QTLs And Candidate Genes Mapping For Rice Root Traits And Comparative Analysis Under Different Water Supply Conditions

Drought is one of the most important agronomic problems. Good root system are associated with crop drought avoidance. To investigate the genetic factors of adaptive and constitutive root morphological traits under different water conditions, a recombinant inbreed line (RILs) population derived from a cross between a lowland rice variety IR1552 and an upland rice variety Azucena with 249 molecular markers was used in cylindrical pot experiments. Quantitative trait loci (QTLs) for root length and root number were detected under different water conditions. Comparative QTLs mapping across three different populations with the same parent of Azucena for the root traits were also conducted. Mapping and expression analysis of genes for cell wall extensibility and cell proliferation, and some cDNA-AFLP clones were performed. The results are summarized as follows:1. Eighteen QTLs were detected for seminal root length (SRL), adventitious root number (ARM), lateral root length (LRL) and lateral root number (LRN) which are defined in a 3 cm fragment on seminal root under flooding and upland conditions. The QTLs for SRL, ARN, LRL and LRN accounted for about 11.5%~12%, 11.4%~20%> 11.8% and 13.4% of the total phenotypic variation under flooding conditions, respectively. Under upland condition, the QTLs for SRL, ARN, LRL and LRN accounted for 12.2%~15%, 12%~14.6%, 11.8%~14.4% and 11.7% of total phenotypic variations, respectively. One identical QTL was found for SRL under both flooding and uplanding conditions.2. A comparative analysis was performed for the QTLs detected in this case and these reported from the other two genetic populations with the same upland rice Azucena as a parent. Several identical QTLs for root elongation across the three populations with the positive alleles from the upland rice Azucena were found, which suggesting that these alleles of Azucena could be involved in water limitation-accelerated elongation of rice root under different genetic backgrounds.3. Genes for cell wall extension (expansins, Xets, Egases and extensin) and the gene for cell proliferation (cyc07) were mapped using the same population as above,and comparation of these genes and QTLs for root elongation and other traits were analyzed. SI 746 (OsEXP2) of three expansin genes was mapped on chromosome 1, which is linked with the QTL for seminal root length under upland conditions. Northern blotting analysis indicated that SI 746 (OsEXP2 ) was up-regulated by water limitation in seminal root tip. One EGase gene El328 was mapped on chromosome 5 linked with RG313, where some QTLs for lateral root length have been detected under upland conditions. Northern blotting analysis indicated that E1328 was up-regulated by water limitation in seminal root tip.4. Four cDNA-AFLP clones were mapped and two of them, T17 and LI 6, were located on chromosome 3 and 2, respectively. Northern blot analysis indicated that the expressions of LI 6, T59 and T82 were induced by water limiting condition, while the expressions of Tl 7 was suppressed. The results of blast in Gene Bank showed that T17 encoded nickel binding protein, which was linked with QTL for lateral root length. LI6 encoded putative SART-1 protein, T59 encoded CLIP associated protein and T82 encoded bHLH protein. The three genes are linked with QTLs for seminal root length, which indicates that these genes may be involved in seminal root elongation under upland conditions.