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Table 2 Putative QTL associated with RCA identified using Sherpa/IRAT109 RIL population

From: Stable and Novel Quantitative Trait Loci (QTL) Confer Narrow Root Cone Angle in an Aerobic Rice (Oryza sativa L.) Production System

Experiment QTL Chr Nearest Marker Mb cM CI (cM) LOD AE Favourable Allele R2
GH qRCA1.1 1 Chr1_39524707 39.52 154.60 148.7–162.4 5.37 2.10 Sherpa 6.99
qRCA3 3 Chr3_16551946 16.55 78.23 71.6–81.0 6.10 −1.90 IRAT109 8.00
qRCA4 4 Chr4_30036160 30.03 101.43 97.0–104.0 12.45 −2.97 IRAT109 17.40
           (36.73)
IWS19 qRCA1.2 1 Chr1_19340596 19.34 84.87 67.2–89.8 5.06 −1.73 IRAT109 5.22
qRCA1.3 1 Chr1_24919134 24.92 99.88 99.0–100.5 7.94 1.81 Sherpa 8.42
qRCA1.1 1 Chr1_39416289 39.42 161.41 150.7–164.9 7.66 1.39 Sherpa 8.10
qRCA2.1 2 Chr2_27972049 27.97 122.53 119.0–133.2 4.64 1.36 Sherpa 4.76
qRCA2.2 2 Chr2_30400561 30.40 134.12 131.4–135.9 9.48 −1.92 IRAT109 10.22
qRCA4 4 Chr4_29775386 29.78 98.97 97.0–99.9 20.13 −2.47 IRAT109 24.18
qRCA11 11 Chr11_19591983 19.59 76.31 73.4–83.3 5.74 −1.16 IRAT109 5.96
           (49.72)
WW20 qRCA1.1 1 Chr1_39524707 39.52 153.61 148.7–162.4 9.35 3.68 Sherpa 10.22
qRCA3 3 Chr3_16551946 16.55 76.34 44.6–100.3 3.31 −1.86 IRAT109 4.12
qRCA4 4 Chr4_30366129 30.37 102.14 99.0–104.6 15.51 −4.29 IRAT109 21.11
           (38.31)
IWS20 qRCA1.2 1 Chr1_23120475 23.12 85.86 78.0–90.8 5.40 −2.44 IRAT109 5.42
qRCA1.3 1 Chr1_24919134 24.92 99.88 99.0–100.5 8.84 2.63 Sherpa 9.18
qRCA1.1 1 Chr1_39416289 39.42 161.41 152.6–164.9 8.90 1.97 Sherpa 9.25
qRCA2.1 2 Chr2_27972049 27.97 122.53 119.0–133.2 4.30 1.71 Sherpa 4.27
qRCA2.2 2 Chr2_30400561 30.40 134.12 131.4–135.9 8.79 −2.42 IRAT109 9.12
qRCA4 4 Chr4_29775386 29.78 98.97 97.0–99.9 20.70 −3.28 IRAT109 24.28
qRCA11 11 Chr11_20763446 20.76 82.62 73.4–84.0 5.02 −1.38 IRAT109 5.03
           (51.22)
  1. Mb - physical map position of each marker based on the Nipponbare sequence at RAP database (http://rapdb.dna.affrc.go.jp/); CI- bayesian credible confidence intervals in centiMorgan (cM); AE: additive effect of the allele from IRAT109 compared with that from the recipient line, Sherpa; R2 - percentage of the genotypic variance explained by each QTL. Numbers in parentheses indicate percentage of the variance explained by multiple QTL; GH - Glasshouse Experiment; IWS19 - intermittent water stress 2019 experiment, WW20 - well-watered 2020 experiment, and IWS20 - intermittent water stress 2020 experiment