Bulked Segregant RNA Sequencing Revealed Difference Between Virulent and Avirulent Brown Planthoppers

The brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most devastating insect pests of rice (Oryza sativa L.), but BPH populations have varying degrees of virulence to rice varieties carrying different resistance genes. To help efforts to characterize these variations we applied bulked segregant RNA sequencing (BSR-seq) to identify differentially expressed genes (DEGs) and genetic loci associated with BPH virulence to YHY15 rice plants carrying the resistance gene Bph15. BPHs that are highly virulent or avirulent to these plants were selected from an F2 population to form two contrasting bulks, and BSR-seq identified 751 DEGs between the bulks. Genes associated with carbohydrate, amino acid and nucleotide metabolism, the endocrine system, and signal transduction were upregulated in the avirulent insects when they fed on these plants. The results also indicated that shifts in lipid metabolism and digestive system pathways were crucial for the virulent BPHs' adaptation to the resistant rice. We identified 24 single-nucleotide polymorphisms (SNPs) in 21 genes linked with BPH virulence. Possible roles of genes apparently linked to BPH virulence are discussed. Our results provide potentially valuable information for further studies of BPH virulence mechanisms and development of robust control strategies.

Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.)

Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called "specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.