Fig. 1. Confirmation of SUB1 allele in the 10 PILs derived from BR11 by GnS2 marker

Table 1. Foreground markers surveyed over two parents of MABC scheme

SN / Primers / Poly morphism / Position (cM) / Position (Mb) / Allele Size / Forward / Reverse / Repeat motif
SC3/ RM8300 / P / 6.8-10.0 / 6.6 / 211-217 / GCTAGTGCAGGGTTGACACA / CTCTGGCCGTTTCATGGTAT / (ACCATTAT)3
SSR1 / M / 6.8-10.0 / 6.5 / 285 (expected) / CTACTTCAATGTCACCAACG / TAGAAGATGGAAGACCTGAT / -
SC23 / P / 4.4-6.8 / 6.1 / 235-238
SC24/ RM23901 / P / 6.8-10.0 / 6.8 / 327-355 / CAGCTATTGAGACAACGCAAACAC / CAAAAATCATCTATTTTCGCAGGC / (AT)45
  1. c
/ SC1 / X / 6.8 / 6.4
SC2 / X / 6.8 / 6.4
SC4 / X / 6.8 / 6.3
SC5 / X / 6.8 / 6.3
SC6 / X / 6.8-10.0 / 6.4
Sub1C173 / P / 4.4-6.8 / 6.2 / 166-178 / AACGCCAAGACCAACTTCC / AGGAGGCTGTCCATCAGGT
DJM1/ GnS2 / P / 4.4-6.8 / 6.3 / 253 (136+ 106) / CTTCTTGCTCAACGACAACG / TCGATGGGGTCTTGATCTCT

Legend: P = Polymophic, M = Monomophic, X = Non-amplification

Table 2. Polymorphic flanking markers of SUB1 QTL between recipient and donor parents on Chromosome 9

SN / Primers / Position (cM) / Position (Mb) / Band Size / Forward1 / Reverse1 / Repeat motif
RM296 / 0.0 / 0.0 / 116.51-121.90 / CACATGGCACCAACCTCC / GCCAAGTCATTCACTACTCTGG / (GA)10
SC32/ RM23668 / 0.0-0.5 / 0.6 / 95.18-101.71 / CAACTAGCCCTACCGTGCAT / CGTGTTAAAGCAGCGAAACA / (ACG) 10
SC34/ RM23679 / 0.5 / 0.8 / 153.19-176.89 / AGTGCATGTTGAGCTTGTGG / ACCTGGCAATGAGAACGAGT / (AGAA)10
RM3609/ SC36 / 0.8 / 1.1 / 154.15-179.62 / GTCGCAGGGACTAGTTAGTTAATGG / TGGCATCTTCTTGGTTGTTAGC / (GA)13
SC41 / 0.8 / 3.4 / 249.30-243.84
SC11/ RM23770 / 0.8 / 3.6 / 271.14-290.97 / GACCTTGTCCAGAGTGATTTTG / ATTTGAGAATAACTTTTCCTACTTCG / (AAT)20
SC12/ RM23778 / 0.8 / 3.9 / 287.56-315.94 / ACACAGCCTAAAGGTGTTCTGAGC / GAGCTTCGGCCCTATAGTCTTCTC / (ATAA)20
RM316 / 1.8 / 194.3-223.69 / CTAGTTGGGCATACGATGGC / ACGCTTATATGTTACGTCAAC / (GT)8-(TG)9 (TTTG)4 (TG)4
SC16/ RM23805 / 2.1 / 4.5 / 257.72-266.42 / CACATAGTTTCCATGCTCGTTCAC / GGTAGAATCCATGACCGTCTCATC / (TG)13
SC21/ RM23843 / 2.4-3.2 / 5.5 / 297.89-323.46 / TCACAGACATAATTGTTTGGAGAAGG / CCAAAAGCTTTCATCTTTTTGTCC / (TA)40
SC25/ RM23902 / 10.0 / 7.0 / 258.67-264.83 / CGATTTGTTGTCAGCGTGAATTAG / GCATGCATGATTGAAGATTTGAAG / (ATA)27
SC26/ RM23915 / 10.0 / 7.1 / 117.52-152.50 / TACATTGGAAGGAAATTCAGCTCC / CATGCAGATATGACCAAGAACCTG / (AC)15
RM219 / 11.7 / 226.86-236.65 / CGTCGGATGATGTAAAGCCT / CATATCGGCATTCGCCTG / (CT)17
SC27/ RM23917 / 10.0-20.7 / 7.2 / 259.10-267.68 / CTCAGCTGTCTGTTCAGCTCTCAC / CTTTGGTGCTGAGGTAGGTATTGG / (CA)12
SC30/ RM23958 / 20.7 / 7.9 / 167.37-180.85 / GAGACAGATGTGTACGGTTTGGTG / TTGACAAGGGAATTGAAGGAGAAG / (CT)15

1

Table 3.List of initial background markers of all 12 chromosomes used in the background selection

Chr 1 / Chr 2 / Chr 3 / Chr 4 / Chr 5 / Chr 6
RM495 / RM154 / RM569 / RM471 / RM153 / RM469
RM84 / RM279 / RM231 / RM17162 / RM413 / RM585
RM259 / RM555 / RM545 / RM273 / RM574 / RM402
RM581 / RM327 / RM218 / RM252 / RM164 / RM541
RM05 / RM424 / RM14963 / RM17391 / RM421 / RM275
RM237 / RM341 / RM411 / RM141
RM212 / RM263 / RM520
RM486 / RM06 / RM468
RM208 / RM570
RM85
Chr 7 / Chr 8 / Chr 9 / Chr 10 / Chr 11 / Chr 12
RM481 / RM407 / SC34 / RM244 / RM286 / RM247
RM346 / RM6208 / SC16 / RM25181 / RM26360 / RM27877
RM336 / RM72 / SC26 / RM25321 / RM167 / RM27933
RM18 / RM256 / SC30 / RM258 / RM26482 / RM463
RM172 / RM458 / RM566 / RM228 / RM229 / RM17
RM242 / RM206
RM278 / RM254

Table 4. The distribution of additional background markers over the genome

Chromosome / Marker / Position (cM) / Chromosome / Marker / Position (cM)
Chr1 / RM488 / 101.4 / RM538 / 132.7
RM543 / 145.6 / Chr6 / RM540 / 0
RM302 / 147.8 / RM217 / 26.2
RM486 / 153.5 / RM584 / 26.2
Chr2 / RM110 / 6.9 / RM314 / 33.6
RM211 / 14.4 / RM549 / 42.7
RM322 / 49.8 / Chr7 / RM298 / 0
RM71 / 49.8 / RM418 / 42.1
RM482 / 187.5 / RM455 / 65.7
Chr3 / RM60 / 0 / Chr8 / RM337 / 1.1
RM489 / 29.2 / RM152 / 9.4
RM227 / 156.3 / RM126 / 57
RM565 / 215.5 / RM547 / 58.1
Chr4 / RM185 / 50.8 / RM264 / 128.6
Chr5 / RM122 / 0 / Chr9 / RM24712 / 83.2
RM405 / 28.6 / RM6643 / 85.6
RM267 / 28.6 / Chr10 / RM222 / 11.3
RM592 / 31.4 / RM311 / 25.2
RM249 / 43 / Chr11 / RM4B / 0
RM437 / 43.4 / RM21 / 85.7
RM509 / 65.8 / Chr12 / RM260 / 61.7
RM430 / 78.7