Phenotypic measurement and genotypic data

In each environment, the number of spikes per m² (SPM2) was determined after anthesis, by manual counting all spikes in two, 1-m long transects per micro-plot. At physiological maturity, all micro-plots were harvested using a combine harvester and the yield components (detailed below) were determined from the harvested grain samples, referred to hereafter as ‘bulk grain’. Grain humidity was measured using a humidimeter (TM, Tripette and Renaud, France) to calculate grain mass yield at a notional 15% humidity basis.

For each grain bulk, a 200 g subsample was oven-dried (60°C for 48 h) before determining TKW, with an automatic seed-weighing and counting device (Opto Agri2, Optomachine, France). From direct measurements of yield (GY), SPM2 and TKW, the numbers of grains per spike (GPS), and numbers of grains per m² (GPM2) were computed.

The device used for TKW determination also provides single-grain-size components. Individual grain size (projected area) was extracted and used as a proxy for individual grain mass (S2 Fig and S3 Fig). Depending on the bulk grain and the season (2016 or 2017), the analyses of individual grain size distributions were based on 300 to 500 individual grains (S3 Table).

The 228 genotypes from the 2016 trial and the 312 genotypes from the 2017 trial were genotyped with the TaBW280K SNP genotyping array [34]. Markers with missing values above 10%, minor allele frequency above 5% and monomorphic markers were removed. Imputation of missing values was carried out with Beagle V4.1 software [35]. The physical map used was the RefSeqV1.0 reference sequence of Chinese Spring [36].