Mapping quantitative trait loci for sheath blight disease resistance in Yangdao 4 rice.

Rice sheath blight (ShB), which is caused by Rhizoctonia solani, has become the most serious rice disease in China. Yangdao 4, a cultivar with partial resistance to ShB, was crossed with Lemont, a susceptible cultivar, to develop mapping populations that were used to analyze quantitative trait loci (QTL) that confer resistance to ShB. QTL analysis were performed in 3 environments (E1-E3) using 2 F2 and 1 F2:3 populations, respectively. Three traits were recorded to evaluate ShB resistance, including disease rating (DR), lesion height (LH), and percentage of lesion height (PLH). Based on field evaluation of ShB resistance and the 2 genetic maps constructed, we identified a total of 8 QTLs for DR (4 in E1, 4 in E2, and 3 in E3), 6 QTLs for LH (1 in E1, 3 in E2, and 2 in E3), and 7 QTLs for PLH (1 in E1, 4 in E2, and 2 in E3). Sixteen of the ShB-QTLs co-localized as 6 clusters on chromosomes 3, 7, 11, and 12. Four of the 6 clusters contained ShB-QTLs that were detected in 2 environments, while the other 2 clusters with ShB-QTLs were detected in 1 environment. Three ShB-QTLs (qSBD-3-2, qSBL-3-1, and qSBPL-3-1) were delimited to a 581-kb region flanked by markers D333B and D334 on chromosome 3. The resistance alleles of Yangdao 4 at the qSBD-3-2 locus decreased DR by 0.68 and 0.79 in E2 and E3, respectively.

Development of 1047 insertion-deletion markers for rice genetic studies and breeding.

In this study, a total of 1047 insertion-deletion (InDel) primer pairs distributed across the rice genome were developed and experimentally validated. The primer pairs were designed based on the InDel length polymorphisms between 93-11 (Oryza sativa ssp indica cv.) and Nipponbare (Oryza sativa ssp japonica cv.), aiming for utilization between indica and japonica rice, or between other inter-subspecific rice cultivars. The 1047 primer pairs were dispersed across all 12 of the rice chromosomes, with one InDel marker found every 371.3 kb on average. The InDel length of the markers varied from 3 to 39 bp: 88.2% of the markers contained 6 to 25 bp, only 6.2% of markers were ≤ 5 bp, and 5.6% were ≥ 26 bp. Six hundred and twenty-three (59.5%) of the 1047 InDel markers were shown to amplify well and were polymorphic between Taichung65 and IR8, and 476 (45.5%) markers were polymorphic between Lemont and Yangdao4, while 398 (38.0%) were polymorphic in both combinations. These results demonstrated that the polymerase chain reaction-based InDel markers developed in this study could be of immediate use for rice genetic studies and breeding programs.