constraction of high density genetic map of common wheat

Common wheat (Triticum aestivum L., genome constitution AABBDD) is an allohexaploid species originated from interspecific hybridization between tetraploid wheat (Triticum turgisum L., AABB) and the wild diploid relative Aegilops tauschii Coss.(DD)(Kihara 1944; McFadden and Sears 1944). In common wheat, its large genome size (17 Gb) and allopolyploidy complicated the construction of high-resorution genetic maps. Diversity arrays technology (DArT), a microarray hybridization-based technique, has been developed in common wheat for high-throughput genotyping without relying on sequence information (Akbari et al., 2006). DArT generates whole-genome fingerprints by scoring the presence versus the absence of DNA fragments in genomic representations generated by digestion of genomic DNA with a combination of two restriction endonucleases (Wenzl et al., 2004). Using wheat PstI(TaqI) v2.6 array, 1,348 DArT markers were mapped in the hexaploid Synthetic W7984 x Opata M85 doubled haploid population (Sorrells et al., 2011). Recent advances in the next-generation sequencing (NGS) technology make it possible to screen a huge number of polymorphic site even in species without reference genome information. Single nucleotide polymorphisms (SNPs) have been discovered by sequencing of complexity-reduced fraction of the tetraploid wheat genome (Trebbi et al., 2011) or cDNA of common wheat (Allen et al., 2011; Lai et al., 2012), and were used to develop high-throuput SNP-typing platforms. Improvements in the throughput of NGS technologies made it possible to conduct the SNP-typing of entire mapping population by direct sequencing, combining the process of polymorphism discovery and genotyping in a single experiment. In tetraploid and hexaploid wheat, the sequence-based genotyping has been performed by sequencing of complexity-reduced genomic DNA (Poland et al., 2012) or targeted genomic region (Winfield et al., 2012). Sequence-based genotyping is cost-effective, but often have significant amount of missing data due to the low coverage of sequencing (Davey et al., 2011). To efficiently construct the high-resolution map in common wheat with few missing data, we developed a microarray-based polymorphism detection system using NGS data obtained from complexity-reduced genomic DNA samples of two common wheat cultivars Chinese Spring (CS) and Mironovskaya 808 (M808), and genotyped 210 recombinant inbred lines (RILs) between the two cultivars. Moreover, quantitative trait locus (QTL) analysis was performed for morphological and agronomically important traits using the constructed high-density map.