IMP-HRM: an automated pipeline for high throughput SNP marker resource development for molecular breeding in orphan crops

Abstract

Orphan crops have played a major role in daily diet, health nourishment, economy and livelihood of marginal farmers in under developed and developing world. For various reasons, the majority of these crops including finger millet and tef in cereals; lentil, cowpea and groundnut in legumes; cassava and yam in root crops; have remained neglected and underutilized. With little or no investment these ‘orphan’ crops have lagged far behind in developing genomic resources and are deprived of the application of advanced molecular breeding approaches for their rapid improvement. Single nucleotide polymorphisms, multiple nucleotide polymorphisms, insertions/deletions (indels) and size polymorphisms are important tools for developing rich molecular marker resources. Cataloguing and use of intron based polymorphism have also been demonstrated for applications in molecular breeding. Currently the process of predicting putative introns and designing flanking primers for their amplification requires multiple computer programs and a high level of human intervention. We automated this process by developing intron mapping pipeline (IMP) which allows the generation of large primer sets with minimal human intervention and greater efficiency. Since IMP can take advantage of the highly conserved nature of the introns flanking sequences across a wide range of species, any available model plant genome can be used to predict intron boundaries in related orphan crop species. IMP combined with high resolution melt analysis demonstrated potential for high throughput polymorphism discovery, validation and molecular marker development platform which can generate genomic resources rapidly in orphan species.