(Mb, AGPV3) / Confidence interval
(cM) / LOD / Additive
effect / SRA / R2(%)
2013 / 1 / 1.02 / SNP50691-SNP45103 / 12.0-13.6 / 4.6-11.4 / 2.5 / 3.5 / C7-2 / 3.9
3 / 3.06-3.07 / SNP16586-SNP17179 / 176.8-209.9 / 98.8-140.2 / 6.5 / -6.0 / H127R / 11.1
4 / 4.07-4.08 / SNP46353-SNP21108 / 177.2-188.2 / 96.8-120.4 / 3.6 / -3.8 / H127R / 4.3
7 / 7.04 / SNP31808-SNP31885 / 157.9-162.2 / 103.8-116.7 / 3.2 / -3.9 / H127R / 4.4
8 / 8.06 / SNP35175-SNP35311 / 158.9-165.1 / 113.1-128.4 / 4.2 / -4.5 / H127R / 6.6
9 / 9.03-9.04 / SNP37204-SNP37731 / 98.0-126.5 / 18.0-29.7 / 5.0 / -5.1 / H127R / 8.2
2014-A / 2 / 2.03 / SNP54161-SNP9291 / 12.0-14.3 / 48.4-57.3 / 3.3 / 4.0 / C7-2 / 5.4
3 / 3.06-3.07 / SNP16586-SNP17179 / 176.8-209.9 / 98.8-140.2 / 5.9 / -5.7 / H127R / 11.1
5 / 5.03-5.04 / SNP53694-SNP24393 / 60.0-126.1 / 89.1-96.4 / 2.8 / -3.8 / H127R / 4.2
7 / 7.04 / SNP31808-SNP31885 / 157.9-162.2 / 103.8-116.7 / 3.1 / -3.9 / H127R / 4.8
2014-B / 2 / 2.09 / SNP13120-SNP49082 / 224.4-233.3 / 178.9-202.9 / 3.9 / -4.9 / H127R / 6.4
3 / 3.06-3.07 / SNP16586-SNP17179 / 176.8-209.9 / 98.8-140.2 / 7.8 / -7.6 / H127R / 15.3
3 / 3.09 / SNP53905-SNP55833 / 222.6-224.7 / 172.5-177.4 / 2.6 / -4.0 / H127R / 4.2
5 / 5.03-5.04 / SNP53694-SNP24393 / 60.0-126.1 / 89.1-97.6 / 3.4 / -4.5 / H127R / 5.2
8 / 8.04-8.05 / SNP33467-SNP34536 / 75.8-127.6 / 69.0-85.0 / 4.2 / -4.0 / H127R / 4.4
BLUP / 3 / 3.06-3.07 / SNP16586-SNP17179 / 176.8-209.9 / 98.8-140.2 / 7.9 / -5.5 / H127R / 11.5
3 / 3.09 / SNP53826-SNP17444 / 217.9-225.6 / 161-6-179.6 / 4.4 / -4.2 / H127R / 6.6
5 / 5.03-5.04 / SNP53694-SNP24908 / 60.0-126.1 / 89.1-97.6 / 5.1 / -4.4 / H127R / 7.2
7 / 7.04 / SNP31808-SNP31891 / 157.9-162.5 / 103.8-117.1 / 4.2 / -3.8 / H127R / 5.7
8 / 8.06 / SNP34910-SNP35175 / 146.4-158.9 / 95.3-113.1 / 5.6 / -4.4 / H127R / 8.0
10 / 10.03-10.04 / SNP39868-SNP40385 / 82.2-107.8 / 28.0-35.4 / 2.9 / 3.0 / C7-2 / 3.9
Supplementary Table S1Parameters associated with theQTL identified with the transformed datasetsfor stalk rot resistance
LOD, logarithm of the odds of linkage; SRA, source of resistance allele;R2 (%), percentage of phenotypic variance explained by the QTL
Supplementary Table S2 Molecular markers developed in the qRfg3 region on chromosome 3
Name / Location (Mb)aAGPV3 / Forward primer / Reverse primer / Tm(℃) / Type
SSR177-3 / 176.5 / TTGACGTTGCTTTCTCTGCC / GGACATTTATCCGGCGCAAA / 60 / SSR
SSR180-2 / 180.3 / ATCCGGCAATCCCATCCC / TGATGGGTTCTTGGGTTGGA / 60 / SSR
STS182-16 / 182.1 / GTGTAGCATGCGTGGCTTC / TCGAATGAAATGTCTTGTCGTTT / 60 / STS
STS182-70 / 182.8 / GGAGCATGGCGTGTTTAGAG / CGGGTGAGCTTAGCGGAATA / 60 / STS
STS7-5 / 183.2 / CGACGTGACGGCTGATTATTA / CGACGTGACGGCTGATTATTA / 60 / STS
STS183-6 / 183.6 / AACAACGATGGCCTTGCTTT / TGACACATATGGGAGTGAGCA / 59 / STS
SSR185-3 / 185.2 / ACCAGATGAGAGCGTAGAGG / GCAACATTGGTCCCATGTGT / 60 / SSR
SSR188-8 / 188.8 / CACCAACGTCAGACCAAGAG / TGGGTAGTGGCAAGAGTCG / 60 / SSR
IDP8572 / 193.1 / CTTCTGTCCGTGAAGGATGG / CTCAGGAGGAGGAAATGTGG / 60 / IDP
SSR195-1 / 195.2 / TGGGAAGTCTGGCCTCATTT / TCTCACCACACAATATACGCTC / 60 / SSR
SSR202-7 / 202.3 / GGTACAGTATGGCGGATGGA / CCAGATGTGACCACTAGCAC / 60 / SSR
SSR212-7 / 212.8 / TTTACAGTTGCGGCTTCCTG / ATTCTTGTCGATCGGGCAAC / 60 / SSR
Ks6 / 182.0 / GAAGGTGACCAAGTTCATGCTACAAGTGTTTTAAGTGGAACAGT b
GAAGGTCGGAGTCAACGCATTACAAGTGTTTTAAGTGGAACAGC c / GGAGACCAGGAAGATCTTGAAT / KASP
Ks85 / 182.9 / GAAGGTGACCAAGTTCATGCTCGTAACTCCACCTTTCCTTTTGAA b / GCATGCATGAACGGACAGTTA / KASP
Ks985-3 / 183.0 / GAAGGTCGGAGTCAACGCATTCGTAACTCCACCTTTCCTTTTGAC c
GAAGGTGACCAAGTTCATGCTATTCTAAGTATTTATGCAACTAGATCAAA b
GAAGGTCGGAGTCAACGCATTATTCTAAGTATTTATGCAACTAGATCAAG c / GCTGTGTAAGGGCAAACAA / KASP
SNP193 / 181.9 / CATGTATGTGCTTGAATAGAGAGAAAAGAAC / CGTGGCTCTACTAAGGAGATTGAG / Taqman
AAGAAAGACGTTGAACTC d , TTAAGAAAGACATTGAACTC e
SNP194 / 183.5 / TTCAGCTGCGTCAACTTTGC / CAGCCCCAGGGTGAACAG / Taqman
CAAGCTGCATGATGGT d , AAGCTGCACGATGGT e
a. Physical location according to B73 reference genome sequence
b. Forward primer specific binding to H127R.
c. Forward primer specific binding to C7-2.
d. Reporter 1 sequence specific to detect H127R.
e. Reporter 2 sequence specific to detect C7-2
Supplementary Fig.S2 Schematic diagram of genetic linkage map and positions of resistance QTL within the RIL population. 189 SNP markers which were evenly distributed across 10 chromosomes were listed on the right of the chromosomes.And genetic distances between adjacent markers were listed on the left. The QTLs identified from three field trials and BLUP are represented as colored rectangles: red for the 2013, purple for the 2014-A, and green for the 2014-B trials, and brown for BLUP. The previous mappedQTL on chr. 3 (Pè 1993) was also marked on the genetic map.
Supplementary Fig. S3Detection of QTLs conferring resistance to Gibberellastalk rot. LOD profiles and additive genetic effects of (a) 13 QTLs and (b) the major QTL qRfg3.qRfg3was consistently detected in each field trail and BLUP. QTL analysis was conducted basedon the raw dataof the 199 RILs in three field trailsas well as the BLUP values.
Supplementary Fig.S4Detection of QTLs conferring resistance to Gibberellastalk rot. LOD profiles and additive genetic effects of (a) 13 QTLs and (b) the major QTL qRfg3.qRfg3wasconsistently detected in each field trail and BLUP. QTL analysis was conducted based on the transformed dataof the 199 RILs in three field trailsas well as the BLUP values.
Supplementary Fig. S5The genetic effect of QTL qRfg3 on maize resistance to Gibberella stalk rot in the field. The mean DSI± SDwas marked forthe homozygous H127R/H127R (blue column), heterozygous H127R/C7-2(red column), and homozygous C7-2/C7-2 (green column). The markers STS 182-70and Ks85 were used to genotype the BC1F4and BC1F6 populations, respectively. *P < 0.05; **P < 0.01; NS, not significant