Validation of QTLs for Resistance to Pre-Harvest Sprouting in a Panel of European Wheat Cultivars
Abstract
1. Introduction
2. Results
2.1. Phenotypic Evaluation of PHS Resistance
2.2. Genotyping
2.3. Allelic Effect of KASP Markers on Germination Index
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Field Experiments
4.2. Sampling of Spikes and Quantification of Seed Dormancy (SD)
4.3. DNA Extraction and KASP Genotyping
4.4. Statistical Analysis of Field Experiments and KASP Marker Validation
4.5. Allelic Effect of KASP Markers on GI
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
Abbreviations
PHS | pre-harvest sprouting |
GI | germination index |
SNP | single-nucleotide polymorphism |
KASP | Kompetitive Allele Specific PCR |
QTL | quantitative trait locus |
SD | seed dormancy |
SE | Southeastern Europe |
MAS | marker-assisted selection |
ABA | abscisic acid |
MAP | mitogen-activated protein |
PAV | presence/absence variation |
NCED | nine-cis-epoxycarotenoid dioxygenase |
GWAS | genome-wide association study |
ABRE | abscisic acid-responsive element |
RNAi | RNA interference |
ANOVA | analysis of variance |
SD | standard deviation |
HSD | honestly significant difference |
DNA | deoxyribonucleic acid |
BLUP | best linear unbiased prediction |
PVE | phenotypic variance explained |
AIC | Akaike’s Information Criterion |
MAGIC | multiparent advanced generation inter-cross |
CDS | coding sequence |
RCBD | randomized complete block design |
PCR | polymerase chain reaction |
SAS | statistical analysis system |
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Source of Variation | Variance | Significance | % of the Total Variance | Heritability |
---|---|---|---|---|
Genotype (G) | 0.031 | <0.001 | 46 | 0.86 |
Environment (E) | 0.015 | <0.001 | 22 | |
G × E | 0.018 | <0.001 | 27 | |
Residual | 0.003 | 5 |
Year | Location | Environment | Mean GI ± SD | GI Range |
---|---|---|---|---|
2018 | Zagreb | ZG2018 | 0.50 ± 0.25 a 1 | 0.03–0.98 |
2019 | Zagreb | ZG2019 | 0.36 ± 0.21 b | 0.02–0.97 |
2020 | Osijek | OS020 | 0.33 ± 0.24 b | 0.02–0.98 |
2020 | Zagreb | ZG2020 | 0.19 ± 0.16 c | 0.01–0.92 |
Mean | 0.35 ± 0.18 | 0.04–0.89 |
SNP Marker Locus (Chr) | Freq (%) | Allele | Change of GI Due to the Effect of Tolerant Allele (%) Proportion of Phenotypic Variance Explained (PVE) | ||||
---|---|---|---|---|---|---|---|
ZG2018 | ZG2019 | ZG2020 | OS2020 | Across Environments | |||
TaPHS1-646 (3A) | 20 | A | ns | −23 (3.5) | −35 (4.6) | −22 (2.2) | −18 (3.1) |
80 | G 1 | ||||||
TaPHS1-666 (3A) | 22 | T | ns | −20 (3.5) | −31 (5.2) | −26 (3.0) | −20 (4.0) |
78 | A | ||||||
KASP765 (3B) | 22 | A | ns | −21 (3.5) | −39 (8.6) | −38 (9.0) | −20 (4.3) |
78 | G | ||||||
BS00037019_51 (4A) | 80 | C | −19 (2.7) | ns | −38 (3.7) | −46 (7.3) | −27 (5.2) |
20 | T | ||||||
BS00072025_51 (4A) | 69 | A | ns | ns | −41 (7.0) | −37 (7.2) | −19 (3.4) |
31 | G | ||||||
IAAV615 (4A) | 80 | G | −17 (2.3) | ns | −33 (3.2) | −41 (5.8) | −22 (4.4) |
20 | A | ||||||
wsnp_Ex_rep_c66324_64493429 (4A) | 61 | C | −24 (6.5) | −25 (5.2) | −43 (10.0) | −49 (16.3) | −31 (12.7) |
39 | T | ||||||
TaMKK3-A (4A) | 42 | T | −29 (11.1) | −18 (3.0) | −48 (17.2) | −51 (25) | −33 (17.5) |
58 | G | ||||||
wsnp_Ex_c908_1754208 (7B) | 30 | C | ns | ns | −28 (3.9) | −23 (2.8) | ns |
70 | T |
Model/Marker | BS00072025_51 (4A) | IAAV615 (4A) | KASP765 (3B) | TaMKK3-A (4A) | TaPHS1-646 (3A) | wsnp_Ex_c908_1754208 (7B) | wsnp_Ex_rep_c66324_64493429 (4A) | PVE | AIC |
---|---|---|---|---|---|---|---|---|---|
Effect of tolerant allele on GI | |||||||||
Model 1 | −0.14 | 18 | −553.13 | ||||||
Model 2 | 0.04 | −0.17 | 19 | −552.72 | |||||
Model 3 | 0.05 | −0.15 | −0.04 | 20 | −552.43 | ||||
Model 4 | −0.13 | −0.03 | 19 | −552.07 | |||||
Model 5 | −0.14 | −0.02 | 19 | −551.51 | |||||
Model 6 | −0.02 | −0.14 | 19 | −551.44 | |||||
Model 7 | −0.14 | −0.01 | 19 | −551.25 | |||||
Model 8 | −0.01 | −0.14 | 18 | −551.22 | |||||
Model 9 | 0.04 | −0.16 | −0.02 | 20 | −551.20 | ||||
Model 10 | 0.05 | −0.02 | −0.16 | 20 | −551.14 |
Model | Combination of KASP Markers | Haplotype | All | ||||||
---|---|---|---|---|---|---|---|---|---|
No. of genotypes | 43 | 56 | 78 | 1 | 178 | ||||
2 | BS00072025_51 | A | G | A | G | ||||
TaMKK3-A | G | G | T | T | |||||
BLUP_GI LSMEAN | 0.26 a | 0.30 b | 0.44 c | 0.41 | |||||
No. of genotypes | 20 | 37 | 21 | 18 | 68 | 7 | 1 | 172 | |
3 | BS00072025_51 | A | G | A | G | A | A | G | |
TaMKK3-A | G | G | G | G | T | T | T | ||
wsnp_Ex_rep_c66324_64493429 | T | T | C | C | C | T | C | ||
BLUP_GI LSMEAN | 0.22 a | 0.26 ab | 0.29 b | 0.36 c | 0.44 d | 0.48 d | 0.41 | ||
No. of genotypes | 63 | 39 | 69 | 7 | 178 | ||||
4 | TaMKK3-A | G | G | T | T | ||||
wsnp_Ex_rep_c66324_64493429 | T | C | C | T | |||||
BLUP_GI LSMEAN | 0.24 a | 0.33 b | 0.44 c | 0.48 c | |||||
No. of genotypes | 78 | 25 | 42 | 28 | 173 | ||||
5 | TaMKK3-A | G | G | T | T | ||||
wsnp_Ex_c908_1754208 | T | C | T | C | |||||
BLUP_GI LSMEAN | 0.28 a | 0.29 a | 0.43 b | 0.48 c | |||||
No. of genotypes | 90 | 17 | 54 | 24 | 185 | ||||
6 | KASP765 | G | A | G | A | ||||
TaMKK3-A | G | G | T | T | |||||
BLUP_GI LSMEAN | 0.27 a | 0.31 a | 0.41 b | 0.48 c | |||||
No. of genotypes | 90 | 12 | 23 | 49 | 174 | ||||
7 | TaMKK3-A | G | G | T | T | ||||
TaPHS1-646 | G | A | A | G | |||||
BLUP_GI LSMEAN | 0.26 a | 0.37 b | 0.42 bc | 0.44 c | |||||
No. of genotypes | 36 | 64 | 79 | 179 | |||||
8 | IAAV615 | A | G | G | |||||
TaMKK3-A | G | G | T | ||||||
BLUP_GI LSMEAN | 0.27 a | 0.28 a | 0.43 b | ||||||
No. of genotypes | 34 | 7 | 47 | 8 | 54 | 23 | 1 | 174 | |
9 | BS00072025_51 | A | A | G | G | A | A | G | |
TaMKK3-A | G | G | G | G | T | T | T | ||
KASP765 | G | A | G | A | G | A | G | ||
BLUP_GI LSMEAN | 0.26 a | 0.27 a | 0.29 a | 0.31 a | 0.41 b | 0.49 c | 0.41 | ||
No. of genotypes | 30 | 11 | 11 | 41 | 42 | 28 | 1 | 164 | |
10 | BS00072025_51 | A | G | A | G | A | A | G | |
TaMKK3-A | G | G | G | G | T | T | T | ||
wsnp_Ex_c908_1754208 | T | T | C | T | T | C | T | ||
BLUP_GI LSMEAN | 0.24 a | 0.24 ab | 0.31 bc | 0.32 c | 0.43 d | 0.48 e | 0.41 |
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Rajković, B.; Lovrić, A.; Maričević, M.; Novoselović, D.; Šarčević, H. Validation of QTLs for Resistance to Pre-Harvest Sprouting in a Panel of European Wheat Cultivars. Plants 2025, 14, 1342. https://doi.org/10.3390/plants14091342
Rajković B, Lovrić A, Maričević M, Novoselović D, Šarčević H. Validation of QTLs for Resistance to Pre-Harvest Sprouting in a Panel of European Wheat Cultivars. Plants. 2025; 14(9):1342. https://doi.org/10.3390/plants14091342
Chicago/Turabian StyleRajković, Bruno, Ana Lovrić, Marko Maričević, Dario Novoselović, and Hrvoje Šarčević. 2025. "Validation of QTLs for Resistance to Pre-Harvest Sprouting in a Panel of European Wheat Cultivars" Plants 14, no. 9: 1342. https://doi.org/10.3390/plants14091342
APA StyleRajković, B., Lovrić, A., Maričević, M., Novoselović, D., & Šarčević, H. (2025). Validation of QTLs for Resistance to Pre-Harvest Sprouting in a Panel of European Wheat Cultivars. Plants, 14(9), 1342. https://doi.org/10.3390/plants14091342