Abstract
BackgroundDevelopment of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported.ResultsRadiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH lines with an average deletion frequency of ~10% were identified for developing high density marker scaffolds of the D-genome.ConclusionsThe RH panel reported here is the first developed for any wild ancestor of a major cultivated plant species. The results provided insight into various aspects of RH mapping in plants, including the genetically effective cell number for wheat (for the first time) and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for mapping gene based markers, developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and functional characterization of genes and gene networks present on the D-genome.
Highlights
Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome
Radiation hybrid mapping is an important tool for mapping/cloning genes in recombination poor regions [14] and developing a marker scaffold for whole genome assembly [8,25] of important crops like wheat with complex and highly repetitive genomes
A Radiation hybrid (RH) panel was developed for the D-genome of Ae. tauschii accession AL8/78 (AL8/78-DGRH1) and is the first reported for any wild ancestor of a cultivated plant species
Summary
Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. Its genetic improvement holds the key to achieving the levels of production necessary to meet the demands of an ever increasing world population Keeping this in mind, the International Wheat Genome Sequencing Consortium (IWGSC; http://www.wheatgenome.org/) was established with the goal to fully sequence the wheat genome. Bread wheat (Triticum aestivum L.), which accounts for ~95% of world wheat production, is evolutionarily the youngest polyploid (segmental allohexaploid) species among the cultivated crops. It has a large genome (~17 Gb) which is about eight times larger than that of maize (Zea mays L.) and 40 times that of rice (Oryza sativa L.) [1]. The large genome size and presence of over 80% repetitive sequences [2] makes the development of a complete physical map, a necessary first step to whole genome assembly of this species, a formidable challenge
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