Genomics-Assisted Breeding for Nematode Resistance in Soybeans

Soybean nematodes, including soybean cyst nematode (SCN), root-knot nematode (RKN), and reniform nematode (RN) are the most destructive pests in soybean production. Over 100 SCN resistant germplasm and several resistant QTL are known. However, more than 90% of commercialized SCN-resistant soybean cultivars in the USA carry only rhg1 from PI 88788. In the past few years, over 1,000 Plant Introductions (PIs) (MG 000-V) were evaluated for nematode resistance. Several PIs with broad-based resistance to multiple SCN HG types and resistance to RKN and/or RN were identified. New SCN resistant QTL in PI 437654 and PI 567516C have been discovered. Whole genome sequencing and haplotype analysis are also being employed to dissect genomic locations and QTL/genes associated with resistance to the multiple-nematodes. To facilitate marker-assisted breeding (MAB), two gene specific SNP markers were developed for rhg1 which can differentiate eight copies (as in PI 88788), three copies (as in Peking), or one copy (as in Williams 82). Other SNP markers were developed which distinguish presence and absence of Rhg4 from Peking. Fine-mapping, cloning, and functional marker development for the QTL in PI 437654 and PI 567516C are underway. A major RKN resistant QTL in PI 438489B was mapped within a 27.6 kb region by whole genome resequencing and SNP markers were developed from two candidate genes. The overall goal of our program is to discover new sources, identify novel QTL/genes providing resistance to multiple nematode species, and develop functional markers as well as new varieties with broad spectrum nematode resistance through MAB.