Genomic heterogeneity and structural variation in soybean near isogenic lines

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.

Keywords: CGH; NIL; heterogeneity; iron; soybean.

Figure 1

Structural genomic analysis of the HiPro versus LoPro near isogenic lines. Two conspicuous polymorphic regions are visible on chromosomes 18 and 20 (boxed regions), corresponding to previously identified loci.

Figure 2

Genomic structural variation on chromosome 03 for seven different “IsoClark” NILs.

Figure 3

A detailed view of thee different “IsoClark” introgressions on chromosome 03. The CGH data is shown as gray spots. Diamonds represent the positions of SNP markers in this region: red diamonds indicate SNPs matching the “T203” haplotype, while blue diamonds indicate SNPs matching the “Clark” haplotype. As expected, the introgressed “T203” regions exhibit structural variation (UpCNV and DownCNV) relative to the “Clark” control. Haplotype 1 (top) appears to be a continuous ∼10 Mb introgression of “T203,” haplotype 2 appears to be a smaller (∼6–8 Mb) introgression, and haplotype three appears to be a quadruple recombinant where part of the introgression is interrupted by the “Clark” haplotype (at position ∼41 Mb).

Figure 4

Yellowing responses of the “IsoClark” sub-lines to hydroponic treatments of limited iron. (A) All nine genotypes (including “Clark” and “T203” control) were grown together within each treatment unit. (B) Conspicuous yellowing of a “T203” trifoliate. (C) Mean separation (LSD) for phenotypes as scored by visual ratings and SPAD measurements over three time points. Letters a, b, c, indicate when treatment means are in significantly different groups.