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. 2021 May 7;10(3):e292. doi: 10.1002/fes3.292

TABLE 1.

Summary of trehalose phosphate synthase (TPS) and trehalose phosphate phosphatase (TPP) genes significantly associated with yield‐related traits from the gene‐based analysis in the wheat HiBAP panel

Gene family Gene class Gene IDa No. of variantsb Ω c Affected traitd Proportion of heritabilitye
Elite Exotic All
Trehalose phosphate synthase TPS1 TraesCS1A02G064800a 136 0(0−0.3) PH 0.48 ± 0.19 0.00 ± 0.07 0.26 ± 0.16
TPS1 TraesCS1B02G083100a 89 1.16(0.2−3) PH* 0.70 ± 0.13* 0.00 ± 0.05 0.62 ± 0.14*
PED* – – –
TPS1 TraesCS1D02G065600a 67 1.91(0.3−5) PH 0.56 ± 0.16* 0.00 ± 0.12 0.49 ± 0.14*
PED 0.26 ± 0.19 0.00 ± 0.03 0.10 ± 0.10
BM 0.14 ± 0.14 0.01 ± 0.06 0.12 ± 0.10
TPS1 TraesCS1B02G351600 10 0.26(0−1) RSGP 0.01 ± 0.04 0.24 ± 0.23 0.13 ± 0.13
TPS6 TraesCS4A02G062900b 8 0 GFR 0.05 ± 0.06 0.00 ± 0.09 0.02 ± 0.03
TPS6 TraesCS4B02G239900b 5 – PH 0.00 ± 0.09 – 0.58 ± 0.34
TPS6 TraesCS5A02G203500 14 0.50(0.2−2) Awns 0.91 ± 0.07 – 0.86 ± 0.11
TPS7 TraesCS1A02G338200 26 0.18(0−0.8)** PGF* 0.85 ± 0.11* 0.01 ± 0.05 0.66 ± 0.21*
SM2 0.35 ± 0.25 – 0.34 ± 0.23
TPS7 TraesCS3A02G289300 19 0.70(0.1−2) SpS 0.00 ± 0.02 0.00 ± 0.09 0.00 ± 0.02
TPS7 TraesCS5A02G116500c 2 0(0−1.4) SpS 0.05 ± 0.07 – 0.05 ± 0.06
RSGP 0.03 ± 0.05 – 0.04 ± 0.05
TPS7 TraesCS5B02G117800c 4 – InfSpS* 0.00 ± 0.03 0.07 ± 0.12 0.00 ± 0.03
Trehalose phosphate phosphatase – TraesCS1A02G210400 4 1.20(0.2−3) PH* 0.02 ± 0.04 0.00 ± 0.09 0.02 ± 0.04
PED* 0.09 ± 0.12 0.00 ± 0.19 0.04 ± 0.06
– TraesCS2A02G161100 14 0.50(0.2−2) PH 0.00 ± 0.03 – 0.00 ± 0.02
PED 0.00 ± 0.02 – 0.00 ± 0.01
– TraesCS3A02G085700a 19 0(0−1.2) InfSpS* 0.00 ± 0.04 0.00 ± 0.06 0.00 ± 0.06
– TraesCS3D02G085800a 65 – GM2* – 0.58 ± 0.22* 0.15 ± 0.13
– TraesCS5D02G200800 2 4(0.2−17) InfSpS 0.04 ± 0.06 0.13 ± 0.15 0.07 ± 0.08
– TraesCS7B02G085800 5 – SpS* 0.00 ± 0.02 0.05 ± 0.12 0.01 ± 0.03
a

Wheat gene ID at EnsemblPlants (IWGSC RefSeq v1.0 annotation). Same letter indicates homoelogues genes.

b

Number of variants inside the gene after applying for quality control using 1% MAF.

c

Ratio (ω = d N/d S) of the number of non‐synonymous mutations (d N) to the number of synonymous mutations (d S). Error depict 95% confidence interval (CI). **Genes detected at α < 0.1 (qglobal, Benjamini–Hochberg adjustment). Values not shown represent that the model did not converge.

d

Traits are plant height (PH, cm), peduncle length (PED, cm), final biomass (BM, g/m2), grains per m2 (GM2), grain filling rate (GFR, yield/grain filling duration, g/m2/day), percentage of grain filling (PGF), spikes per m2 (SM2), infertile spikelets per spike (InfSpS, number), spikelets per spike (SpS, number), rapid spike growth phase percentage (RSGP) and awn length (Awns, cm). *Significant trait detected using MAF ≥ 0.01 and MAF≥0.05 by at least one gene‐based model.

e

Proportion of heritability per single gene from elite, exotic derivatives and the complete panel. Values are mean ± standard errors. Values not shown represent that the model did not converge. *Significant genes by Bonferroni correction at α = 0.05 detected using the regional heritability mapping (RHM).