Fig. 2.

MAM identified the location of the P10 transgene. a) The parental and backcrosses that yield the F2 progeny (b) used for MAM. In this example, P (the P10 GFP transgene insertion) is the gene to be mapped. Two flanking markers, the dominant male-determining locus M and a wild-type black-eye allele B (or +), are used to assist the mapping of P. The corresponding alleles m and re on the homologous chromosome are not shown. M/m individuals are males and m/m individuals are females. B/re (or +/re) individuals are black eyed and re/re individuals are red eyed. The genotype of the females in both the parental and the backcross is m/m, N/N (negative for the transgene insertion), and re/re. The genotype of the F1 male is M/m, P/N, and B/re (or +/re) and only the dominant alleles are shown for simplicity. b) Identifying the informative recombinants in the progenies of the backcross: the phenotype of the F2 progeny, which is solely determined by the genotype of the gamete of the F1 male, is used for MAM. The presence of the easily scorable markers (sex and eye color) flanking the gene of interest P enables the identification of the vast number of noninformative F2 progenies, which maintain the parental linkage: MPB, males (M) that are positive for GFP (P) and black eyed (B); or FNR, females (m) that are negative for GFP (N) and red eyed (re). Thus, we are able to exclude the noninformative progeny and focus on the informative recombinants MPR, FBP, MNR, and FNB. The numbers below each genotype/phenotype are the actual numbers of individuals identified from the backcross. More than 3,000 (1,556 + 1,511 = 3,067) noninformative individuals are excluded from the MAM analysis. The number of individuals sequenced is indicated in materials and methods. c) Expected Δ(SNP index) values differ under 3 sampling scenarios: (1) MAM, only the informative F2 progeny (P and N progeny showing recombination between markers M and B) are genotyped; (2) extreme genotyping (EG), thousands of P and N progeny are genotyped; and (3) limited genotyping (LG), a limited sample of the P and N progeny is genotyped. As shown in (d), Δ(SNP index) is the signal used for mapping. The recombination rate between M and B is approximately 2.5% in the current example. Thus, genotyping 1,000 P and 1,000 N progeny will likely only include 25 informative P and 25 informative N progeny having recombination between the flanking markers, severely limiting both the signal-to-noise ratio and the resolution of the mapping result. The position of the “peak” in LG could also be misleading due to limited sampling. d) MAM identifies the location of the P10 transgene insertion. The tricube‐smoothed Δ(SNP index) is shown in 1-Mb sliding windows. The Δ(SNP index) value is calculated by comparing all informative P10 positive recombinants (MPR and FPB) with all informative P10 negative recombinants (FNB and MNR). The corresponding 2-sided confidence intervals are shown as red (90%) or blue (95%) lines. X-axis is the genomic position on the homomorphic sex chromosome 1. The confidence intervals were estimated using 10,000 replicate simulations for all SNP positions with the given read depths. Positions from 223,288,153 to 226,114,389 exceed 95% confidence and the left and right inflection points of this peak are 223,412,798–225,833,455, respectively.