Developing resistant cultivars to soybean cyst nematode (SCN) for changing climate and genetic dissection of the resistance using advanced functional genomic tools

Objectives:

• Development of Ontario-adapted resilient soybean cultivars and germplasm carrying soybean cyst nematode (SCN) resistance genes from multiple sources (i.e., PI 88788, PI 548402, and PI 437654).
• Dissection of the genetic basis of the resistance using functional genomics techniques of RNA-seq and quantitative proteomics for the development of genomics-based breeding approaches.

Impacts:

• A wide range of SCN-resistant elite cultivars with different sources of SCN resistance provides Ontario’s soybean growers with tools to not only mitigate losses from SCN during a single season, but also different resistance sources to rotate among to slow resistance development in SCN populations in the longer term.
• A wide range of soybean germplasm with different sources of SCN resistance provides Ontario/Canadian-based soybean breeders with adapted SCN resistance sources for integrating the traits into their cultivars, reducing SCN-related yield losses.
• The functional and molecular-based genomic tools for discriminating genotypes carrying different SCN genes from multiple sources enable the University of Guelph (U of G) soybean breeding programs, and other interested public and private breeding programs, to accelerate the SCN-resistant cultivar development process with limited or no need to carry out greenhouse bioassay evaluations.

Project Overview:

Soybean is the most common field crop grown in Ontario. Soybean cyst nematode (SCN) (Heterodera glycines, Ichinohe) is the main yield-limiting parasite of soybean in most soybean production regions, especially in southwestern Ontario. Growing resistant cultivars is currently the most effective practice for increasing yield and controlling the SCN population density in SCN-infested soils. Due mainly to limited knowledge about the genetic basis of the resistance to SCN, and lack of effective molecular breeding tools, the development of high-yielding SCN-resistant soybeans using various sources of resistance has been very slow. Therefore, farmers over rely on limited sources of resistance, making it easier for SCN populations to develop resistance to the available SCN-resistance sources.

While numerous exotic soybean germplasm have been reported to be resistant to SCN, more than 98% of available commercial cultivars in Ontario are developed from PI 88788, and a few from Peking (PI 548402). Repeated use of cultivars with the same resistance sources has led to the increase of SCN races that can overcome current resistance sources in North America, including in the southern part of Ontario (i.e., Essex and Chatham-Kent) and this issue is projected to worsen. Although polymorphic DNA-based molecular tools such as quantitative trait loci (QTL) have provided breeders with powerful tools for improving specific traits through marker-assisted selection (MAS), the usefulness of these approaches has been limited for breeding SCN-resistant lines. While over 230 SCN-related QTL are reported from different studies, only two QTL have been used in MAS. Therefore, this project aimed to develop Ontario-adapted SCN-resistant cultivars through the introduction of new sources of SCN (i.e., PI88788, Peking, and Hartwig), and to develop new genomics-based toolkits for breeding for SCN resistance using functional genomic approaches of RNA sequencing (RNA-seq) and Shotgun proteomics.

Results:

In this project, we aimed to develop Ontario-adapted SCN-resistant cultivars from the three main sources of SCN, i.e., PI 88788, PI 548402 (aka. Peking), and PI 437654 (aka. Hartwig) and to develop genomics-based selection tools using omics approaches to facilitate and accelerate the breeding process for SCN. To develop Ontario-adapted SCN-resistant cultivars with different sources, three crosses were made between OAC Avatar (an Ontario-adapted SCN-susceptible commercial soybean) and U16-905030, U14-925152, and AR15-258059 (SCN-resistant lines containing PI 88788, PI 548402, and PI 437654 resistance sources, respectively).

For the genomics toolkit development, we used genomics, transcriptomics and proteomics approaches. By transcriptomics, we did dual RNA-seq analysis of the SCN HG type 1.2.5.7 and four soybean PI lines (e.g. PI 437654, PI 548402, PI88788, and Lee74) simultaneously to identify promising resistance mechanisms against SCN and H. glycines virulence genes involved in resistance breakdown. The current results indicated the importance of phenylpropanoid biosynthesis, MAPK signalling pathway and plant hormone signal transduction, and biosynthesis of secondary metabolites for the resistance. We also found that the key defense mechanism of PI437654, which shows strong resistance (FI = 0%), involves the expression of several genes that strengthen the cell wall as the first layer of defense, along with many oxidative enzyme genes, reactive oxygen species (ROS) scavengers, and Ca²⁺ sensors that can activate the salicylic acid pathway. These are important outcomes that may help us discover new tools to facilitate the breeding of resistant cultivars.

The three bi-parental populations, from crosses between OAC Avatar and each of the SCN-resistant sources (PI 88788, PI 548402, and PI 437654), were also used to detect molecular markers associated with SCN using QTL linkage analysis and genome-wide association studies (GWAS). The combined results from GWAS and linkage analysis led to the identification of six molecular markers associated with resistance to SCN HG type 1.2.5.7, the most prevalent and concerning HG type for soybean growers in southern Ontario. Notably, three of these markers are novel discoveries.

Furthermore, we have now developed Ontario-adapted SCN-resistant genotypes from all three parental sources of resistance. These genotypes can serve as valuable breeding material for the development of new soybean cultivars with diverse sources of SCN resistance, an essential tool to help farmers manage SCN populations in their fields and potentially slow the pace of race shifts over time.

Recommendations:

Our research findings have highlighted the pressing need to develop Ontario-adapted cultivars that are resistant to SCN, particularly focusing on Hartwig and Peking sources of resistance. Our observations have shown that Hartwig has a strong defense mechanism against various effectors produced by SCN. Furthermore, we have found that nematodes modify their gene expression to overcome the resistance. As such, diversifying the sources of SCN-resistant genes in commercial cultivars is highly recommended to assist farmers, including those in Ontario, with managing SCN populations in their fields. This will not only increase yield but will also help prevent a shift toward more resistant SCN populations. Our study further demonstrated the efficacy of cultivating PI 88788-based resistant cultivars in fields infested with SCN HG types capable of overcoming this resistance. This approach remains advantageous for controlling SCN population sizes compared to utilizing non-SCN lines. We are also positive about the development of superior Ontario-adapted cultivars with wide ranges of SCN sources in the near future.

External Funding Partners:

The project was funded in part by the Ontario Agri-Food Innovation Alliance, a collaboration between the Government of Ontario and the University of Guelph.

Project Related Publications:

Torabi, S., Seifi, S., Geddes-McAlister, J., Tenuta, A., Wally, O., Torkamaneh, D., and Eskandari, M. 2023. Soybean-SCN Battle: Novel insight into soybean’s defense strategies against Heterodera glycines. International Journal of Molecular Science. 24(22): 16232.