Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains
Abstract
:1. Introduction
2. Materials and Methods
2.1. Tetraploid Wheat Mapping Populations
2.2. Growing Conditions and Experimental Design
2.3. QTL Analysis
2.4. Genome-Based Meta- Quantitative Trait Loci Analysis
2.5. Identification of Wheat Orthologs to Yield-Related Genes in Rice
2.6. GRF4-A Single Nucleotide Polymorphism Marker Development
2.7. Development and Evaluation of Introgression Line IL-21.1
2.8. Allelic Variation Studies
3. Results
3.1. Phenotypic Characterization of Grain Parameters in Parental Lines
3.2. QTL Analysis
3.3. Meta-QTL Analysis
3.4. Validation of mQTL-GW-6A Using Sv × Zv Introgression Lines
3.5. Wheat Orthologs to Yield-Related Genes in Rice
3.6. GRF4-A Polymorphisms
3.7. Allelic Diversity Study of GRF4-A
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Trait | Environment | Sv | Zv |
---|---|---|---|
Mean spike weight (g) | 2014R | 3.9 ± 0.1 | 2.5 ± 0.1 |
2015A | 4.0 ± 0.1 | 1.6 ± 0.8 | |
TKW (g) | 2014R | 61.9 ± 0.2 | 45.8 ± 0.1 |
2015A | 55.7 ± 0.1 | 29.1 ± 0.1 | |
Grain area (mm2) | 2014R | 21.6 ± 0.2 | 23.3 ± 0.3 |
2015A | 23.0 ± 0.3 | 18.6 ± 0.4 | |
Grain width (mm) | 2014R | 3.2 ± 0.03 | 2.8 ± 0.0 |
2015A | 3.7 ± 0.03 | 2.5 ± 0.0 | |
Grain length (mm) | 2014R | 8.1 ± 0.08 | 10.2 ± 0.1 |
2015A | 8.5 ± 0.05 | 10.1 ± 0.1 |
Rice Gene | Rice Gene Function | Source | Wheat Chr. | Wheat Alignment Start | Wheat Alignment End | Wheat Gene Function | WEW Gene ID |
---|---|---|---|---|---|---|---|
D11/DWARF11 | Cytochrome P450 (CYP724B1) enzyme | Reviewed by [14] | 2A | 561795447 | 561798557 | Cytochrome P450 superfamily protein | TRIDC2AG048380 |
2B | 496938005 | 496941148 | Cytochrome P450 superfamily protein | TRIDC2BG050840 | |||
D2 | Cytochrome P450 (CYP90D) enzyme | Reviewed by [14] | 2A | 4843464 | 5209969 | Cytochrome P450 superfamily protein | TRIDC2AG001470 |
2B | 5686865 | 5987817 | Cytochrome P450 superfamily protein | TRIDC2BG001370 | |||
D61 | BR insensitive (BRI)-like leucine-rich repeat (LRR) receptor kinase | Reviewed by [14] | 3A | 465976238 | 465979780 | Leucine-rich receptor-like protein kinase family protein | TRIDC3AG036670 |
3B | 453931439 | 453935096 | receptor-like protein kinase 2 | TRIDC3BG041310 | |||
GIF1 | Cell wall invertase | Reviewed by [14] | 2A | 503854205 | 503855081 | Beta-fructofuranosidase, insoluble isoenzyme 2 (Cell wall invertase 2) | TRIDC2AG042730 |
2B | 447195335 | 447196211 | Beta-fructofuranosidase, insoluble isoenzyme 2 (Cell wall invertase 2) | TRIDC2BG045820 | |||
GRF4/GS2 | Growth-Regulating Factor 4 (OsGRF4) | [18,29] | 2A | 680343644 | 680346735 | Growth-regulating factor 3 | TRIDC2AG062550 |
2B | 649416512 | 649417723 | Growth-regulating factor 3 | TRIDC2BG066890 | |||
6A | 497985063 | 497985958 | Growth-regulating factor 4 | TRIDC6AG041360 | |||
6B | 517412993 | 517416246 | Growth-regulating factor 4 | TRIDC6BG048340 | |||
GS3 | Membrane protein with multiple domains | Reviewed by [14] | 4A | 714924235 | 714925670 | Grain length protein | TRIDC4AG069340 |
7A | 5283743 | 5283958 | Grain length protein | TRIDC7AG001510 | |||
GS5 | Serine carboxypeptidase | Reviewed by [14] | 3A | 182355936 | 182359086 | serine carboxypeptidase-like 33 | TRIDC3AG023140 |
3B | 212372375 | 212373474 | Carboxypeptidase Y homolog A | TRIDC3BG026960 | |||
GW2 | RING-type E3 ubiquitin ligase | Reviewed by [14] | 6A | 230789449 | 230809149 | Protein SIP5 (*TaGW2) | TRIDC6AG027660 |
6B | 294434000 | 294448424 | Protein SIP5 | TRIDC6BG033820 | |||
GW5 | Arginine-rich protein of 144 amino acids | Reviewed by [14] | 1A | 142379896 | 142381359 | IQ-domain 26 | TRIDC1AG017640 |
1B | 185320338 | 185321816 | IQ-domain 26 | TRIDC1BG021520 | |||
3A | 69160021 | 69161092 | IQ-domain 26 | TRIDC3AG013280 | |||
3B | 111226601 | 111227636 | IQ-domain 26 | TRIDC3BG017740 | |||
GW8/SPL16 | SQUAMOSA promoter-binding protein-like 16 | Reviewed by [14] | 7A | 251030195 | 251034936 | undescribed protein | TRIDC7AG033770 |
7B | 230000953 | 230005263 | Squamosa promoter-binding-like protein 16 | TRIDC7BG025060 | |||
qGL3 | Ser/Thr phosphatase of the protein phosphatase kelch-like (PPKL) family | Reviewed by [15] | 5A | 683802818 | 683803388 | Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein | TRIDC5AG075900 |
SRS3 | Kinesin 13 protein | Reviewed by [14] | 1A | 131830406 | 131835083 | Kinesin-related protein 6 | TRIDC1AG016970 |
1B | 142745967 | 142751957 | Kinesin-related protein 6 | TRIDC1BG017960 | |||
3A | 274848912 | 274857469 | Kinesin-related protein 6 | TRIDC3AG027550 | |||
3B | 295258442 | 295261011 | Kinesin-related protein 6 | TRIDC3BG032430 | |||
DEP1 | G protein γ subunit | [16] | 5A | 422466437 | 422469555 | Guanine nucleotide-binding protein subunit gamma 3 | TRIDC5AG033880 |
5B | 391766206 | 391769237 | undescribed protein | TRIDC5BG035790 |
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Avni, R.; Oren, L.; Shabtay, G.; Assili, S.; Pozniak, C.; Hale, I.; Ben-David, R.; Peleg, Z.; Distelfeld, A. Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains. Genes 2018, 9, 636. https://doi.org/10.3390/genes9120636
Avni R, Oren L, Shabtay G, Assili S, Pozniak C, Hale I, Ben-David R, Peleg Z, Distelfeld A. Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains. Genes. 2018; 9(12):636. https://doi.org/10.3390/genes9120636
Chicago/Turabian StyleAvni, Raz, Leah Oren, Gai Shabtay, Siwar Assili, Curtis Pozniak, Iago Hale, Roi Ben-David, Zvi Peleg, and Assaf Distelfeld. 2018. "Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains" Genes 9, no. 12: 636. https://doi.org/10.3390/genes9120636
APA StyleAvni, R., Oren, L., Shabtay, G., Assili, S., Pozniak, C., Hale, I., Ben-David, R., Peleg, Z., & Distelfeld, A. (2018). Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains. Genes, 9(12), 636. https://doi.org/10.3390/genes9120636