A High-Density Genetic Map with Array-Based Markers Facilitates Structural and Quantitative Trait Locus Analyses of the Common Wheat Genome

Abstract

The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map.

Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high‐density, high‐resolution consensus genetic map

“…Detection of QTLs for important development and growth traits has already been done in some of the populations from this study (Prioul et al ., ; Lejeune‐Henaut et al ., ; Bourion et al ., ; Bourgeois et al ., ; Hamon et al ., ; Klein et al ., ). The increase in the number of markers will certainly allow better precision and resolution in QTL detection in each population, as reported for example in T. aestivum (Iehisa et al ., ). The number of common markers between maps is also expected to ease the evaluation of QTL synteny and meta‐QTL analysis.…”

DNA Marker Linked to Everbearing Flowering Gene in Cultivated Strawberry, with High Applicability to Various Breeding Populations

“…The DNA fragments obtained were sequenced on HiSeq 2000 and MiSeq sequencers (Illumina, San Diego, CA, USA). On the basis of the sequence data, we designed 291,041 probes with a length of 50-60 bp according to the procedures described by Iehisa et al (2014), and constructed a microarray including the probes.…”

Genomics of Wild Relatives and Alien Introgressions

“…A new version of DArT marker technology (DArT-seq) is based on next-generation sequencing where the polymorphisms are genotyped by sequencing. Because of their advantages, DArT has been employed extensively in genetic mapping, genotyping, and diversity assessment in wheat (Cabral et al 2014;Jighly et al 2015;Bentley et al 2014;Yu et al 2014;Colasuonno et al 2013;Iehisa et al 2014), and more recently in its wild and cultivated relatives (Montilla-Bascón et al 2015;Kalih et al 2015;Castillo et al 2014;Bolibok-Brągoszewska et al 2014;Alheit et al 2014;Yabe et al 2014;Cabral et al 2014;Jing et al 2009).…”