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United States Department of Agriculture

Agricultural Research Service


Location: Plant Science Research

Title: Genomic heterogeneity and structural variation in soybean near isogenic lines

item Stec, Adrian
item Bhaskar, Pudota
item Bolon, Yung-tsi
item Nolan, Rebecca
item Shoemaker, Randy
item Vance, Carroll
item Stupar, Robert

Submitted to: Frontiers in Plant Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/4/2013
Publication Date: 4/24/2013
Publication URL:
Citation: Stec, A.O., Bhaskar, P.B., Bolon, Y., Nolan, R.K., Shoemaker, R.C., Vance, C.P., Stupar, R.M. 2013. Genomic heterogeneity and structural variation in soybean near isogenic lines. Frontiers in Plant Genetics and Genomics. DOI:10.3389/fpls.2013.00104.

Interpretive Summary: Plant traits involved in seed quality and nutrient use are usually controlled by several genes. These genetic areas controlling these traits are called quantitative trait loci QTLs. We are characterizing the plant QTLs controlling iron deficiency chlorosis (IDC) in soybean. The IDC trait is important because yield and quality of soybean seed are reduced when the plants cannot take up iron in sufficient quantities to grow. In this study we used novel genome mapping techniques identified the QTLs involved in IDC. We found that the major genomic location for this trait is on soybean Chromosome 3. Identification of the location of this trait will improve the efficiency of selecting plants for IDC tolerance.

Technical Abstract: 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 a 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.

Last Modified: 06/26/2017
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