ABSTRACT
Availability of transcriptome datasets for use in accelerated molecular-based breeding in Musa species is limited. IlluminaHiseq technology was employed to determine differential gene expression between the contrasting cultivars for threedifferent stresses (Eumusae leaf spot –Mycosphaerella eumusae, root lesion nematode – Pratylenchus coffeae and moisturedeficit stress) under challenged and unchallenged conditions. An average of 34.72 million of reads was assembled into*47629 contigs, and *5,466 simple sequence repeats (SSR) from each library were identified. GO annotation and KEGGpathway analysis were carried for all the transcripts and the SSR, SNPs were also detected. Based on this information, aMusatransSSRDB has been developed. Currently, the database consists of 32,800 SSRs with the unique information likeputative function of the SSR-containing genes and their metabolic pathway and expression profiling under various stressconditions. This database provides information on in silico polymorphic SSRs (2830 SSRs) between the contrastingcultivars for each stress and within stress. Information on in silico polymorphic SSRs specific to differentially expressedgenes under challenged condition for each stress can also be accessed. This database facilitates the retrieval of results bynavigating the tabs for cultivars, stress and polymorphism. This database was developed using HTML, Java and PHP;datasets are stored in MySQL database and accessible in the public domain (http://bioinfnrcb.byethost7.com/nrcbbio/). Thisunique information facilitates the banana breeder to select the SSR primers based on specific objectives. MusatransSSRDBalong with other genomics databases will facilitate the genetic dissection and breeding for complex traits in banana. Thus,this database is a step forward in economizing cost, time, manpower and other resources.
ABSTRACT
Nearly 65,000 citrus EST (Expressed Sequence Tags) have been investigated using the CitEST project database. Microsatellites were investigated in the unigene sequences from Citrus spp. and Poncirus trifoliata. From these sequences, approximately 35 percent of the non-redundant ESTs contained SSRs. The frequencies of different SSR motifs were similar between Citrus spp and trifoliate orange. In general, mononucleotide repeats appeared to be the most abundant SSRs in the CitEST database, but we also identify di-, tri-, tetra-, penta- and hexanucleotide repeats. The AG/CT and AAG/CTT were the most common dinucleotide and trinucleotide motifs, with frequencies of 54.4 percent and 25.2 percent, respectively. Primer sequences flanking SSR motifs were successfully designed and synthesized. After in silico polymorphism analysis, a subset of sixty-eight primers was validated in different Citrus spp. and Poncirus trifoliata. PCR-amplification revealed polymorphism in citrus with all tested primer pairs and showed the potential of these markers for linkage mapping. Our study showed that the CitEST database can be exploited for the development of SSR markers that can amplify Citrus spp. and related genus for comparative mapping and other genetic analyses.