Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks
Abstract
:1. Introduction
2. Results
2.1. DSNP Mining
2.2. Genetic Linkage Maps of Tetraploid Swingle Citrumelo and Volkamer Lemon
2.3. Recombination Rate
2.4. Parental Heterozygosity Restitution and Meiotic Inheritance Analysis
2.5. Impact of Preferential Pairing on Tetraploid Hybrid Diversity Structure
2.6. Inheritance in the Tetraploid Hybrids of Candidate Genes for Pest and Disease Resistance
2.7. Root Phenotyping and Genomic Association
3. Discussion
3.1. GBS Coupled with TraceAncestor Was Efficient for Estimating Haplotype Ancestral Doses All along the Genome of the Tetraploid Hybrids
3.2. The Tetraploid Volkamer Lemon and Swingle Citrumelo Parents Display Intermediate Inheritance with a Disomic Tendency and Variability between Parents and Chromosomes for Preferential Chromosome Pairing
3.3. Apparent Interspecific and Intergeneric Recombination Rates Are Limited by Preferential Pairing and Are Very Low in Centromeric-Pericentromeric Areas
3.4. Preferential Chromosome Pairing in Tetraploid Rootstock Resulting from Chromosome Doubling of Interspecific Hybrids Is Unfavorable for QTL Analysis
3.5. Implication for Rootstock Breeding Programs
4. Materials and Methods
4.1. Plant Material
4.2. DNA Extraction and Genotyping by Sequencing (GBS)
4.3. SNP Calling
4.4. DSNPs Identification
4.5. Matrix Preparation
4.6. Mapping Analysis
4.7. Recombination Rate
4.8. Parental Heterozygosity Restitution (PHR)
4.9. Estimation of Preferential Pairing (PP)
4.10. Analysis of the Deviation from Expected Gametic Segregation under a Tetrasomic Model
4.11. Inheritance of Candidate Genes in the Hybrid Population
4.12. Root System Architecture Phenotyping
4.13. Quantitative Trait Locus Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Chromosome | C. maxima | C. medica | C. reticulata | P. trifoliata | Total |
---|---|---|---|---|---|
C1 | 1101 | 2220 | 1338 | 3028 | 7687 |
C2 | 1153 | 2654 | 1923 | 3724 | 9454 |
C3 | 1579 | 3938 | 2420 | 5024 | 12,961 |
C4 | 977 | 2221 | 1577 | 2962 | 7737 |
C5 | 1118 | 2193 | 1471 | 2970 | 7752 |
C6 | 885 | 1924 | 1325 | 2485 | 6619 |
C7 | 880 | 1975 | 1320 | 2626 | 6801 |
C8 | 935 | 2018 | 1319 | 2570 | 6842 |
C9 | 816 | 2087 | 1248 | 2448 | 6599 |
Total | 9444 | 21,230 | 13,941 | 27,837 | 72,452 |
% | 13.03 | 29.3 | 19.24 | 38.42 | 100 |
Swingle Citrumelo | Volkamer Lemon | |||
---|---|---|---|---|
LG | Mks/LG | LG Size cM | Mks/LG | LG Size cM |
1 | 149 | 36.47 | 106 | 49.16 |
2 | 172 | 68.94 | 126 | 27.10 |
3 | 236 | 98.46 | 187 | 105.41 |
4 | 143 | 37.09 | 108 | 26.40 |
5 | 139 | 43.34 | 105 | 79.72 |
6 | 116 | 46.59 | 94 | 30.25 |
7 | 128 | 34.59 | 96 | 30.09 |
8 | 119 | 28.20 | 97 | 20.10 |
9 | 116 | 38.97 | 97 | 56.78 |
Total | 1318 | 432.64 | 1016 | 425 |
Chromosome | Swingle Citrumelo | Volkamer Lemon | ||
---|---|---|---|---|
PHR (Rank) | PP (Rank) | PHR (Rank) | PP (Rank) | |
Chr1 | 0.889 ± 0.004 (a) | 0.742 ± 0.007 (d) | 0.826 ± 0.008 (a) | 0.583 ± 0.019 (d) |
Chr2 | 0.802 ± 0.006 (b) | 0.625 ± 0.033 (b) | 0.911 ± 0.008 (b) | 0.81 ± 0 (f) |
Chr3 | 0.790 ± 0.007 (c) | 0.69 ± 0.054 (c) | 0.719 ± 0.008 (c) | 0.317 ± 0.061 (c) |
Chr4 | 0.919 ± 0.004 (d) | 0.85 ± 0.043 (e) | 0.872 ± 0.005 (d) | 0.548 ± 0.061(d) |
Chr5 | 0.849 ± 0.011 (e) | 0.848 ± 0.040 (e) | 0.692 ± 0.008 (e) | 0 ± 0 (a) |
Chr6 | 0.890 ± 0.012 (adf) | 0.925 (f) | 0.869 ± 0.006 (d) | 0.675 ± 0.012 (e) |
Chr7 | 0.817 ± 0.003 (g) | 0.502 ± 0.029 (a) | 0.874 ± 0.007 (d) | 0.663 ± 0.036 (e) |
Chr8 | 0.933 ± 0.006 (h) | 0.923 ± 0.050 (f) | 0.897 ± 0.006 (f) | 0.672 ± 0.057 (e) |
Chr9 | 0.917± 0.003 (f) | 0.76 ± 0.045 (d) | 0.764 ± 0.008 (g) | 0.25 ± 0.054 (b) |
Whole genome | 0.859 ± 0.004 | 0.763 ± 0.054 | 0.817 ± 0.005 | 0.502 ± 0.099 |
(a) Chromosome | N | −log(q-Value) | N < −log(0.05) | % |
---|---|---|---|---|
Chr1 | 149 | 4.276 ± 0.149 (c) | 149 | 100% |
Chr2 | 172 | 1.874 ± 0.129 (ef) | 124 | 72.09% |
Chr3 | 236 | 1.634 ± 0.171 (f) | 108 | 45.76% |
Chr4 | 143 | 5.300 ± 0.115 (b) | 143 | 100% |
Chr5 | 139 | 3.345 ± 0.275 (d) | 122 | 87.77% |
Chr6 | 116 | 4.368 ± 0.378 (c) | 108 | 93.10 |
Chr7 | 128 | 2.084 ± 0.102 (e) | 120 | 93.75% |
Chr8 | 119 | 5.628 0.201 (a) | 119 | 100% |
Chr9 | 116 | 5.097 ± 0.111 (b) | 116 | 100% |
Total | 1318 | 3.492 ± 0.104 | 1109 | 84.14% |
(b) Chromosome | N | −log(q-value) | N > −log(0.05) | % |
Chr1 | 106 | 2.565 ± 0.178 (d) | 94 | 88.68% |
Chr2 | 126 | 4.700 ± 0.222 (a) | 126 | 100% |
Chr3 | 187 | 0.549 ± 0.087 (f) | 18 | 9.63% |
Chr4 | 108 | 3.738 ± 0.113 (c) | 108 | 100% |
Chr5 | 105 | 0.407 ± 0.098 (f) | 7 | 6.67% |
Chr6 | 94 | 3.594 ± 0.153 (c) | 94 | 100% |
Chr7 | 96 | 3.578 ± 0.210 (c) | 96 | 100% |
Chr8 | 97 | 4.346 ± 0.190 (b) | 97 | 100% |
Chr9 | 97 | 0.959 ± 0.157 (e) | 24 | 24.74% |
Total | 1016 | 2.568 ± 0.113 | 664 | 65.35% |
Gene ID | Trait | Location on P. trifoliata Reference Genome | Hybrids % with n Dose of Poncirus | |||||
---|---|---|---|---|---|---|---|---|
Scaffold | Start | End | 0 | 1 | 2 | N | ||
Ptrif.0006s1501.1 | Huanglongbing tolerance | Scaffold 6 | 17843557 | 17847864 | 4.21 | 83.16 | 9.47 | 3.16 |
Ptrif.0009s1449.1 | Scaffold 9 | 16743738 | 16750183 | 5.26 | 90.53 | 1.05 | 3.16 | |
Ptrif.0009s1451.1 | Scaffold 9 | 16761424 | 16771587 | |||||
Ptrif.0009s1453.1 | Scaffold 9 | 16803290 | 16817272 | |||||
Ptrif.0009s1458.2 | Scaffold 9 | 16966396 | 16974146 | |||||
Ptrif.0009s2550.1 | Scaffold 9 | 16873308 | 16878288 | |||||
Ptrif.0009s2650.1 | Scaffold 9 | 16878879 | 16881473 | |||||
Ptrif.0009s1595.1 | Scaffold 9 | 19302619 | 19305258 | 4.21 | 88.42 | 2.11 | 5.26 | |
Ptrif.0009s1596.1 | Scaffold 9 | 19351433 | 19355794 | |||||
Ptrif.0009s1599.1 | Scaffold 9 | 19383517 | 19386756 | |||||
Ptrif.0009s1600.1 | Scaffold 9 | 19400932 | 19403616 | |||||
Ptrif.0007s1586.1 | Citrus tristeza virus disease resistance | Scaffold 7 | 11780276 | 11787445 | 10.53 | 77.89 | 9.47 | 2.11 |
Ptrif.0007s1587.1 | Scaffold 7 | 11823916 | 11826636 | |||||
Ptrif.0007s1590.1 | Scaffold 7 | 11860949 | 11863630 | |||||
Ptrif.0007s1595.1 | Scaffold 7 | 11908817 | 11912236 | |||||
Ptrif.0007s1378.1 | Nematode resistance | Scaffold 7 | 9840644 | 9843519 | 11.58 | 78.95 | 7.37 | 2.11 |
Ptrif.0007s1394.1 | Scaffold 7 | 9974384 | 9977152 | 11.58 | 76.84 | 9.47 | 2.11 | |
Ptrif.0007s1395.1 | Scaffold 7 | 9985962 | 9988577 | |||||
Ptrif.0007s1396.1 | Scaffold 7 | 9990366 | 9991216 | |||||
Ptrif.0007s1398.1 | Scaffold 7 | 10007442 | 10010437 | |||||
Ptrif.0007s1402.1 | Scaffold 7 | 10043069 | 10045927 | |||||
Ptrif.0007s1404.1 | Scaffold 7 | 10056890 | 10060283 | |||||
Ptrif.0007s1406.2 | Scaffold 7 | 10065703 | 10067962 | |||||
Ptrif.0007s1411.2 | Scaffold 7 | 10097497 | 10100154 | |||||
Ptrif.0007s1415.1 | Scaffold 7 | 10123503 | 10126433 | |||||
Ptrif.0007s2703.1 | Scaffold 7 | 10139209 | 10144561 | |||||
Ptrif.0007s1481.1 | Scaffold 7 | 10687572 | 10691702 | 11.58 | 78.95 | 9.47 | 0 | |
Ptrif.0007s1484.1 | Scaffold 7 | 10729463 | 10732201 | |||||
Ptrif.0007s1501.1 | Scaffold 7 | 10812404 | 10852651 | |||||
Ptrif.0007s1502.1 | Scaffold 7 | 10860634 | 10863348 |
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Calvez, L.; Dereeper, A.; Perdereau, A.; Mournet, P.; Miranda, M.; Bruyère, S.; Hufnagel, B.; Froelicher, Y.; Lemainque, A.; Morillon, R.; et al. Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks. Plants 2023, 12, 1630. https://doi.org/10.3390/plants12081630
Calvez L, Dereeper A, Perdereau A, Mournet P, Miranda M, Bruyère S, Hufnagel B, Froelicher Y, Lemainque A, Morillon R, et al. Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks. Plants. 2023; 12(8):1630. https://doi.org/10.3390/plants12081630
Chicago/Turabian StyleCalvez, Lény, Alexis Dereeper, Aude Perdereau, Pierre Mournet, Maëva Miranda, Saturnin Bruyère, Barbara Hufnagel, Yann Froelicher, Arnaud Lemainque, Raphaël Morillon, and et al. 2023. "Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks" Plants 12, no. 8: 1630. https://doi.org/10.3390/plants12081630
APA StyleCalvez, L., Dereeper, A., Perdereau, A., Mournet, P., Miranda, M., Bruyère, S., Hufnagel, B., Froelicher, Y., Lemainque, A., Morillon, R., & Ollitrault, P. (2023). Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks. Plants, 12(8), 1630. https://doi.org/10.3390/plants12081630