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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Publications at this Location » Publication #325438

Research Project: Defining the Genetic Diversity and Structure of the Soybean Genome and Applications to Gene Discovery in Soybean, Wheat and Common Bean Germplasm

Location: Soybean Genomics & Improvement Laboratory

Title: Genetic diversity and phylogenetic relationships of annual and perennial Glycine species

Author
item HWANG, EUN-YOUNG - UNIVERSITY OF MARYLAND
item Schroeder, Steven - Steve
item Fickus, Edward
item Quigley, Charles - Chuck
item CREGAN, PERRY - RETIRED ARS EMPLOYEE
item Song, Qijian

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/15/2019
Publication Date: 5/17/2019
Citation: Hwang, E., Schroeder, S.G., Fickus, E.W., Quigley, C.V., Cregan, P., Song, Q. 2019. Genetic diversity and phylogenetic relationships of annual and perennial Glycine species. G3, Genes/Genomes/Genetics. https://doi.org/10.1534/g3.119.400220.
DOI: https://doi.org/10.1534/g3.119.400220

Interpretive Summary: Soybean (Glycine max), which is native to East Asia has a number of perennial Glycine relatives that mainly originate from Australia and other locations with warm and drought prone environments. The perennial species are a source of genes for pest resistance and could carry genes that would be useful in the face of global warming. It was our objective to define the level of genetic variability in six perennial Glycine species versus cultivated soybean and wild soybean from which cultivated soybean arose. We determined the DNA sequence of 76 genes in cultivated and wild soybean accessions as well as six perennial Glycine species and found that one of the perennial species, Glycine canescens, had a level of genetic diversity that was four times greater than that of cultivated soybean. The DNA sequence of another set of 52 genes was used to determine the relationships among the cultivated and wild soybeans and the six perennial Glycine species. In the case of the 11 accessions of the perennial species G. canescens, the three accessions from the dry and warm region of western Australia were demonstrated to be genetically distinct from the other eight accessions from central and eastern Australia. These three accessions may be of particular interest as a source of genes that provide resistance to warm and dry growth conditions. These data are most likely to influence scientists at universities, government agencies and companies trying to breed new soybean varieties tolerant to heat and drought.

Technical Abstract: The genus Glycine Willds. includes two annual species, Glycine max (L.) Merr. and Glycine soja Sieb. & Zucc. and the perennial Glycine species. In this study, we estimated the average genetic diversity of the two annual and six perennial species based upon 76 orthologous gene sets and performed a phylogenetic analysis among 77 accessions of the eight species using 52 orthologous gene sets 87.6 Kbp in length. In addition, 367 orthologous gene sets with 462 Kbp of sequence were used to estimate the relationships of 11 G. canescens accessions. The nucleotide diversity (theta) of G. max and G. soja was 0.0011 and 0.0022, respectively. Among the perennials, G. canescens showed the highest nucleotide diversity (theta=0.0043) and, with the exception of G. tomentella (theta=0.0016), the other perennials had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the Glycine showed a similar genome grouping with the previous report based upon Histone H3-D, except G. cyrtoloba and G. stenophita formed a sister clade in the study. The relationships among the 11 G. canescens showed one clade including the genome group G3 accessions and two additional clades, the first with the U and ND accessions and the second with the group G1 and G2 accessions. The greater genetic diversity of most of the perennial Glycine species and their origins from the warmer and in some cases drier climates of Australia suggested the perennials as potential sources of heat and drought resistance that will be of value in the face of global warming.