Abstract
BackgroundGuar [Cyamopsis tetragonoloba, L. Taub.] is an important industrial crop because of the commercial applications of the galactomannan gum contained in its seeds. Plant breeding programmes based on marker-assisted selection require a rich resource of molecular markers. As limited numbers of such markers are available for guar, molecular breeding programmes have not been undertaken for the genetic improvement of this important crop. Hence, the present work was done to enrich the molecular markers resource of guar by identifying high quality SSR, SNP and InDel markers from the RNA-Seq data of the roots of two guar varieties.ResultsWe carried out RNA-Seq analysis of the roots of two guar varieties, namely, RGC-1066 and M-83. A total of 102,479 unigenes with an average length of 1016 bp were assembled from about 30 million high quality pair-end reads generated by an Illumina HiSeq 2500 platform. The assembled unigenes had 86.55% complete and 97.71% partially conserved eukaryotic genes (CEGs). The functional annotation of assembled unigenes using BLASTX against six databases showed that the guar unigenes were most similar to Glycine max. We could assign GO terms to 45,200 unigenes using the UniProt database. The screening of 102,479 unigenes with MISA and SAMtools version 1.4 softwares resulted in the identification of 25,040 high-confidence molecular markers which consisted of 18,792 SSRs, 5999 SNPs and 249 InDels. These markers tagged most of the genes involved in root development, stress tolerance and other general metabolic activities. Each of the 25,040 molecular markers was characterized, particularly with respect to its position in the unigene. For 71% of the molecular markers, we could determine the names, products and functions of the unigenes. About 80% of the markers, from a random sample of molecular markers, showed PCR amplification.ConclusionsWe have identified and characterized 25,040 high confidence SSR, SNP and InDel molecular markers in guar. It is expected that these markers will be useful in molecular breeding programmes and will also be helpful in studying molecular mechanisms of root development, stress tolerance and gum synthesis in guar.
Highlights
The numbers of clean reads generated after trimming adaptors and removing low quality bases were 17,305,480 and 17,517,086 in guar varieties RGC-1066 and M-83, respectively
We report here the development and characterization of simple sequence repeat (SSR), Single nucleotide polymorphism (SNP) and Insertions and deletions (InDels) markers for the guar crop by sequencing of the root transcriptome
A total of 102,479 unigenes were assembled from the Ribonucleic acid sequence (RNA-Seq) data of two guar varieties, namely, RGC-1066 and M-83
Summary
Taub.] is a diploid, annual and drought-tolerant leguminous crop mainly cultivated in the semi-arid areas of India, Pakistan and the United States of America. It is generally grown in marginal soils having nitrogen and water deficiencies and often containing high salt concentrations. The guar gum, which is mainly galactomannan, is a natural thickener used in petroleum, food, paper, textile, cosmetics and pharmaceutical industries [3] It has shown a potential in the treatment of diseases like irritable bowel syndrome, diarrhea, high cholesterol and diabetes [4,5,6]. Due to the high demand of guar gum all over the world, improved varieties of guar, having increased amounts of high quality gum and able to grow under adverse conditions, have become a necessity
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