Genetic bases of resistance to the rice hoja blanca disease deciphered by a QTL approach

Rice hoja blanca (RHB) is one of the most serious diseases in rice growing areas in tropical Americas. Its causal agent is Rice hoja blanca virus (RHBV), transmitted by the planthopper Tagosodes orizicolus Müir. Genetic resistance is the most effective and environment-friendly way of controlling the disease. So far, only one major quantitative trait locus (QTL) of Oryza sativa ssp. japonica origin, qHBV4.1 , that alters incidence of the virus symptoms in two Colombian cultivars has been reported. This resistance has already started to be broken, stressing the urgent need for diversifying the resistance sources. In the present study we performed a search for new QTLs of O. sativa indica origin associated with RHB resistance. We used four F2:3 segregating populations derived from indica resistant varieties crossed with a highly susceptible japonica pivot parent. Beside the standard method for measuring disease incidence, we developed a new method based on computer-assisted image processing to determine the affected leaf area (ALA) as a measure of symptom severity. Based on the disease severity and incidence scores in the F3 families under greenhouse conditions, and SNP genotyping of the F2 individuals, we identified four new indica QTLs for RHB resistance on rice chromosomes 4, 6 and 11, namely qHBV4.2WAS208 , qHBV6.1PTB25 , qHBV11.1 and qHBV11.2 . We also confirmed the wide-range action of qHBV4.1 . Among the five QTLs, qHBV4.1 and qHBV11.1 had the largest effects on incidence and severity, respectively. These results provide a more complete understanding of the genetic bases of RHBV resistance in the cultivated rice gene pool, and can be used to develop marker-aided breeding strategies to improve RHB resistance. The power of joint-and meta-analyses allowed precise mapping and candidate gene identification, providing the basis for positional cloning of the two major QTLs qHBV4.1 and qHBV11.1 . ### Competing Interest Statement The authors have declared no competing interest. * ### List of abbreviations ALA : affected leaf area Badka : Badkalamkati variety, accession number IRGC 45011 BBT 50 : Bluebonnet 50 variety CIAT : Centro Internacional de Agricultura Tropical (now Alliance Bioversity-CIAT) CIM : composite interval mapping cM : centimorgan CTV : Citrus tristeza virus DAI : days after infestation DNA : deoxyribonucleic acid EDTA : ethylenediaminetetraacetic acid EHBV : Echinochloa hoja blanca virus FD 50 : Fedearroz 50 variety, accession number IRGC 1799-1-1 FD 2000 : Fedearroz 2000 variety, accession number IRGC 124388 FLAR : Fondo Latinoamericano para Arroz de Riego fsGBS : flexible and scalable genotyping by sequencing IFC : integrated fluidic circuit LOD : logarithm in base 10 of likelihoods odds MATAB : mixed alkyltri-methylammonium bromide MEG : maternally expressed gene MLGM : generalized linear mixed model NBS-LRR : nucleotide binding site-leucine-rich repeat PCR : polymerase chain reaction PTGS : post-transcriptional gene silencing PTB 25 : PTB 25 variety, accession number IRGC 6386 PVY : Potato virus Y QTL : quantitative trait locus RHB : rice hoja blanca disease RHBV : Rice hoja blanca virus RNA : ribonucleic acid RSV : Rice stripe virus SD : segregation distortion SIM : simple interval mapping SMR : single-marker regression SNP : single nucleotide polymorphism TBSV : Tomato bush dwarf virus TGS : transcriptional gene silencing UHBV : Urochloa hoja blanca virus WAS 208 : WAS 208-B-B-5-1-1-3 variety, accession number IRGC 121855 WGS : whole-genome sequencing