Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

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.

A System for Dosage-Based Functional Genomics in Poplar

“…Ionizing radiations induce DNA breaks, resulting in chromosomal deletions and insertions (indel mutations) of various lengths (Shirley et al, 1992). In plants, dosage mutants can be generated rapidly in a single step, by irradiation of pollen followed by fertilization (Khush and Rick, 1968;Pfahler, 1967;Vizir et al, 1994;Liharska et al, 1997;Farbos et al, 1999;Vizir and Mulligan, 1999;Gao et al, 2006;Kumar et al, 2012). The resulting progeny display male-specific indel mutations that have been used in plant genetic studies in various crops for nearly half a century (Khush and Rick, 1968), mostly in a forward genetics mode.…”

A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A

“…It was significantly lower when compared to RH panels developed by seed irradiation. In these cases, the average retention frequency was 80–90% (Kumar et al, 2012a,b, 2015; Michalak de Jimenez et al, 2013; Mazaheri et al, 2015). The main reason for higher retention frequencies in seed panels is the fact, that seeds with higher chromosome breakage level would not produce viable plants (Kumar et al, 2014).…”

“…For comparison, RH map of barley chromosome 3H constructed using 113 EST and RJM markers on 202 RH lines resulted in a map of 3066 cR (Mazaheri et al, 2015). The fourth map was developed for wheat chromosome 2D using 92 RH lines and 25 markers with the final length of 453 cR (Kumar et al, 2012b). …”

A noise-aware method for building radiation hybrid maps

“…The simulated annealing [16], taboo search [17] and LinKernighan heuristic [18] are used to find a map with a better loglikelihood over an initial map. These algorithms have been used to construct several maps in [19,20,13].…”