Transcriptome dataset from Solanum lycopersicum L. cv. Micro-Tom; wild type and two mutants of INDOLE-ACETIC-ACID (SlIAA9) using long-reads sequencing oxford nanopore technologies.

OBJECTIVE: Tomatoes are the most widely consumed fruit vegetable and are relatively easy to cultivate. However, an increase in temperature causes some plants to respond with a decrease in fruit production. So, it is necessary to develop plants resistant to extreme temperature changes. The tomato cv. Micro-Tom has genetic variations in the gene of INDOLE-ACETIC-ACID, namely SlIAA9-3 and SlIAA9-5. However, the genetic information regarding the full-length transcript of the gene from this type of tomato plant is unknown. Therefore, this study aimed to determine the full-length transcript of the genes of these three types of tomatoes using long-reads sequencing technology from Oxford Nanopore. DATA DESCRIPTION: The total RNA from three types of Micro-Tom was isolated with the RNeasy PowerPlant Kit. Then, the RNA sequencing process used PCR-cDNA Barcoding kit - SQK-PCB109 and continued with the processing of raw reads based on the protocol from microbepore protocol ( https://github.com/felixgrunberger/microbepore ). The resulting raw reads were 578 374, 409 905, and 851 948 for wildtype, iaa9-3, and iaa9-5, respectively. After obtaining cleaned reads, each sample was mapped to the tomato reference genome (S. lycopersicum ITAG4.0) with the Minimap2 program. In particular, 965 genes were expressed only in the iaa9-3 mutant, and 2332 genes were expressed only in the iaa9-5 mutant. Whereas in the wild type, 1536 genes are specifically expressed. In cluster analysis using the heatmap analysis, separate groups were obtained between the wild type and the two mutants. This proves an overall difference in transcript levels between the wild type and the mutants.

Parthenocarpic tomato mutants, iaa9-3 and iaa9-5, show plant adaptability and fruiting ability under heat-stress conditions.

Fruit set is one of the main problems that arise in tomato plants under heat-stress conditions, which disrupt pollen development, resulting in decreased pollen fertility. Parthenocarpic tomatoes can be used to increase plant productivity during failure of the fertilisation process under heat-stress conditions. The aim of this study were to identify the plant adaptability and fruiting capability of ?iaa9-3 and iaa9-5 tomato mutants under heat-stress conditions. The iaa9-3 and iaa9-5 and wild-type Micro-Tom (WT-MT) plants were cultivated under two temperature conditions: normal and heat-stress conditions during plant growth. The results showed that under the heat-stress condition, iaa9-3 and iaa9-5 showed delayed flowering time, increased number of flowers, and increased fruit set and produced normal-sized fruit. However, WT-MT cannot produce fruits under heat stress. The mutants can grow under heat-stress conditions, as indicated by the lower electrolyte leakage and H2O2 concentration and higher antioxidant activities compared with WT-MT under heat-stress conditions. These results suggest that iaa9-3 and iaa9-5 can be valuable genetic resources for the development of tomatoes in high-temperature environmental conditions.

SlIAA9 Mutation Maintains Photosynthetic Capabilities under Heat-Stress Conditions.

Tomato is one of the most widely consumed horticultural products. However, tomato is very sensitive to changes in temperature. Daily average temperatures above 32 °C severely reduced tomato plant growth, development, and productivity. Therefore, climate change-induced global warming is a major threat to future tomato production. Good photosynthetic capability under heat stress conditions is known to be a major sign of heat tolerance. Tomato INDOLE-ACETIC-ACID (SlIAA9) is a transcriptional repressor in auxin signaling. SlIAA9 mutation caused heightened endogenous auxin response and biosynthesis within plant tissues. In this study, we studied the photosynthetic capability of iaa9-3 and iaa9-5 mutants under heat-stress conditions. We discovered that both iaa9-3 and iaa9-5 could maintain their photosynthetic capability after 14 days of heat treatment (>40 °C), differing from Wild Type-Micro-Tom (WT-MT) tomato. Both iaa9 mutants had higher net photosynthetic rate, stomatal conductance, leaf total chlorophyll, leaf carotenoids, Fv/Fm value, and lower leaf MDA than WT-MT. These results suggested that the SlIAA9 mutation benefits plant adaptation to heat stress.

Development of PCR-RFLP Technique for Identify Several Members of Fusarium incarnatum-equiseti Species Complex and Fusarium fujikuroi Species Complex.

Fusarium incarnatum-equiseti species complex (FIESC) contain over 40 members. The primer pair Smibo1FM/Semi1RM on the RPB2 partial gene has been reported to be able to identify Fusarium semitectum. The F. fujikuroi species complex (FFSC) contains more than 50 members. The F. verticillioides as a member of this complex can be identified by using VER1/VER2 primer pair on the CaM partial gene. In this research, the Smibo1FM/Semi1RM can amplify F. sulawesiense, F. hainanense, F. bubalinum, and F. tanahbumbuense, members of FIESC at 424 bp. The VER1/VER2 can amplify F. verticillioides, F. andiyazi, and F. pseudocircinatum, members of FFSC at 578 bp. Polymerase chain reaction-restriction fragment length polymorphism by using the combination of three restriction enzymes EcoRV, MspI, and HpyAV can differentiate each species of FIESC used. The two restriction enzymes HpaII and NspI can distinguish each species of FFSC used. The proper identification process is required for pathogen control in the field in order to reduce crop yield loss.

Phytophthora palmivora from Sulawesi and Java Islands, Indonesia, reveals high genotypic diversity and lack of population structure.

Phytophthora palmivora is the causal agent of cocoa black pod disease, one of the primary diseases of cocoa in Indonesia. A better understanding of P. palmivora population genetics is needed to aid the development of relevant disease management strategies. This study is the first population genetic study of P. palmivora in Indonesia using microsatellite markers based on the alleles genotyping method. The microsatellite markers were used to determine the genotype of 44 P. palmivora isolates from Sulawesi (24) and Java (20) islands. The total number of observed multilocus genotypes (MLG) from both populations was 34. The genotypic diversity of P. palmivora from Sulawesi (2.90; 16.0; 0.938) and Java (2.76; 14.3; 0.930) islands was high as seen from Shannon's diversity index (H), Stoddart and Taylor's Index (G), and Simpson's Index (λ) respectively. Evenness and Nei's unbiased gene diversity exhibited similarly high levels from both populations. The linkage disequilibrium test indicated that sexual recombination occurred in the Java population (P = 0.312). Analysis of molecular variance (AMOVA) and Bayesian clustering revealed five genetic clusters, and isolates from both islands were evenly distributed across the five gene clusters. All genetic diversity was from within individuals. P. palmivora from Sulawesi and Java showed a high genotypic diversity but a lack of genetic differentiation among populations (Fst = 0.006). Both populations formed one highly diverse group. Minimum spanning network analysis showed no particular grouping of MLGs, and shared MLGs from both populations indicated long-distance migration of P. palmivora facilitated by human activities.

Variability of Lecanicillium spp. Mycoparasite of Coffee Leaf Rust Pathogen (Hemileia vastatrix) in Indonesia.

<b>Background and Objective:</b> Coffee leaf rust disease caused by <i>Hemileia vastatrix</i> resulted in high yield loss and difficult to control. Several chemical fungicides have been used to control this disease. However, the effectiveness of chemical control is low, so it is necessary to find other methods such as biological control. <i>Lecanicillium</i> spp. is well-known as mycoparasite on <i>H. vastatrix</i> uredospores but the study in Indonesia is still limited. This study aimed to collect and investigated the genetic variability of <i>Lecanicillium</i> spp. at various coffee plantations in Indonesia. <b>Materials and Methods:</b> Samples of <i>Lecanicillium </i>spp. were collected from 20 districts in 7 provinces throughout Indonesia. Morphology of colony and conidia were identified by visual examination and by viewed under the light microscope. Genetic variability was conducted using Rep-PCR and clustered with UPGMA. <b>Results:</b> Morphological observation in this study revealed all isolates collected from uredospores of <i>H. vastatrix</i> were similar with <i>Lecanicillium </i>spp. Genetic variability analysis clustered the 80 isolates into eight clusters with their specific characters. <b>Conclusion:</b> Morphological identification in this study showed that 80 isolates of mycoparasite on <i>H. vastatrix</i> belong to <i>Lecanicillium</i> spp. Further study using the molecular technique is needed to identity the species of <i>Lecanicillium</i>.

Multi-genetic Analysis of Colletotrichum spp. Associated with Postharvest Disease of Fruits Anthracnose in Special Region of Yogyakarta, Indonesia.

BACKGROUND AND OBJECTIVE: Postharvest disease caused by Colletotrichum spp. caused major losses. The species of Colletotrichum are difficult to distinguish if only seen from their morphology. This study investigated Colletotrichum isolates associated with tropical fruits anthracnose using multi-genetic analysis and the cross-infection potency of each isolate among tropical fruits. MATERIALS AND METHODS: The fruit samples were collected from markets in the Special Region of Yogyakarta, Indonesia and its surrounding area. The fruits affected by anthracnose subjected to isolation, resulting in 15 isolates. Morphology of colony and conidia then characterized and clustered with UPGMA. The seven representative isolates were selected for molecular identification. The multi-genetic analysis was used by combining ITS, Glyceraldehyde 3-phosphate dehydrogenase (gapdh) and tub2 sequence genes. A cross-infection test was conducted by using selected species from the multi-genetic analysis. RESULTS: Multi-genetic analysis clustered the selected isolates into four species. Isolates from banana, avocado, papaya and citrus belonged to gloeosporioides species complex, including C. siamense, C. asianum and C. gloeosporioides. Isolates from apple, guava, mango and citrus belonged to acutatum species complex, including C. sloanei. The cross-infection test in this study showed that C. siamense could cause anthracnose on banana, apple, citrus and avocado, C. asianum on avocado, papaya, apple and citrus, C. gloeosporioides on citrus and apple, C. sloanei on apple, guava, citrus and papaya. CONCLUSION: The C. siamense, C. asianum, C. gloeosporioides and C. sloanei found associated with tropical fruits anthracnose. The potency of the cross-infection test revealed the board range in the pathogenicity of the Colletotrichum isolates.

Effect of corn steep liquor on lettuce root rot (Fusarium oxysporum f.sp. lactucae) in hydroponic cultures.

BACKGROUND: Recent reports indicate that organic fertilisers have a suppressive effect on the pathogens of plants grown under hydroponic systems. Furthermore, microorganisms exhibiting antagonistic activity to diseases have been observed in organic hydroponic systems. This study evaluated the effect of corn steep liquor (CSL) on controlling lettuce root rot disease [Fusarium oxysporum f.sp. lactucae (FOL)] in a hydroponic system. The effect of CSL and Otsuka A (a chemical fertiliser) on the inhibition of FOL in terms of mycelial growth inhibition was tested in vivo. RESULTS: Addition of CSL suppressed FOL infection rates. CSL inhibited FOL infection by 26.3-42.5% from 2 days after starting incubation. In comparison, Otsuka A inhibited FOL growth by 5.5-19.4%. In addition, four of 10 bacteria isolated from the nutrient media containing CSL exhibited inhibition zones preventing FOL mycelial growth. CONCLUSIONS: We found that CSL suppressed FOL in lettuce via its antifungal and biostimulatory effects. We suggest that activation of beneficial microorganisms present in CSL may be used to decrease lettuce root rot disease and contribute to lettuce root growth.