Sequence variation and phylogenetic relationship analysis of starch branching enzyme I gene (SBEI) in rice varieties from China, Laos and Thailand

The coding sequence of starch branching enzyme I gene (SBEI) of 30 rice varieties from China, Laos and Thailand were cloned. All thirty sequences contain 2,463 bp and 14 exons and encode for 820 amino acids. Three sites of Single Nucleotide Polymorphisms (SNPs) A < C, T < C, and T < C were found at positions 1,107, 2,156 and 2,271 in Exon with 6, 13 and 14 respectively. The SNPs at position 1,107 A < C and position 2,271 T < C were silent mutations. The SNP at position 2,156 T < C was a missense mutation and induced a mutation from valine (GTG) to alanine (GCG). Three haplotypes A/T/T, C/T/C and C/C/C were observed. The phylogenetic analysis of 81 SBEI CDS sequences, out of which 30 are from this study and 51 are from previous, classifies them into 2 major groups using 4 sequences as outgroup. The group of monocot comprised of rice, barley, wheat, sorghum whereas maize and the group of dicot comprised of potato, cassava, poplar, Chinese chestnut, bean, legumes and apple. The group of rice SBEI CDS was a major clade in monocot group with high bootstrap value. SBEI gene of rice from China, Laos and Thailand, wheat, apple and poplar contain 14 exons while SBEI gene of rice from Japan and Korea contained only 12 exons. The GC content of SBEI gene of rice varieties was lower than that of wheat and apple but higher than that of poplar

Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice

Bacterial leaf blight (BLB) is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which poses a significant threat to global rice production. In this study, a genomewide association study (GWAS) was conducted using the genotyping-by-sequencing (GBS) approach to identify candidate single nucleotide polymorphisms (SNPs) associated with BLB resistance genes. The study utilized 200 indica rice accessions inoculated with seven distinct Xoo isolates and filtered highly significant SNPs using a minor allele frequency (MAF) of >5% and a call rate of 75%. Four statistical models were used to explore potential SNPs associated with BLB resistance, resulting in the identification of 32 significant SNPs on chromosomes 1–8 and 12 in the rice genome. Additionally, 179 genes were located within 100 kb of the SNP region, of which 49 were selected as candidate genes based on their known functions in plant defense mechanisms. Several candidate genes were identified, including two genes in the same linkage disequilibrium (LD) decay as the well-known BLB resistance gene (Xa1). These findings represent a valuable resource for conducting further functional studies and developing novel breeding strategies to enhance the crop’s resistance to this disease

Genetic analysis of wheat domestication and evolution under domestication

Wheat is undoubtedly one of the world's major food sources since the dawn of Near Eastern agriculture and up to the present day. Morphological, physiological, and genetic modifications involved in domestication and subsequent evolution under domestication were investigated in a tetraploid recombinant inbred line population, derived from a cross between durum wheat and its immediate progenitor wild emmer wheat. Experimental data were used to test previous assumptions regarding a protracted domestication process. The brittle rachis (Br) spike, thought to be a primary characteristic of domestication, was mapped to chromosome 2A as a single gene, suggesting, in light of previously reported Br loci (homoeologous group 3), a complex genetic model involved in spike brittleness. Twenty-seven quantitative trait loci (QTLs) conferring threshability and yield components (kernel size and number of kernels per spike) were mapped. The large number of QTLs detected in this and other studies suggests that following domestication, wheat evolutionary processes involved many genomic changes. The Br gene did not show either genetic (co-localization with QTLs) or phenotypic association with threshability or yield components, suggesting independence of the respective loci. It is argued here that changes in spike threshability and agronomic traits (e.g. yield and its components) are the outcome of plant evolution under domestication, rather than the result of a protracted domestication process. Revealing the genomic basis of wheat domestication and evolution under domestication, and clarifying their inter-relationships, will improve our understanding of wheat biology and contribute to further crop improvement

Alternative splicing of barley clock genes in response to low temperature:evidence for alternative splicing conservation

Alternative splicing (AS) is a regulated mechanism that generates multiple transcripts from individual genes. It is widespread in eukaryotic genomes and provides an effective way to control gene expression. At low temperatures, AS regulates Arabidopsis clock genes through dynamic changes in the levels of productive mRNAs. We examined AS in barley clock genes to assess whether temperature-dependent AS responses also occur in a monocotyledonous crop species. We identify changes in AS of various barley core clock genes including the barley orthologues of Arabidopsis AtLHY and AtPRR7 which showed the most pronounced AS changes in response to low temperature. The AS events modulate the levels of functional and translatable mRNAs, and potentially protein levels, upon transition to cold. There is some conservation of AS events and/or splicing behaviour of clock genes between Arabidopsis and barley. In addition, novel temperature-dependent AS of the core clock gene HvPPD-H1 (a major determinant of photoperiod response and AtPRR7 orthologue) is conserved in monocots. HvPPD-H1 showed a rapid, temperature-sensitive isoform switch which resulted in changes in abundance of AS variants encoding different protein isoforms. This novel layer of low temperature control of clock gene expression, observed in two very different species, will help our understanding of plant adaptation to different environments and ultimately offer a new range of targets for plant improvement

Pleiotropic effects of the wheat domestication gene Q on yield and grain morphology

Transformation from q to Q during wheat domestication functioned outside the boundary of threshability to increase yield, grains m−2, grain weight and roundness, but to reduce grains per spike/spikelet. Mutation of the Q gene, well-known affecting wheat spike structure, represents a key domestication step in the formation of today’s free-threshing, economically important wheats. In a previous study, multiple yield components and spike characteristics were associated with the Q gene interval in the bread wheat ‘Forno’ × European spelt ‘Oberkulmer’ recombinant inbred line population. Here, we reported that this interval was also associated with grain yield, grains m−2, grain morphology, and spike dry weight at anthesis. To clarify the roles of Q in agronomic trait performance, a functional marker for the Q gene was developed. Analysis of allelic effects showed that the bread wheat Q allele conferred free-threshing habit, soft glumes, and short and compact spikes compared with q. In addition, the Q allele contributed to higher grain yield, more grains m−2, and higher thousand grain weight, whereas q contributed to more grains per spike/spikelet likely resulting from increased preanthesis spike growth. For grain morphology, the Q allele was associated with reduced ratio of grain length to height, indicating a rounder grain. These results are supported by analysis of four Q mutant lines in the Chinese Spring background. Therefore, the transition from q to Q during wheat domestication had profound effects on grain yield and grain shape evolution as well, being a consequence of pleiotropy

A phenotypic test for delay of abscission and non-abscission oil palm fruit and validation by abscission marker gene expression analysis

International Horticultural Congress on Horticulture : Sustaining Lives, Livelihoods and Landscapes : International Symposia on Abscission Processes in Horticulture and Non-Destructive Assessment of Fruit Attributes, Brisbane, AUS, 17-/08/2014 - 22/08/2014Knowledge of the cell separation processes underlying organ abscission is limited mainly to the eudicot model systems tomato and Arabidopsis, while less is known about the mechanisms in crop species in general, and monocots in particular. Here we describe a simple phenotypic screen for oil palm plant lines with delayed or non-abscising fruit. The phenotypic test was used on the two species of oil palm including Elaeis guineensis and E. oleifera, in addition to their interspecific hybrids, and hybrids backcrossed to E. guineensis. A large variation in abscission phenotypes was observed. Histological analysis revealed similarities and differences in the abscission zone (AZ) of E. guineensis and E. oleifera, and dominant traits were observed in the AZ of the interspecific crosses. The expression of abscission marker genes for a polygalacturonase (EgPG4) and an ethylene synthesis ACO synthase (EgACO) were monitored during abscission of a randomly selected set of plants and in a non-abscising individual identified by the phenotypic test

Proceedings of international symposia on abscission processes in horticulture and non-destructive assessment of fruit attributes

Knowledge of the cell separation processes underlying organ abscission is limited mainly to the eudicot model systems tomato and Arabidopsis, while less is known about the mechanisms in crop species in general, and monocots in particular. Here we describe a simple phenotypic screen for oil palm plant lines with delayed or non-abscising fruit. The phenotypic test was used on the two species of oil palm including Elaeis guineensis and E. oleifera, in addition to their interspecific hybrids, and hybrids backcrossed to E. guineensis. A large variation in abscission phenotypes was observed. Histological analysis revealed similarities and differences in the abscission zone (AZ) of E. guineensis and E. oleifera, and dominant traits were observed in the AZ of the interspecific crosses. The expression of abscission marker genes for a polygalacturonase (EgPG4) and an ethylene synthesis ACO synthase (EgACO) were monitored during abscission of a randomly selected set of plants and in a non-abscising individual identified by the phenotypic test

A phenotypic test for delay of abscission and non-abscission oil palm fruit and validation by abscission marker gene expression analysis

International audienceKnowledge of the cell separation processes underlying organ abscission is limited mainly to the eudicot model systems tomato and Arabidopsis, while less is known about the mechanisms in crop species in general, and monocots in particular. Here we describe a simple phenotypic screen for oil palm plant lines with delayed or non-abscising fruit. The phenotypic test was used on the two species of oil palm including Elaeis guineensis and E. oleifera, in addition to their interspecific hybrids, and hybrids backcrossed to E. guineensis. A large variation in abscission phenotypes was observed. Histological analysis revealed similarities and differences in the abscission zone (AZ) of E. guineensis and E. oleifera, and dominant traits were observed in the AZ of the interspecific crosses. The expression of abscission marker genes for a polygalacturonase (EgPG4) and an ethylene synthesis ACO synthase (EgACO) were monitored during abscission of a randomly selected set of plants and in a non-abscising individual identified by the phenotypic test

Magnaporthe grisea Infection Triggers RNA Variation and Antisense Transcript Expression in Rice1[W]

Rice blast disease, caused by the fungal pathogen Magnaporthe grisea, is an excellent model system to study plant-fungal interactions and host defense responses. In this study, comprehensive analysis of the rice (Oryza sativa) transcriptome after M. grisea infection was conducted using robust-long serial analysis of gene expression. A total of 83,382 distinct 21-bp robust-long serial analysis of gene expression tags were identified from 627,262 individual tags isolated from the resistant (R), susceptible (S), and control (C) libraries. Sequence analysis revealed that the tags in the R and S libraries had a significant reduced matching rate to the rice genomic and expressed sequences in comparison to the C library. The high level of one-nucleotide mismatches of the R and S library tags was due to nucleotide conversions. The A-to-G and U-to-C nucleotide conversions were the most predominant types, which were induced in the M. grisea-infected plants. Reverse transcription-polymerase chain reaction analysis showed that expression of the adenine deaminase and cytidine deaminase genes was highly induced after inoculation. In addition, many antisense transcripts were induced in infected plants and expression of four antisense transcripts was confirmed by strand-specific reverse transcription-polymerase chain reaction. These results demonstrate that there is a series of dynamic and complex transcript modifications and changes in the rice transcriptome at the M. grisea early infection stages