4D Wheat Activity 2.2: Genetic maps of synthetic hexaploid wheat derived populations to investigate recombination, to identify quantitative traits and isolate genes.

Five backcross BC1F5 populations were developed by crossing the synthetic hexaploid wheat (SHW) lines C44, C45, C52, C65 and C66 to the recurrent elite wheat cultivar Carberry. Genomic DNA of a total of 910 BC1F5 lines and the six parental lines were restricted with PstI and MspI and reduced representation libraries were constructed following the protocol described in Colston-Nepali et al. (2029; https://doi.org/10.1007/s10592-019-01223-y). The libraries were pooled and sequenced using Illumina NovaSeq 6000 using paired-end 150. The two 96-well plates comprising the 18C66CAR individuals were sequenced on ~0.5% of a NovaSeq lane per individual. Individuals of the remaining four populations were sequenced on ~0.25% of a lane per individual or 4 x 96-well plates per NovaSeq lane. The parental libraries were more deeply sequenced to ensure a high-call rate. The depth with percentages of NovaSeq lane in brackets were as follows: C44 (~2.25%), C45 (~2.25%), C52 (~1.91%), C65 (~2.97%), C66 (~2.61%) and Carberry (~5.43%).