Structural variants in the soybean genome localize to clusters of biotic stress-response genes.
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.
Department of Horticulture and Crop Science, Ohio State University, Columbus, Ohio 43210, USA.
Leah K
LK
McHale
William J
WJ
Haun
Wayne W
WW
Xu
Pudota B
PB
Bhaskar
Justin E
JE
Anderson
David L
DL
Hyten
Daniel J
DJ
Gerhardt
Jeffrey A
JA
Jeddeloh
Robert M
RM
Stupar
D032461:Chromosomes, Plant / Q000235:genetics; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics; D060146:Ecotype; D059472:Exome / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D005838:Genotype; D060005:Genotyping Techniques; D005810:Multigene Family / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics* / Q000276:immunology / Q000502:physiology*; D013312:Stress, Physiological / Q000235:genetics*