A Roadmap for Functional Structural Variants in the Soybean Genome

Author:

Anderson Justin E1,Kantar Michael B12,Kono Thomas Y1,Fu Fengli1,Stec Adrian O1,Song Qijian3,Cregan Perry B3,Specht James E4,Diers Brian W5,Cannon Steven B6,McHale Leah K7,Stupar Robert M11

Affiliation:

1. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108

2. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4

3. United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705

4. Agronomy and Horticulture Department, University of Nebraska, Lincoln, Nebraska 68583

5. Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801

6. United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011

7. Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio 43210

Abstract

Abstract Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.

Publisher

Oxford University Press (OUP)

Subject

Genetics (clinical),Genetics,Molecular Biology

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