Allele Alliance: An Accurate Detection of Allelic Diversity within Breeding Populations

Efficient breeding involves crossing several founder lines to create genetically complex, multi-allelic progeny. Despite their importance in breeding programs for crop improvement, many economically significant complex traits, including yield and environmental stress tolerance, are not sufficiently well explained by the commonly used sets of DNA markers. Consequently, plant breeders depend almost entirely on phenotypic evaluation for the selection of beneficial individuals for the next breeding cycle.

To aid in the process of selection, NRGENE focuses on mapping traits using actual breeding populations. NRGENE's GenoMAGIC^TM platform utilizes next generation sequencing (NGS) and novel algorithms to identify superior marker sets for the allelic diversity in each and every locus.

NRGENE has used the GenoMAGIC^TM platform to analyze the genetic makeup of commercial inbred lines and hybrids of rice (Oryza sativa), tomato (Solanum lycopersicum) and maize (Zea mays). Our results demonstrate great differences in the breeding populations’ genetic architecture. While rice exhibits multi-allelic loci and approximately 50% heterozygosity, tomato displays a rather uniform genetic background with large introgressions from wild germplasm. Conversely, maize hybrids are composed of extremely diverse parental lines. We identified several alleles associated with commercially important traits for these crops.