of habitats and stresses, wild species of cultivated crops offer new sources of genetic diversity for germplasm improvement. Using an Infinium array representing a genome-wide set of 8303 single nucleotide polymorphisms (SNPs), phylogenetic relationships and allelic diversity were evaluated within a diversity panel of germplasm from Solanum sect. Petota. This panel consists of 74 plant introductions (PIs) representing 25 species and provides a diverse representation of tuber-bearing Solanum germplasm. Unlike other molecular markers, genome-wide SNPs have not been widely implemented in potato. To determine relatedness between current species classifications and SNP-based genetic distances, a phylogeny was generated based on random individuals from each core collection PI. With few exceptions, SNP-based estimates of species relationships revealed general agreement with the existing taxonomic grouping of species in Solanum sect. Petota. Genotype comparisons between the Solanum sect. Petota diversity panel and a panel of 213 tetraploid cultivars and breeding lines indicated a greater extent of diversity between populations of native Andean landraces than among modern cultivated varieties. Comparison of SNP allele frequencies between the Solanum sect. Petota panel and tetraploid cultivars identified loci with extreme divergence between cultivated potato and its tuber-bearing relatives. Several of these loci are associated with genes related to carbohydrate metabolism and tuber development, suggesting potential roles in potato domestication. The Infinium SNP data offer a new taxonomic view of potato germplasm, while further identifying candidate alleles likely to differentiate wild germplasm and cultivated potato, possibly underlying key agronomic traits. T he ability to exploit genetic diversity is critical to modern crop breeding, as it enables the introduction of new, useful genes and allelic variants into existing germplasm. Germplasm diversity offers a source of novel traits of agronomic value and can increase the variety of alleles within breeding populations (Bamberg and Del Rio 2005; Bradshaw et al., 2006; Lam et al., 2010; Pavek and Corsini, 2001; Tester and Langridge, 2010). A large extent of genetic diversity can be found in wild and landrace relatives of cultivated crop species (Bradshaw et al., 2006; Pavek and Corsini, 2001) and evaluation of the diversity in these wild species and landraces at the sequence level facilitates its use in developing new cultivars. Surveying wild genotypes across broad sets of loci can provide clues to genes that differentiate primitive and cultivated germplasm, suggesting key loci involved in the domestication and enhanced agronomic performance of modern varieties (Huang et al., 2012; Hufford et al., 2012; Olsen and Wendel, 2013; Qi et al., 2013). Such genes offer candidates for breeders in selecting elite cultivars and have implications for the expression of important field traits. Understanding the taxonomy of wild relatives of cultivated crops is also important, as it increases the efficiency of germplasm conservation and may lend predictive power to the implementation of diverse plant species in breeding programs (Daly et al., 2001, Spooner and Salas, 2006). Potato taxonomy has changed throughout recent history, depending on whether intermediate interspecific Published in The Plant Genome 8 doi: 10.3835/plantgenome2014.06.0025 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. M. A. Hardigan and C. R.Buell, Dep. of Plant Biology, Michigan State Univ., East Lansing, MI 48824-1312; J. Bamberg, USDA-ARS, Sturgeon Bay, WI 54235-9620; and D. S. Douches, Dep. of Plant, Soil, and Microbial Sciences, Michigan State Univ., East Lansing, MI 48824-1312. Received 6 June 2014. *Corresponding author