Submitted to: PLoS One
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/14/2014
Publication Date: 6/1/2014
Publication URL: handle.nal.usda.gov/10113/59010
Citation: Chang, S., Thurber, C.S., Brown, P.J., Hartman, G.L., Lambert, K.N., Domier, L.L. 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. Interpretive Summary: Soybean (Glycine max), like many cultivated crops, has a relatively narrow genetic base and lacks diversity for some economically important traits. In contrast, wild perennial relatives of soybean are more genetically diverse and show high levels of resistance to multiple soybean pathogens and pests. However, it has been extremely difficult to cross soybean with its wild perennial relatives to capture genes for these valuable traits. To investigate possible differences in chromosome structure between soybean and one of its perennial relatives, Glycine latifolia, and to generate molecular resources for gene mapping and identification, high-density linkage maps were constructed for G. latifolia using single nucleotide polymorphism markers. The orders of molecular markers were very similar in two G. latifolia populations, and between 12 of 20 soybean and G. latifolia chromosomes. The remaining eight chromosomes appeared to contain multiple interchromosomal rearrangements, which would disrupt chromosome pairing when crossing soybean with its wild perennial relatives and greatly reduce the chances of recovering fertile offspring. These experiments will be of interest to scientist working to utilize diverse soybean germplasm for cultivar improvement and to study the relationships of the species within the genus Glycine.
Technical 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, a perennial wild relative of 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, only limited information is available on the genomes of 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 F2 population and confirmed in an F5 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 F2 and F5 populations. To examine the relationships between G. latifolia linkage groups and G. max chromosomes, SNP-containing sequences from G. latifolia were aligned to the genome sequence of G. max, which showed that 12 of 20 G. latifolia linkage groups were nearly collinear with G. max chromosomes. Relative to G. max, eight linkage groups appeared to be products of multiple interchromosomal translocations. These experiments are the first to compare genome organizations of annual and perennial Glycine species. The development of molecular resources for species closely related to G. max provides information into the evolution of genomes with in the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production.