2007. Signaling dynamics in rice expressing constitutively active Nicotiana protein kinase 1

2007. Signaling dynamics in rice expressing constitutively active Nicotiana protein kinase 1

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ABSTRACT

Signaling components such as mitogen-activated protein kinases (MAPKs) regulate stress-induced pathways and are potentially a powerful means of genetically engineering plant tolerance to abiotic stress. The kinase domain of tobacco mitogen-activated protein kinase Nicotiana protein kinase 1 (NPK1) into rice cultivar Nipponbare. Four-week old transgenic and wild type plants treated with moderate (150mM) or severe (300mM) salt stress did not differ in visible signs of leaf damage, electrolyte leakage, malondialdehyde content or ion content within leaves. Expression of caNPKl alters gene transcript abundance in the absence of stress as assessed by microarray analysis. Genes potentially related to flowering and development are downregulated while biotin biosynthesis and methionine recycling pathway as well as thirteen transcripts with matches to stress-related genes appear upregulated in the transgenic plants. Quantitative real-time PCR analysis indicates no significant difference in expression of several known rice MAPKs between caNPKl transgenics and wild type  .

2007. Rice plant traits dissection for early vigor and competitiveness with Echinochloa phyllopogon (Stapf) Koss.

2007. Rice plant traits dissection for early vigor and competitiveness with Echinochloa phyllopogon (Stapf) Koss.

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ABTRACT

Resistance to herbicides in the most important weeds threatens the sustainability of California rice. Weed-competitive rice cultivars could be a low-cost and safe nonchemical addition to an integrated weed management program. Tradeoffs between competitiveness and productivity and inconsistent trait expression could complicate the breeding of competitive rice cultivars. A two-year competition experiment was conducted. Competition reduced average rice yield from 32% to 48%, and watergrass biomass from 44% to 77%. Path analysis suggested that enhancing rice weed-suppressive ability and weed tolerance while minimizing possible productivity tradeoffs should promote early (12 d after seeding) (DAS) growth and light-capture traits followed by moderate growth rates before heading and a vigorous grain filling period. Late-season competitiveness can lower productivity. A second study focused on the identification and interrelationships among traits for early vigor. In a greenhouse two-year experiment, the growth characteristics ofwatergrass and 21 rice seedlings differed after three destructive harvests for growth analysis at 4-5 leaf stage, early and mid to late tillering. Semidwarf rice seedlings had greater growth traits. However, watergrass had later superior growth rates and tallness. Cluster analysis found that vigorous seedling had more leaf area and early tillering. Seedling height was not associated with the clustering of genotypes into high vigor groups. Overall, these results suggest that rice early vigor, as a component of competitiveness, can be enhanced through selection for leafier, rapidly elongating, and highly tillered plants. A third study identified rice QTLs for early vigor and competitiveness. A population of 137 F2 recombinant inbred lines derived from the cross M-202 x IR50 was grown in the field during 2003 and 2004. Phenotyping was performed at 20, 30 and 60 DAS. A genetic linkage map was generated using 180 microsatellite markers. Path analysis was used to clarify the relationships among diverse variables, including molecular markers, in hypothetical cause-effect models. We located about 40 putative genetic loci associated with rice traits related to plant vigor and competitiveness. Results would be useful for using marker-aided selection for identification of genotypes with superior vigor and competitiveness, and for combining these characteristics into a highly productive ideotype  .

2007. Physiological and biochemical analysis of transgenic rice over-expressing C4 genes from maize and the diversity and plasticity of C4 photosynthesis in Eleocharis (Cyperaceae)

2007. Physiological and biochemical analysis of transgenic rice over-expressing C4 genes from maize and the diversity and plasticity of C4 photosynthesis in Eleocharis (Cyperaceae)

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ABSTRACT

From a photosynthetic point of view, yield of some crops may be further improved by increasing the photosynthetic capacity of the source leaves and/or by increasing partitioning of photoassimilate to organs of economic importance. C4 plants are able to overcome photorespiration, and thus photosynthesize more efficiently, through an additional photo synthetic pathway (C4) and specialized leaf anatomy (Kranz) that work together as a "CO2 pump" to supply Rubisco with enriched CO2 edging out O2 as a competitive substrate. This photosynthetic mechanism endows C4 plants a selective advantage over C3 plants especially in warmer climates and during water deficits: higher photo synthetic capacity, and higher water and nutrient use efficiency. The C4 syndrome is characterized by high activities of C4 enzymes and Kranz anatomy (mesophyll and bundle-sheath cells). Traditionally, Kranz anatomy, which allows for the spatial separation of the C4 biochemical steps, was believed to be required for the C4 CO2 concentrating mechanism in terrestrial plants. However, it is known that C4-like mechanisms can be induced, without the presence of Kranz anatomy, in two submersed aquatic species (Hydrilla verticillata and Egeria dens a). Most recently, the terrestrial C4 plants Bienertia cycloptera, B. sinuspersici, and Suaeda aralocaspica (Chenopodiaceae) from Central Asia have been found to lack Kranz anatomy and function with specialized intracellular compartmentation. Thus, by introducing the necessary genes of the C4 pathway to C3 plants, it may be possible to engineer a C4-like mechanism and improve photosynthesis without a requirement for Kranz anatomy. In this study, C3 rice was transformed with two genes encoding C4 photosynthetic enzymes (phosphoenolpyruvate carboxylase and pyruvate orthophosphate dikinase) and the photosynthetic, biochemical, and anatomical changes were documented.

Additionally, research with the genus Eleocharis shows that the C4 syndrome may be more plastic than formerly believed. Within the genus, species were shown to possess the full range from C3 to intermediate to C4. In a species dependant manner, plants changed photosynthctic types whether grown terrestrially or submerged with concomitant changes in the C4 enzyme activities, carbon isotope composition and leaf anatomy  .

2007. Microarray analysis of rice grain abscission regulated by sh4

2007. Microarray analysis of rice grain abscission regulated by sh4

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ABSTRACT

Abscission is the programmed organ separation from the main body of the mother plant. Separation takes place at predetermined positions called abscission zones. Although abscission is essential for the plant life cycle, the molecular regulation of abscission remains poorly understood. The rice grain shattering gene sh4, which encodes a putative MYB3 transcription factor, is involved in the development and function of the abscission zone between a rice grain and its pedicel. To investigate genes potentially regulated by sh4 during the abscission process, microarray analysis was conducted using sh4 transgenic plants. The study identified several categories of genes that were up-regulated by sh4. These include cell wall hydrolytic enzymes, expansins, pathogenesis-related genes, and abscisic acid (ABA) and stress responsive genes. Further studies indicated that exogenous ABA was capable of promoting flower abscission in wild rice species and the sh4 transgenic plants. ABA from the developing embryo may have served as the signal for the initiation of rice grain abscission. The study suggests that ABA is the hormone that signals rice grain abscission and sh4 is a regulator in the signaling pathway  .



 

2007. Identification of molecular markers and association mapping of selected loci associated with agronomic traits in rice.

2007. Identification of molecular markers and association mapping of selected loci associated with agronomic traits in rice.

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ABSTRACT

Discriminate Analysis as a procedure was evaluated to select molecular markers associated with complex traits in US rice germplasm. Markers for percent head rice, percent total rice, and grain yield were identified with high levels of correct classification that mapped within or near traditional Quantitative Trait Loci (QTL).

Mixed model-regression procedure to identify molecular markers that predict phenotypic variance associated with four agronomic traits was created and validated in two distinct rice inbred populations. Main and epistatic effects were identified by standard hypothesis testing and Bayesian information criteria in a multivariate format. The new procedure increased power and enhanced prediction ability of markers in validation samples from both populations.

 A new SNP discovery and genotyping protocol referred to as Alternative Ecotilling has identified four previously reported and 14 new SNPs in the alk and waxy genes among 57 accessions based on comparisons with sequencing results. The new procedure has been published in 2006 in the journal Plant Molecular Biology Reporter.

Application of haplotype-specific markers in exon 7 of the BAD2 gene for marker-assisted identification and introgression of the aroma gene in U.S. rice was evaluated. Aromatic/non-aromatic phenotypes were consistent with corresponding marker haplotypes for all progeny tested which shows the potential of this procedure for marker assisted breeding of new
aromatic varieties.

Similarly, an allele-specific PCR assays were developed to distinguish between homozygous and heterozygous imazethapyr-resistant S653D and G654E SNP alleles of the rice ALS gene. Field collections were successfully screened for the presence of S653D SNP, and F2 progeny lines of natural CL 121 x red rice outcrosses were screened for the presence of the G654E SNP. These assays were proven successful and are currently used for detection of outcrossing and seed purity for the LSU AgCenter Rice Breeding Project  .

 

2006. Mapping QTL controlling durable resistance to rice blast in the cultivar Oryzica Llanos 5

2006. Mapping QTL controlling durable resistance to rice blast in the cultivar Oryzica Llanos 5

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ABSTRACT

The rice cultivar Oryzica Llanos 5 (OL5) possesses a high level of resistance to the fungus Magnaporthe grisea. The number and chromosomal location of quantitative trait loci (QTL) conferring resistance against eight isolates of the blast fungus were tested in two different populations of recombinant inbred lines from the cross Fanny x OL5. Twenty one QTL were detected and associated with the resistance traits, disease leaf area and lesion type, on 9 rice chromosomes. Eight of these 21 resistance loci had significant resistance effects in both experiments, while the others had effects that were only statistically significant in one experiment. Most, but not all, of the QTL occurred in the same genomic regions as either genes with major race-specific effects or other resistance QTL that had been described in previous experiments. Most of the QTL appeared to be race-specific in their effects but it is possible some of the QTL with smaller effects were nonspecific. One of the blast isolates used was FL440, which causes limited disease on OL5 and was probably virulent on most or all of the major genes from OL5. Three QTL affected resistance to FL440 in both experiments, one of which mapped to a region on chromosome 9 where no blast resistance genes have yet been mapped. An advanced backcross strategy with marker-assisted selection for OL5 alleles in QTL regions was used to generate five BC2F3 populations carrying five different target regions associated with partial resistance to rice blast disease. Three of five of these populations were analyzed for segregation for resistance to the M. grisea isolate FL440. One QTL designated qrbr-11.3 near the bottom of rice chromosome 11 was found to be significantly associated with partial blast resistance in 120 lines of a BC2F3 population (P< 0.01). This QTL accounted for 12.4% and 8.0% of the phenotypic variation in diseased leaf area and lesion type observed under greenhouse inoculation. Examination of the genomic sequence at the qrbr-11.3 locus showed that twenty-nine candidate resistance genes are present at that locus (~1.8 Mb), twenty-seven of which are predicted NBS-LRR genes. Ultimately, the information from this study can be integrated into the development of improved lines with OL5-derived QTL for resistance  .

2006. Analysis of transcriptome in rice and Arabidopsis

2006. Analysis of transcriptome in rice and Arabidopsis

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ABSTRACT

Transcriptional regulation is a fundamental issue in plant biology. With the availability of completed sequenced genomes and tools for large-scale analysis of gene transcription, such as DNA microarrays, the dynamics of transcriptomes and their developmental regulation are being revealed. In this dissertation, I focused my research primarily on genome-wide analysis of the transcriptome in rice and Arabidopsis, with special interest on light-regulation. First, I investigated blue light regulation of Arabidopsis transcription factor gene expression. Studies of various photoreceptor mutants revealed the predomiant role of cryptochromes in blue light control of genome transcription. Second, I compared light-regulated genome expression in rice and Arabidopsis and found a higher correlation of expression in light than in darkness. Organ-specific expression profiles provide evidence for divergent light effects in different organs with specific light-responsive promoter c/s-elements involved. Next, I used a tiling microarray to analyze the transcription of rice chromosome 4. This analysis provided expression support for most of the gene models, detected transcriptional activities in non-annotated regions, and identified correlation between transcriptional activity and chromosome organization. Further, I examined transcriptional activities of selected rice transposon-related genes. Expression was detected and actively transcribed clades were identified, supporting potential adapted host function or active expression (and possible transposition). Finally, I participated in the construction and analysis of RICEATLAS, a cellular transcriptional atlas of rice. My research significantly advanced our knowledge of the genome expression and their regulation in the two plant model species with their genome complete sequenced  .