The rice SPINDLY gene functions as a negative regulator of gibberellin signaling by controlling the suppressive function of the DELLA protein, SLR1, and modulating brassinosteroid synthesis

SPINDLY (SPY) encodes an O-linked N-acetylglucosamine transferase that is considered to be a negative regulator of gibberellin (GA) signaling through an unknown mechanism. To understand the function of SPY in GA signaling in rice, we isolated a rice SPINDLY homolog (OsSPY) and produced knockdown transgenic plants in which OsSPY expression was reduced by introducing its antisense or RNAi construct. In knockdown plants, the enhanced elongation of lower internodes was correlated with decreased levels of OsSPY expression, similar to the spindly phenotype of Arabidopsis spy mutants, suggesting that OsSPY also functions as a negative factor in GA signaling in rice. The suppressive function of OsSPY in GA signaling was supported by the findings that the dwarfism was partially rescued and OsGA20ox2 (GA20 oxidase) expression was reduced in GA-deficient and GA-insensitive mutants by the knockdown of OsSPY function. The suppression of OsSPY function in a GA-insensitive mutant, gid2, also caused an increase in the phosphorylation of a rice DELLA protein, SLR1, but did not change the amount of SLR1. This indicates that the function of OsSPY in GA signaling is not via changes in the amount or stability of SLR1, but probably involves control of the suppressive function of SLR1. In addition to the GA-related phenotypes, OsSPY antisense and RNAi plants showed increased lamina joint bending, which is a brassinosteroid-related phenotype, indicating that OsSPY may play roles both in GA signaling and in the brassinosteroid pathway.     

Sugar starvation- and GA-inducible calcium-dependent protein kinase 1 feedback regulates GA biosynthesis and activates a 14-3-3 protein to confer drought tolerance in rice seedlings

Germination followed by seedling growth constitutes two essential steps in the initiation of a new life cycle in plants, and in cereals, completion of these steps is regulated by sugar starvation and the hormone gibberellin. A calcium-dependent protein kinase 1 gene (OsCDPK1) was identified by differential screening of a cDNA library derived from sucrose-starved rice suspension cells. The expression of OsCDPK1 was found to be specifically activated by sucrose starvation among several stress conditions tested as well as activated transiently during post-germination seedling growth. In gain- and loss-of-function studies performed with transgenic rice overexpressing a constitutively active or RNA interference gene knockdown construct, respectively, OsCDPK1 was found to negatively regulate the expression of enzymes essential for GA biosynthesis. In contrast, OsCDPK1 activated the expression of a 14-3-3 protein, GF14c. Overexpression of either constitutively active OsCDPK1 or GF14c enhanced drought tolerance in transgenic rice seedlings. Hence, our studies demonstrated that OsCDPK1 transduces the post-germination Ca²⁺ signal derived from sugar starvation and GA, refines the endogenous GA concentration and prevents drought stress injury, all essential functions to seedling development at the beginning of the life cycle in rice.     

Thai Jasmine Rice Carrying QTLch9 (SubQTL) is Submergence Tolerant

Submergence tolerance is an important agronomic trait for ricegrown in South-East Asia, where flash flooding occurs frequentlyand unpredictably during the monsoons. Although mapping locationsof one major and several minor quantitative trait loci (QTL)were known previously, improving submergence tolerance in agronomicallydesirable types of rice has not been achieved. KDML105 is jasminerice widely grown in rain-fed lowland regions of Thailand. Thiscultivar is very intolerant of submergence stress. To improvesubmergence tolerance in this cultivar, three submergence-tolerantcultivars, FR13A, IR67819F2-CA-61 and IR49830-7-1-2-2, werecross-pollinated with KDML105. Transferring the major QTL forsubmergence tolerance was facilitated by four back-crossingsto the recipient KDML105. Molecular markers tightly linked tothe gene(s) involved were developed to facilitate moleculargenotyping. We demonstrated that individuals of a BC4F3 linethat retained a critical region on chromosome 9 transferredfrom tolerant lines were also tolerant of complete submergencewhile retaining all the agronomically desirable traits of KDML105.In addition, effects of secondary QTLch2 were detected statisticallyin back-cross progenies. Effects of secondary QTLch7 were notstatistically significant. The close association between tightlylinked markers of the tolerance locus on chromosome 9 and submergencetolerance in the field demonstrates the considerable promiseof using these markers in lowland rice breeding programmes forselecting increased submergence tolerance.     

An overview of gibberellin metabolism enzyme genes and their related mutants in rice

To enhance our understanding of GA metabolism in rice (Oryza sativa), we intensively screened and identified 29 candidate genes encoding the following GA metabolic enzymes using all available rice DNA databases: ent-copalyl diphosphate synthase (CPS), ent-kaurene synthase (KS), ent-kaurene oxidase (KO), ent-kaurenoic acid oxidase (KAO), GA 20-oxidase (GA20ox), GA 3-oxidase (GA3ox), and GA 2-oxidase (GA2ox). In contrast to the Arabidopsis genome, multiple CPS-like, KS-like, and KO-like genes were identified in the rice genome, most of which are contiguously arranged. We also identified 18 GA-deficient rice mutants at six different loci from rice mutant collections. Based on the mutant and expression analyses, we demonstrated that the enzymes catalyzing the early steps in the GA biosynthetic pathway (i.e. CPS, KS, KO, and KAO) are mainly encoded by single genes, while those for later steps (i.e. GA20ox, GA3ox, and GA2ox) are encoded by gene families. The remaining CPS-like, KS-like, and KO-like genes were likely to be involved in the biosynthesis of diterpene phytoalexins rather than GAs because the expression of two CPS-like and three KS-like genes (OsCPS2, OsCPS4, OsKS4, OsKS7, and OsKS8) were increased by UV irradiation, and four of these genes (OsCPS2, OsCPS4, OsKS4, and OsKS7) were also induced by an elicitor treatment.     

Enhanced insect resistance in Thai rice varieties generated by particle bombardment

We used particle bombardment to transform two elite Thai rice varieties, Khao Dawk Mali 105 (KDML105) and Supanburi 60 (SP60), with the snowdrop lectin gene gna (Galanthus nivalis agglutinin). This gene confers resistance to sap-sucking insects such as the brown planthopper (BPH; Nilaparvata lugens), which is one of the most damaging pests of rice. Traditionally, KDML105 and SP60 have been regarded as recalcitrant to transformation, and this is the first account of successful gene transfer to these varieties. By molecular analysis, we confirmed the recovery of over thirty gna-transgenic lines. GNA protein expression was characterised by western blot analysis, and we achieved expression levels of up to 0.25% total soluble protein. GNA-producing R₁ transgenic plants were significantly more resistant to BPH than control plants (P<0.0001), with 37% and 42% reduction in nymphal survival for constitutive and phloem-specific expression, respectively. Transferring the gna gene to these superior rice varieties thus represents a major step forward for crop improvement in Thailand, and should help to reduce the damage caused by rice pests, and hence increase yields for this vital domestic and export market.     

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 cookingand eating qualities. Amylose content (AC), gel consistency(GC) and gelatinization temperature (GT) are important traitsdetermining rice quality. A population of recombinant inbredlines (RIL) derived from KDML105 x CT9993 cross was used tostudy the genetic control of AC, GC and GT traits. A total of191 markers were used in the linkage map construction. The 1605.3cM linkage map covering nearly the whole rice genome was usedfor QTL (define QTL) analysis. Four QTLs for AC were detectedon chromosomes 3, 4, 6 and 7. These QTLs accounted for 80% ofphenotypic variation explained (PVE) in AC. The presence ofone major gene as well as several modifiers was responsiblefor the expression of the trait. Two QTLs on chromosome 6 andone on chromosome 7 were detected for GC, which accounts for57% of PVE. A single gene of major effect along with modifiergenes controls GC from this cross. The QTLs in the vicinityof waxy locus were major contributors in the expression of ACand GC. The finding that the position of QTLs for AC and GCwere near each other may reflect tight linkage or pleiotropy.Three QTLs were detected, one on chromosome 2 and two on chromosome6, which accounted for 67% of PVE in GT. Just like AC and GC,one major gene and modifier genes governed the variation inGT resulting from the KDML105 x CT9993 cross. Breeding for cookingand eating qualities will largely rely on the preferences ofthe end users.     

Marker-assisted breeding of Thai fragrance rice for semi-dwarf phenotype, submergence tolerance and disease resistance to rice blast and bacterial blight

Rice is a staple food crop for more than half of the world’s population. However, rice production is affected by many types of abiotic and biotic stress. Genetic breeding by utilizing natural resistance or tolerance genes is the most economic and efficient way to combat or adapt to these stresses. Khao Dawk Mali 105 (KDML 105) is an elite cultivar of aromatic rice mainly grown in Thailand. However, the production of KDML 105 is affected by lodging problems due to its tall plant type, regular flash floods or short-term submergence during the monsoon season, and diseases such as blast and bacterial blight. Here we report the pyramiding of semi-dwarf gene sd1, submergence tolerance gene Sub1A, blast resistance gene Pi9 and bacterial blight resistance genes Xa21 and Xa27 in KDML 105 by marker-assisted selection. The improved line, designated T5105, has a semi-dwarf phenotype with improved lodging resistance and a greater harvest index. T5105 survives after 2 weeks of complete submergence without significant loss of viability. T5105 confers high resistance to all five Magnaporthe oryzae isolates tested and provides resistance or moderate resistance to 25 of the 27 Xanthomonas oryzae pv. oryzae strains tested. In addition, T5105 produced higher yield than KDML 105 in two field trials and retains similar good grain quality to KDML 105. The development of T5105 provides a new line to boost the production of high-quality aromatic rice in tropical regions.