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. 2018 May 7;16(11):1825–1835. doi: 10.1111/pbi.12918

Table 2.

SNPs significantly associated with white mould resistance and a subset of candidate genes identified by RNA‐seq from greenhouse trials

Panel Loci SNP Chr. Positiona P Allele R 2 (%) QTLb Subset of candidate genesc based on RNA‐seq
Name Annotation Log2(fold change) TPd (hpi)
Improved lines 1 ss715588043 4 44059284 1.1 × 10−5 A/G 4.0 Glyma.04G184400 F‐box only protein 1.5 12
2 ss715596204 7 10951353 6.1 × 10−5 A/G 3.6 1‐2 Glyma.07G109600 SBP domain 1.7 12
3 ss715607404 10 44648970 6.0 × 10−5 C/A 3.2 Glyma.10G214500 Unknown 1.6 12
4 ss715616839 13 15951647 1.4 × 10−5 A/G 3.8 Glyma.13G062000 NAM protein −2.0 48
5 ss715616533 13 44344336 7.1 × 10−5 A/G 4.1 Glyma.13G355600 NAD‐dependent epimerase 1.7 12
ss715616535 13 44357080 5.9 × 10−5 T/C 4.2
6 ss715625406 16 7257702 9.1 × 10−5 T/C 4.1 Glyma.16 g071700 LOB domain containing 2.5 12
ss715625408 16 7265131 8.1 × 10−6 C/T 5.2
ss715625410 16 7272893 3.3 × 10−5 T/G 4.5
ss715625414 16 7302240 9.7 × 10−5 A/G 4.0
PIs 7 ss715595608 6 8486465 5.6 × 10−5 T/C 4.7
ss715595609 6 8488833 1.1 × 10−5 T/G 4.6 Glyma.06G107800 Serine hydroxyl methyltransferase 1.8 12
8 ss715597461 7 36664586 2.2 × 10−5 C/T 5.1
ss715597466 7 36679589 3.6 × 10−5 C/T 4.9
ss715597467 7 36684209 4.1 × 10−5 A/G 4.8
ss715597472 7 36740564 4.7 × 10−6 T/C 5.0 Glyma.07G199800 MAC/Perforin domain 1.5 48
ss715597474 7 36745679 5.6 × 10−5 T/C 4.8
ss715597504 7 36936795 7.9 × 10−5 T/C 3.7
9 ss715605211 9 5948655 2.6 × 10−5 C/T 4.3 1‐3 Glyma.09G062100 LRR 2.8 12
10 ss715611206 11 8151411 6.4 × 10−5 T/G 3.8 3‐3 Glyma.11G107000 Amino acid transporters 1.6 48
11 ss715612432 12 34480040 2.8 × 10−5 G/A 4.2 Glyma.12G183400 Acyl‐CoA reductase 1.6 12
a

Position in base pairs for the peak SNP according to soya bean reference sequence (a2. v1) of Williams 82.

b

The position of significant SNP is located in one of the QTL intervals (defined as physical position of associated markers) as reported previously (http://www.soybase.org/search/index.php?qtl=white mould).

c

Candidate genes selected by RNA‐seq analysis as having the significant changes (FDR<0.05) in abundance between partially resistant and susceptible genotypes by comparisons of Log2 (fold change) of reads per kilobase per million (FPKM) around peak SNP.

d

TP stands for time point in hours (hours postinoculation).