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PMID: 22696021 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Structural variants in the soybean genome localize to clusters of biotic stress-response genes.

Plant physiology ·Vol. 159 ·No. 4 ·2012-08-00 ·Pages 1295-308

McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM

Abstract

Genome-wide structural and gene content variations are hypothesized to drive important phenotypic variation within a species. Structural and gene content variations were assessed among four soybean (Glycine max) genotypes using array hybridization and targeted resequencing. Many chromosomes exhibited relatively low rates of structural variation (SV) among genotypes. However, several regions exhibited both copy number and presence-absence variation, the most prominent found on chromosomes 3, 6, 7, 16, and 18. Interestingly, the regions most enriched for SV were specifically localized to gene-rich regions that harbor clustered multigene families. The most abundant classes of gene families associated with these regions were the nucleotide-binding and receptor-like protein classes, both of which are important for plant biotic defense. The colocalization of SV with plant defense response signal transduction pathways provides insight into the mechanisms of soybean resistance gene evolution and may inform the development of new approaches to resistance gene cloning.

MeSH Terms
Chromosomes, Plant/genetics Comparative Genomic Hybridization DNA Copy Number Variations/genetics Disease Resistance/genetics Ecotype Exome/genetics Genes, Plant/genetics Genotype Genotyping Techniques Multigene Family/genetics Polymorphism, Single Nucleotide/genetics Reproducibility of Results Sequence Analysis, DNA Soybeans/genetics,immunology,physiology Stress, Physiological/genetics
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
McHale Leah K
Department of Horticulture and Crop Science, Ohio State University, Columbus, Ohio 43210, USA.
Haun William J
Xu Wayne W
Bhaskar Pudota B
Anderson Justin E
Hyten David L
Gerhardt Daniel J
Jeddeloh Jeffrey A
Stupar Robert M
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Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
1532-2548
DOI
10.1104/pp.112.194605
Published
2012-08-00
Epub
2012-00-13
Pages
1295-308
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC3425179
Subset
IM
Databases
GEO
GSE28905
External Links
PubMed source DOI: 10.1104/pp.112.194605 PMC Full Text View journal details
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