Unigene derived microsatellite markers for the cereal genomes

Abstract

Unigene derived microsatellite (UGMS) markers have the advantage of assaying variation in the expressed component of the genome with unique identity and positions. We characterized the microsatellite motifs present in the unigenes of five cereal species namely, rice, wheat, maize, Sorghum and barley and compared with those in Arabidopsis. The overall UGMS frequency in the five cereal species was 1/7.6 kb. The maximum UGMS frequency was in rice (1/3.6 kb) and the lowest in wheat (1/10.6 kb). GC-rich trinucleotide repeat motifs coding for alanine followed by arginine and the dinucleotide repeat motif GA were found to be abundant UGMS classes across all the five cereal species. Primers could be designed for 95% (wheat and barley) to 97% (rice) of the identified microsatellites. The proportion and frequency of occurrence of long hypervariable class I (> or = 20 nucleotides) and potentially variable class II (12-20 nucleotides) UGMS across five cereal species were characterized. The class I UGMS markers were physically mapped in silico on to the finished rice genome and bin-mapped in wheat. Comparative mapping based on class I UGMS markers in rice and wheat revealed syntenic relationships between the two genomes. High degree of conservation and cross-transferability of the class I UGMS markers were evident among the five cereal species, which was validated experimentally. The class I UGMS-conserved orthologous set (COS) markers identified in this study would be useful for understanding the evolution of genes and genomes in cereals.

Mining of microsatellites using next generation sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome

“…The amino acids serine, leucine, glutamine, and phenylalanine were predominant. Similar predominance of these amino acids has also been reported in other plant species (Jung et al 2005;Lawson et al 2006;Parida et al 2006;Roorkiwal and Sharma 2011).…”

Flow cytometric chromosome sorting from diploid progenitors of bread wheat, T. urartu, Ae. speltoides and Ae. tauschii

“…Our findings confirm and expand the results of previous studies indicating the high transferability of COS markers between species (Parida et al 2006;Burt and nicholson 2011;Howard et al 2011;Molnár et al 2013). The fact that 64.2 % of the products obtained with chromosomes isolated from wild relatives were polymorphic relative to those obtained in hexaploid wheat suggested that the substantial genetic diversity of wild progenitors is due to the variability of intron regions (Yu et al 2005).…”

Development and linkage mapping of unigene-derived microsatellite markers in Brassica rapa L.

“…UGMS markers have been recently developed in order to use unique functional genes in the plant genomes as molecular markers (Parida et al 2006(Parida et al , 2010. This has reduced the redundancy, i.e., multiple copies of genes or repeats of the same DNA sequences, which is a general problem when SSRs are designed from random genomic DNA or EST sequences.…”

“…However, due to the problem of sequence redundancy yielding multiple sets of markers at the same locus, random EST sequences are being assembled into unique gene sequences called unigenes (http://www. ncbi.nlm.nih.gov/), and SSRs are designed from these transcribed genes in order to have unique identities and positions in the genome (Parida et al 2006, Sharma et al 2009). The availability of increasingly large unigene databases now makes systematical and easy identification of microsatellites from a large number of plants possible, greatly facilitating the study of functional diversity in the natural populations and many germplasm collections as well as comparative mapping and evolutionary studies (Ishikawa et al 2008, Parida et al 2006.…”