B the Number and Types of Markers for Background Selection

Supplementary Table 1 Summary of the development of near-isogenic lines with marker-assisted selection

Recurrent parent / Generation / Plant number / Marker a / Year / Selection pressure (%) / Recurrent parent recovered (%) / Marker number
/Location / /Marker type b
Chang7-2 / umc1656 / umc1595 / umc1918 / Q8 / umc1979 / phi031 / nc010
BC1F1 / 1037 / H / H / H / H / H / H / H / 2007/Beijing / 0.2
BC2F1 / 253 / H / H / H / H / H / H / H / 2007/Hainan / 1
BC3F1 / 320 / H / H / H / H / H / H / H / 2008/Beijing / 1 / 93 / 40/SSR
HO53-1 / HO76-13 / DGAT1-2-3' / DGAT1-2-F / DGAT1-2-5' / HO47-9 / HO26-8
BC4F1 / 154 / H / H / H / H / H / H / H / 2008/Hainan / 7 / 96 / 40/SSR
BC5F1 / 09BJ 40-8 / A / A / H / H / H / H / H / 2009/Beijing / 1 / 93 / 128/SSR
BC6F1 / 09HN 27-1 / A / A / H / H / H / A / A / 2009/Hainan / 3 / 98 / 128/SSR
BC6F2 / N / A / A / B / B / B / A / A / 2010/Beijing / 99.5 / 53,757/SNP
Zheng58 / umc1656 / umc1595 / umc1918 / Q8 / umc1979 / phi031 / nc010
BC1F1 / 482 / H / H / H / H / H / H / H / 2007/Beijing / 1
BC2F1 / 158 / H / H / H / H / H / H / H / 2007/Hainan / 3
BC3F1 / 220 / H / H / H / H / H / H / H / 2008/Beijing / 1 / 87 / 40/SSR
HO53-1 / HO76-13 / DGAT1-2-3' / DGAT1-2 / DGAT1-2-5' / HO47-9 / HO26-8
BC4F1 / 165 / H / H / H / H / H / H / H / 2008/Hainan / 6 / 95 / 40/SSR
BC5F1 / 09BJ 106-8 / H / H / H / H / H / H / A / 2009/Beijing / 1 / 91 / 128/SSR
09BJ 94-2 / A / A / H / H / H / H / H
BC6F1 / 09HN 88-1 / A / A / H / H / H / A / A / 2009/Hainan / 4 / 97 / 128/SSR
BC6F2 / 7 / A / A / B / B / B / A / A / 2010/Beijing / 98.8 / 53,757/SNP

a The markers used for forward selection and the corresponding genotypes of each locus in the target genomic region in each generation. A, genotype of the recurrent line; B, genotype of the donor line; H, heterozygous genotype.

b The number and types of markers for background selection.

Supplementary Table 2 Primers for the markers of the target genomic region

Marker / Primer sequence / Position (Mb) a / Position (cM) b / Note
umc1656 / 5′-AGTTTTGACCGCGCAAAAGTTA-3′ / 5′-GTACGAGCAGGCCATTAACCC-3′ / 89.1 / 43.3 / -
umc1595 / 5′-GCTGCTGGTCTACAACCTCTTGTT-3′ / 5′-CGCTTGAAATGGAAAGGTAGAAAG-3′ / 95.0 / 51.4 / -
Q8 / 5′-AAGCTCTTGAACCGCATTAAGGAT-3′ / 5′-GCATTTCCTGGTGGTGAAGTTATC-3′ / 102.4 / 57.0 / -
umc1918 / 5′-CACAAGAACATTATGACGACCGAG-3′ / 5′-AAGCAGGAGACATCGTTTAAGTCG-3′ / 104.6 / 55.0 / -
HO53-1 / 5′-GATTACCCAATAGCTGAATAAGCC-3′ / 5′-TATGGTCAACAGTATTAGAGGAGGG-3′ / 104.6 / - / -
HO76-13 / 5′-TCATCTTATCGCTCTTTGGCATC-3′ / 5′-CTTCTTGTTGTATCTGAACACTCCC-3′ / 104.7 / - / -
DGAT1-2-3 / 5′-CTTGGGATGGAGGGAGAAC-3′/ 5′-CGGGTGGATGGATATTTTG-3′ / 104.8 / - / 3′-UTR of DGAT1-2
DGAT1-2-F / 5′-TGCCACTACCTAACCATC-3′/ 5′-ACATCGGCTGTCCGACTA-3′ / 104.8 / - / the last exon of DGAT1-2
DGAT1-2-5 / 5′-TGGCGTCAGAGCTGAGGGG-3′ / 5′-CGGTAGGCTTGCGGGAGAAC-3′ / 104.8 / - / 3′-UTR DGAT1-2
HO47-9 / 5′-GGCTTTGGTTTGTTTAGGGTG-3′ / 5′-CCAACTTCAGTGTACCGAGTGC-3′ / 104.9 / - / -
HO26-8 / 5′-CGCAGCCGGACAGCA-3′ / 5′-TCACAAACAGAGCAAAGGGA-3′ / 105.2 / - / -
umc1979 / 5′-AATTTCGGGAAACAGGCCAT-3′ / 5′-GAGTCCCCGAAACTGAACACC-3′ / 106.0 / 65.9 / -
phi031 / 5′-GCAACAGGTTACATGAGCTGACGA-3′ / 5′-CCAGCGTGCTGTTCCAGTAGTT-3′ / 108.3 / 74.8 / -
nc010 / 5′-TGAGCTGACGACGAGCAG-3′ / 5′-CATTATCTGTTCGGCCCG-3′ / 108.3 / 74.8 / -

a Position in base pairs for each locus according to version 5b.60 of the B73 reference sequence (MaizeSequence, http://www.maizesequence.org);

b The genetic distance estimated in a By804/B73 RIL population.

Supplementary Table 3 List of 16 flanking markers of QTL for oil content for background selection

Chromosome / Markers / Genetic distance (cM) a
1 / umc2217 / 74.7
bnlg2086 / 87.8
ols1 / 215
phi308707 / 223.1
2 / phi96100 / 0
kt2 / 23.4
4 / dupssr28 / 104.8
bnlg2162 / 109.1
5 / umc2373 / 82.3
umc1221 / 92.8
8 / umc1130 / 65.8
umc1562 / 66.6
9 / bnlg1401 / 21
umc2213 / 31.9
10 / umc1367 / 40.2
umc2016 / 40.9

a Genetic distance estimated in a By804/B73 recombinant inbred line population.

Supplementary Table 4 List of 128 markers for background selection

Chromosome / Marker a / Genetic distance (cM) / Chromosome / Marker a / Genetic distance (cM) /
Chr1 / umc1177 / 0 / Chr6 / umc2208 / 0
bnlg1429 / 38.1 / phi075 / 10.2
umc1403 / 58.3 / umc1753 / 24.3
umc1598 / 69.5 / umc1133 / 28
bnlg1811 / 79 / umc1195 / 28.7
umc1626 / 127.8 / c6-33 / 33.9
umc1601 / 135.7 / umc1257 / 41.8
umc1122 / 153.7 / umc1595 / 49.9
bnlg400 / 158.4 / umc1979 / 64.4
umc2047 / 207.7 / nc009 / 73.8
umc1553 / 233 / umc1857 / 86.9
umc1605 / 251.5 / umc2006 / 104
umc2100 / 252.2 / phi129 / 106.1
umc1725 / 258.1 / umc1614 / 106.9
phi064 / 269.6 / nc013 / 125.4
Chr2 / phi96100 / 0 / umc2162 / 141.4
umc1265 / 16.2 / phi299852 / 155.1
umc1422 / 70.2 / Chr7 / umc1241 / 0
umc1776 / 86.8 / umc1695 / 5.7
umc2032 / 86.8 / mmc0171 / 14
umc1003 / 95.6 / phi034 / 44.9
phi092 / 98.4 / umc1433 / 46.4
umc1065 / 101.3 / phi091 / 64.5
nc003 / 105.9 / umc1112 / 77.6
umc2372 / 107.9 / umc2332 / 100.7
c9-3 / 112.3 / phi328175 / 101.5
umc0271 / 135.9 / dupssr13 / 103.4
umc1551 / 162.6 / umc1125 / 115.6
bnlg1520 / 166.9 / umc2197 / 127.7
Chr3 / umc2105 / 0 / phi082 / 133.1
umc2101 / 1 / Chr8 / umc1139 / 0
umc2256 / 7.2 / umc2042 / 1.8
bnlg1144 / 28 / umc1304 / 31
umc1012 / 49.6 / phi119 / 37.2
bnlg1638 / 86.5 / umc1360 / 54.2
umc1655 / 93.4 / bnlg1863 / 57.9
mmc0132 / 98.1 / phi121 / 59.4
phi053 / 103.1 / bnlg2046 / 61.7
bnlg197 / 141.5 / umc1130 / 64.4
bnlg1605 / 146.1 / umc1141 / 78.6
umc1399 / 146.6 / umc1673 / 115.8
phi046 / 172.3 / umc1663 / 123.8
Chr4 / umc1017 / 0 / umc1069 / 125.3
phi026 / 58.1 / bnlg1131 / 129.7
bnlg1217 / 61.1 / Chr9 / phi028 / 1.5
umc1299 / 74.3 / bnlg1401 / 15.9
bnlg2291 / 86.6 / umc1037 / 21.5
bnlg1189 / 95 / umc2213 / 26.8
dupssr28 / 104.8 / umc1688 / 29.1
bnlg2162 / 109.1 / umc1654 / 36.4
umc2286 / 117.9 / umc1471 / 49
bnlg1023 / 124.9 / umc1794 / 55
umc1649 / 159.2 / bnlg1525 / 81.5
Chr5 / umc1491 / 0 / bnlg1904 / 118.7
umc1097 / 6.4 / Chr10 / phi118 / 0
phi024 / 25.6 / umc1367 / 40.2
umc2036 / 40 / bnlg1655 / 43
c6-23 / 68.7 / phi062 / 46.7
umc1692 / 74.7 / MZETC034 / 48.7
umc2373 / 82.4 / umc1506 / 58.7
umc1221 / 93 / bnlg1082 / 67.8
phi085 / 148.6 / umc1933 / 76.6
bnlg2305 / 157.4 / umc1196 / 83.7
umc2143 / 179.3 / umc1645 / 98.9

a Markers in bold were used for background selection of BC3 to BC4 generations.

Supplementary Table 5 List of genes in the target genomic region

Gene ID / Start position / End position / Functional annotation / References
GRMZM2G449817 / 104671217 / 104674448 / LRR receptor-like kinase / Li J, Wen J, Lease K A, et al. Cell, 2002, 110(2): 213–222.
GRMZM2G151015 / 104676733 / 104709112 / Glycosyl transferase / Gantt R W, Peltier-Pain P, Singh S, et al. Proc Natl Acad Sci USA, 2013, 110(19): 7648–7653.
GRMZM2G109009 / 104715306 / 104721588 / Polynucleotide adenylyltransferase / Forbes K P, Addepalli B, Hunt A G. J Biol Chem, 2006, 281(1): 176–186.
GRMZM2G103526 / 104755709 / 104760627 / Acid phosphatase 1 / Jaquinod M, Villiers F, Kieffer-Jaquinod S, et al. Mol Cell Proteomics, 2007, 6(3): 394–412.
GRMZM5G800610 / 104828445 / 104828661 / Unknown
GRMZM2G169114 / 104848940 / 104858629 / K(+) efflux antiporter 4 / Mäser P, Thomine S, Schroeder J I, et al. Plant Physi, 2001, 126(4): 1646–1667.
GRMZM2G169089 / 104859135 / 104866019 / Diacylglycerol acyltransferase / Zheng P, Allen W B, Roesler K, et al. Nat Genet, 2008, 40(3): 367–372.
GRMZM2G367631 / 104947474 / 104950989 / Plant transposase / Feschotte C, Jiang N, Wessler S R. Nat Genet Rev 2002, 3(5): 329–341.
GRMZM2G331283 / 104963322 / 104965389 / Transmembrane amino acid transporter protein / Lee Y H, Foster J, Chen J, et al. The Plant Journal, 2007, 50(2): 305–319.
GRMZM2G029685 / 104965877 / 104967497 / 40S ribosomal protein S24 / Carroll A J, Heazlewood J L, Ito J, et al. Mol Cell Proteomics, 2008, 7(2): 347–369.

Supplementary Table 6 Comparisons of the measured traits between hybrid Zhengdan958 and the improved hybrid Zhengdan958-qHO6

Traits / Mean ± SD / Absolute difference / Relative difference (%) / P-value
Zhengdan958 / Zhengdan958-qHO6
Kernel oil content (%) a / 3.76 ± 0.2 / 4.47 ± 0.3 / 0.71 / 18.89 / 3.9E-30
Grain weight per ear (g) a / 210.2 ± 4.7 / 212.8 ± 4.5 / 2.5 / 1.19 / 0.34
Ear length (cm) a / 16.9 ± 1.6 / 17.2 ± 1.7 / +0.3 / 1.78 / 0.30
Ear row number a / 15.3 ± 0.5 / 15.3 ± 0.5 / 0.0 / 0.00 / 0.82
Kernel number per row a / 36.6 ± 3.6 / 36.1 ± 3.8 / −0.5 / 1.37 / 0.33
Embryo oil content (%) b / 42.9 ± 2.8 / 48.6 ± 2.0 / 0.58 / 13.50 / 3.14E-12
Embryo weight (mg) b / 62.47 ± 8.4 / 65.82 ± 11.3 / 3.36 / 5.38 / 0.03
Endosperm weight (g) b / 2.88 ± 0.5 / 2.98 ± 0.3 / 0.1 / 3.47 / 0.24
Endosperm/embryo weight b / 46.45 ± 8.9 / 46.17 ± 6.0 / −0.28 / 0.60 / 0.85
Kernel width (mm) b / 9.94 ± 0.5 / 10.02 ± 0.5 / 0.08 / 0.80 / 0.09
Kernel length (mm) b / 12.74 ± 0.2 / 12.76 ± 0.2 / 0.02 / 0.16 / 0.97
Kernel thickness (mm) b / 5.43 ± 0.3 / 5.48 ± 0.3 / 0.05 / 0.92 / 0.1
Embryo length (mm) b / 9.95 ± 0.2 / 9.89 ± 0.2 / −0.06 / 0.60 / 0.83
Embryo width (mm) b / 4.31 ± 0.1 / 4.38 ± 0.2 / 0.07 / 1.62 / 0.42
Embryo thickness (mm) b / 3.27 ± 0.2 / 3.28 ± 0.3 / 0.01 / 0.31 / 0.88

a The traits were investigated in five locations with two repetitions in 2011 and 2012.

b The traits were investigated in three locations with two repetitions in 2011.