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 .

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The effects of eight different doses (0, 10, 20, 25, 35, 40, 60, and 100 Gy) of acute gamma irradiation on 44 (three varieties of Curcuma alismatifolia: Chiang Mai Red, Sweet Pink, Kimono Pink, and one Curcuma hybrid (Doi Tung 554) individual plants were investigated. Radiation sensitivity tests revealed that the LD50 values of the varieties were achieved at 21 Gy for Chiang Mai Red, 23 Gy for Sweet Pink, 25 Gy for Kimono Pink, and 28 Gy for Doi Tung 554. From the analysis of variance (ANOVA), significant variations were observed for vegetative traits, flowering development, and rhizome characteristics among the four varieties of Curcuma alismatifolia and dose levels as well as the dose × variety interaction. In irradiated plants, the leaf length, leaf width, inflorescence length, the number of true flowers, the number of pink bracts, number of shoots, plant height, rhizome size, number of storage roots, and number of new rhizomes decreased significantly (P < 0.05) as the radiation dose increased. The cophenetic correlation coefficient (CCC) between genetic dissimilarity matrix estimated from the morphological characters and the UPGMA clustering method was r = 0.93, showing a proof fit. In terms of genetic variation among the acutely irradiated samples, the number of presumed alleles revealed by simple sequence repeats ranged from two to seven alleles with a mean value of 3.1, 4.5, and 5.3 alleles per locus for radiation doses of 0, 10, and 20 Gy, respectively. The average values of the effective number of alleles, Nei's gene diversity, and Shannon's information index were 2.5–3.2, 0.51–0.66, and 0.9–1.3, respectively. The constructed dendrogram grouped the entities into seven clusters. Principal component analysis (PCA) supported the clustering results. Consequently, it was concluded that irradiation with optimum doses of gamma rays efficiently induces mutations in Curcuma alismatifolia varieties.

Problem statement: Curcuma alismatifolia Gagnep., commonly known as 'Thai tulip' or pathumma is a member of the family Zingiberaceae. This herbaceous perennial which can be grown from rhizomes have a great potential for use as a cut flower, flowering potted plant and as a garden plant for tropical landscaping. Unlike other bulbous floral crops, research on C. alismatifolia using gamma irradiation has been a least subject of investigation. Approach: Presently, the use of induced mutation in plant improvement had become a proven way that can generate new sources of genetic variations in creating new varieties. This additional tool is important in plant improvement, which was a valuable approach to plant breeding in the world of ornamental industry. A study on the effects of gamma irradiation on mutagenesis of Curcuma alismatifolia was conducted to determine the optimal dose for radiosensitivity test (LD 50) of the plants and also to determine the effects of induced mutation on the species. This study was carried out at the Malaysian Nuclear Agency (Nuclear Malaysia), Bangi. Ten levels (dose rate) of gamma irradiation were used in this study. Data collection for days of shoot emergence, plants height, number of leaves and shoots, days to bloom, height of flowering stalks, inflorescence size and the days to anthesis (post-production longevity) were taken. Results: Results obtained showed that the highest survival rate was 67% obtained from the non-irradiated rhizomes (0 Gy). Fifty percent when were treated with 10 Gy and 63% survival rate when treated at 20 Gy. Mean survival rate fell sharply from 63% at 20 Gy to 7% at 30 Gy. This decreasing trend was followed by 2% survival at 40 Gy. Results indicated that the radiosensitivity test (LD 50) for the Curcuma alismatifolia was approximately at 25 Gy. Conclusion: Gamma irradiation had exerted various effects on growth of C. alismatifolia, including the survival rate of rhizomes, extension of days to shoot emergence, plant height, leaves and shoots number as well as modifications in plant morphology and flower development.