Conservation and utilization of crop genetic resources in Malaysia: Mardi’s Effort

Abstract: Malaysian Agriculture Research and Development Institute (MARDI) is the country’s major custodian of the nation’s crops genetic resources. It has a global responsibility in the conservation of genetic resources of banana, sweet potato and citrus, and national responsibility for the conservation of crops, such as rice, tropical fruits and some herbs and medicinal plant species. MARDI rice seed genebank at Seberang Prai in the state of Penang was established in 1984 and currently holds 12,770 registered rice accessions, of which 53% are of local origin. In addition, MARDI also conserves genes in the field, mostly for underutilized tropical fruit genetic resources. At present, about 168 species of underutilized, rare and wild tropical fruit species consisting of about 2,000 accessions, the largest in the country, are being conserved. The species include “kuini” (Mangifera odorata), “bacang” (Mangifera foetida), “binjai” (Mangifera caesia), “cerapu” (Garcinia praniana), “rambai” (Baccaurea motleyana), “asam gelugor” (Garcinia atroviridis), “terap” (Arthocarpus odoratissimus) and “pulasan” (Nephellium rambutan-ake). The accessions are mostly conserved ex situ in field genebanks located at the various MARDI stations throughout the country. Although the conservation of the various crop species genetic resources is important, the real challenge is enhancing its utilisation. The main objective of the paper was to share and disseminate information related to works conducted and strategies opted by MARDI on the conservation and utilization of crop genetic resources. Information on species of crops that are available in MARDI’s genebank was also highlighted together with brief information of some of the associated traits of significant importance posses by those genetic resources

Determination of the chromosome number and genome size of Garcinia mangostana L. via cytogenetics, flow cytometry and k-mer analyses

Mangosteen (Garcinia mangostana L.) is one of the most popular tropical fruit of South-East Asia. It has considerable economic potential for local and export markets. This paper describes a research work to determine the number of chromosomes and genome size of G. mangostana through chromosome counting, flow cytometry and k-mer analyses. Chromosome count analysis revealed that the chromosome number of G. mangostana varied from 74 to 110. The high number observed could be due to the occurrence of mutation and aneuploidy in G. mangostana. Using flow cytometry with Glycine max cv. Polanka (2C = 2.5 pg) used as standard, G. mangostana genome size was found to be 2C = 6.00 ± 0.17 pg. Meanwhile, a genome survey of G. mangostana was performed using Illumina HiSeq 2000 DNA sequencing; k-mer analysis revealed that the genome size of G. mangostana was approximately 5.92 Gbp, or approximately 6.05 pg (1 pg DNA = 0.9780 × 109 bp). Based on the flow cytometry and genome survey, the study concludes that the genome size of G. mangostana is between 6.00 and 6.05 pg

The homestay program in Malaysia: Motivation for participation and development impact

The main purpose of this study is to identify the characteristics and factors affecting the participation and perception of homestay operators about the impact of homestay development on their local communities in Johor. The research instruments used were questionnaires and face to face interviews in 8 major homestay areas. A total of 80 operators were selected via stratified random sampling for the interviews. The study found that majority of the operators in Johor involved in the homestay program are full time operators. Their involvement was driven by various factors such as their own desire to be operators, encouragement from communities, families and associations as well as government incentives. The reasons for being involved in this program are: gaining new experiences, acquiring better source of income, spending their leisure time, improving skills and interests of individuals and the SME businesses they owned. With regard to perception, their homestay operators believed that the development of homestay tourism has positive impacts on their local communities. Based on the 1-5 Likert scale, the impact of cultural heritage is the highest of the overall impacts with a mean score of 4.81, followed by the economic impact with value of 4.80, social and environmental impacts at 4.70 and 4.43, respectively. Overall, from the perspective of homestay operators, the homestay program in Johor has positive impact and is successful. Nonetheless, collaboration and networking with government and private organizations are still needed to further improve the development of homestay program

SMRT sequencing data for Garcinia mangostana L. variety Mesta

The “Queen of Fruits” mangosteen (Garcinia mangostana L.) produces commercially important fruits with desirable taste of flesh and pericarp rich in xanthones with medicinal properties. To date, only limited knowledge is available on the cytogenetics and genome sequences of a common variety of mangosteen (Abu Bakar et al., 2016 [1]). Here, we report the first single-molecule real-time (SMRT) sequencing data from whole genome sequencing of mangosteen of Mesta variety. Raw reads of the SMRT sequencing project can be obtained from SRA database with the accession numbers SRX2718652 until SRX2718659

Predicting storage life of sapodilla (Manilkara zapota L.) by non-destructive technique

Non-destructive technique using Kiwifirm device was useful in detecting the maturity stage of sapodilla fruit, predicting the quality at ripening stage and also days of the fruits to ripen. The power line (Y = 0.02x3.6026) which was derived from the relationship of score resultant from the impact response of Kiwifirm device and duration for the fruit to ripen at 12 °C can be used as a chart to predict and separate the fruit according to the predicted storage duration. Thus the technique could be used to group the fruit into either storage-marketing and utilization purposes, or only suitable group for certain market. This strategy can be used to promote sapodilla fruit for distance market or export. Post-harvest losses, which occurred during storage and transportation can be minimized

Screening rice (Oryza sativa L.) genotypes for resistance against drought

Drought is regarded as one of the limiting factors in rice production nationally and globally. The present study was conducted to study morpho-physiological and biochemical responses of rice genotypes to drought stress, to identify potential traits for use as a selection criterion in breeding drought-tolerant rice at seedling stage and finally to identify rice genotype resistant to drought stress for use as parents in future breeding. The experimental design used was a split-plot design with three replications, with drought stress as the main plot and rice genotypes as the sub-plot. The main plots consisted of control (normal irrigation) and drought stress. The sub-plots consisted of twelve rice genotypes namely Apami (V1), Boewani (V2), Basmati 370 (V3), Cica-4 (V4), Dular (V5), Jarom mas (V6), Kalarata (V7), Biris (V8), Haiboq (V9), Moroberekan (V10), MR 297 (V11) and Aerob 1 (V12). Results showed that drought stress led to a decrease in plant height, leaves size, root length, total dry weight, and number of leaves but an increment in proline content. The genotype Apami and Kalarata were found to accumulate higher proline content indicating potential resistant ability towards drought stress. Dular and Aerob1, along with tolerant control genotype, Moroberekan, on the other hand, recorded a lower SES score. Leave size, root length, and plant height could also be used as a selection criterion in breeding drought-tolerant rice due to high values of broad-sense heritability and genetic advance by percentage of mean (GAM). Nevertheless, further study on the genetics and physiological basis of tolerant ability at reproductive growth stages are necessary in order to assess grain yield potential of the potentially tolerant genotype reported in this study

Cytotoxicity and genotoxicity studies of synthesized amino acid thiourea derivatives on acanthamoeba spp. and human corneal epithelial cells

Two newly-synthesized amino acids thiourea derivatives; 2-(3-benzoylthioureido)-3-mercaptopropanoic acid and 2-(3-benzoylthioureido)-4-(methylthio)butanoic acid, which were labeled as M1 and M2 respectively, were evaluated for their potential as anti-amoebic agent, aiming for a new discovery in amoebic keratitis treatment. The compounds were tested on Acanthamoeba castellanii (CCAP 1501/2A) and Acanthamoeba sp. (Hospital Kuala Lumpur isolate), and also on human corneal epithelial cells (HCEC). Experiments conducted consisting of IC50 determination by eosin dye and MTT assay, morphological observation by light microscopy, evaluation of membrane integrity by acridine orange/propidium iodide staining, mode of cell death determination by DNA fragmentation test and assessment of DNA damage by alkaline comet assay. The IC50 obtained for M1 were 6.26 μM for A. castellanii, and 9.00 μM for Acanthamoeba sp. (HKL isolate) while for M2 the values were 6.97 and 8.63 μM respectively, indicating that these compounds are cytotoxic against both Acanthamoeba. They shortened acanthopodia structures, transformed the amoeba cells to become rounded, and exhibited no distinct vacuoles and nucleus. The membrane integrity was also disrupted, making them non-intact, and promoted apoptosis in amoeba but did not significantly affected the DNA. Both thiourea derivatives showed moderate cytotoxicity toward HCEC with IC50 at 132.69 and 98.20 μM respectively. The compounds did not significantly alter corneal cells’ cellular morphology. These derivatives were found to disrupt HCEC’s membrane integrity and promoted apoptosis but non-genotoxic on HCEC’s DNA

Susceptibility of Malaysian Rice (Oryza sativa L.) Cultivar to Saline Water Submergence Based on the Morphological Traits

Saline water submergence is a newly emerge abiotic stress jeopardizing rice production especially for the rice fields located nearby or alongside coastal areas. The stress was caused by the intrusion of sea water into those rice fields causing flash flood mainly during monsoon season. The present study was conducted to evaluate susceptibility level of selected Malaysian rice cultivars to saline water submergence at seedling stage based on the morphological traits and survival rate. There were six genotypes involved in the study mainly IR64-Sub1 as submergence tolerant control, Pokkali as salinity tolerant control, IR64 as susceptible control and MR297, MR284 and MR253 as local rice cultivars, respectively. The experiment was conducted using split plot design with three replications. On the day 14 after germination, all rice seedlings were totally submerged of about one-meter depth in a polyethylene tank containing saline water at 0, 4, 8 and 12 dS/m for 14 days while the non-submerged plant was control of the experiment. Seedling growth attributes and survival rate were recorded before, right after de-submerged and 14 days after de-submerged. All genotypes however were susceptible to saline water submergence at 4, 8 and 12 dS/m. In contrast, under 0 dS/m, IR64-Sub1 recorded significantly higher survival rate at 83% as compared to MR284 (17%), MR297 (17%), Pokkali (8%), MR253 (0%) and IR64 (0%).  All genotypes were not survived under saline submergence. Therefore, further phenotypic screening of rice genetic resources originated from or nearby coastal areas could be suggested in order to increase chance of identifying potentially tolerant genotype to saline water submergence

Morphological, Biochemical and Genetic Variation of Rice (Oryza sativa L.) Genotypes to Vegetative Stage Salinity Stress

Salinity is one of the most serious issues in rice cultivation and production. Salt stress significantly reduced seedling growth performance of rice. This research was conducted to study the effects of vegetative stage salinity stress on morphological, biochemical, molecular and genetic variation of 12 rice genotypes as well as 2 check varieties, MR297 (susceptible) and Pokkali (tolerant). The experiment was arranged in a split-plot design with 3 replications. Normal freshwater at 0 dS m-1 (L1), saline water at 6 dS m-1 (L2) and saline water at 12 dS m-1 (L3) were the main plot and rice genotypes were the sub-plot. In general, morphological and biochemical traits of all genotypes showed an overall reduction of about 47.41% in L3 as compared to L1 except for the tolerant check, Pokkali. The genetics and correlation analysis indicated that plant height, leaf size and standard evaluation system (SES) score might be used as a selection criterion in developing salt tolerant rice. The multivariate analysis revealed that a Malaysian landraces, Jarom Mas was clustered together with Pokkali as tolerant genotype. Screening using tightly linked Simple Sequence Repeat (SSR) markers (RM1287, RM10748, RM493) of salinity tolerant QTL, Saltol indicated that this QTL was absence in Jarom Mas. This finding might indicate the presence of other QTL associated with salinity tolerance in Jarom Mas. Further study on identifying the speculated QTL may be conducted to confirm this postulation