Comparative Mapping of the Wild Perennial Glycine latifolia and Soybean (G. max) Reveals Extensive Chromosome Rearrangements in the Genus Glycine Sungyul Chang 1 , Carrie S. Thurber 1 , Patrick J. Brown 1 , Glen L. Hartman 1,2 , Kris N. Lambert 1 , Leslie L. Domier 1,2 * 1 Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America, 2 United States Department of Agriculture, Agricultural Research Service, Urbana, Illinois, United States of America Abstract Soybean (Glycine max L. Mer.), like many cultivated crops, has a relatively narrow genetic base and lacks diversity for some economically important traits. Glycine latifolia (Benth.) Newell & Hymowitz, one of the 26 perennial wild Glycine species related to soybean in the subgenus Glycine Willd., shows high levels of resistance to multiple soybean pathogens and pests including Alfalfa mosaic virus, Heterodera glycines Ichinohe and Sclerotinia sclerotiorum (Lib.) de Bary. However, limited information is available on the genomes of these perennial Glycine species. To generate molecular resources for gene mapping and identification, high-density linkage maps were constructed for G. latifolia using single nucleotide polymorphism (SNP) markers generated by genotyping by sequencing and evaluated in an F 2 population and confirmed in an F 5 population. In each population, greater than 2,300 SNP markers were selected for analysis and segregated to form 20 large linkage groups. Marker orders were similar in the F 2 and F 5 populations. The relationships between G. latifolia linkage groups and G. max and common bean (Phaseolus vulgaris L.) chromosomes were examined by aligning SNP- containing sequences from G. latifolia to the genome sequences of G. max and P. vulgaris. Twelve of the 20 G. latifolia linkage groups were nearly collinear with G. max chromosomes. The remaining eight G. latifolia linkage groups appeared to be products of multiple interchromosomal translocations relative to G. max. Large syntenic blocks also were observed between G. latifolia and P. vulgaris. These experiments are the first to compare genome organizations among annual and perennial Glycine species and common bean. The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production. Citation: Chang S, Thurber CS, Brown PJ, Hartman GL, Lambert KN, et al. (2014) Comparative Mapping of the Wild Perennial Glycine latifolia and Soybean (G. max) Reveals Extensive Chromosome Rearrangements in the Genus Glycine. PLoS ONE 9(6): e99427. doi:10.1371/journal.pone.0099427 Editor: Matthew N. Nelson, The University of Western Australia, Australia Received February 21, 2014; Accepted May 14, 2014; Published June 17, 2014 This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Funding: This study was supported by funding from the National Sclerotinia Initiative and the United States Department of Agriculture-Agricultural Research Service. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: leslie.domier@ars.usda.gov Introduction Soybean (Glycine max L. Mer.) is a major source of dietary protein and oil in animal production and for human consumption worldwide [1]. With increasing utilization of soybean for animal feed in countries like China, there is added demand for soybean production [2]. Most of the increased demand for soybean products has been met by expanding the land area devoted to soybean production [3]. However, it is not clear if the expansion of soybean production areas alone will be able to keep pace with this growing demand. In addition, the global movement of soybean pathogens and pests and the emergence of new pathogens, as illustrated by the recent identification of soybean aphids (Aphis glycines Matsumura), soybean rust (Phakopsora pachyrhizi Syd. & P. Syd) and Soybean vein necrosis virus in North America [4–6], necessitates the identification of novel genes that will enable producers to meet the ever increasing demand for soybean production in the face of changing abiotic and biotic stresses. Because of its narrow genetic base, soybean, like many cultivated crops, lacks diversity found in some of its wild relatives. The genus Glycine consists of 28 species split between two subgenera, Glycine Willd. and Soja (Moench) F. J. Hermann. The subgenus Soja contains two annual species, G. max, the domesti- cated species in the genus, and G. soja Sieb. & Zucc., both of which are native to Asia. The Glycine subgenus contains 26 species, including G. latifolia (Benth.) Newell & Hymowitz, that are native to Australia and surrounding islands, and have been shown to possess genes for agronomically valuable traits, such as resistance to Heterodera glycines Ichinohe and tolerance to Sclerotinia sclerotiorum (Lib.) de Bary. and drought [7–13]. To date however, it has not been possible to utilize genes from the perennial Glycine species for soybean improvement even though G. max and the perennial Glycine species share a relatively recent whole genome duplication that occurred between 5 and 13 million years ago [14,15]. Attempts to hybridize G. max and Glycine perennials have, with the exception of G. tomentella (2n = 78) Hayata, been unsuccessful, even with in vitro embryo rescue PLOS ONE | www.plosone.org 1 June 2014 | Volume 9 | Issue 6 | e99427