Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan
Abstract
:1. Introduction
2. Results
2.1. Seedling Resistance to Pt and Pgt Races
2.2. Adult Plant Resistance to LR and SR
2.3. Identification of QTLs Associated with LR and SR Resistance Using GWAS
2.4. Comparison of QTLs with Genes for LR and SR Resistance and Resistance QTLs from Literature Survey
3. Discussion
3.1. Resistance to LR and SR in the Studied Tetraploid Wheat Collection at Seedling and Adult Plant Growth Stages
3.2. QTLs Identified for LR and SR Resistance and Comparison of Them to Genes and QTLs from the Literature
3.3. Potentially Novel LR and SR Resistance Loci for Durum Wheat
4. Materials and Methods
4.1. Germplasm and Genotyping
4.2. Assessment of Seedling Resistance and Adult Plant Resistance to Leaf and Stem Rust
4.3. Statistical and Association Mapping Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Pathogen (Races) | Mean IT * | Immune Genotypes (IT) | Susceptible Genotypes (IT) |
---|---|---|---|
Pt (TGTGT and TQTGT) | 2+ | 5-BIL42, Athena, Cannizzo, Kronos, Orfeo, Tito, Tiziana, PI 289606 (0) | PI 573182 (4) |
Pgt (QHHSF and THMTF) | 2+ | 5-BIL42, Cannizzo, Orfeo, Ethiopia (0) | MG 15516/1, Nauryz 2, Bezenchukskaya 139 (4) |
Disease | Race | CV | H2 (%) | GA | GAM (%) |
---|---|---|---|---|---|
LR | TGTGT | 23.3 | 90.1 | 5.2 | 137.7 |
TQTGT | 19.4 | 93.6 | 6.4 | 148.0 | |
SR | QHHSF | 23.2 | 93.4 | 5.7 | 173.4 |
THMTF | 21.6 | 89.7 | 5.2 | 124.5 |
Disease | Factor | df | SS | MS | F-value | p-Value | % SS |
---|---|---|---|---|---|---|---|
LR | Genotype | 192 | 5129.5 | 26.7 | 36.3 | 3.4 × 10−171 | 69.5 |
Race | 1 | 52.9 | 52.9 | 71.7 | 5.3 × 10−16 | 2.2 | |
Genotype × Race | 192 | 1804.1 | 9.4 | 12.8 | 1.6 × 10−95 | 24.5 | |
Residuals | 384 | 282.9 | 0.7 | 3.8 | |||
SR | Genotype | 192 | 5020 | 26.1 | 37.2 | 3 × 10−173 | 75.8 |
Race | 1 | 148.9 | 148.9 | 212.1 | 1.5 × 10−38 | 2.4 | |
Genotype × Race | 192 | 1171.4 | 6.1 | 8.7 | 3.6 × 10−71 | 17.7 | |
Residuals | 384 | 269.5 | 0.7 | 4.1 |
Pt_TGTGT | Pt_TQTGT | Pgt_QHHSF | Pgt_THMTF | |
---|---|---|---|---|
Pt_TGTGT | 1 | 0.41 *** | 0.10 ns | 0.30 *** |
Pt_TQTGT | 0.41 *** | 1 | 0.11 ns | 0.34 *** |
Pgt_QHHSF | 0.10 ns | 0.11 ns | 1 | 0.59 *** |
Pgt_THMTF | 0.30 *** | 0.34 *** | 0.59 *** | 1 |
Infection | Min * | Max * | Mean * | Resistant Genotypes (IT) | Susceptible Genotypes (IT) |
---|---|---|---|---|---|
LR | MR | S | MR | Pedroso, PI 157985, Zenit, Neodur, Primadur, Brindur, CLTR11390, PI 278350, PI 330554, PI 352488 (MR) | PI 134946, PI 68287, PI 286075 (S) |
SR | MR | S | MR | Pedroso, PI 157985, Zenit, Neodur, PI 223171 (MR) | PI 289606, PI 134946, PI 68287 (S) |
Pt_APR | Pt_TGTGT | Pt_TQTGT | Pgt_QHHSF | Pgt_THMTF | NFS | WKP | TKW | GY | |
---|---|---|---|---|---|---|---|---|---|
Pt_APR | 1 | −0.05 ns | −0.09 ns | 0.31 * | 0.21 * | 0 ns | −0.2 * | 0.17 * | −0.33 * |
Pgt_APR | 0.56 ** | −0.13 ns | −0.16 * | 0.18 * | 0.08 ns | −0.09 ns | −0.15 * | 0.35 * | −0.3 * |
# | QTL | SNP | Chr. | Position (cM) | p-Value | R2 (%) | Allele | Effect | Environment |
---|---|---|---|---|---|---|---|---|---|
1 | QLr.tw.ipbb_2A.1 | IWB53298 | 2A | 107.7–109.9 | 1.7 × 10−4 | 7.6 | G | 1.2 | GH (TGTGT) |
2 | QLr.tw.ipbb_2A.2 | IWB2020 | 2A | 159.1 | 7.9 × 10−4 | 6.3 | A | 1.1 | GH (TQTGT) |
3 | QLr.tw.ipbb_2B.1 | IWB63235 | 2B | 137.9–138.1 | 6.1 × 10−4 | 6.2 | A | 1.0 | GH (TQTGT) |
4 | QLr.tw.ipbb_2B.2 | IWB28191 | 2B | 166.3 | 4.0 × 10−4 | 6.4 | T | 0.4 | APR_KAES17, APR_KAES_mean |
5 | QLr.tw.ipbb_3A.1 | IWB50321 | 3A | 16.5 | 3.8 × 10−4 | 6.7 | C | 1.2 | GH (TGTGT) |
6 | QLr.tw.ipbb_3A.2 | IWB71659 | 3A | 122.3 | 8.5 × 10−5 | 8.8 | G | 0.5 | APR_KAES17, APR_KAES_mean |
7 | QLr.tw.ipbb_3B.1 | IWB74764 | 3B | 12.3 | 7.6 × 10−4 | 6.4 | A | 0.5 | APR_KAES17 |
8 | QLr.tw.ipbb_3B.2 | IWB60584 | 3B | 70.1 | 8.4 × 10−4 | 5.9 | A | 1.5 | GH (TGTGT) |
9 | QLr.tw.ipbb_3B.3 | IWA211 | 3B | 77.7 | 3.9 × 10−4 | 6.8 | A | 1.4 | GH (TQTGT, TGTGT) |
10 | QLr.tw.ipbb_3B.4 | IWB9095 | 3B | 157.8 | 7.9 × 10−4 | 6.0 | C | 1.2 | GH (TGTGT) |
11 | QLr.tw.ipbb_6A.1 | IWB67075 | 6A | 34.9 | 5.2 × 10−4 | 6.8 | G | 0.6 | APR_KAES_mean |
12 | QLr.tw.ipbb_6B.1 | IWB25753 | 6B | 64.8 | 6.4 × 10−4 | 6.2 | A | 1.0 | GH (TGTGT) |
13 | QLr.tw.ipbb_6B.2 | IWB52925 | 6B | 154.6–155.1 | 4.0 × 10−4 | 7.1 | A | 0.5 | APR_KAES17, APR_KAES_mean |
14 | QLr.tw.ipbb_7A.1 | IWB7431 | 7A | 33.6 | 8.8 × 10−4 | 5.9 | A | 0.9 | GH (TGTGT) |
15 | QLr.tw.ipbb_7A.2 | IWB55071 | 7A | 201 | 4.9 × 10−4 | 6.4 | A | 1.0 | GH (TQTGT) |
16 | QLr.tw.ipbb_7B.1 | IWB11945 | 7B | 66.2–67.2 | 7.6 × 10−4 | 6.4 | T | 0.5 | APR_KAES17 |
17 | QLr.tw.ipbb_7B.2 | IWB9330 | 7B | 193.3–194.8 | 1.1 × 10−4 | 8.1 | C | 1.0 | GH (TGTGT), APR_KAES17 |
# | QTL | SNP | Chr. | Position (cM) | p-Value | R2 (%) | Allele | Effect | Environment |
---|---|---|---|---|---|---|---|---|---|
1 | QSr.tw.ipbb_1A.1 | IWB7910 | 1A | 150.2 | 1.9 × 10−4 | 7.2 | G | 1.0 | GH (QHHSF) |
2 | QSr.tw.ipbb_1B.1 | IWB32261 | 1B | 54.5–67.2 | 4.2 × 10−4 | 7.2 | T | 0.7 | APR_KAES18, APR_KAES_mean |
3 | QSr.tw.ipbb_1B.2 | IWB901 | 1B | 72.9–81.2 | 8.7 × 10−4 | 6.4 | G | 0.4 | GH (THMTF, QHHSF), APR_KAES_mean |
4 | QSr.tw.ipbb_2A.1 | IWB54981 | 2A | 36.6 | 9.9 × 10−4 | 6.2 | T | 0.7 | APR_KAES_mean |
5 | QSr.tw.ipbb_2A.2 | IWB71948 | 2A | 186.1 | 2.6 × 10−4 | 6.9 | G | 0.8 | GH (QHHSF) |
6 | QSr.tw.ipbb_2B.1 | IWB70548 | 2B | 124.9–131.6 | 4.2 × 10−4 | 7.2 | A | 0.5 | APR_KAES17 |
7 | QSr.tw.ipbb_2B.2 | IWB25313 | 2B | 153.3 | 8.0 × 10−4 | 6.0 | A | 0.9 | GH (THMTF) |
8 | QSr.tw.ipbb_3A.1 | IWB39004 | 3A | 170 | 7.5 × 10−4 | 6.5 | A | 0.6 | APR_KAES_mean |
9 | QSr.tw.ipbb_3B.1 | IWB60584 | 3B | 70.1–79.6 | 8.6 × 10−4 | 7.2 | A | 1.5 | GH (QHHSF) |
10 | QSr.tw.ipbb_3B.2 | IWB12192 | 3B | 132.8 | 7.5 × 10−4 | 7.7 | C | 0.2 | APR_KAES18 |
11 | QSr.tw.ipbb_5A.1 | IWB31092 | 5A | 105 | 4.1 × 10−4 | 6.4 | G | 1.6 | GH (QHHSF) |
12 | QSr.tw.ipbb_5B.1 | IWB68299 | 5B | 44 | 7.0 × 10−4 | 5.9 | T | 1.1 | GH (QHHSF) |
13 | QSr.tw.ipbb_5B.2 | IWB71503 | 5B | 121.7 | 5.0 × 10−4 | 6.5 | C | 0.8 | GH (THMTF) |
14 | QSr.tw.ipbb_5B.3 | IWB72666 | 5B | 151.9–158.6 | 1.5 × 10−4 | 8.4 | C | 0.5 | APR_KAES_mean |
15 | QSr.tw.ipbb_6A.1 | IWA6999 | 6A | 4.8-5.9 | 2.3 × 10−5 | 9.7 | G | 1.8 | GH (THMTF) |
16 | QSr.tw.ipbb_6A.2 | IWA6406 | 6A | 86.3 | 1.4 × 10−4 | 7.8 | G | 1.6 | GH (THMTF) |
17 | QSr.tw.ipbb_6B.1 | IWA2451 | 6B | 71.9 | 3.9 × 10−4 | 7.3 | C | 0.6 | APR_KAES17 |
18 | QSr.tw.ipbb_7A.1 | IWB60043 | 7A | 17.8 | 5.1 × 10−4 | 6.9 | G | 0.5 | APR_KAES_mean |
19 | QSr.tw.ipbb_7A.2 | IWB7431 | 7A | 33.6 | 2.2 × 10−4 | 7.9 | G | 0.4 | APR_KAES17, APR_KAES_mean |
20 | QSr.tw.ipbb_7A.3 | IWA8390 | 7A | 62.4 | 6.4 × 10−4 | 6.2 | T | 0.8 | GH (THMTF) |
21 | QSr.tw.ipbb_7A.4 | IWB9275 | 7A | 192.9–193 | 3.9 × 10−4 | 6.5 | A | 1.0 | GH (QHHSF) |
Leaf Rust (LR) | |||||
---|---|---|---|---|---|
# | QTL | Position (cM) | Candidate Leaf Rust QTLs | Candidate Lr Genes | |
Tetraploid Wheat | Hexaploid Wheat | ||||
1 | QLr.tw.ipbb_2A.1 | 107.7–109.9 | [43] | [50] | |
2 | QLr.tw.ipbb_2A.2 | 159.1 | [51] | ||
3 | QLr.tw.ipbb_2B.1 | 137.9–138.1 | [30] | ||
4 | QLr.tw.ipbb_2B.2 | 166.3 | [30] | ||
5 | QLr.tw.ipbb_3A.1 | 16.5 | [30] | Lr63, Lr66 | |
6 | QLr.tw.ipbb_3A.2 | 122.3 | |||
7 | QLr.tw.ipbb_3B.1 | 12.3 | [50] | Lr27 | |
8 | QLr.tw.ipbb_3B.2 | 70.1 | [51] | ||
9 | QLr.tw.ipbb_3B.3 | 77.7 | |||
10 | QLr.tw.ipbb_3B.4 | 157.8 | |||
11 | QLr.tw.ipbb_6A.1 | 34.9 | |||
12 | QLr.tw.ipbb_6B.1 | 64.8 | [52] | [53] | |
13 | QLr.tw.ipbb_6B.2 | 154.6–155.1 | [54] | Lr3 | |
14 | QLr.tw.ipbb_7A.1 | 33.6 | |||
15 | QLr.tw.ipbb_7A.2 | 201 | Lr20 | ||
16 | QLr.tw.ipbb_7B.1 | 66.2–67.2 | |||
17 | QLr.tw.ipbb_7B.2 | 193.3–194.8 | Lr14a | ||
Stem Rust (SR) | |||||
# | QTL | Position (cM) | Candidate Stem Rust QTLs | Candidate Sr Genes | |
Tetraploid Wheat | Hexaploid Wheat | ||||
1 | QSr.tw.ipbb_1A.1 | 150.2 | [55] | ||
2 | QSr.tw.ipbb_1B.1 | 54.5–67.2 | [56] | [23,31] | |
3 | QSr.tw.ipbb_1B.2 | 72.9–81.2 | [57] | ||
4 | QSr.tw.ipbb_2A.1 | 36.6 | [57] | ||
5 | QSr.tw.ipbb_2A.2 | 186.1 | |||
6 | QSr.tw.ipbb_2B.1 | 124.9–131.6 | [55,58] | [59] | |
7 | QSr.tw.ipbb_2B.2 | 153.3 | [57,58] | [60] | Sr28 |
8 | QSr.tw.ipbb_3A.1 | 170 | |||
9 | QSr.tw.ipbb_3B.1 | 70.1–79.6 | [57] | [61] | |
10 | QSr.tw.ipbb_3B.2 | 132.8 | [62] | ||
11 | QSr.tw.ipbb_5A.1 | 105 | [57] | [63] | |
12 | QSr.tw.ipbb_5B.1 | 44 | |||
13 | QSr.tw.ipbb_5B.2 | 121.7 | [64,65] | ||
14 | QSr.tw.ipbb_5B.3 | 151.9–158.6 | [57] | ||
15 | QSr.tw.ipbb_6A.1 | 4.8–5.9 | [66,67,68] | ||
16 | QSr.tw.ipbb_6A.2 | 86.3 | [57] | ||
17 | QSr.tw.ipbb_6B.1 | 71.9 | [69] | [23] | |
18 | QSr.tw.ipbb_7A.1 | 17.8 | |||
19 | QSr.tw.ipbb_7A.2 | 33.6 | |||
20 | QSr.tw.ipbb_7A.3 | 62.4 | [58,69] | ||
21 | QSr.tw.ipbb_7A.4 | 192.9–193 | [67,70] |
Environment | Average Temperature, °C | Rainfall, mm | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
May | June | July | August | Mean | May | June | July | August | Overall | |
KAES17 | 13.5 | 18.7 | 19.7 | 20.3 | 18.1 | 50.9 | 79.3 | 69.7 | 37.8 | 237.7 |
KAES18 | 12.1 | 17.0 | 22.8 | 18.3 | 17.6 | 32.7 | 46.5 | 78.7 | 39.6 | 197.5 |
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Genievskaya, Y.; Pecchioni, N.; Laidò, G.; Anuarbek, S.; Rsaliyev, A.; Chudinov, V.; Zatybekov, A.; Turuspekov, Y.; Abugalieva, S. Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan. Plants 2022, 11, 1904. https://doi.org/10.3390/plants11151904
Genievskaya Y, Pecchioni N, Laidò G, Anuarbek S, Rsaliyev A, Chudinov V, Zatybekov A, Turuspekov Y, Abugalieva S. Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan. Plants. 2022; 11(15):1904. https://doi.org/10.3390/plants11151904
Chicago/Turabian StyleGenievskaya, Yuliya, Nicola Pecchioni, Giovanni Laidò, Shynar Anuarbek, Aralbek Rsaliyev, Vladimir Chudinov, Alibek Zatybekov, Yerlan Turuspekov, and Saule Abugalieva. 2022. "Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan" Plants 11, no. 15: 1904. https://doi.org/10.3390/plants11151904