Table 2  Chromosomal locations, candidate genes and other parameters of the six SNPs identified as being significantly associated with HTR in this study
ChromosomeSNP physical position (bp)HTRCandidate gene containing SNP (AGP v2 position in bp)LES
P-valueq-ValueAlleleaNbAllele effectc(R2)dP-valueAllele effectsR2
5183,737,260e3.8 × 10−50.267G142−0.1017.7RING-H2 finger/U-box domain-containing protein: 183,736,532–183,737,7768.6 × 10−3+0.6263.1e
A890.00.0
7148,173,418e3.5 × 10−50.267G198+0.1627.8NEP-interacting protein 2/RING-H2 finger domain: 148,172,765–148,175,8641.4 × 10−4−1.3376.6
A310.00.0
9121,167,503e2.9 × 10−50.267A161+0.1308.6EF1-α protein family: 121,171,302–121,173,7799.4 × 10−4−0.9165.4e
G520.00.0
1021,693,685e3.3 × 10−70.014A83+0.12812.0DNA polymerase α/ε-subunit B: 21,678,999–21,694,2478.1 × 10−6−1.0939.1e
G1470.00.0
1021,722,883f4.1 × 10−6C65+0.10910.1HSP70: 21,722,658–21,727,7708.2 × 10−7−1.20511.9e
T1560.00.0
1021,823,409e8.7 × 10−50.182A96+0.1089.8UEV/ELC/Vps23p/TSG101: 21,821,274–21,820,2222.2 × 10−5−1.0329.7e
C1190.00.0
  • a Alleles are from homozygote genotypes.

  • b N, total number of lines with the specific SNP genotype.

  • c Positive allelic effects for HTR and LES imply a suppressive and enhancing effect on the HR phenotype, respectively.

  • d R2, proportion of phenotypic variance explained by SNP.

  • e Based on SNPs from Illumina chip.

  • f Based on SNPs obtained by GBS.