Molecular genetics of submergence tolerance in rice: QTL analysis of key traits.

Flash flooding of young rice plants is a common problem for rice farmers in south and south-east Asia. It severely reduces grain yield and increases the unpredictability of cropping. The inheritance and expression of traits associated with submergence stress tolerance at the seedling stage are physiologically and genetically complex. We exploited naturally occurring differences between certain rice lines in their tolerance to submergence and used quantitative trait loci (QTL) mapping to improve understanding of the genetic and physiological basis of submergence tolerance. Three rice populations, each derived from a single cross between two cultivars differing in their response to submergence, were used to identify QTL associated with plant survival and various linked traits. These included total shoot elongation under water, the extent of stimulation of shoot elongation caused by submergence, a visual submergence tolerance score, and leaf senescence under different field conditions, locations and years. Several major QTL determining plant survival, plant height, stimulation of shoot elongation, visual tolerance score and leaf senescence each mapped to the same locus on chromosome 9. These QTL were detected consistently in experiments across all years and in the genetic backgrounds of all three mapping populations. Secondary QTL influencing tolerance were also identified and located on chromosomes 1, 2, 5, 7, 10 and 11. These QTL were specific to particular traits, environments, or genetic backgrounds. All identified QTL contributed to increased submergence tolerance through their effects on decreased underwater shoot elongation or increased maintenance of chlorophyll levels, or on both. These findings establish the foundations of a marker-assisted scheme for introducing submergence tolerance into agriculturally desirable cultivars of rice.

Thai jasmine rice carrying QTLch9 (SubQTL) is submergence tolerant.

Submergence tolerance is an important agronomic trait for rice grown in South-East Asia, where flash flooding occurs frequently and unpredictably during the monsoons. Although mapping locations of one major and several minor quantitative trait loci (QTL) were known previously, improving submergence tolerance in agronomically desirable types of rice has not been achieved. KDML105 is jasmine rice widely grown in rain-fed lowland regions of Thailand. This cultivar is very intolerant of submergence stress. To improve submergence tolerance in this cultivar, three submergence-tolerant cultivars, FR13A, IR67819F2-CA-61 and IR49830-7-1-2-2, were cross-pollinated with KDML105. Transferring the major QTL for submergence tolerance was facilitated by four back-crossings to the recipient KDML105. Molecular markers tightly linked to the gene(s) involved were developed to facilitate molecular genotyping. We demonstrated that individuals of a BC4F3 line that retained a critical region on chromosome 9 transferred from tolerant lines were also tolerant of complete submergence while retaining all the agronomically desirable traits of KDML105. In addition, effects of secondary QTLch2 were detected statistically in back-cross progenies. Effects of secondary QTLch7 were not statistically significant. The close association between tightly linked markers of the tolerance locus on chromosome 9 and submergence tolerance in the field demonstrates the considerable promise of using these markers in lowland rice breeding programmes for selecting increased submergence tolerance.

Mapping of quantitative trait locus related to submergence tolerance in rice with aid of chromosome walking.

The major QTL for submergence tolerance was locate in the 5.9 cM interval between flanking RFLP markers. To narrow down this region, a physical map was constructed using YAC and BAC clones. A 400-kb YAC was identified in this region and later its end fragments were used to screen a rice BAC library. Through chromosome walking, 24 positive BAC clones formed two contigs around linked-RFLP markers, R1164 and RZ698. Using one YAC end, six BAC ends and three RFLP markers, a fine-scale map was constructed of the 6.8-cM interval of S10709-RZ698 on rice chromosome 9. The submergence tolerance and related trait were located in a small, well-defined region around BAC-end marker 180D1R and RFLP marker R1164. The physical-to-map distance ratio in this region is as small as 172.5 kb/cM, showing that this region is a hot spot for recombination in the rice genome.

Mapping of genes for cooking and eating qualities in Thai jasmine rice (KDML105).

Thai jasmine rice, KDML 105, is known as the best quality rice. It is known not only for its aroma but also for its good cooking and eating qualities. Amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) are important traits determining rice quality. A population of recombinant inbred lines (RIL) derived from KDML105 x CT9993 cross was used to study the genetic control of AC, GC and GT traits. A total of 191 markers were used in the linkage map construction. The 1605.3 cM linkage map covering nearly the whole rice genome was used for QTL (define QTL) analysis. Four QTLs for AC were detected on chromosomes 3, 4, 6 and 7. These QTLs accounted for 80% of phenotypic variation explained (PVE) in AC. The presence of one major gene as well as several modifiers was responsible for the expression of the trait. Two QTLs on chromosome 6 and one on chromosome 7 were detected for GC, which accounts for 57% of PVE. A single gene of major effect along with modifier genes controls GC from this cross. The QTLs in the vicinity of waxy locus were major contributors in the expression of AC and GC. The finding that the position of QTLs for AC and GC were near each other may reflect tight linkage or pleiotropy. Three QTLs were detected, one on chromosome 2 and two on chromosome 6, which accounted for 67% of PVE in GT. Just like AC and GC, one major gene and modifier genes governed the variation in GT resulting from the KDML105 x CT9993 cross. Breeding for cooking and eating qualities will largely rely on the preferences of the end users.

Mapping of rice Rf gene by bulked line analysis.

A method, bulked line analysis (BLA), was developed for identification of the RFLP markers associated with a target gene. Instead of segregating progenies, conventional lines sharing the same trait were bulked by the BLA method. This method is an alternative approach to the identification of DNA markers linked with a target gene. A major advantage of this method is time-saving for genetic stock development. The advantage is very significant for organisms having a long generation period. This method has been tested by using fertility restoration of rice cytoplasmic male sterility of wild abortive type as a target trait. A fertility-restoring gene was successfully identified by linkage with RFLP markers. This gene was mapped in the middle of the long arm of chromosome 10 of the rice genome.

Cloning and Characterization of Aerobactin Biosynthesis Genes of the Biological Control Agent Enterobacter cloacae.

Five strains of Enterobacter cloacae that are biological control agents of Pythium damping-off diseases produced the hydroxamate siderophore aerobactin under iron-limiting conditions. Genes determining aerobactin biosynthesis of the biocontrol strain E. cloacae EcCT-501 were localized to a 12.3-kb region, which conferred aerobactin production to Escherichia coli DH5alpha. The aerobactin biosynthesis genes of E. cloacae hybridized to those of the pColV-K30 plasmid of E. coli, but restriction patterns of the aerobactin regions of pColV-K30 and E. cloacae differed. A derivative strain with a deletion in the aerobactin biosynthesis locus was as effective as strain EcCT-501 in biological control of Pythium damping-off of cucumber. Thus, aerobactin production did not contribute significantly to the biological control activity of EcCT-501 under the conditions of this study.