Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping
Abstract
:1. Introduction
2. Results and Discussion
2.1. Descriptive Statistics
2.2. Correlations
2.3. GWAS
2.3.1. QPed.shared.2H-1
2.3.2. QPed.shared.2H-2
2.3.3. QPed.shared.2H-3
2.3.4. QPed.shared.3H-1
2.3.5. QPed.shared.3H-2
2.3.6. QPed.shared.3H-3
2.3.7. QPed.shared.4H-1
2.4. Impact of Plant Development on Peduncle Morphology
3. Materials and Methods
3.1. Plant Material and Field Trials
3.2. Phenotyping
3.3. Statistics and Significance Tests
3.4. Genome-Wide Association Study (GWAS)
3.5. Exome Capture Sequencing
4. 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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Trait a | N b | Mean c | SD d | Min e | Max f | CV g | Barke h |
---|---|---|---|---|---|---|---|
DIA17 | 1232 | 1202.82 | 141.08 | 776.00 | 1640.91 | 0.12 | 1239.35 |
DIA18 | 1343 | 1204.25 | 137.89 | 833.50 | 1931.10 | 0.11 | 1309.98 |
DIA | 1411 | 1204.33 | 126.87 | 841.76 | 1876.26 | 0.11 | 1274.66 |
WAL17 | 1232 | 279.01 | 24.01 | 179.96 | 385.95 | 0.09 | 270.66 |
WAL18 | 1343 | 247.32 | 19.98 | 178.74 | 322.83 | 0.08 | 238.83 |
WAL | 1411 | 263.16 | 18.84 | 179.35 | 338.69 | 0.07 | 254.74 |
AREA17 | 1232 | 8.14 × 105 | 1.57 × 105 | 3.78 × 105 | 1.35 × 106 | 0.19 | 8.24 × 105 |
AREA18 | 1343 | 7.46 × 105 | 1.32 × 105 | 4.12 × 105 | 1.37 × 106 | 0.18 | 8.04 × 105 |
AREA | 1411 | 7.81 × 105 | 1.29 × 105 | 4.04 × 105 | 1.29 × 106 | 0.16 | 8.16 × 105 |
Trait | Vg a | Ve b | Vr c | H2 d |
---|---|---|---|---|
DIA | 57.8 | 0.0 | 42.2 | 73.3 |
WAL | 17.4 | 51.1 | 31.4 | 52.6 |
AREA | 45.2 | 10.4 | 44.4 | 67.0 |
Trait | Prediction Ability | ⌀Number of Sig. SNPs |
---|---|---|
DIA | 0.47 | 36.81 |
DIA17 | 0.45 | 31.67 |
DIA18 | 0.28 | 25.75 |
WAL | 0.20 | 27.15 |
WAL17 | 0.10 | 21.41 |
WAL18 | 0.21 | 24.42 |
AREA17 | 0.33 | 28.46 |
AREA18 | 0.28 | 23.35 |
AREA | 0.40 | 32.70 |
QTL Region | DIA [µm] | WAL [µm] | AREA [µm2] | Candidate Gene | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
shared-QTL | chromosome | Position a | 2017 | 2018 | BLUEs | 2017 | 2018 | BLUEs | 2017 | 2018 | BLUEs | ||
QPed.shared.2H-1 | 2H | 18.3–26.8 cM | 21,508,891–29,254,219 bp | −101.5 | - | −67.5 | 5.6 | 6.5 | 5.5 | −8.3 × 104 | - | −4.4 × 104 | PPD-H1 [20] |
QPed.shared.2H-2 | 2H | 55.5–60.8 cM | 164,050,763–518,354,808 bp | −181.6 | −153.7 | −168.0 | −10.2 | −7.5 | −9.5 | −1.8 × 105 | −1.4 × 105 | −1.6 × 105 | HvCEN [22] |
QPed.shared.2H-3 | 2H | 82.0 cM | 586,582,931–586,594,551 bp | 11.3 | - | 16.3 | - | - | - | −1.3 × 104 | - | 1.0 × 104 | |
QPed.shared.3H-1 | 3H | 47.7–51.8 cM | 128,830,583–394,780,497 bp | 72.7 | 100.9 | 91.1 | 10.5 | 14.4 | 14.2 | 8.8 × 104 | 1.2 × 105 | 1.1 × 105 | |
QPed.shared.3H-2 | 3H | 71.5 cM | 517,985,664 bp | - | 17.0 | 16.3 | - | - | - | - | - | 2.1 × 104 | |
QPed.shared.3H-3 | 3H | 106.6–109.5 cM | 569,528,666–573,503,074 bp | −50.3 | - | - | −8.8 | - | −2.0 | −6.0 × 104 | - | −2.4 × 104 | HvGA20ox2 [23] |
QPed.shared.4H-1 | 4H | 0.9–2.1 cM | 393,618–3,342,910 bp | - | 25.8 | - | 5.1 | 8.1 | 6.3 | - | 3.7 × 104 | 2.5 × 104 |
QTL | HEA a | WAL b | DIA b | AREA b |
---|---|---|---|---|
QFt.HEB25-1b a | −1.4 | - | - | - |
QPed.shared.2H-1 | −9.5 | 5.5 | −67.5 | −4.4 × 104 |
QPed.shared.2H-2 | −3.0 | −9.5 | −168.0 | −1.6 × 105 |
QPed.shared.3H-1 | - | 14.2 | 91.1 | 1.1 × 105 |
QPed.shared.3H-3 | −3.1 | −2.0 | −22.3 | −2.4 × 104 |
QPed.shared.4H-1 | 3.2 | 6.3 | 25.2 | 2.5 × 104 |
QFt.HEB25-4e a | 2.2 | - | - | - |
QFt.HEB25-5d a | 3.8 | −1.3 | −22.7 | - |
QFt.HEB25-7a a | 4.1 | - | - | - |
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Zahn, S.; Schmutzer, T.; Pillen, K.; Maurer, A. Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping. Plants 2021, 10, 10. https://doi.org/10.3390/plants10010010
Zahn S, Schmutzer T, Pillen K, Maurer A. Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping. Plants. 2021; 10(1):10. https://doi.org/10.3390/plants10010010
Chicago/Turabian StyleZahn, Sebastian, Thomas Schmutzer, Klaus Pillen, and Andreas Maurer. 2021. "Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping" Plants 10, no. 1: 10. https://doi.org/10.3390/plants10010010
APA StyleZahn, S., Schmutzer, T., Pillen, K., & Maurer, A. (2021). Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping. Plants, 10(1), 10. https://doi.org/10.3390/plants10010010