Table 5.

The designed TaqMan® assays used in this study

Target	Flesh color	Code	Assay Name	Pd.cM	BCn	Context Sequence
qPM2	G	R1	2_382892_C-A	7.47	1	TAATAAATGTTTTAACTTTTCTAGT[C/A]TTTTTGGAAGAGGAATTGAAAGAAA
	G	F1	2_621190_A-G	9.73	1 + 2	CGTCCCTAGTTACTTCTGTTTGTTT[A/G]CCTCATTATACCACTGAAGCAACAA
	G	F2	2_1603309_A-T	19.32	1 + 2	TCGGTTCTGATAAGCAGGATGCTTC[A/T]GGAAATAAGCTTCTTCAAGATATTG
	G	R2	2_2351587_A-C	28.67	1	GGCTTGTGGAGAAGATCAACAATTC[A/C]ATTGGGCAAGACCCAAATTCTAAAT
	O	R1	2_103153_C-A	1.40	1	TCTTCTCACCCTCCATCTCATTAAC[C/A]AACTGTCAGCACCCTAAGATTCCCT
	O	F1.2	2_627533_C-T	9.78	2	GAATANTATCGTTGCATTTGATGAA[C/T]TTAAGGCTCTCCTAAGTTTAGAGCT
	O	F1.1	2_778333_T-A	10.72	1	ACGAAAATGTCACATAGCCTACAAC[T/A]CCTCCATTGACGGCATCATTCTCCC
	O	F2	2_816421_C-G	11.06	1 + 2	CCATTCTCAAATCCATCCAAAACAC[C/G]AATCCAACAAAGAACAAATAAAACC
	O	R2	2_1410652_T-C	17.03	1	CTGGTATGCTCAGTTATGCAAAGAG[T/C]GTTGCAGCTGATAACTGGTTGGCAT
qPM5	G/O	R1	5_24520366_C-T	86.51	1	CAACTTTCCATTTTAACTATTGGAA[C/T]GTGAGTTACTATTATTCCTTTCTTT
	G/O	F1.2	5_24941008_G-C	89.02	2	GCTTGTTCAATCTTGTGAGTTGGAT[G/C]AGATGATTTAGTTGAAGCGTGANTG
	G/O	F1.1	5_25264851_C-T	89.31	1	TTCTCCTAGTCACTTGTTTCTTACA[C/T]GAGATCTTTTGTTTCACTAGGAGGA
	G/O	F2	5_25862218_T-C	96.52	1 + 2	AACATGAAACACATCTCAATGATGA[T/C]GACGACGATGAATACCAGGCTGATT
	G/O	R2	5_26105586_T-A	99.27	1	AGGGACATCTTCATGGTTTGGTGGC[T/A]ACTTTAGCAAACTAAATTTTAGACA
qPM12	G	R1	12_21800139_A-G	71.69	1 + 2	CAACAAAAAATTTGTTTGATGGCCG[A/G]TAGGATTGTAACCTAATAAAAAAAC
	O	R1	12_21116734_T-G	63.61	1 + 2	GGACTATTATTCTGAACCTACCCAG[T/G]TCACAAGAGGCCCTTGTTCTTCTGA
	G/O	F1	12_22418198_A-G	78.87	1 + 2	TGAAGTAAAGTGAAAAGAAATAATC[A/G]TGTATGGCTCGCTGTTGACGTTTGT
	G/O	F2	12_23222171_G-A	84.38	1 + 2	TGATCGCCAAAGACGAGAAACTTGC[G/A]ACTTCATACCGTGATGAGAAATGGA
	G/O	R2	12_23491653_A-G	87.74	1	CCGTGGTTTGTCTATCAAGTTTTTA[A/G]AATCAACCTATGTGACAATCGCATT

The flesh colors G and O indicate the assays used for the green- or orange-fleshed recurrent parents, and G/O indicates the assay used for both recurrent parents in MABC

Codes R and F indicate the assays used for recombinant or foreground selection. The R1, R2, F1, and F2 indicate the physical position order of the TaqMan assays. The F1.1 and F1.2 indicate the F1 TaqMan assays but the different versions for their slight adjustment of the physical positions

Pd.cM indicates the predicted genetic position (cM) of the TaqMan assays through the LOESS regression models within each chromosome

BC_n filled with 1, 2, and 1 + 2 values indicate that the TaqMan assays were used during BC₁, BC_2, or both BC₁ and BC₂ generations