Multi-parent advanced generation inter-cross in barley: high-resolution quantitative trait locus mapping for flowering time as a proof of concept

The choice of mapping population is one of the key factors in understanding the genetic effects of complex traits and determines the power and precision of quantitative trait locus (QTL) mapping. We present the results of the first eight-way multi-parent advanced generation inter-cross (MAGIC) doubled haploid (DH) population in barley (Hordeum vulgare ssp. vulgare) applied to mapping complex traits. The results of the genetic architecture within the barley MAGIC population allowed QTL mapping in 533 DH lines with 4,550 single nucleotide polymorphisms (SNPs) with a newly developed mixed linear model in SAS v9.2, incorporating multi-locus analysis and cross validation for flowering time. Two QTL mapping approaches, the binary approach (BA), which is widely used in QTL and association mapping, and a novel haplotype approach (HA) were compared based on their efficiency, precision for QTL detection and estimation of genetic effects. The analysis detected 17 QTLs, five of which were shared between the two approaches; five and two were specifically found with the BA and HA approaches, respectively. The combination of the two mapping approaches enabled high-precision QTL mapping for flowering time. The QTLs corresponded to the genomic regions of major flowering-time genes Vrn-H1, Vrn-H3, HvGI, Ppd-H1, HvFT2, HvFT4, Co1 and linked genes for plant height (sdw1). These results confirm the proof of concept of QTL mapping in a multi-parent population, highlight the advantages and demonstrate that the barley MAGIC DH lines in combination with an advanced QTL mapping approach are valuable resources for mapping complex traits.