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United States Department of Agriculture

Agricultural Research Service

Research Project: FUNCTIONAL AND STRUCTURAL GENETIC ANALYSIS OF SOYBEAN AND OTHER LEGUMES Title: Genomic heterogeneity and structural variation in soybean near-isogenic lines

Authors
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 Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 4, 2013
Publication Date: April 24, 2013
Citation: Stec, A., Bhaskar, P., Bolon, Y., Nolan, R., Shoemaker, R.C., Vance, C.P., Stupar, R. 2013. Genomic heterogeneity and structural variation in soybean near-isogenic lines. Frontiers in Plant Science. 4:104.

Interpretive Summary: Important soybean biological resources are the many pairs of genetic lines that differ predominantly in a region of a chromosome containing a gene for a specific trait. Some of these paired lines have been instrumental in uncovering the gene responsible for the trait. Unfortunately other chromosomal regions are also different between the lines, and these may or may not play a role in the expression of the trait. In this manuscript the authors compared the chromosome structure between two pairs of lines; one for iron efficiency and one for seed protein content. They used an array of single base mutations that cover the entire soybean genome to identify the location of differences between the chromosomes of the pairs. They were surprised to find that within genetic lines of the pairs, there are sub-lines indicating that there is more variation in the lines than once thought. However, they also found that the variation in the sub-lines did not cause determinable changes in the expression of the trait. These findings are important for geneticists who are attempting to identify causative genes for a trait using paired genetic lines. They will need to be very cautious to ensure they are searching in the correct chromosomal region.

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 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: 12/22/2014
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