The soybean cyst nematode (SCN, Heterodera glycines) is the most damaging pathogen of soybean and is widespread in Minnesota and most soybean-growing regions of the world. As a species, SCN contains significant variations in virulence (ability to reproduce on different soybean lines) and morphology. For this project we propose to study the phenotypic and genotypic diversity of SCN. Specifically, we will phenotype 182 inbred lines of cyst nematodes randomly selected from Minnesota soybean fields for their virulence on the SCN-resistant germplasm lines PI 88788, Peking (PI 548402), Pickett (PI 548988), PI 567516C, PI 438489B, and PI 90763. These germplasm lines contain diverse SCN resistance genes. We will study variations in SCN virulence to the soybean lines and morphometric traits. The genomes of the SCN lines have been sequenced, and their genetic diversity will be studied. Genome-wide association study (GWAS) will be performed to identify QTLs (quantitative trait loci) and candidate genes associated with SCN virulence to each of the soybean germplasm lines and SCN morphometric traits. The knowledge of SCN phenotypic and genotypic diversity will be highly useful for strategically breeding soybean cultivars resistant to SCN with the most effective sources of resistance. This project will advance technology to manage the most destructive pest of soybean and maintain the soybean productivity in Minnesota.

Objective 1: Study genetic diversity and population structure of the SCN.
The genome of a total of 178 SCN inbred lines have been sequenced. Currently, we are analyzing the
data to identify single nucleotide polymorphisms (SNPs) or DNA markers. The 178 SCN inbred lines
can represent the SCN populations across the state of Minnesota. Genetic diversity and population
structure (difference in gene allele frequencies between the lines) of the SCN will be analyzed. If
a nematode line does not fit in SCN genome, further DNA sequences of nematode specific region and
morphology will be examined to determine species identity; particularly we will determine if any of
the lines belongs to the white soybean cyst nematode (WSCN, Heterodera sojae).

Objective 2: Identify SNP markers and candidate genes associated with virulence phenotype and
morphological traits of SCN.
We will compare the genomic (SNP) data to virulence phenotype data to identify factors (gene or
genome region containing multi-genes) controlling virulence phenotype and morphological traits. To
our knowledge, nothing like this has ever been done. The unique collection of 182 SCN
inbred lines (178 lines sequenced) at our proposal makes this possible.

1. This project will develop knowledge of diversity of SCN virulence in Minnesota, which can be
used to strategically deploy effective types of resistance in soybean cultivars.
2. The study will result in a better understanding of the basic biology of soybean cyst nematode,
including genetic diversity, population structure, and virulence genes of SCN.
3. If virulence genes can be tagged by molecular markers, it is possible that in the future a
simple lab test could be used to characterize field populations of SCN, which would help farmers
choose the most effective sources of SCN resistance for their fields.
4. The information developed from this project will be shared at extension education events such as
the Agronomy Field Tour, Open House at the University of Minnesota Southern Research and Outreach
Center, MN Ag Expo, and Prairie Grains Conference.
5. The results has been or will be presented at scientific meetings such Soybean Nematode
Conference, Society of Nematologist meetings, North Central Nematology Research Committee meetings,
American Society of Agronomy meetings, and/or International Plant & Animal Genome Conference.
6. The research will be published in scientific journals for a broader dissemination.

The soybean cyst nematode is widely spread in soybean fields in Minnesota and it is the most
important biological factor limiting soybean yield ³. Use of SCN-resistant soybean cultivars is the
most common and effective strategy to manage SCN. This study advances the knowledge of SCN
virulence diversity and genetics that is useful for soybean breeders to select appropriate sources
of resistance and evaluate SCN resistance in breeding commercial soybean cultivars. The knowledge
is also useful for soyban growers to use the SCN-resistant soybean cultivars correctly and
effectively. There is a high possibility that in future molecular markers of SCN virulence could be
developed and used to characterize field populations of SCN, which would help farmers choose the
most effective sources of SCN resistance for their fields. With the effective SCN management,
soybean growers and enterprise will have economic benefit of improved soybean
yield.