We selected 355 lines as the RH panel based on the genotypes determined using the 21 6B-specific SSR markers.
Then, we used MAS to select 23 BC1F1 plants carrying one or two target chromosome segments, based on the genotypes of 86 DNA markers distributed across the genome.
A scoring system was developed to determine the minor contributors in DNA mixtures based on the genotypes identified using MPS.
Using hybriddetective we simulated multigenerational (viz. pure wild, pure farm, F1, F2, and backcrosses to wild and farm) hybrid datasets based on the genotypes of our wild and farmed baselines at the 95 SNPs in our panel.
A clear separation based on the genotypes site of origin among the genotypes for drought tolerance could not be established when analyzed using principal component analysis.
Second, a small fraction of case and control individuals in each data set are genotyped at all the loci, and a dynamic programming algorithm is used to determine the haplotype blocks and the tag SNPs based on the genotypes of the sampled individuals.
The genotypes of the hybrids were deduced based on the genotypes of the parental lines.
A total of 241 introgressions, including 207 homozygous and 34 heterozygous segments, were detected on 12 chromosomes based on the genotypes of 133 SSR markers in 96 ILs (Additional file 1: Table S1).
Seven markers were used to screen 26 BC4F3 lines, and these lines were evaluated for the TGW and SPP. The 26 lines were classified into 8 groups based on the genotypes of the SSR markers.
Based on the genotypes determined by the five markers, three plants (15 2, 15 27 and 15 183) with homozygous YXZ genotypes and three plants (15 193, 15 307 and 15 398) with homozygous SBSM genotypes were selected.
We classified the progeny into four groups based on the genotypes of the QTL regions (Figure 5A): individuals harboring QTLs qPbm11 and qPbm9 (Type 1, qPbm11/qPbm9); individuals harboring qPbm11 (Type 2, qPbm11/-); individuals harboring qPbm9 (Type 3, −/qPbm9); and individuals lacking both QTLs (Type 4, −/−).
