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

Principal Investigator: Milad Eskandari

Research Institution: University of Guelph (U of G)

Timeline: April 2020 – March 2023

Objectives:

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

Impacts:

  • The development of a wide range of SCN-resistant elite cultivars with different sources of SCN resistance will provide Ontario’s soybean growers with tools to not only mitigate SCN resistance losses during a single season, but also to rotate among to slow resistance development in SCN populations in the longer term.
  • The development of a wide range of soybean germplasm with different sources of SCN will provide Ontario/Canadian-based soybean breeders with adapted SCN sources for integrating the trait in their cultivars, which is the key factor for sustainable soybean production in Ontario and Canada.
  • The development of functional and molecular-based genomic tools for discriminating genotypes carrying different SCN genes from multiple sources will help the 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.

Scientific Summary:

Soybean is the most common cash crop grown in Ontario. The sustainable production of soybeans is vital for renewing the financial, social, and environmental resources on which our farming depends. 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 and, therefore, our 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 the southern part of Ontario (i.e., Essex and Chatham-Kent) and this issue is projected to worsen due to climate change. 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 aims 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.

External Funding Partners:

Ontario Agri-Food Innovation Alliance (Tier 1)  

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.

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