2016. Adaptation to drought in rice. Dissecting the role of Jamonates for the response to drought in rice

2016.  Adaptation to drought in rice. Dissecting the role of Jamonates for the response to drought in rice

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABTRACT

The various adaptive responses of drought stressed plants are strongly influenced by chemical messengers called phytohormones, which help the plants to regulate growth and development also in adverse conditions such as drought. One such important phytohormone is jasmonic acid (JA). However, little is known about its direct involvement in drought response or about its cross-talk to other phytohormones such as abscisic acid (ABA), which is intricately involved in drought stress adaptations. Previously, it was shown that the rice mutant cpm2, impaired in the function of allene oxide cyclase (AOC), a key enzyme in JA biosynthesis, was less sensitive to salt stress. In the present study, comparative changes under drought in some physiological traits and in the root proteome of cpm2 and the wild type (WT) were analyzed. When the stomatal conductance in WT and cpm2 under drought conAdition was measured, cpm2 had lower stomatal conductance under drought stress as compared to WT and this also correlated with increased ABA levels in shoots. Under drought, higher Water Use Efficiency (WUE) in cpm2 as compared to WT also indicated improved drought tolerance. Importantly, roots of cpm2 were better developed under both control and moderate drought stress. To assess if the roots of cpm2 and WT respond differentially to drought at the molecular level, root proteome analysis was undertaken using Tandem Mass Tag (TMT) approach. At the protein level, AOC was unique to WT and highly abundant under drought. This confirmed the lack of AOC in cpm2. Another protein, OPDA reductase (0PR7) which is downstream of AOC in JA biosynthesis pathway became more abundant in cpm2 while its amount decreased in the WT in drought stress. These results suggest that OPDA, a precursor of JA, and not JA itself is accumulating in response to drought stress. Analysis of other differentially expressed proteins revealed more active ROS detoxification and metabolism in cpm2 under drought. In addition, a number of proteins involved in pathways related to cell wall remodeling and cell growth were also abundant in cpm2 roots. These results suggested that JA signaling might negatively influence drought tolerance by orchestrating a block on critical morpho-physiological and molecular changes necessary for stress adaptation. Mutant analysis suggested benefits of blocking JA synthesis which might be useful for improving drought tolerance in rice  .

2012. Genome wide association mapping of drought resistance traits in rice

2012.  Genome wide association mapping of drought resistance traits in rice

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABTRACT

Rice, (Oryza sativa L.) is one of the most important crops providing staple food for a large segment of the world population. Drought stress is a major limitation to rice yields and its stability in rainfed areas. Developing drought resistant cultivars will help to increase production of rice in rainfed area. However, conventional breeding for drought resistance is slow in attaining progress due to poor understanding of genetic control of drought resistance and difficulty in phenotyping breeding progenies for drought tolerance. Molecular markers help in identification of quantitative trait loci (QTLs) associated with drought resistance traits and their use in breeding high yielding rice varieties suitable for drought-prone areas through marker-assisted breeding, thus reducing the need for extensive field testing over space and time. Conventional QTL mapping requires genotyping large mapping progenies derived from biparental crossing, demanding time and labour. Genome-wide association mapping is a powerful approach to identify associations between traits of interest and genetic markers using diverse genotypes. Thus, in the present study, a total of 48 rice accessions from different geographic locations and ecotypes were evaluated for plant production and root traits under irrigated and rainfed conditions in target populations of environment. Rice accessions showed significant differences for plant phenology, production and root traits. The rice accessions were screened using a total of 510 SSR markers selected from across the rice genome. Among them, 323 SSR markers were found to be polymorphic among the accessions. Structure analysis grouped the 48 accessions into six populations, broadly corresponding to the major geographic regions. Genome-wide association analysis using TASSEL identified a total of 444 marker-trait associations at P<0.05, P<0.001 and PO.OOOl for the various traits. Among them, 155 markers were associated with yield traits and 82 markers for root traits in these rice accessions. The markers viz., RM170 chromosome 6 (ch. 6), RM5720 (ch. 7), RM318 (ch. 2), RM3843 (ch. 4), RM29 (ch. 2), RM540 (ch. 6), RM585 (ch. 6) and RM36 (ch. 3) are linked to both yield and root traits under drought stress in this study. These markers were earlier identified to be linked to drought resistance and yield traits in rice through conventional QTL mapping efforts. The consistent markers for yield and root traits can be used in marker-assisted breeding for rainfed rice improvement. Thus, genome wide association mapping is ideal to detect markers linked to plant production and drought resistance traits in rice using diverse genotypes  .

2011. Defense response signaling for disease resistance in rice

2011. Defense response signaling for disease resistance in rice

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABTRACT

Plant disease resistance is often associated with a type of programmed cell death (PCD) called the hypersensitive response (HR). Upon recognition of pathogen proteins or their activity, the affected cell and surrounding cells commit to the HR to limit pathogen spread throughout the plant. This mechanism of plant disease resistance renders a pathogen avirulent on the host plant. Lesion mimics (LM) are a class of mutant or transgenic plants that spontaneously show lesions resembling the HR in the absence of biotic stress. Based on the association of the LM phenotype to cell death and its similarity to disease symptoms and the HR, this phenotype is a useful tool to dissect and understand the plant defense response.

To identify genes that when mutated result in the LM phenotype in rice, we used a microarray approach. By hybridizing labeled genomic DNA from an allelic series of deletion mutants to an oligonucleotide microarray, we identified candidate genes and genic regions that were deleted in a set of mutants. For one mutant, spll, mutations in a cytochrome P450 gene were confirmed to confer the LM phenotype. A genome browser developed to handle these microarray data is a community resource that enables researchers to rapidly identify untagged deletion mutations in rice.

Members of the 14-3-3 protein family were recently shown to be positive regulators of cell death and the HR in Arabidopsis. In contrast, the work herein shows that a rice 14-3-3 protein is a negative regulator of cell death and resistance. Transgenic plants carrying a construct that silences the rice 14-3-3 gene GF14e exhibit a LM phenotype and enhanced resistance to two distinct rice pathogens, Xanthomonas oryzae pv. oryzae and Rhizoctonia solani. These Gf74<?-silenced plants also showed enhanced expression of genes associated with salicylic acid (SA) mediated defense responses, including members of the peroxidase gene family. The GF/4<?-silenced plants did not show enhanced expression of marker genes associated with the ethylene response pathway, indicating that GF14e may negatively regulate SA mediated defense responses, but does not affect ethylene regulated responses.

Silencing GF14e results in the upregulation of several defense responsive peroxidases. cDNA from GF14e silenced plants was used in quantitative PCR (qPCR) to assay expression of four peroxidase genes. Of these, three showed significant upregulation in 2 weeks after sowing (WAS) and 5 WAS GF1^-silenced plants. The promoters of the three upregulated genes (PO-C1, PoxS.l, Pox22.3) contain at least one W-box element. In contrast, the peroxidase (Pox5.1) that did not show upregulation and is not upregulated in R gene mediated responses had no W-box elements. W-box elements are binding sites for the WRKY class of transcription factors. This result, coupled with bioinformatic predictions of potential rice 14-3-3 clients, and the observation that some WRKY genes are upregulated in GF14e silenced lines indicates that GF14e may negatively regulate WRKY transcription factors related to cell death and defense responses.

Based on the implication that one 14-3-3 protein negatively regulates defense responses related cell death, provides a framework to develop a model for how this protein might function in the plant disease  resistance repsonse  .

2010. Genome organization and genetic diversity of wildrice (Zizania palustris L.)

2010. Genome organization and genetic diversity of wildrice (Zizania palustris L.)

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABSTRACT

The large amount of molecular marker and DNA sequence information in rice (Oryza sativa L.) has allowed for comparative genetics between rice and wildrice (Zizania palustris L.). In particular, rice simple sequence repeat (SSR) markers were used to develop an SSR-based linkage map in wildrice and to determine the amount of genetic diversity within and among populations of the species. The same set of markers was analyzed in a wildrice population segregating for the pistillate trait to find marker genotypes that correlated with the trait. Rice genome DNA sequences for three well-characterized genes were used to determine the relatedness between Oryza species and wildrice.

Six-hundred-eleven rice SSR markers were tested in wildrice. Approximately 42% of the markers can be amplified in wildrice and about 30% of those markers exhibit polymorphism in the newly developed SRT X BRL mapping population. SRT is a shattering resistant tester line used in the wildrice breeding program. BRL is a breeding line resulting from selection on a population collected from Big Rice Lake in Cass County, Minnesota. An additional 36 SSR markers were developed in Zizania palustris using DNA sequences from the endangered wildrice species Z. texana. About 47% of these markers exhibited co-dominant polymorphism and 23% dominant polymorphism in the SRT X BRL mapping population. In all, seventy-five of these polymorphic markers were used to develop the first SSR-based molecular genetic map of wildrice.

In contrast to the RFLP-based wildrice map, the SSR-based map indicates little synteny between rice and wildrice. This difference may be due to some non-specific amplification with the rice SSR markers. It may also be an indication of the amount of DNA sequence conservation between the two species as the RFLP markers were generated from cDNAs representing expressed DNA sequences. The majority of the rice SSR markers were generated from genomic DNA sequences where SSR motifs are largely in intron or even non-genic sequences. Such regions of eukaryotic genomes are known to be subject to rearrangement which may be reflected in what appears to be a reduced level of detected synteny (Langham et al. 2004).

A molecular genetic marker was identified to be associated with the pistillate gene. Using this genetic marker to select for the pistillate gene would be useful for developing significantly larger mapping populations than are currently possible in wildrice allowing for more precise mapping and QTL studies. In the short-term, use of pistillate wildrice could benefit the wildrice breeding program by increasing cultivar yields as much as 50%. In the long-term, a true breeding pistillate wildrice could facilitate the development of recombinant inbred lines and near isogenic lines for use in producing wildrice hybrids and genetic stocks. Zizania palustris is more closely related to wild Oryza species than to the cultivated species Oryza sativa based on direct comparison of gene sequences from Adhl, Waxy and MatK.

The Rc gene is known to control rice seed pericarp color via the presence of a 14-bp indel sequence. Comparison of the Rc gene sequence among Zizania palustris, Oryza. rufipogon and O. sativa revealed that wildrice contains the indel sequence conferring red pericarp color in O. rufipogon. Further comparative genetics between Z. palustris and wild Oryza species such as O. brachyantha, O. granulata and O. rufipogon may uncover greater synteny than with O. sativa.

Genetic diversity studies of recently collected natural wildrice from lakes in Minnesota and Wisconsin do not appear to correlate with geographic distribution. The assessment of the available genetic diversity in wildrice is important for continued improvements in wildrice breeding. Generally, wildrice genetic diversity analysis has shown that allele uniqueness and frequency are specific to a given natural population. This may be a result of adaptation to the unique environment of each lake. Further diversity analysis using a larger set of populations may lead to a greater understanding of specific alleles involved in wildrice adaptation that could be utilized to produce varieties that would be more uniformly adapted to the varying cultivated conditions in northern Minnesota  .

2009. Identification and characterization of quantitative trait loci for drought resistance in upland rice (Oryza sativa L.).

2009. Identification and characterization of quantitative trait loci for drought resistance in upland rice (Oryza sativa L.).

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABSTRACT

Breeding improved drought-resistant upland rice cultivars could be accelerated if suitable quantitative trait loci (QTL) with large and consistent effects on grain yield under drought conditions in the desired genetic backgrounds were identified. Experiments were performed with the aim of identifying, characterizing and validating a QTL with the potential to be used in marker-assisted selection. A population from the cross Vandana/Way Rarem was field tested during two consecutive years. A large-effect QTL (qtl!2.1) for grain yield under reproductive-stage drought was identified. This locus had an additive effect equivalent to 47% of the trial mean yield over two years and had a very low level of QTL x year interaction. The favorable effect was contributed by Way Rarem, the drought-susceptible parent. A subset of lines was subsequently tested in a total of 21 trials, in order to confirm the effect of qtl!2.1 under a wider range of environments, stress intensities and stress timing. The QTL had a very consistent effect across trials, as it improved grain yield in 9 out of 10 moderately to severely drought-stressed trials. The locus had no effect under well-watered conditions. The results from those trials confirm that qtl!2.1 is a drought-specific locus that is consistent across environments. Physiological experiments on a subset of lines having contrasting genotypes at qtll2.1 revealed that the Way Rarem-derived allele of qtl!2.1 improves grain yield under drought mainly through a slight improvement (7 to 9 %) in plant water uptake under water-limited conditions. Such an increase in water uptake could explain the large effect on grain yield observed under field conditions. This improvement of plant water uptake is likely associated with improved root architecture. Finally, QTL mapping for drought resistance was also performed in an IR55419-04/ Way Rarem population evaluated under similar conditions as the Vandana/Way Rarem population. This revealed that qtll2.1 had no effect on grain yield under stress in the IR55419-04/Way Rarem population, suggesting QTL x genetic background interaction for qtl!2.1  .


 

2008. Genome-wide analysis of the nitrogen stress transcriptome of red rice (Oryza sativa L.).

2008. Genome-wide analysis of the nitrogen stress transcriptome of red rice (Oryza sativa L.).

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABTRACT

The weedy red rice (Oryza sativa L.) competes with cultivated rice (O. sativa) for N fertilizers, as demonstrated in field and greenhouse experiments. The ability of red rice to accumulate more N than cultivated rice even at low-N was hypothesized to be due to a molecular mechanism that helps it tolerate N deficiency stress better than the cultivated rice. Microarray analysis of the N stress transcriptome of the weedy red rice was conducted to identify expression patterns that could reveal signaling and response pathways in N deficiency stress adaptation. Candidate genes identified by microarray analysis were validated and their expression patterns in red rice were compared with those in Wells by semi-quantitative real-time RT-PCR. Microarray analysis revealed transcription factors and genes associated with signaling and response regulation, NH4+ assimilation, starch synthesis, stress response, protein fate, and energy metabolism. Gene expression profiles suggested that these genes compose an N deficiency stress response pathway that is likely underlying the greater tolerance of weedy red rice to N-limiting conditions compared to the cultivated rice. Real-time RT-PCR gene assays revealed that genes coding for two transcription factors as well as enzymes involved in starch synthesis, N assimilation, protein folding, and signaling and response regulation were differentially expressed in red rice and cultivated rice. Although these findings confirm the hypothesis that red rice has adaptive molecular mechanisms different from Wells rice, further experiments need to be done to investigate the specific processes involved in the response pathways regulated by these transcription factors and enzymes, particularly at time points immediately after N deficiency  .


 

2008. Genetic and molecular characterization of the low phytic acid (Lpa1) locus in rice

2008. Genetic and molecular characterization of the low phytic acid (Lpa1) locus in rice 

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABTRACT

The rice low phytic acid (lpa\) mutant has a 45 % reduction in seed phytic acid and a molar equivalent increase in inorganic P. The rice /pal mutation was mapped to rice chromosome 2L. This research aims to identify the rice Lpal gene using a positional cloning and candidate gene approach, characterize the rice Lpal gene expression and identify lpal mutant alleles for functional analysis. High resolution genetic mapping of the rice lpal mutation resulted in the identification of an 8 kb region on chromosome 2 containing a single candidate gene (LOC_Os02g57400) with homology to 2-phosphoglycerate kinase. Sequence analysis of the candidate gene from the two independent mutants (KB 1-1 and DR1331-2) confirmed that (LOC_Os02g57400) is the rice Lpa\ gene {OsLpa 1). This gene has three alternative splice variants which have been confirmed by expression analysis. The location and nature of the two mutations suggests that the lesion affects the translation of the predicted protein derived from the longest transcript. OsLpa 1 represents a novel gene involved in phytic acid metabolism. The identification of Lpa\ gene as well as generation of additional mutants for future study will contribute to the understanding of the phytic acid biosynthesis and accumulation in plants  .

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

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

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

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.

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

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)

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

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

 DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

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.

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

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

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

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

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

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  .

2005.Large-scale gene expression analysis of barley and rice under salinity stress

2005.Large-scale gene expression analysis of barley and rice under salinity stress

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABSTRACT

Salinity stress imposes significant yield restriction on irrigated and rainfed agricultural systems. Rice is one of the most economically important crop species which is salt-sensitive. A related cereal, barley, has significant morphological and developmental similarity with rice but is among the most salt-tolerant crop species. In an effort to identify genes which may be involved in adaptation of rice and barley to salinity stress we have conducted large-scale gene expression analysis in species. Identification of components that distinguish the response of barley from that of rice, and of tolerant genotypes from sensitive ones, could improve our understanding of tolerance mechanisms. Such an understanding is necessary for efforts to improve salinity tolerance of rice. We performed transcriptional profiling of a barley genotype, Morex, under salinity stress at three time points over a short duration. Considerably different sets of genes were induced by salinity stress at the three time points, indicating the dynamic nature of the transcriptome. Genes related to jasmonic acid (JA) biosynthesis and known to be JA-responsive were induced by salinity stress in barley. In an effort to elucidate the role of JA in salinity response of barley, we characterized the performance and gene expression of barley plants which were pretreated with JA before salinity stress. Phenotypic characterization of pretreated plants indicated that JA partial ameliorated salinity stress by JA as evident in increased photosynthetic performance and decreased Na+ accumulation in shoot tissue. Transcriptional profiling was further extended to rice genotypes which differed in salt-tolerance at early vegetative stage and reproductive stage. These studies revealed that different genotypes induced strikingly different set of genes in response to salinity. One key feature was that the sensitive genotypes induce a much larger set of genes in response to salinity relative to tolerant lines. One of the approaches used to identify genes with a potential role in salinity adaptation was to co-localize responsive genes with known salinity tolerance quantitative trait loci (QTL). This approach resulted in identification of a cation transporter which was later reported to be the gene responsible for significant variation in salinity tolerance of rice. Such an integrated approach of combining genetic information with large-scale genomics data has potential use in crop improvement  .

2005. Physiological and molecular responses to abiotic stress in rice (Oryza sativa)

2005. Physiological and molecular responses to abiotic stress in rice (Oryza sativa)

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

OBJECTIVES OF THE STUDY

The general objective of this study was to identify genes with important roles in cold-stress tolerance and to understand how they function. Identification and characterization of these genes in the context of cellular biochemistry and physiology are major challenges for the plant molecular biologist following completion of the full genomic sequences of the model plant species Arabidopsis and Oryza.

The specific objectives were:

1-    To characterize the involvement of the OsLti6 gene family in abiotic stress responses.

2-    To elucidate the functional role of OsLti6 in cold stress and to identify proteins with which it may interact.

3-    To identify the physiological responses of rice genotypes to abiotic stress.

4-    To examine expression profile differences between cold tolerant and sensitive rice genotypes in a semi-global manner using cDNA-AFLP   .

2004. Comparative analysis of the wheat and rice genomes based on DNA sequence

2004. Comparative analysis of the wheat and rice genomes based on DNA sequence

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

INTRODUCTION

Comparative Genetics is a broad discipline that has as it’s first objective the estimation of genetic similarity between two or more species to establish evolutionary relationships. Comparisons may be at the phenotypic and morphologic level of the whole organism or at deeper levels of complexity such as biochemical traits in the cell or the DNA sequence in the nucleus. A second objective utilizes the recognized levels of similarity between two or more organisms for the transfer and complementation of knowledge from one organism to another. This can accelerate the discovery process when one of them is a model species or has been studied more thoroughly, all of this within a framework of genes in common. The typical example is the use of the mouse as a model for mammalian genetics and the transferability of knowledge acquired from this system to the study of human genetics and medicine  .

2003. Fine mapping and candidate gene analysis for root traits in rice (Oryza sativa L.)

2003. Fine mapping and candidate gene analysis for root traits in rice (Oryza sativa L.)

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABSTRACT

Rice is a major staple food for more than 30% of the world’s population with 85% of its production devoted to human consumption (IRRI, 1997). Rice is grown in diverse agro-ecological conditions, ranging from deepwater lowland areas to high altitude upland areas. Nearly half of the areas planted in rice are in rainfed ecosystems. Drought is one of the main abiotic constraints in rice, causing huge yield losses each year. A thick and deep root system is considered a favorable component allowing rice crops to maintain their water status under conditions in which there is water available at deep soil layers (Nguyen et al., 1997). The presence of sub-soil compaction layers in many rainfed lowland areas impedes optimal growth in rice cultivars without these characters.

To fully understand biological processes underlying rice root growth, it is important to isolate and characterize the genes involved in these processes. In the present study, two approaches were employed in order to identify genes involved in rice root growth, a Differential Display Reverse Transcription (DDRT) analysis and a “map-based cloning” strategy. In the DDRT analysis, 2 candidate cDNA clones putatively involved in rice root penetration ability (CR19C1 and CR23A1) were identified. Results from sequence homology searches indicated that the DD fragment CR19C1 has some similarity to the locus AT1G72960 on chromosome 1 of the Arabidopsis genome. This locus is a putative gene conferring root hair defects in Arabidopsis thaliana. The DD fragment CR23A1 was similar to the locus AT1G76490 on chromosome 1 of Arabidopsis thaliana. This locus is a putative gene coding for 3-hydroxy-3-methylglutaryl CoA reductase (HMGR), the enzyme involved in cell division in many species. These findings give us some ideas about the functions of candidate genes involved in root growth mechanisms in rice.

In a map-based cloning strategy, 1,037 NILs derived from the BC4F2 population were used for fine mapping of the BRT QTL on rice chromosome 4. So far, the marker R1408B has been mapped in the target QTL between the flanking markers RG939 and RZ905, leading to the dissection of the target QTL into 2 smaller segments with a genetic distance of 2.3 and 2.8 cM, respectively. More RFLP markers are being screened with the aim of narrowing the genetic distance of the target QTL down to 1 cM or less. Chromosome substitution lines have been selected for further root characteristic evaluation in the greenhouse. Results from this experiment will facilitate fine mapping of the target QTL  .

2003, Genetic mapping of agronomic traits from the interspecific cross Oryza sativa (L.) and Oryza glaberrima (Steud.)

2003, Genetic mapping of agronomic traits from the interspecific cross Oryza sativa (L.) and Oryza glaberrima (Steud.)

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABTRACT

Wild relatives of cultivated rice varieties offer new genetic sources for enhancing economic value, but traditional interval mapping techniques have not gained widespread support among applied researchers for marker assisted selection. The objectives of this study were to detect quantitative trait loci (QTL) for agronomic traits in a hybrid mapping population and compare the non-parametric Discriminant Analysis (DA) procedure with traditional approaches for accuracy and precision. In addition, the effects of population structure on marker-assisted classification were explored. A molecular linkage map comprising 100 SSR markers that spanned the rice genome at intervals of 10.5 cM on the average was constructed based on 312 doubled haploid lines derived from the cross interspecific Oryza sativa x O. glaberrima.

The mapping population was evaluated in replicated field plots in Colombia and Louisiana in 2001 and 2002, respectively. QTLs were identified for grain, milling and eating qualities and important agronomic traits such as heading date, plant height, number of tillers per plant, panicle length, grain yield and 1000-grain weight. A total of 28 QTLs were detected for 10 grain quality traits, and 22 QTLs for six agronomic traits were detected that were significant in at least one environment, but only seven were significant in both environments. SSR markers that best discriminated between pre-defined groups of high and low trait values were selected by stepwise DA. Using a A>nearest neighbor algorithm, the largest phenotypic differentiation (3 standard deviations) between two contrasting phenotypic groups resulted in 100% correct classification. Adjustments for population structure resulted in a 5-fold decrease in number of markers needed to achieve the same level of accuracy. These results demonstrated that procedures such as DA and consideration of population structure can be used for efficient marker-based allocation of the doubled haploid lines into pre-defined groups for yield and other agronomic traits. Finally, DA-selected markers pointed to the same or closely linked regions on the linkage map that in turn underscored the validity of the DA approach for genetic mapping  .

2002. Genetic studies on traits related to cold tolerance in rice

2002. Genetic studies on traits related to cold tolerance in rice

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABSTRACT

Low temperature stress is commonly associated with rice cultivation in temperate growing areas where successful cultivars have to possess a high degree of cold tolerance at sensitive growth stages. This research was conducted to identify and tag quantitative trait loci associated with low temperature tolerance at the seedling and booting stage of rice. Cold tolerance was assessed using several parameters measured in replicated experiments under controlled environment and natural field conditions using 191 recombinant inbred lines developed from a cross between the japonica cultivar M-202 and the indica cultivar IR50. A genetic map composed of 181 microsatellite loci was constructed for QTL analysis implemented using the composite interval mapping approach. At the seedling stage, a major QTL associated with cold-induced wilting in the growth chamber experiment was identified on chromosome 12 accounting for 41% of the phenotypic variation. Another QTL with large effect on chromosome 1 explained 68% of the phenotypic variation for cold tolerance in the field. At the booting stage, two QTL on chromosomes 2 and 9 were associated with spikelet fertility assessed in the growth chamber and greenhouse; both explained a total of 18% of the phenotypic variation. QTL associated with heading date, plant height, panicle exsertion and length, number of grains per panicle and tillering were also identified in this research. To elucidate the relationships between several cold tolerance parameters and agronomic trait measurements using controlled and field environments, correlation analysis was performed. Several interesting QTL have been identified as potential targets in breeding for cold tolerant rice and for further study  .

2002. Development and mapping of markers linked to the rice bacterial leaf blight resistance gene Xa7

2002. Development and mapping of markers linked to the rice bacterial leaf blight resistance gene Xa7

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABSTRACT

Markers were generated that are linked to the rice bacterial blight resistance gene Xa7. AFLP analysis of a segregating, near-isogenic F3 population of IR24 X IRBB7 revealed one polymorphic fragment, M1, which was mapped to position 107.3 centimorgans (cM) on the RGP map. Sequence comparisons of resistant and susceptible lines near M1 were used to develop additional markers. A STS named M2 was mapped proximal to M1 that indicated that Xa7 is on the distal side of M1. On the distal side of M1, two SSRs, M3 and M4, were mapped 0.5 cM and 1.8 cM, respectively, from Xa7. The pattern of recombinants was consistent with the order of M1-Xa7-M3-M4, and the map distances indicated that Xa7 is located in the region corresponding to the ends of the physically mapped CUGI BAC contigs 96 and 143. A complex repeat was identified in the DNA sequence from rice cultivars '93-11' and 'Nipponbare' that matched the end of contig 96 and a previously mapped EST marker (C52865S). Amplification of the repeat and flanking sequences revealed the presence and absence of the repeat in IR24 and IRBB7, respectively. The polymorphic STS was named M5. No recombinants were identified between Xa7 and M5 in 277 F3 susceptible progeny of the IR24 X IRBB7 cross. Comparison of the physical and genetic maps of rice indicates that Xa7 could lie within 40 kb of M5, a distance suitable for gene pyramiding efforts and Xa7 cloning strategies .

2000. Physiology of submergence tolerance in rice A functional study of the rice Sub1 gene

2000.  Physiology of submergence tolerance in rice  A functional study of the rice Sub1 gene

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABSTRACT

Submergence stress limits yield on 22 million hectares of lowland rice in South and Southeast Asia, demonstrating the need for varieties with improved submergence tolerance (ST). ST may also benefit irrigated systems where controlled flooding suppresses weed growth. The response of rice to submergence depends on flooding regime. In regions where flash-flooding occurs and water recedes within two weeks, ST cutivars predominate. In contrast to deepwater rice, which avoids submergence stress by elongating in response to flooding, ST cultivars exhibit little or no elongation, but have enhanced capacity for tolerance of submergence. ST in rice, previously viewed as a quantitative trait, is now associated with the Subl gene. This study, which examines the effect of Subl on physiology of ST in rice, represents a considerable improvement in methodology in the examination of flooding tolerance. Previous studies utilized flooding intolerant species or made comparisons between species or cultivars. According to the results of this study, Subl alters fermentation, carbohydrate metabolism and growth under anoxia and is associated with reduced submergence-induced shoot elongation. Treatments which increase leaf elongation have no effect on carbohydrate reserves but decrease glutathione reductase activity, increase oxidative stress, and decrease survival. These data indicate a relationship between elongation growth and oxidative stress defense responses and the lack of a relationship between carbohydrate reserves and leaf elongation. This finding suggests that some mechanisms controlled by Subl may occur independent of the gene's effect on elongation and indicate the possibility of combining ST with elongation. Subl engenders a suite of physiological responses including altered fermentation, carbohydrate metabolism, elongation, and oxidative stress tolerance. Subl increases coleoptile growth under anoxia but decreases leaf growth under submergence. Such a diversity of effects indicates that Subl encodes a transcription factor, or a protein involved in the perception or transduction of a signal generated by submergence stress. Rice varieties transformed with Subl will improve rice production and provide an excellent model system to advance basic understanding of the Subl gene and of flooding tolerance in plants. This study provides a framework for ultimately establishing the link between Subl structure and function  .

1992. Embryogenic suspension culture of rice and NaCl selection from suspension culture derived somaclones

1992. Embryogenic suspension culture of rice and NaCl selection from suspension culture derived somaclones

DOWNLOAD: PDF
SÐT: 0981800855 (A. LONG)
PRICE: 100.000 VND
EMAIL: FOODCROPS@GMAIL.COM

ABSTRACT

Embryogenic suspension cultures of rice (Oryza sativa L. cv. Basmati-370 and Taipei-309) were established. Various explants, types, and different concentrations of growth regulators, different concentrations of sucrose, and transfer techniques were investigated to identify parameters which control the initiation of and plant regeneration from rice callus.

The types of calli induced in various media also were tested for ability to initiate suspensions which could regenerate plants. Friable embryogenic calli from caryopses on LS medium supplemented with 1 or 2 mg-L'1 2,4-D and 1 or 2 g-L'1 sucrose proved to be the most suitable starting material.

Histological studies demonstrated embryogenesis in somatic cell suspensions. Friable calli developed embryoids after two to three months in suspensions. "Proembryogenic masses" formed at the peripheries of the inoculated callus clumps. Fragmentation of the proembryogenic masses gave rise to embryoids in the cell cultures. Embryogenic masses also arose from the development of cell aggregates into organized structures. Plant regeneration occurred from embryoids transferred to solid LS medium with or without NAA and BAP. Plants could be obtained from long term suspensions of Basmati-370 (up to 9.5 months old) by adding GA3 or NaCl to the medium. Two embryogenic cell lines were cultured in 200 mM NaCl for two months with increased regenerability. Greenspots and formation of leafy structures were obtained from forty-four months and one week old suspension cultures by adding sorbitol, ABA, and NaCl.

Somaclonal variations were observed in suspension culture-derived somaclones of rice cv. Taipei-309. Variants expressed inferior and superior agricultural traits, such as height, maturity, and yield. Most somaclones were shorter, later in maturity, and low yielding compared to the check.

Seedling screens and whole plant testings were conducted over four generations to select somaclones for NaCl tolerance. Heritable tolerance was obtained. X-ray microanalyses and ion analyses revealed that tolerant lines accumulated fewer Na+ ions in the plant tissues compared to susceptible lines. Tolerant plants also secreted less salt through their leaves compared to the susceptible ones.

This study indicated that somaclones derived from rice embryogenic suspension cultures may be a potential source for NaCl selection and that the acquired traits also are heritable  .