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Fulltext Combining ability analysis in complete diallel cross of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai)

Bahari M, Rafii MY, Saleh GB, Latif MA

ScientificWorldJournal, 2012;2012:543158.
PMID: 22566772 DOI: 10.1100/2012/543158

The experiments were carried out in two research stations (MARDI Bukit Tangga, Kedah, and MARDI Seberang Perai, Penang) in Malaysia. The crossings were performed using the four inbred lines in complete diallel cross including selfs and reciprocals. We evaluated the yield components and fruit characters such as fruit yield per plant, vine length, days to fruit maturity, fruit weight, total soluble solid content, and rind thickness over a period of two planting seasons. General combining ability and its interaction with locations were statistically significant for all characteristics except number of fruits per plant across the environments. Results indicated that the additive genetic effects were important to the inheritance of these traits and the expression of additive genes was influenced greatly by environments. In addition, specific combining ability effect was statistically evident for fruit yield per plant, vine length, days to first female flower, and fruit weight. Most of the characters are simultaneously controlled by additive and nonadditive gene effects. This study demonstrated that the highest potential and promising among the crosses was cross P2 (BL-14) × P3 (6372-4), which possessed prolific plants, with early maturity, medium fruit weight and high soluble solid contents. Therefore this hybrid might be utilized for developing high yielding watermelon cultivars and may be recommended for commercial cultivation.

Matched MeSH terms: Genes, Plant
Fulltext Expression patterns of genes involved in the defense and stress response of Spiroplasma citri infected Madagascar Periwinkle Catharanthus roseus

Nejat N, Vadamalai G, Dickinson M

Int J Mol Sci, 2012;13(2):2301-2313.
PMID: 22408455 DOI: 10.3390/ijms13022301

Madagascar periwinkle is an ornamental and a medicinal plant, and is also an indicator plant that is highly susceptible to phytoplasma and spiroplasma infections from different crops. Periwinkle lethal yellows, caused by Spiroplasma citri, is one of the most devastating diseases of periwinkle. The response of plants to S. citri infection is very little known at the transcriptome level. In this study, quantitative real-time PCR (RT-qPCR) was used to investigate the expression levels of four selected genes involved in defense and stress responses in naturally and experimentally Spiroplasma citri infected periwinkles. Strictosidine β-glucosidase involved in terpenoid indole alkaloids (TIAs) biosynthesis pathway showed significant upregulation in experimentally and naturally infected periwinkles. The transcript level of extensin increased in leaves of periwinkles experimentally infected by S. citri in comparison to healthy ones. A similar level of heat shock protein 90 and metallothionein expression was observed in healthy, naturally and experimentally spiroplasma-diseased periwinkles. Overexpression of Strictosidine β-glucosidase demonstrates the potential utility of this gene as a host biomarker to increase the fidelity of S. citri detection and can also be used in breeding programs to develop stable disease-resistance varieties.

Matched MeSH terms: Genes, Plant
Fulltext Assessment of four molecular markers as potential DNA barcodes for red algae Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta)

Tan J, Lim PE, Phang SM, Hong DD, Sunarpi H, Hurtado AQ

PLoS One, 2012;7(12):e52905.
PMID: 23285223 DOI: 10.1371/journal.pone.0052905

DNA barcoding has been a major advancement in the field of taxonomy, seeing much effort put into the barcoding of wide taxa of organisms, macro and microalgae included. The mitochondrial-encoded cox1 and plastid-encoded rbcL has been proposed as potential DNA barcodes for rhodophytes, but are yet to be tested on the commercially important carrageenophytes Kappaphycus and Eucheuma. This study gauges the effectiveness of four markers, namely the mitochondrial cox1, cox2, cox2-3 spacer and the plastid rbcL in DNA barcoding on selected Kappaphycus and Eucheuma from Southeast Asia. Marker assessments were performed using established distance and tree-based identification criteria from earlier studies. Barcoding patterns on a larger scale were simulated by empirically testing on the commonly used cox2-3 spacer. The phylogeny of these rhodophytes was also briefly described. In this study, the cox2 marker which satisfies the prerequisites of DNA barcodes was found to exhibit moderately high interspecific divergences with no intraspecific variations, thus a promising marker for the DNA barcoding of Kappaphycus and Eucheuma. However, the already extensively used cox2-3 spacer was deemed to be in overall more appropriate as a DNA barcode for these two genera. On a wider scale, cox1 and rbcL were still better DNA barcodes across the rhodophyte taxa when practicality and cost-efficiency were taken into account. The phylogeny of Kappaphycus and Eucheuma were generally similar to those earlier reported. Still, the application of DNA barcoding has demonstrated our relatively poor taxonomic comprehension of these seaweeds, thus suggesting more in-depth efforts in taxonomic restructuring as well as establishment.

Matched MeSH terms: Genes, Plant
Phylogeny of Hopea (Dipterocarpaceae) inferred from chloroplast DNA and nuclear PgiC sequences

Choong CY, Wickneswari R, Norwati M, Abbott RJ

Mol Phylogenet Evol, 2008 Sep;48(3):1238-43.
PMID: 18280183 DOI: 10.1016/j.ympev.2008.01.004
Matched MeSH terms: Genes, Plant
HnRNP-like proteins as post-transcriptional regulators

Yeap WC, Namasivayam P, Ho CL

Plant Sci, 2014 Oct;227:90-100.
PMID: 25219311 DOI: 10.1016/j.plantsci.2014.07.005

Plant cells contain a diverse repertoire of RNA-binding proteins (RBPs) that coordinate a network of post-transcriptional regulation. RBPs govern diverse developmental processes by modulating the gene expression of specific transcripts. Recent gene annotation and RNA sequencing clearly showed that heterogeneous nuclear ribonucleoprotein (hnRNP)-like proteins which form a family of RBPs, are also expressed in higher plants and serve specific plant functions. In addition to their involvement in post-transcriptional regulation from mRNA capping to translation, they are also involved in telomere regulation, gene silencing and regulation in chloroplast. Here, we review the involvement of plant hnRNP-like proteins in post-transcription regulation of RNA processes and their functional roles in control of plant developmental processes especially plant-specific functions including flowering, chloroplastic-specific mRNA regulation, long-distance phloem transportation and plant responses to environmental stresses.

Matched MeSH terms: Genes, Plant
Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Song BK, Chuah TS, Tam SM, Olsen KM

Mol Ecol, 2014 Oct;23(20):5003-17.
PMID: 25231087 DOI: 10.1111/mec.12922

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild-to-weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed-shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.

Matched MeSH terms: Genes, Plant
Fulltext Fine mapping of a grain weight quantitative trait locus, qGW6, using near isogenic lines derived from Oryza rufipogon IRGC105491 and Oryza sativa cultivar MR219

Ngu MS, Thomson MJ, Bhuiyan MA, Ho C, Wickneswari R

Genet. Mol. Res., 2014;13(4):9477-88.
PMID: 25501158 DOI: 10.4238/2014.November.11.13

Grain weight is a major component of rice grain yield and is controlled by quantitative trait loci. Previously, a rice grain weight quantitative trait locus (qGW6) was detected near marker RM587 on chromosome 6 in a backcross population (BC2F2) derived from a cross between Oryza rufipogon IRGC105491 and O. sativa cv. MR219. Using a BC2F5 population, qGW6 was validated and mapped to a region of 4.8 cM (1.2 Mb) in the interval between RM508 and RM588. Fine mapping using a series of BC4F3 near isogenic lines further narrowed the interval containing qGW6 to 88 kb between markers RM19268 and RM19271.1. According to the Duncan multiple range test, 8 BC4F4 near isogenic lines had significantly higher 100-grain weight (4.8 to 7.5% over MR219) than their recurrent parent, MR219 (P < 0.05). According to the rice genome automated annotation database, there are 20 predicted genes in the 88-kb target region, and 9 of them have known functions. Among the genes with known functions in the target region, in silico gene expression analysis showed that 9 were differentially expressed during the seed development stage(s) from gene expression series GSE6893; however, only 3 of them have known functions. These candidates provide targets for further characterization of qGW6, which will assist in understanding the genetic control of grain weight in rice.

Matched MeSH terms: Genes, Plant
Fulltext TRANSPARENT TESTA GLABRA1 Regulates the Accumulation of Seed Storage Reserves in Arabidopsis

Chen M, Zhang B, Li C, Kulaveerasingam H, Chew FT, Yu H

Plant Physiol, 2015 Sep;169(1):391-402.
PMID: 26152712 DOI: 10.1104/pp.15.00943

Seed storage reserves mainly consist of starch, triacylglycerols, and storage proteins. They not only provide energy for seed germination and seedling establishment, but also supply essential dietary nutrients for human beings and animals. So far, the regulatory networks that govern the accumulation of seed storage reserves in plants are still largely unknown. Here, we show that TRANSPARENT TESTA GLABRA1 (TTG1), which encodes a WD40 repeat transcription factor involved in many aspects of plant development, plays an important role in mediating the accumulation of seed storage reserves in Arabidopsis (Arabidopsis thaliana). The dry weight of ttg1-1 embryos significantly increases compared with that of wild-type embryos, which is accompanied by an increase in the contents of starch, total protein, and fatty acids in ttg1-1 seeds. FUSCA3 (FUS3), a master regulator of seed maturation, binds directly to the TTG1 genomic region and suppresses TTG1 expression in developing seeds. TTG1 negatively regulates the accumulation of seed storage proteins partially through transcriptional repression of 2S3, a gene encoding a 2S albumin precursor. TTG1 also indirectly suppresses the expression of genes involved in either seed development or synthesis/modification of fatty acids in developing seeds. In addition, we demonstrate that the maternal allele of the TTG1 gene suppresses the accumulation of storage proteins and fatty acids in seeds. Our results suggest that TTG1 is a direct target of FUS3 in the framework of the regulatory hierarchy controlling seed filling and regulates the accumulation of seed storage proteins and fatty acids during the seed maturation process.

Matched MeSH terms: Genes, Plant
Introgression of blast resistance genes into the elite rice variety MR263 through marker-assisted backcrossing

Hasan MM, Rafii MY, Ismail MR, Mahmood M, Alam MA, Abdul Rahim H, et al.

J Sci Food Agric, 2016 Mar 15;96(4):1297-305.
PMID: 25892666 DOI: 10.1002/jsfa.7222

Blast caused by the fungus Magnaporthe oryzae is a significant disease threat to rice across the world and is especially prevalent in Malaysia. An elite, early-maturing, high-yielding Malaysian rice variety, MR263, is susceptible to blast and was used as the recurrent parent in this study. To improve MR263 disease resistance, the Pongsu Seribu 1 rice variety was used as donor of the blast resistance Pi-7(t), Pi-d(t)1 and Pir2-3(t) genes and qLN2 quantitative trait locus (QTL). The objective was to introgress these blast resistance genes into the background of MR263 using marker-assisted backcrossing with both foreground and background selection.

Matched MeSH terms: Genes, Plant
Recurrent parent genome recovery analysis in a marker-assisted backcrossing program of rice (Oryza sativa L.)

Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Latif MA

C. R. Biol., 2015 Feb;338(2):83-94.
PMID: 25553855 DOI: 10.1016/j.crvi.2014.11.003

Backcross breeding is the most commonly used method for incorporating a blast resistance gene into a rice cultivar. Linkage between the resistance gene and undesirable units can persist for many generations of backcrossing. Marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and accelerates recurrent parent genome (RPG) recovery. The MABC approach was employed to incorporate (a) blast resistance gene(s) from the donor parent Pongsu Seribu 1, the blast-resistant local variety in Malaysia, into the genetic background of MR219, a popular high-yielding rice variety that is blast susceptible, to develop a blast-resistant MR219 improved variety. In this perspective, the recurrent parent genome recovery was analyzed in early generations of backcrossing using simple sequence repeat (SSR) markers. Out of 375 SSR markers, 70 markers were found polymorphic between the parents, and these markers were used to evaluate the plants in subsequent generations. Background analysis revealed that the extent of RPG recovery ranged from 75.40% to 91.3% and from 80.40% to 96.70% in BC1F1 and BC2F1 generations, respectively. In this study, the recurrent parent genome content in the selected BC2F2 lines ranged from 92.7% to 97.7%. The average proportion of the recurrent parent in the selected improved line was 95.98%. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in backcross generations. The application of MAS with the MABC breeding program accelerated the recovery of the RP genome, reducing the number of generations and the time for incorporating resistance against rice blast.

Matched MeSH terms: Genes, Plant
Expression profiles of defence related cDNAs in oil palm (Elaeis guineensis Jacq.) inoculated with mycorrhizae and Trichoderma harzianum Rifai T32

Tan YC, Wong MY, Ho CL

Plant Physiol Biochem, 2015 Nov;96:296-300.
PMID: 26322853 DOI: 10.1016/j.plaphy.2015.08.014

Basal stem rot is one of the major diseases of oil palm (Elaies guineensis Jacq.) caused by pathogenic Ganoderma species. Trichoderma and mycorrhizae were proposed to be able to reduce the disease severity. However, their roles in improving oil palm defence system by possibly inducing defence-related genes in the host are not well characterized. To better understand that, transcript profiles of eleven putative defence-related cDNAs in the roots of oil palm inoculated with Trichoderma harzianum T32 and mycorrhizae at different time points were studied. Transcripts encoding putative Bowman-Birk protease inhibitor (EgBBI2) and defensin (EgDFS) increased more than 2 fold in mycorrhizae-treated roots at 6 weeks post inoculation (wpi) compared to those in controls. Transcripts encoding putative dehydrin (EgDHN), glycine-rich RNA binding protein (EgGRRBP), isoflavone reductase (EgIFR), type 2 ribosome inactivating protein (EgT2RIP), and EgDFS increased in the oil palm roots treated with T. harzianum at 6 and/or 12 wpi compared to those in the controls. Some of these genes were also expressed in oil palm roots treated with Ganoderma boninense. This study provides an insight of some defence-related genes induced by Trichoderma and mycorrhizae, and their roles as potential agents to boost the plant defence system.

Matched MeSH terms: Genes, Plant
Fulltext Identification and validation of hub genes associated with biotic and abiotic stresses by modular gene co-expression analysis in Oryza sativa L

Razalli II, Abdullah-Zawawi MR, Zainal Abidin RA, Harun S, Che Othman MH, Ismail I, et al.

Sci Rep, 2025 Mar 12;15(1):8465.
PMID: 40069264 DOI: 10.1038/s41598-025-92942-5

Rice, a staple food consumed by half of the world's population, is severely affected by the combined impact of abiotic and biotic stresses, with the former causing increased susceptibility of the plant to pathogens. Four microarray datasets for drought, salinity, tungro virus, and blast pathogen were retrieved from the Gene Expression Omnibus database. A modular gene co-expression (mGCE) analysis was conducted, followed by gene set enrichment analysis to evaluate the upregulation of module activity across different stress conditions. Over-representation analysis was conducted to determine the functional association of each gene module with stress-related processes and pathways. The protein-protein interaction network of mGCE hub genes was constructed, and the Maximal Clique Centrality (MCC) algorithm was applied to enhance precision in identifying key genes. Finally, genes implicated in both abiotic and biotic stress responses were validated using RT-qPCR. A total of 11, 12, 46, and 14 modules containing 85, 106, 253, and 143 hub genes were detected in drought, salinity, tungro virus, and blast. Modular genes in drought were primarily enriched in response to heat stimulus and water deprivation, while salinity-related genes were enriched in response to external stimuli. For the tungro virus and blast pathogen, enrichment was mainly observed in the defence and stress responses. Interestingly, RPS5, PKG, HSP90, HSP70, and MCM were consistently present in abiotic and biotic stresses. The DEG analysis revealed the upregulation of MCM under the tungro virus and downregulation under blast and drought in resistant rice, indicating its role in viral resistance. HSP70 showed no changes, while HSP90 was upregulated in susceptible rice during blast and drought. PKG increased during drought but decreased in japonica rice under salinity. RPS5 was highly upregulated during blast in both resistant and susceptible rice. The RT-qPCR analysis showed that all five hub genes were upregulated in all treatments, indicating their role in stress responses and potential for crop improvement.

Matched MeSH terms: Genes, Plant
Isolation and characterization of an oil palm constitutive promoter derived from a translationally control tumor protein (TCTP) gene

Masura SS, Parveez GK, Ti LL

Plant Physiol Biochem, 2011 Jul;49(7):701-8.
PMID: 21549610 DOI: 10.1016/j.plaphy.2011.04.003

We have characterized an oil palm (Elaeis guineensis Jacq.) constitutive promoter that is derived from a translationally control tumor protein (TCTP) gene. The TCTP promoter was fused transcriptionally with the gusA reporter gene and transferred to monocot and dicot systems in order to study its regulatory role in a transient expression study. It was found that the 5' region of TCTP was capable of driving the gusA expression in all the oil palm tissues tested, including immature embryo, embryogenic callus, embryoid, young leaflet from mature palm, green leaf, mesocarp and stem. It could also be used in dicot systems as it was also capable of driving gusA expression in tobacco leaves. The results indicate that the TCTP promoter could be used for the production of recombinant proteins that require constitutive expression in the plant system.

Matched MeSH terms: Genes, Plant/genetics*
Fulltext The draft genomes of five agriculturally important African orphan crops

Chang Y, Liu H, Liu M, Liao X, Sahu SK, Fu Y, et al.

Gigascience, 2019 03 01;8(3).
PMID: 30535374 DOI: 10.1093/gigascience/giy152

BACKGROUND: The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few plants of special significance to agriculture, agroforestry, and nutrition) could be a partial solution.
RESULTS: Here, we present draft genome information for five agriculturally, biologically, medicinally, and economically important underutilized plants native to Africa: Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. Assembled genomes range in size from 217 to 654 Mb. In V. subterranea, L. purpureus, F. albida, S. birrea, and M. oleifera, we have predicted 31,707, 20,946, 28,979, 18,937, and 18,451 protein-coding genes, respectively. By further analyzing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors, and starch biosynthesis-related genes in these genomes.
CONCLUSIONS: These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused, and predictable crop improvement programs.

Matched MeSH terms: Genes, Plant
EgRBP42 from oil palm enhances adaptation to stress in Arabidopsis through regulation of nucleocytoplasmic transport of stress-responsive mRNAs

Yeap WC, Namasivayam P, Ooi TEK, Appleton DR, Kulaveerasingam H, Ho CL

Plant Cell Environ, 2019 05;42(5):1657-1673.
PMID: 30549047 DOI: 10.1111/pce.13503

Abiotic stress reduces plant growth and crop productivity. However, the mechanism underlying posttranscriptional regulations of stress response remains elusive. Herein, we report the posttranscriptional mechanism of nucleocytoplasmic RNA transport of stress-responsive transcripts mediated by EgRBP42, a heterogeneous nuclear ribonucleoprotein-like RNA-binding protein from oil palm, which could be necessary for rapid protein translation to confer abiotic stress tolerance in plants. Transgenic Arabidopsis overexpressing EgRBP42 showed early flowering through alteration of gene expression of flowering regulators and exhibited tolerance towards heat, cold, drought, flood, and salinity stresses with enhanced poststress recovery response by increasing the expression of its target stress-responsive genes. EgRBP42 harbours nucleocytoplasmic shuttling activity mediated by the nuclear localization signal and the M9-like domain of EgRBP42 and interacts directly with regulators in the nucleus, membrane, and the cytoplasm. EgRBP42 regulates the nucleocytoplasmic RNA transport of target stress-responsive transcripts through direct binding to their AG-rich motifs. Additionally, EgRBP42 transcript and protein induction by environmental stimuli are regulated at the transcriptional and posttranscriptional levels. Taken together, the posttranscriptional regulation of RNA transport mediated by EgRBP42 may change the stress-responsive protein profiles under abiotic stress conditions leading to a better adaptation of plants to environmental changes.

Matched MeSH terms: Genes, Plant
Fulltext Organ-Specific Analysis of Morus alba Using a Gel-Free/Label-Free Proteomic Technique

Zhu W, Zhong Z, Liu S, Yang B, Komatsu S, Ge Z, et al.

Int J Mol Sci, 2019 Jan 16;20(2).
PMID: 30654535 DOI: 10.3390/ijms20020365

Morus alba is an important medicinal plant that is used to treat human diseases. The leaf, branch, and root of Morus can be applied as antidiabetic, antioxidant, and anti-inflammatory medicines, respectively. To explore the molecular mechanisms underlying the various pharmacological functions within different parts of Morus, organ-specific proteomics were performed. Protein profiles of the Morus leaf, branch, and root were determined using a gel-free/label-free proteomic technique. In the Morus leaf, branch, and root, a total of 492, 414, and 355 proteins were identified, respectively, including 84 common proteins. In leaf, the main function was related to protein degradation, photosynthesis, and redox ascorbate/glutathione metabolism. In branch, the main function was related to protein synthesis/degradation, stress, and redox ascorbate/glutathione metabolism. In root, the main function was related to protein synthesis/degradation, stress, and cell wall. Additionally, organ-specific metabolites and antioxidant activities were analyzed. These results revealed that flavonoids were highly accumulated in Morus root compared with the branch and leaf. Accordingly, two root-specific proteins named chalcone flavanone isomerase and flavonoid 3,5-hydroxylase were accumulated in the flavonoid pathway. Consistent with this finding, the content of the total flavonoids was higher in root compared to those detected in branch and leaf. These results suggest that the flavonoids in Morus root might be responsible for its biological activity and the root is the main part for flavonoid biosynthesis in Morus.

Matched MeSH terms: Genes, Plant
The effect of adenosine monophosphate deaminase overexpression on the accumulation of umami-related metabolites in tomatoes

Chew BL, Fisk ID, Fray R, Tucker GA, Bodi Z, Ferguson A, et al.

Plant Cell Rep, 2017 Jan;36(1):81-87.
PMID: 27662835 DOI: 10.1007/s00299-016-2058-z

KEY MESSAGE: This study highlights the changes in umami-related nucleotide and glutamate levels when the AMP deaminase gene was elevated in transgenic tomato. Taste is perceived as one of a combination of five sensations, sweet, sour, bitter, salty, and umami. The umami taste is best known as a savoury sensation and plays a central role in food flavour, palatability, and eating satisfaction. Umami flavour can be imparted by the presence of glutamate and is greatly enhanced by the addition of ribonucleotides, such as inosine monophosphate (IMP) and guanosine monophosphate (GMP). The production of IMP is regulated by the enzyme adenosine monophosphate (AMP) deaminase which functions to convert AMP into IMP. We have generated transgenic tomato (Solanum lycopersicum) lines over expressing AMP deaminase under the control of a fruit-specific promoter. The transgenic lines showed substantially enhanced levels of AMP deaminase expression in comparison to the wild-type control. Elevated AMP deaminase levels resulted in the reduced accumulation of glutamate and increased levels of the umami nucleotide GMP. AMP concentrations were unchanged. The effects on the levels of glutamate and GMP were unexpected and are discussed in relation to the metabolite flux within this pathway.

Matched MeSH terms: Genes, Plant
The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica

Song BK, Hein I, Druka A, Waugh R, Marshall D, Nadarajah K, et al.

Funct Integr Genomics, 2009 Feb;9(1):97-108.
PMID: 18633654 DOI: 10.1007/s10142-008-0091-x

Common wild rice (Oryza rufipogon) plays an important role by contributing to modern rice breeding. In this paper, we report the sequence and analysis of a 172-kb genomic DNA region of wild rice around the RM5 locus, which is associated with the yield QTL yld1.1. Comparative sequence analysis between orthologous RM5 regions from Oryza sativa ssp. japonica, O. sativa ssp. indica and O. rufipogon revealed a high level of conserved synteny in the content, homology, structure, orientation, and physical distance of all 14 predicted genes. Twelve of the putative genes were supported by matches to proteins with known function, whereas two were predicted by homology to rice and other plant expressed sequence tags or complementary DNAs. The remarkably high level of conservation found in coding, intronic and intergenic regions may indicate high evolutionary selection on the RM5 region. Although our analysis has not defined which gene(s) determine the yld1.1 phenotype, allelic variation and the insertion of transposable elements, among other nucleotide changes, represent potential variation responsible for the yield QTL. However, as suggested previously, two putative receptor-like protein kinase genes remain the key suspects for yld1.1.

Matched MeSH terms: Genes, Plant
The genetic and molecular origin of natural variation for the fragrance trait in an elite Malaysian aromatic rice through quantitative trait loci mapping using SSR and gene-based markers

Golestan Hashemi FS, Rafii MY, Ismail MR, Mohamed MT, Rahim HA, Latif MA, et al.

Gene, 2015 Jan 25;555(2):101-7.
PMID: 25445269 DOI: 10.1016/j.gene.2014.10.048

MRQ74, a popular aromatic Malaysian landrace, allows for charging considerably higher prices than non-aromatic landraces. Thus, breeding this profitable trait has become a priority for Malaysian rice breeding. Despite many studies on aroma genetics, ambiguities considering its genetic basis remain. It has been observed that identifying quantitative trait loci (QTLs) based on anchor markers, particularly candidate genes controlling a trait of interest, can increase the power of QTL detection. Hence, this study aimed to locate QTLs that influence natural variations in rice scent using microsatellites and candidate gene-based sequence polymorphisms. For this purpose, an F2 mapping population including 189 individual plants was developed by MRQ74 crosses with 'MR84', a non-scented Malaysian accession. Additionally, qualitative and quantitative approaches were applied to obtain a phenotype data framework. Consequently, we identified two QTLs on chromosomes 4 and 8. These QTLs explained from 3.2% to 39.3% of the total fragrance phenotypic variance. In addition, we could resolve linkage group 8 by adding six gene-based primers in the interval harboring the most robust QTL. Hence, we could locate a putative fgr allele in the QTL found on chromosome 8 in the interval RM223-SCU015RM (1.63cM). The identified QTLs represent an important step toward recognition of the rice flavor genetic control mechanism. In addition, this identification will likely accelerate the progress of the use of molecular markers for gene isolation, gene-based cloning, and marker-assisted selection breeding programs aimed at improving rice cultivars.

Matched MeSH terms: Genes, Plant
Fulltext Variations in DREB1A and VP1.1 Genes Show Association with Salt Tolerance Traits in Wild Tomato (Solanum pimpinellifolium)

Rao ES, Kadirvel P, Symonds RC, Geethanjali S, Thontadarya RN, Ebert AW

PLoS One, 2015;10(7):e0132535.
PMID: 26161546 DOI: 10.1371/journal.pone.0132535

Association analysis was conducted in a core collection of 94 genotypes of Solanum pimpinellifolium to identify variations linked to salt tolerance traits (physiological and yield traits under salt stress) in four candidate genes viz., DREB1A, VP1.1, NHX1, and TIP. The candidate gene analysis covered a concatenated length of 4594 bp per individual and identified five SNP/Indels in DREB1A and VP1.1 genes explaining 17.0% to 25.8% phenotypic variation for various salt tolerance traits. Out of these five alleles, one at 297 bp in DREB1A had in-frame deletion of 6 bp (CTGCAT) or 12 bp (CTGCATCTGCAT), resulting in two alleles, viz., SpDREB1A_297_6 and SpDREB1A_297_12. These alleles individually or as haplotypes accounted for maximum phenotypic variance of about 25% for various salt tolerance traits. Design of markers for selection of the favorable alleles/haplotypes will hasten marker-assisted introgression of salt tolerance from S. pimpinellifolium into cultivated tomato.

Matched MeSH terms: Genes, Plant

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