Abstract
Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.
Highlights
Cereals occupy the major share in global food supply in terms of production, acreage and source of nutrition
We investigated the genetic basis of Rice root-knot nematode (RRKN) resistance in wild rice accessions (constituting O. nivara, O. rufipogon and the intermediate O. sativa f. spontanea types) from India using Genome-wide association study (GWAS) with a three-pronged approach–(1) screening nematode resistant accessions among 272 diverse rice germplasm, (2) identifying genomic regions significantly associated with RRKN resistance via SNP markers genotyped by 50K “OsSNPnks” genic Affymetrix chip, and (3) expression analysis of candidate genes in nematode-infected plant tissues by reverse-transcription quantitative PCR (RT-qPCR)
Resistance to grassy stunt virus, bacterial leaf blight, neck blast and brown plant hopper was successfully introgressed into the cultivated rice from their wild relatives [42,43,44]
Summary
Cereals occupy the major share in global food supply in terms of production, acreage and source of nutrition. Rice as a staple food crop meets the nutrient demand of at least two-thirds of the global population ([1]; http://www.ricepedia.org/). The yield of rice is substantially afflicted by several biotrophic pathogens including rice root-knot nematode (RRKN), Meloidogyne graminicola. This sedentary endoparasite occurs in a wide range of rice-based. GWAS of wild rice for nematode resistance
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