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Grain minerals in rice, especially those in milled grains, are important sources of micro-nutrition elements, such as iron (Fe), zinc (Zn), manganese (Mn), copper (Cu), and selenium (Se), and of toxic heavy metal elements, especially cadmium (Cd), for populations consuming a rice diet. To date, the genetic mechanism underlying grain mineral concentrations (GMCs) in milled grain remains largely unknown. In this report, we adopted a set of 698 germplasms consisting of two subsets [indica/Xian (X-set) and japonica/Geng (G-set)], to detect quantitative trait loci (QTL) affecting GMC traits of Fe, Zn, Cd, Mn, Cu, and Se in milled grains. A total of 47 QTL regions, including 18 loci and 29 clusters (covering 62 Cd loci), responsible for the GMCs in milled grains were detected throughout the genome. A joint exploration of favorable haplotypes of candidate genes was carried out as follows: (1) By comparative mapping, 10 chromosome regions were found to be consistent with our previously detected QTL from linkage mapping. (2) Within eight of these regions on chromosomes 1, 4, 6, 7, and 8, candidate genes were identified in the genome annotation database. (3) A total of 192 candidate genes were then submitted to further haplotype analysis using million-scale single nucleotide polymorphisms (SNPs) from the X-set and the G-set. (4) Finally, 37 genes (19.3%) were found to be significant in the association between the QTL targeting traits and the haplotype variations by pair-wise comparison. (5) The phenotypic values for the haplotypes of each candidate were plotted. Three zinc finger (like) genes within two candidate QTL regions (qFe6-2 and qZn7), and three major GMC traits (Fe, Zn, and Cd) were picked as sample cases, in addition to non-exhausted cross validations, to elucidate this kind of association by trait value plotting. Taken together, our results, especially the 37 genes with favorable haplotype variations, will be useful for rice biofortification molecular breeding.

The rice line carrying the nonhost gene Rxo1, which was cloned from maize, exhibits a rapid hypersensitive response (HR) to Xanthomonas oryzae pv. oryzicola (Xoc). In this study, a microarray experiment was carried out to analyze the genome-wide gene expression responses to Xoc at the early stage in the rice transgenic line and its wild type. 175 and 379 differentially regulated genes (DRGs) were detected in 9804-Rxo1 and 9804 at 36 h post-inoculation (hpi), respectively. The patterns of DRGs induced by Xoc in the transgenic rice line and its wild type were distinctly different: 92.00% of the DRGs were up-regulated in inoculated 9804-Rxo1 and 48.22% of the DRGs were sorted as defense-related genes. In contrast, 40.69% of the DRGs were up-regulated in inoculated 9804 and 40.00% were sorted as injury-induced genes. Some genes specifically up-regulated in infected 9804-Rxo1 were defenserelated, including the genes encoding pathogenesis-related protein, terpene synthase family, transcription factors (TFs) AP2 domain containing protein, myb-like deoxyribonucleic acid (DNA)- binding domain containing protein, and C 2 H 2 -type zinc-finger transcription factors. Six peroxidase (POD) genes were significantly up-regulated and POD activity consistently rose in the inoculated 9804- Rxo1, whereas seven POD genes were down-regulated in its wild type, indicating that POD may also play a role in the complex process of resistant response to Xoc in the transgenic line. Instead of focusing only on the R-gene-mediated defense, this study also discusses the susceptible response in the wild types to virulent pathogen infection in transcription level. Key words: Rice bacterial leaf streak, nonhost resistance, expression profile, Rxo1.

Drought is an important constraint to productivity in rainfed rice environments. Improvement in the various components of rice drought tolerance is now possible through the identification and manipulation of DNA markers linked with genes controlling these quantitative traits. A recombinant inbred line population was derived from the cross IAC165 x Co39. A molecular map was built that contained 182 RFLP and microsatellite markers. Segregation distortions were limited to a few chromosomal segments. Constitutive root traits, including maximum root length, root thickness and root dry weight in various layers, were measured on 125 lines in a greenhouse replicated experiment. QTL analysis was performed using composite interval mapping. Between 1 and 4 main effect QTLs, which explained individually between 5.5 and 24.8% of the variability, were identified for each trait. The most important genomic regions, which carried QTLs for several traits, were found on chromosomes 1, 4, 9, 11 and 12. The QTL locations were in good agreement with previous studies on these traits, confirming the value of the QTLs in a different genetic background. Epistasis represented a non-negligible component of the observed variability for some of the traits but was not detected for others. These results add to the understanding of the genetic control of root morphology in rice, which is necessary to strengthen marker-aided selection programs to improve varieties for water-limited environments.

Drought is an increasingly important constraint limiting rice world production. Drought tolerance, however, is a complex character resulting from many interacting component traits that QTL mapping studies have shown to be quantitative. To demonstrate the efficiency of marker-aided selection (MAS) to manipulate QTLs, two examples of selection based on markers only are described. The first study aimed at introgressing alleles for root depth. QTL detection had already been conducted in the appropriate background and the MAS step was therefore implemented directly. The interesting alleles were coming from Azucena, a deep-rooted variety, and IR64, the target for introgression, was used as the recurrent parent in 3 cycles of marker-assisted backcrosses. Several QTLs were manipulated at once. BC3F2 progenies were genotyped to select plants with Azucena alleles at the QTLs and assess the return to the recurrent parent. The phenotypic evaluation of BC3F3 families showed that the introgressed QTLs were expressed in the recipient background. It also highlighted the importance of the initial QTL analysis methods. In standard breeding programs, however, specific QTL detection results are seldom available. The advanced backcross QTL analysis method allows the simultaneous discovery and transfer of interesting QTLs from an unadapted donor to an elite variety. We used this method to transfer QTLs for osmotic adjustment, an important component of true tolerance, from IR62266, an indica donor, to IR60080-46A, a japonica elite line. BC3F3 plants were produced and QTL analysis of osmotic adjustment was conducted to determine the best plants to cross to construct improved near-isogenic lines. (Texte intégral)