Genomic heterogeneity and structural variation in soybean near isogenic lines

Adrian O. Stec, Pudota B. Bhaskar, Yung Tsi Bolon, Rebecca Nolan, Randy C. Shoemaker, Carroll P. Vance, Robert M. Stupar

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Near isogenic lines (NILs) are a critical genetic resource for the soybean research community. The ability to identify and characterize the genes driving the phenotypic differences between NILs is limited by the degree to which differential genetic introgressions can be resolved. Furthermore, the genetic heterogeneity extant among NIL sub-lines is an unaddressed research topic that might have implications for how genomic and phenotypic data from NILs are utilized. In this study, a recently developed high-resolution comparative genomic hybridization (CGH) platform was used to investigate the structure and diversity of genetic introgressions in two classical soybean NIL populations, respectively varying in protein content and iron deficiency chlorosis (IDC) susceptibility. There were three objectives: assess the capacity for CGH to resolve genomic introgressions, identify introgressions that are heterogeneous among NIL sub-lines, and associate heterogeneous introgressions with susceptibility to IDC. Using the CGH approach, introgression boundaries were refined and previously unknown introgressions were revealed. Furthermore, heterogeneous introgressions were identified within seven sub-lines of the IDC NIL "IsoClark." This included three distinct introgression haplotypes linked to the major iron susceptible locus on chromosome 03. A phenotypic assessment of the seven sub-lines did not reveal any differences in IDC susceptibility, indicating that the genetic heterogeneity among the lines does not have a significant impact on the primary NIL phenotype.

Original languageEnglish (US)
Article number104
JournalFrontiers in Plant Science
Issue numberAPR
StatePublished - Apr 24 2013


  • CGH
  • Heterogeneity
  • Iron
  • NIL
  • Soybean


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