Valentina Dwi Suci Handayani

Indonesian rice cultivars represent valuable genetic resources, yet many remain poorly characterized at the genomic level. Here, we generated 95.40 Gb of PacBio HiFi sequence data from seven Indonesian rice cultivars and constructed cultivar-specific consensus genomes using the telomere-to-telomere Nipponbare reference AGIS1.0. Sequencing coverage ranged from 27.92× to 41.58×, and the resulting consensus genomes spanned 387.93-390.54 Mb, with BUSCO completeness of approximately 98.3-98.5%. OrthoFinder assigned 99.1% of predicted proteins to 40,737 orthogroups, including 27,514 core orthogroups represented across all seven cultivars, indicating a highly conserved predicted gene space within the reference-guided framework. Targeted analysis recovered 278 of 280 cultivar-by-locus combinations representing 40 genes or gene family entries associated with grain pigmentation, nitrogen and amino-acid metabolism, and starch properties. Comparative predicted protein analysis prioritized ANS1 , SBE2b , SSIIa/ALK , Wx/GBSSI , OsAAP6/qPC1 , and SSI as candidates for further investigation. Among 269 completed AGIS1.0-anchored promoter comparisons, 159 passed quality-control criteria, whereas 110 were flagged for gene-model, boundary, synteny, or structural concerns. Notably, these flagged comparisons accounted for more than 90% of the alignment-derived sequence variation, emphasizing the importance of rigorous quality control when interpreting apparent promoter divergence. Collectively, these reference-guided genomic resources provide a standardized framework for investigating sequence variation in Indonesian rice germplasm and prioritize testable coding and regulatory candidates for functional validation and future genomics-assisted crop improvement.

Beet tubers are perishable horticultural commodities, cannot be stored for long, and are commonly consumed in fresh conditions. Postharvest handling of beet tubers needs to be carried out to maintain their freshness Chitosan and other packaging used in postharvest handling of fresh beet tubers have not yet been reported. This study aims to determine the effect of chitosan coating and types of packaging on beet tubers on the physical quality of beet tubers. The study was a randomly designed group with two factors; the first factor was chitosan concentration, and the second factor was the kinds of packaging. Chitosan concentration consists of 5 levels, namely 0, 0.5%, 1%, 1.5%, and 2%, and the type of packaging includes no packaging (Without), plastic packaging with holes (Perforated), ordinary plastic packaging (Ordinary) and plastic vacuumed (Vacuum). The beet tubers were soaked in chitosan solution of 0, 0.5%, 1%, 1.5%, and 2% for 1 minute, air-dried, then were packaged with no packaging, plastic packaging with holes, ordinary plastic packaging, and plastic vacuumed. . The physical quality parameters observed were moisture content, weight loss respiration rate,electrolyte leakage, total dissolved solid (TDS), ascorbic acid, betacyanin, betaxanthins, tuber firmness, damage percentage, and visual quality rating (VQR). Data were analyzed using Anova variant analysis and then continued with Tuckey tests with a 95% confidence level using R studio software. The results showed that chitosan coating did not affect the physical quality of beet tubers, while packaging affected the quality of beet tubers. The most suitable packaging to maintain the physical quality of beet tubers is plastic packaging with holes (perforated).

Garlic is a bulbous plant that grows and produces superb bulb yields in environments with temperatures between 15−25°C and humidity levels of 60−70%. A challenge in garlic growing in lowland areas is the suboptimal bulb growth caused by elevated air temperatures (23−37°C). Through experimentation with the 'Lumbu Putih' variety, predominantly cultivated at low elevations in Gunung Kidul Regency, the use of shade nets is anticipated to modify the microclimate, hence establishing optimal circumstances for garlic plant development. This research specifically targeted to identify the shade net colors that can alter the microclimate to optimize the development, productivity, and quality of garlic production. The study was performed in Logandeng Village, Playen District, Gunung Kidul Regency, Yogyakarta Special Region, at an elevation of approximately 215 meters above sea level. The treatments were organized according to a randomized complete block design (RCBD) including three levels: open land as a control, white shade nets, and black shade nets. Each treatment level comprised five replications organized as blocks. The data collected was analysed by analysis of variance (ANOVA) and the least significant difference (LSD) test at a significance threshold of 5%. The findings indicated that the shade net treatment enhanced the leaf count, leaf surface area, plant development rate, and dry weight per plant. The black shade net treatment yielded a superior quantity of cloves and an increased bulb density relative to the white shade net. According to the findings of structural equation modeling (SEM) study, garlic production is directly controlled by the yield component of 96.2% and indirectly affected by the growth component of 88.3%. The yield and growth component factors that generate direct and positive contributions, as indicated by the Stepwise Multiple Regression analysis, include total root length, plant dry weight, bulb diameter, and clove count.

Produktivitas bawang merah nasional masih di bawah potensi hasil yang diharapkan. Tidak optimalnya produktivitas bawang merah disebabkan interferensi gulma. Interferensi gulma dapat menjadi penyebab kehilangan hasil pada proses budidaya karena adanya kompetisi dan dampak dari alelopati. Penelitian ini bertujuan untuk melihat dampak interferensi gulma terhadap kualitas dan hasil bawang bawang merah. Penelitian menggunakan Rancangan Acak Kelompok Lengkap (RAKL) dengan tiga blok sebagai ulangan. Perlakuan yang diujikan adalah pengendalian gulma dan tanpa pengendalian. Hasil penelitian menunjukkan pengendalian gulma pada lahan pertanian menyebabkan perubahan kelimpahan dan keragaman komunitas gulma. Pengendalian gulma pada saat 3 dan 6 minggu setelah tanam (mst) menyebabkan perbedaan kelimpahan gulma dan perubahan dominasi gulma yaitu dari rumputan menjadi daun lebar yang terjadi pada pengamatan 6 mst dan 9 mst. Kelimpahan dan dominansi gulma berdampak pada penurunan diameter umbi, bobot segar umbi dan bobot umbi bawang merah kering jemur (susut bobot). Pengendalian gulma pada lahan pertanian dapat mencegah kehilangan hasil bawang merah dengan rerata 3 ton/ha dibandingkan lahan tanpa pengendalian.

Generally, cucumber plants have more male flowers than female flowers. The fewer number of female flowers is one of the problems of cucumber production. Flowering regulation can be performed by applying growth regulators and water management. The study aims to determine the effects of paclobutrazol concentrations and watering frequencies on the flowering ratio of cucumber plants. The experiment was arranged in a factorial Randomized Completely Block Design at the Agricultural, Food, and Fishery Extension Center, Seyegan, Yogyakarta. The first factor was the paclobutrazol concentrations consisting of four levels (a control, 0.187 mL.L-1, 0.375 mL.L-1, and 0.562 mL.L-1). Meanwhile, the second factor was the watering frequency consisting of three levels (once a day, once every two days, and once every three days). The observed data were performed using the analysis of variance (ANOVA) and followed with Duncan’s Multiple Range Test at α= 5 %. The paclobutrazol concentrations resulted in a significant effect on all of the observed variables. Meanwhile, watering frequencies showed no significant effect on the male flowers, female flowers and ratio of male to female flowers in cucumber. There was an interaction effect of paclobutrazol concentration and watering frequency on the plant height and flowering age of cucumber plants. The treatment of paclobutrazol at a concentration of 0.375 mL.L-1, decreased of male flowers and increased of female flowers, reducing the ratio of male and female flowers of cucumber plants at various watering frequencies.-1

The pandemic situation experienced by the world are currently threatening food security in various regions including Indonesia. In these regions, the flow of traffic in the agricultural and fisheries sectors, from the means of production to the distribution of the harvest, is choked up due to social restrictions in various parts of the region. As a strategic step to reduce the impact on the agricultural sector, it is necessary to accelerate information to support the stability of production and also to distribute production results. Digital media in agriculture are needed to provide education with a variety of contents, such as technical production, marketing, and agricultural finance information. The Faculty of Agriculture of Universitas Gadjah Mada (UGM) has supported digital information dissemination through the Desa Apps application. Desa Apps aims to be an application platform that provides agricultural extension and develops digital farmer communities. The information that has been carried out by Desa Apps so far includes agrocomplex sector (agriculture, animal husbandry and fisheries) problems related to cultivation methods and obstacles faced in the land such as attack by plant pest and disease. As a digital media, the Desa Apps has educated farmer and aquaculturists. Optimization needs to be done to improve the performance of Desa Apps as a digital media, one of which is the marketing system that this application actually has. This study evaluates whether farmers and aquaculturists under the auspices of the Faculty of Agriculture are interested in being able to get education and at the same time be able to market their product directly to consumers with one application, the Desa Apps. The findings of the study showed that the pandemic period greatly affected the incomes of the assisted target community, and they required media that can help market their product. The decline in turnover due to pandemic conditions reached 70% with an average decrease of 39.2%. The method of selling products has changed from conventional to online sales by 20% of the total respondents. Changes in sales methods occurred due to distribution limitations due to regional and activity restrictions during the pandemic. Therefore, it is necessary to optimize the Desa Apps application as a digital media to support food security.

Italian ryegrass ( Lolium multiflorum Lam.) is a non‐native annual winter grass that has seriously infested rice paddy levees and wheat fields in Japan. Recently, glyphosate‐resistant Italian ryegrass was found on paddy levees in central Japan, thereby making control of the grass by using glyphosate less effective. In this study, physical control methods were tested that combined the timing and frequency of mowing in order to more effectively control glyphosate‐resistant Italian ryegrass on rice paddy levees. A 3 year field experiment was conducted from 2012 to 2014 in a western region of Shizuoka Prefecture, where glyphosate‐resistant Italian ryegrass has become dominant. Five treatments were tested: (i) mowing once before the flowering of the grass (i.e. conventional mowing measure); (ii) mowing once during flowering; (iii) mowing twice during flowering; (iv) glyphosate application before flowering (i.e. one of the conventional mowing measures); and (v) no treatment. The above‐ground biomass, seed production, soil seed bank and seedling occurrence of Italian ryegrass were measured to determine the effectiveness of these treatments. Mowing during the flowering period resulted in reduced above‐ground biomass, seed production and soil seed bank when compared with the other treatments. Additionally, mowing twice during the flowering period resulted in a lower seedling density than mowing once. The results suggest that, in this region, physical control by mowing during the flowering period would be more effective than conventional measures for controlling glyphosate‐resistant Italian ryegrass.

Recently, glyphosate‐resistant Italian ryegrass (Lolium multiflorum Lam.) was found on rice paddy levees in a western region of Shizuoka Prefecture, Japan. Naturalized populations of Italian ryegrass are frequently infected with fungal Epichloë endophytes. Endophytes often confer benefits to their host grasses. This study investigated the influence of five weed management treatments on glyphosate resistance and endophyte infection in Italian ryegrass that was growing on paddy levees where glyphosate‐resistant individuals were dominant. The weed management treatments were: (i) mowing once before the grass flowered; (ii) mowing once during flowering; (iii) mowing twice during flowering; (iv) glyphosate application before flowering; and (v) no treatment. The seeds were collected from the treatment plots in 2013 and 2014. The seeds were examined for endophyte infection and the seedlings that had been grown from the seeds were tested for the frequency of glyphosate resistance. The seedlings that had been derived from the glyphosate treatment showed higher frequencies of glyphosate resistance than those seedlings that had been derived from all the other treatments. Endophytes were found in all populations of the seeds from the paddy levees, with higher infection rates in the seeds that had been derived from the glyphosate treatment and the twice‐mowed treatment. There was a significant relationship between the endophyte infection frequency in the seeds and glyphosate resistance in the seedlings that had been grown from the same populations. The results indicate that where glyphosate herbicides are frequently used, selection for glyphosate‐resistant Italian ryegrass occurs, and along with this, the frequency of endophyte infection also increases.