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United States Department of Agriculture

Agricultural Research Service

Research Project: Defining the Genetic Diversity and Structure of the Soybean Genome and Applications to Gene Discovery in Soybean, Wheat and Common Bean Germplasm

Location: Soybean Genomics and Improvement

Title: Distinct copy number, coding sequence and locus methylation patterns underlie Rhg1-mediated soybean resistance to soybean cyst nematode

Authors
item Cook, David -
item Bayless, Adam -
item Wang, Kai -
item Guo, Xiaoli -
item Song, Qijian
item Jiang, Jiming -
item Bent, Andrew -

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 19, 2014
Publication Date: April 25, 2014
Citation: Cook, D.E., Bayless, A., Wang, K., Guo, X., Song, Q., Jiang, J., Bent, A.F. 2014. Distinct copy number, coding sequence and locus methylation patterns underlie Rhg1-mediated soybean resistance to soybean cyst nematode. Plant Physiology. 164(4):1-54 DOI:10.1104/pp.114.235952.

Interpretive Summary: The soybean cyst nematode (SCN) is the economically most important pest of soybean in the U.S. The Rhg1 genetic locus that provides resistance to the SCN has been widely used to breed soybean varieties with SCN resistance. The objective of the research reported here was to determine the DNA sequence of the Rhg1 genetic locus in various soybean lines that carry resistance to SCN controlled by the Rhg1 genetic locus. A number of approaches were used to analyze the DNA sequence of soybean lines carrying resistance including the determination of the DNA sequence of a diverse set of 41 soybean lines. The soybean lines included SCN susceptible lines as well as those with Rhg1 resistance derived from different sources. From the analysis and comparison of the DNA sequence from the different soybean lines it was determined that one group of resistant lines carried 7 to 10 copies of a large DNA segment, another group of resistant lines carried only three copies of the large DNA segment. In contrast, those lines that did not carry SCN resistance had only a single copy of the large DNA segment at the Rhg1 locus. These discoveries of DNA sequence variation that relate copy number variation of DNA sequence to resistance to nematode are a useful first step to developing a general definition of copy number variation and its relationship to biotic or abiotic stress resistance. The two types of resistance defined here will also be of use in the selection of soybean breeding lines that carry the two different type of resistance.

Technical Abstract: Copy number variation of kilobase-scale genomic DNA segments, beyond presence/absence polymorphisms, can be an important driver of adaptive traits. Rhg1 is a widely utilized quantitative trait locus that makes the strongest known contribution to resistance against soybean cyst nematode (SCN; Heterodera glycines), the most damaging disease of soybean (Glycine max). Rhg1 is a complex locus at which resistance-conferring haplotypes carry up to ten tandem repeat copies of a 31 kb DNA segment, and three disparate genes present on each repeat contribute to SCN resistance. Here we use whole-genome sequence data, fiber-FISH and other methods to describe the genetic variation at Rhg1 across 41 diverse soybean accessions. Based on copy number variation, differential transcript abundance, nucleic acid polymorphisms and differentially methylated DNA regions, the multi-copy Rhg1 haplotypes associated with SCN resistance formed two groups distinct from a single-copy group associated with all tested SCN-susceptible accessions. The tested accessions in the high copy-number group, including PI 88788, contain 7 to 10 copies of the 31 kb Rhg1 repeat, form a distinct clade based on DNA sequence polymorphisms, and contain the previously identified alternate allele of Glyma18g02590 (a predicted alpha-SNAP). We also identified a low copy-number Rhg1 group, from accessions that include PI 548402/Peking and PI 437654, that all contain 3 copies of the 31 kb Rhg1 sequence and a newly identified allele of the Glyma18g02590 alpha-SNAP. There is strong evidence for a shared origin of the two resistance-conferring multi-copy Rhg1 groups and subsequent independent evolution. Differentially methylated DNA regions were identified that correlate with soybean cyst nematode resistance and likely play a role in the expression of the locus. The data provide insights into copy number variation of multi-gene segments, and do so in an example that confers a stress tolerance trait of high economic importance.

Last Modified: 12/19/2014
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