Only clearly distinguishable polymorphic AFLP bands were scored for mapping in the present study.
This brought the total number of sequence contigs that could be scored for SNPs in the bin mapping progeny to 954, covering 28,045,768 bp (74%) of the draft genome assembly.
Recombinant F2 progeny were scored for presence of the mapping dominant markers and for absence of the balancer dominant marker (see genetic scheme in Figure 1A).
Each synthesis map was scored for organization (both between concepts and within concepts), accuracy, and completeness using the rubric described in the Supplemental Material.
The Nipponbare X Kasalath CSSL mapping population was scored for NIS to the GUY11 isolate (see Methods). A. The CSSL5, CSSL19 lines and two recombinant lines (19-42-2 and 19-42-4) identify chromosome 1 as carrying a Kasalath locus conferring susceptibility under high nitrogen treatment.
For the SPC gene, each F2 plant of the mapping population was scored for pod coiling (clockwise or anticlockwise) and the marker was treated as dominant.
The mapping population was scored for resistance to cane botrytis (B. cinerea), spur blight (Didymella applanata), cane spot (Elsinoe veneta) and yellow rust (Phragmidium rubi-idaei).
For the Mtsym6 gene, each F2 plant of the mapping population was scored for its symbiotic phenotype by testing a minimum of 10 F3 plants inoculated with Sinorhizobium meliloti strain A145 as described by Tirichine et al[ 31].
After the parental genotypes were scored for their alleles, any polymorphic microsatellites were mapped using the recombinant inbred line (RIL) population from Blair et al. [ 10] based on the cross DOR364 × G19833 where DOR364 is a Mesoamerican advanced breeding line from CIAT and G19833 is an Andean germplasm accession from Peru.
The relative content of the predominant non-acylated anthocyanin pigment Cy3XGG, had a clear bimodal distribution in the F2 compatible with a simply-inherited dominant trait, and for mapping purposes was scored as a dominant phenotypic marker.
