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Advancements in breeding, genetics, and genomics for resistance to three nematode species in soybean

Kim, Ki-Seung, Vuong, Tri D., Qiu, Dan, Robbins, Robert T., Grover Shannon, J., Li, Zenglu, Nguyen, Henry T.
Theoretical and applied genetics 2016 v.129 no.12 pp. 2295-2311
Glycine max, Meloidogyne incognita, Rotylenchulus reniformis, bioinformatics, cultivars, genes, genetic analysis, genetic markers, genetic resistance, genome-wide association study, genomics, genotyping by sequencing, haplotypes, host plants, loci, marker-assisted selection, molecular biology, pests, plant breeding, quantitative trait loci, single nucleotide polymorphism, soybeans
KEY MESSAGE: Integration of genetic analysis, molecular biology, and genomic approaches drastically enhanced our understanding of genetic control of nematode resistance and provided effective breeding strategies in soybeans. Three nematode species, including soybean cyst (SCN, Heterodera glycine), root-knot (RKN, Meloidogyne incognita), and reniform (RN, Rotylenchulus reniformis), are the most destructive pests and have spread to soybean growing areas worldwide. Host plant resistance has played an important role in their control. This review focuses on genetic, genomic studies, and breeding efforts over the past two decades to identify and improve host resistance to these three nematode species. Advancements in genetics, genomics, and bioinformatics have improved our understanding of the molecular and genetic mechanisms of nematode resistance and enabled researchers to generate large-scale genomic resources and marker-trait associations. Whole-genome resequencing, genotyping-by-sequencing, genome-wide association studies, and haplotype analyses have been employed to map and dissect genomic locations for nematode resistance. Recently, two major SCN-resistant loci, Rhg1 and Rhg4, were cloned and other novel resistance quantitative trait loci (QTL) have been discovered. Based on these discoveries, gene-specific DNA markers have been developed for both Rhg1 and Rhg4 loci, which were useful for marker-assisted selection. With RKN resistance QTL being mapped, candidate genes responsible for RKN resistance were identified, leading to the development of functional single nucleotide polymorphism markers. So far, three resistances QTL have been genetically mapped for RN resistance. With nematode species overcoming the host plant resistance, continuous efforts in the identification and deployment of new resistance genes are required to support the development of soybean cultivars with multiple and durable resistance to these pests.