Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.

Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, ‘Chiang Mai Pink’ and ‘UB Snow 701’, to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.

The present study was conducted in order to assess the effect of various doses of acute gamma irradiation (0, 10, 15, and 20 Gy) on the improvement of bioactive compounds and their antioxidant properties of Curcuma alismatifolia var. Sweet pink. The high performance liquid chromatography (HPLC) and gas chromatography (GC) analysis uncovered that various types of phenolic, flavonoid compounds, and fatty acids gradually altered in response to radiation doses. On the other hand, antioxidant activities determined by 1,1-Diphenyl-2-picryl-hydrazyl (DPPH), ferric reduction, antioxidant power (FRAP), and 2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) radical scavenging assay showed a higher irradiation level significantly increased the antioxidant properties. This study revealed an efficient effect of varying levels of gamma radiation, based on the pharmaceutical demand to enhance the accumulation and distribution of bioactive compounds such as phenolic and flavonoid compounds, fatty acids, as well as their antioxidant activities in the leaves of C. alismatifolia var. Sweet pink.

Problem statement: Huanglongbing (HLB) is a phloem limited disease in citrus caused by a fastidious bacterium called ’Candidatus’ Liberibacter found in Africa, Asia and United States of America (USA). HLB can severely reduce vigor and yield or kill all citrus trees within 5 years. There is a need to screen and identify suitable rootstock for propagation of clean plan materials for citrus in the tropics. This study was conducted to detect the presence of HLB on 18 selected citrus species and to categorize the level of infection and susceptibility of citrus species to HLB. Approach: Eighteen citrus species were assessed for susceptibility to HLB by graft transmission from source infection (Citrus reticulata). Results: HLB was detected in 15 species 6 months after grafting using PCR test. Conclusion: The species could be categorized in five groups: Severe group (72-58% severity) which includes C. reticulata, C. sinensis, C. reshni cv. cleopatra, moderate group (50- 41% severity) includes Fortunella sp. cv. Kasturi Chinai, C. macrophylla, C. microcarpa, mild group (25-17% severity) which included C. medica, C. aurantifolia, Citrus sp. (natural biotype), C. jambhiri. The tolerant group which did not show any HLB symptoms but tested positive by PCR test includes C. aurantium and C. aurantifolia. The resistant groups which include C. grandis cv. Limau Bali, C. hysterix and Citrus sp. cv. Limau Tembikai showed no symptoms and were tested negative for HLB.

Zingiber zerumbet (L.) Smith, known as Lempoyang in Malaysia, belongs to the family Zingiberaceae. Previous studies on Lempoyang mainly focused on the chemical properties and biological activities of the rhizome extracts of this plant. Despite the tremendous demand for the rhizomes of Z. zerumbet, there is a lack of information on cultivation practices and a scarcity of planting materials. By using the pre-soaked technique, the challenges posed by Z. zerumbet dormancy can be overcome, obtaining good quality and uniform planting material throughout the year. Besides that, it is also crucial to determine the optimum shade level and NPK fertilizer rates to obtain a high yield and good quality rhizomes of Lempoyang. Six concentrations of 6-benzylaminopurine (BAP, 0, 50, 100, 150, 200, and 250 mg/L) and ethephon (0, 150, 300, 450, 600, and 750 mg/L) were tested to evaluate their effects on breaking rhizome dormancy. Three different shade levels (full sun, 30%, and 50% shade levels) and four combinations of Nitrogen (N), phosphorus (P), and potassium (K) (NPK) fertilizer at different rates were evaluated to study their effects on plant growth and yield performance. The results showed that BAP at 100 mg/L and ethephon at 300 mg/L performed better than the other compound concentrations tested in promoting the breaking of bud dormancy. A significant interaction effect was observed between shade levels and NPK fertilizer rates in all the growth parameters examined, except for the number of tillers per plant. Plants grown under 30% shade with NPK 4 produced the highest rhizome fresh weight, dry weight, and yield, but plants grown under 50% shade with NPK 4 showed the highest plant height and number of tillers per plant.