Kyaw Thu Moe

Sequence Information on Simple Sequence Repeats and Single Nucleotide Polymorphisms through Transcriptome Analysis of Mungbean

Mungbean (Vigna radiata (L.) Wilczek) is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs (≥ 500 bp) with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat (SSR) motifs was identified in Jangan (1 630) compared with that of Sunhwa (1 334). A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms (SNPs) and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was approximately 860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.

Trends in genomics and molecular marker systems for the development of some underutilized crops

The term ‘underutilized’ is often used to characterize the range of plant species whose potential contribution to food security, health, income generation, and environmental services has not yet been fully exploited. To harness unexploited resources, the first step is to prevent them from extinction and to conserve them in- and/or ex-situ. To utilize plant species as crops, plants must be collected, conserved, evaluated, and then if necessary manipulated. In this context, significant international efforts have focused on impeding the erosion of genetic diversity. Thousands of new accessions are introduced into germplasm institutes each year. Assessment of their molecular diversity is necessary to eliminate redundant genotypes. Marker systems have been used not only for genotyping to reduce redundancy and develop a core set, but also for a wide variety of other purposes. The use of markers based on single nucleotide polymorphisms, copy number variation, and insertions/deletions, as well as genotyping by sequencing, is becoming popular for genetic mapping and analyses of quantitative trait loci. This review discusses current marker systems and genomic analyses of a number of underutilized crops.