Inclusive Composite Interval Mapping Of QTLs For Some Important Agronomic Traits In Rice

Composite interval mapping (CIM) is a commonly used method for QTL mapping with populations derived from biparental crosses. However, the algorithm used in CIM may result in biased estimation of QTL effect. Inclusive Composite Interval Mapping (ICIM) retains all advantages of CIM over interval mapping, and avoids the possible increase of sampling variance and the complicated background marker selection process in CIM.Based on advanced backcross QTL analysis (AB-QTL), inclusive composite interval mapping (ICIM) and composite interval mapping (CIM) were used for detecting QTLs for plant height, effective tiller number, grain thickness, grain width and grain length of advanced backcross inbred lines (RP2334/R0380//RP2334 BIL). The QTLs detected were mapped in the molecular marker linkage maps from the BIL and the recombinant inbred lines (RIL) respectively. Total 35 QTLs for the six traits were detected by ICIM, and 25 QTLs by CIM. Among these QTLs (total 39),21 QTLs could be found by ICIM and CIM together. ICIM has increased detection power especially in the detecting of QTLs for grain thickness and grain length. The detection power of ICIM was similar to that of CIM on mapping QTLs for plant height; effective tiller number and grain width. The false detection is not impossible, the QTLs found both by ICIM and CIM are more reliable. Total 32 QTLs for the six traits were detected by ICIM based on the linkage map of the BIL population. Although the linkage map of the BIL population is smaller than that of the RIL population, the QTLs detected on the map of the BIL population are similar to those detected on the map of the RIL population.Total 4 additive loci and 2 pairs of epistatic loci for hypoxic germinability were identified by ICIM in BIL population, which significantly influenced the coleoptile length under hypoxic together. The epistatic loci on chromosome 5 interacted with those on chromosomes 4 and 10, which explained 50.73% of the phenotypic variation. A rice variety Feidongtangdao having strong hypoxic germinability was selected from 256 accessions of rice core collection, and would be used to achieve a set of CSSL with IR26 (weak hypoxic germinability) as a recurrent parent for the further research of rice hypoxic germinability and the breeding of direct seeding rice.