Rice Hoja blanca disease

Mapping of Resistance QTLs to RHBV

Rice hoja blanca disease occurs in cyclic epidemics that cause severe yield losses in rice crop in LAC. The causal agent Rice hoja blanca virus (RHBV) is transmitted by the planthopper vector Tagosodes orizicolus, but cannot be transmitted mechanically, which makes breeding for resistance to RHBV very difficult. Controlled infestations of rice with viruliferous vectors helps to select lines possessing various degrees of resistance, however at high cost. The indica varieties Fedearroz 2000 (Fd2000) and Fedearroz 50 (Fd50), both showing fair levels of resistance to RHBV and T. orizicolus, were crossed with the highly susceptible tropical japonica line WC366, and F2/F3 families were produced (218 and 291 families, respectively). The F2 plants were genotyped with evenly-dispersed SSRs, and the F3 populations were scored for their resistance to RHBV and feeding damage by T. orizicolus. A major QTL explaining about 50 % of the resistance to RHBV was found at the same location on chromosome 4 in both populations. Two QTLs were identified for resistance to T. orizicolus on chromosome 5 in the cross Fd2000 x WC366 and chromosome 7 in the cross Fd50 x WC366 (Romero et al, 2013). This comparative study using two distinct rice populations has allowed a better understanding of the genetics and interaction of resistance to RHBV and its vector. We are currently using this information to introgress the resistance QTLs in elite germplasm (see section “Marker-Assisted Breeding”).

MABC for Resistance to RHBV

Resistance to RHBV is an important trait to consider in rice breeding for LAC. We initiated with Fedearroz (Bogotá, Colombia) a pilot project that aims to introgress the QTLs found in Fd2000 variety (see above section “Mapping of Resistance QTLs to RHBV”) in the two eline indica backgrounds Fd174 and CT-12. We used marker-assisted backcrossing (MABC) to generate two BC3F4 populations, selecting for QTL presence at each generation using SSR markers. No phenotypic selection was done at any step. The obtained families showed significantly increased resistance to RHBV in both glasshouse and field experiments. These very encouraging results lead us to start a new MABC experiment in four indica elite lines or cultivars, using a set of SNPs specifically designed for the purpose. The SNPs were extracted from the genomic sequences of Fd2000 and eight other indica sequences, obtained by 10 X resequencing on the Illumina HighSeq 2000® platform at Dr. Stephen Dellaporta’s lab (Yale University, CT). We used SNP Extractor (see “Software Development” section) to choose highly informative, evenly dispersed markers. We retained 177 loci and converted them for the Fluidigm® platform. This technology allow us to control both QTL introgression (forward selection) and genetic background (backward elimination) at each backcross generation, resulting in a significant increase of efficiency and reduction of labour and time.