Identification and cloning of a submergence-induced gene OsGGT (glycogenin glucosyltransferase) from rice (Oryza sativa L.) by suppression subtractive hybridization

The role of OsBZR4 as a brassinosteroid-signaling component in mediating atrazine and isoproturon degradation in rice

Development of a biotechnological system for rapid degradation of pesticides is important to mitigate the environmental, food security, and health risks that they pose. Degradation of atrazine (ATZ) and isoproturon (IPU) in rice crops promoted by the brassinosteroid (BR) signaling component BRASSINAZOLE RESISTANT4 (OsBZR4) is explored. OsBZR4 is localized in the plasma membrane and nucleus, and is strongly induced by ATZ and IPU exposure. Transgenic rice OsBZR4-overexpression (OE) significantly enhances resistance to ATZ and IPU toxicity, improving growth, and reducing ATZ and IPU accumulation (particularly in grains) in rice crops. Genetic destruction of OsBZR4 (CRISPR/Cas9) increases rice sensitivity and leads to increased accumulation of ATZ and IPU. OE plants promote phase I, II, and III metabolic reactions, and expression of corresponding pesticide degradation genes under ATZ and IPU stress. UPLC-Q-TOF-MS/MS analysis reveals increased relative contents of ATZ and IPU metabolites and conjugates in OE plants, suggesting an increased OsBZR4 expression and consequent detoxification of ATZ and IPU in rice and the environment. The role of OsBZR4 in pesticide degradation is revealed, and its potential application in enhancing plant resistance to pesticides, and facilitating the breakdown of pesticides in rice and the environment, is discussed.

Global identification of quantitative trait loci and candidate genes for cold stress and chilling acclimation in rice through GWAS and RNA-seq

Associated analysis of GWAS with RNA-seq had detected candidate genes responsible for cold stress and chilling acclimation in rice. Haplotypes of two candidate genes and geographic distribution were analyzed. To explore new candidate genes and genetic resources for cold tolerance improvement in rice, genome-wide association study (GWAS) mapping experiments with 351 rice core germplasms was performed for three traits (survival rate, shoot length and chlorophyll content) under three temperature conditions (normal temperature, cold stress and chilling acclimation), yielding a total of 134 QTLs, of which 54, 59 and 21 QTLs were responsible for normal temperature, cold stress and chilling acclimation conditions, respectively. Integrated analysis of significant SNPs in 134 QTLs further identified 116 QTLs for three temperature treatments, 53, 43 and 18 QTLs responsible for normal temperature, cold stress and chilling acclimation, respectively, and 2 QTLs were responsible for both cold stress and chilling acclimation. Matching differentially expressed genes from RNA-seq to 43 and 18 QTLs for cold stress and chilling acclimation, we identified 69 and 44 trait-associated candidate genes, respectively, to be classified into six and five groups, particularly involved in metabolisms, reactive oxygen species scavenging and hormone signaling. Interestingly, two candidate genes LOC_Os01g04814, encoding a vacuolar protein sorting-associating protein 4B, and LOC_Os01g48440, encoding glycosyltransferase family 43 protein, showed the highest expression levels under chilling acclimation. Haplotype analysis revealed that both genes had a distinctive differentiation with subpopulation. Haplotypes of both genes with more japonica accessions have higher latitude distribution and higher chilling tolerance than the chilling sensitive indica accessions. These findings reveal the new insight into the molecular mechanism and candidate genes for cold stress and chilling acclimation in rice.

Basal differences in the transcriptional profiles of tomato leaves associated with the presence/absence of the resistance gene Mi-1 and changes in these differences after infestation by the whitefly Bemisia tabaci

The tomato Mi-1 gene mediates plant resistance to whitefly Bemisia tabaci, nematodes, and aphids. Other genes are also required for this resistance, and a model of interaction between the proteins encoded by these genes was proposed. Microarray analyses were used previously to identify genes involved in plant resistance to pests or pathogens, but scarcely in resistance to insects. In the present work, the GeneChip™ Tomato Genome Array (Affymetrix®) was used to compare the transcriptional profiles of Motelle (bearing Mi-1) and Moneymaker (lacking Mi-1) cultivars, both before and after B. tabaci infestation. Ten transcripts were expressed at least twofold in uninfested Motelle than in Moneymaker, while other eight were expressed half or less. After whitefly infestation, differences between cultivars increased to 14 transcripts expressed more in Motelle than in Moneymaker and 14 transcripts less expressed. Half of these transcripts showed no differential expression before infestation. These results show the baseline differences in the tomato transcriptomic profile associated with the presence or absence of the Mi-1 gene and provide us with valuable information on candidate genes to intervene in either compatible or incompatible tomato-whitefly interactions.

Molecular cloning and characterization of a novel H+-translocating pyrophosphatase gene inZea mays

A cDNA encoding a putative H+-translocating pyrophosphatase (H+-PPase) has been cloned from Zea mays by suppression subtractive hybridization (SSH) coupled with in silico cloning approach. The isolated 2974 bp full-length cDNA named ZmGPP contains a single 2400 bp open reading frame encoding a putative protein of 799 amino acids. The predicted protein has 16 transmembrane domains and is significantly similar to Golgi apparatus resident type-II H+-PPase from Arabidopsis thaliana. DNA gel blotting analysis shows that ZmGPP is a low-copy gene. Organ expression pattern analysis reveals that ZmGPPexpressed highly in leaf and tassel, followed by in stem, root, and ear. The Real-time RT-PCR assays showed that the expression of ZmGPP was up-regulated both in shoots and roots of maize seedlings under dehydration, cold and high salt stresses. Those results suggest that the ZmGPP product may play an important role in abiotic stress tolerance of Z. mays.

ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity

Drought, flood, salinity, or a combination of these limits rice production. Several rice varieties are well known for their tolerance to specific abiotic stresses. We determined genetic relationship among 12 rice varieties including 9 tolerant to drought, flood, or salinity using inter-simple sequence repeat (ISSR) markers. Based on all markers, the nine tolerant varieties formed one cluster distinct from the cluster of three control varieties. The salt-tolerant varieties were closest to two flood-tolerant varieties, and together they were distinct from the drought-tolerant varieties. (GA)(8)YG was the most informative primer, showing the highest polymorphic information content (PIC) and resolving power (Rp). The drought-, flood-, and salt-tolerant varieties grouped in three distinct clusters within the group of tolerant varieties, when (GA)(8)YG was used. Sabita was the only exception. The two aus varieties, Nagina22 and FR13A, were separated and grouped with the drought- and flood-tolerant varieties, respectively, but they were together in dendrograms based on other primers. The results show that ISSR markers associated with (GA)(8)YG delineated the three groups of stress-tolerant varieties from each other and can be used to identify genes/new alleles associated with the three abiotic stresses in rice germplasm.

Expression of a novel OSPGYRP (rice proline-, glycine- and tyrosine-rich protein) gene, which is involved in vesicle trafficking, enhanced cold tolerance in E. coli

A novel OSPGYRP gene encoding a rice proline-, glycine- and tyrosine-rich protein was isolated from cold-stress treated rice seedlings using suppression subtractive hybridization. Both amino acid sequence analysis and subcellular localization confirm that OsPGYRP is a novel protein involved in vesicle trafficking. The expression of the OSPGYRP gene was induced by cold, salt, and osmotic stress. In addition, expression of the OSPGYRP gene in E. coli increased the resistance to cold stress. These results show that OsPGYRP is a novel protein involved in vesicle trafficking and plays an important role in plant adaptation to stress.

Comprehensive transcriptome profiling in tomato reveals a role for glycosyltransferase in Mi-mediated nematode resistance

Root-knot nematode (RKN; Meloidogyne spp.) is a major crop pathogen worldwide. Effective resistance exists for a few plant species, including that conditioned by Mi in tomato (Solanum lycopersicum). We interrogated the root transcriptome of the resistant (Mi+) and susceptible (Mi-) cultivars 'Motelle' and 'Moneymaker,' respectively, during a time-course infection by the Mi-susceptible RKN species Meloidogyne incognita and the Mi-resistant species Meloidogyne hapla. In the absence of RKN infection, only a single significantly regulated gene, encoding a glycosyltransferase, was detected. However, RKN infection influenced the expression of broad suites of genes; more than half of the probes on the array identified differential gene regulation between infected and uninfected root tissue at some stage of RKN infection. We discovered 217 genes regulated during the time of RKN infection corresponding to establishment of feeding sites, and 58 genes that exhibited differential regulation in resistant roots compared to uninfected roots, including the glycosyltransferase. Using virus-induced gene silencing to silence the expression of this gene restored susceptibility to M. incognita in 'Motelle,' indicating that this gene is necessary for resistance to RKN. Collectively, our data provide a picture of global gene expression changes in roots during compatible and incompatible associations with RKN, and point to candidates for further investigation.