High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing
Abstract
:1. Introduction
2. Results
2.1. Variation and Correlation Analysis of Fruit- and Oil-Related Traits
2.2. Analysis of ddRAD Data and SNP Markers
2.3. Genetic Map Construction and Its Basic Characteristics
2.4. QTL Analysis of Fruit- and Oil-Related Traits Based on the High-Density Genetic Map
2.4.1. Fruit-Related Traits
2.4.2. Oil-Related Traits
2.5. Identification of Fruit- and Oil-Related Candidate Genes and Potential Regulatory Network
3. Discussion
3.1. Mapping Population and Phenotypic Variation
3.2. Density and Accuracy of the C. oleifera Genetic Map
3.3. QTL Analysis of Economic Traits in C. oleifera
3.4. Identification and Analysis of the Candidate Genes
4. Materials and Methods
4.1. Plant Materials
4.2. Phenotypic Data Collection
4.3. DNA Extraction
4.4. ddRAD Libraries Sequencing and SNPs Identification
4.5. Genetic Map Construction
4.6. QTL Mapping and Genetic Mode Analysis of SNPs
4.7. Identification of Fruit- and Oil-Related Candidate Genes and Potential Regulatory Networks
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sources of Variation | Year | Genotypes | Error | |
---|---|---|---|---|
df | 2 | 179 | 358 | |
FY | MS | 269.4273 | 2.8638 | 1.8835 |
F value | 143.049 ** | 1.521 ** | ||
RSF | MS | 3488.9907 | 72.3878 | 37.9708 |
F value | 91.886 ** | 1.906 ** | ||
RKS2 | MS | 291.5984 | 27.5792 | 6.5039 |
F value | 44.834 ** | 4.24 ** | ||
RKS1 | MS | 268.7622 | 26.0167 | 5.7166 |
F value | 47.015 ** | 4.551 ** | ||
OC | MS | 75.0375 | 27.4846 | 15.3854 |
F value | 4.877 ** | 1.786 ** | ||
C16:0 | MS | 102.5323 | 0.5838 | 0.1932 |
F value | 530.75 ** | 3.022 ** | ||
C18:0 | MS | 4.6355 | 0.1403 | 0.0551 |
F value | 84.199 ** | 2.549 ** | ||
C18:1 | MS | 657.5575 | 4.0707 | 1.4652 |
F value | 448.777 ** | 2.778 ** | ||
C18:2 | MS | 245.2011 | 2.6365 | 0.8135 |
F value | 301.403 ** | 3.241 ** | ||
C18:3 | MS | 0.0264 | 0.0018 | 0.0008 |
F value | 33.577 ** | 2.266 ** | ||
C20:1 | MS | 0.0143 | 0.004 | 0.0015 |
F value | 9.765 ** | 2.754 ** |
LG ID | Total Markers | Total Distance (cM) | Average Distance (cM) | Gaps > 5 cM(%) | Max Gap (cM) |
---|---|---|---|---|---|
LG01 | 231 | 203.79 | 0.89 | 1.74 | 20.62 |
LG02 | 187 | 220.89 | 1.19 | 5.91 | 14.28 |
LG03 | 197 | 196.62 | 1.00 | 2.04 | 10.63 |
LG04 | 138 | 253.02 | 1.85 | 5.84 | 40.67 |
LG05 | 192 | 222.04 | 1.16 | 4.71 | 26.96 |
LG06 | 187 | 196.19 | 1.05 | 2.69 | 12.75 |
LG07 | 258 | 319.60 | 1.24 | 4.28 | 19.77 |
LG08 | 164 | 262.68 | 1.61 | 7.98 | 16.16 |
LG09 | 118 | 211.33 | 1.81 | 5.98 | 19.35 |
LG10 | 186 | 205.40 | 1.11 | 2.70 | 15.22 |
LG11 | 262 | 224.30 | 0.86 | 2.30 | 22.44 |
LG12 | 181 | 201.07 | 1.12 | 2.22 | 10.37 |
LG13 | 171 | 196.04 | 1.15 | 2.35 | 19.84 |
LG14 | 145 | 207.60 | 1.44 | 5.56 | 15.29 |
LG15 | 163 | 206.47 | 1.27 | 5.56 | 17.51 |
Total | 2780 | 3327.02 | 1.20 | 3.88 | 40.67 |
Average | 185 | 415.88 | 1.20 | 3.88 | --- |
Traits | Year | Number of QTLs | Linkage Group | PVE a (%) | LOD Value |
---|---|---|---|---|---|
FY | 2015 | 10 | 1, 2, 5, 6, 10, 13 | 7.4–9.4 | 3.0–3.87 |
2016 | 5 | 3, 5, 7, 9 | 7.4–9.0 | 3.02–3.7 | |
2017 | 8 | 3, 4, 7, 11, 13, 15 | 7.6–9.9 | 3.07–4.07 | |
RSF | 2015 | 14 | 2, 4, 6, 7, 9, 10, 11, 14 | 9.3–11.4 | 3.0–3.72 |
2016 | 8 | 2, 3, 6, 7, 8, 11 | 10.5–14.0 | 3.01–4.1 | |
2017 | 10 | 3, 9, 10, 12, 13, 14 | 8.2–11.2 | 3.06–4.25 | |
RKS2 | 2015 | 5 | 1, 6, 8, 10, 11 | 9.8–16.6 | 3.17–5.57 |
2016 | 14 | 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 15 | 10.4–15.1 | 3.0–4.48 | |
2017 | 5 | 4, 5, 6, 10, 13 | 7.5–9.0 | 3.02–3.66 | |
RKS1 | 2015 | 5 | 2, 6, 10, 11 | 9.6–14.3 | 3.09–4.71 |
2016 | 14 | 1, 2, 3, 4, 6, 7, 9, 13, 14, 15 | 10.6–14.5 | 3.08–4.27 | |
2017 | 8 | 4, 5, 6, 7, 8, 10, 14 | 7.5–10.0 | 3.0–4.08 | |
OC | 2015 | 6 | 3, 13, 14, 16 | 9.4–13.3 | 3.03–4.37 |
2016 | 4 | 1, 10, 11 | 11.5–14.5 | 3.36–4.28 | |
2017 | 3 | 1, 2, 11 | 7.5–8.3 | 3.03–3.35 | |
C16:0 | 2015 | 9 | 1, 2, 7, 8, 11, 13, 15 | 9.5–13.9 | 3.07–4.58 |
2016 | 11 | 1, 3, 4, 7, 10, 11, 12, 14, 15 | 10.4–14.6 | 3.02–4.31 | |
2017 | 7 | 3, 6, 7, 10, 11 | 7.9–11.9 | 3.17–4.89 | |
C18:0 | 2015 | 5 | 2, 5, 7, 13 | 9.7–12.5 | 3.13–4.09 |
2016 | 5 | 3, 4, 12, 15 | 10.4–12.6 | 3.01–3.67 | |
2017 | 4 | 2, 9, 13, 14 | 7.7–8.8 | 3.09–3.56 | |
C18:1 | 2015 | 4 | 5, 7, 8, 15 | 10.1–12.2 | 3.26–3.99 |
2016 | 6 | 10, 11, 12, 15 | 10.4–14.5 | 3.0–4.3 | |
2017 | 0 | ||||
C18:2 | 2015 | 5 | 3, 5, 7, 11, 15 | 9.6–10.8 | 3.07–3.5 |
2016 | 7 | 2, 6, 10, 11, 12, 13 | 10.5–13.4 | 3.05–3.95 | |
2017 | 4 | 5, 10, 11 | 7.5–9.8 | 3.0–3.99 | |
C18:3 | 2015 | 14 | 1, 3, 4, 8, 9, 10, 11, 14, 15 | 9.4–13.0 | 3.02–4.26 |
2016 | 9 | 3, 4, 5, 7, 11, 12, 13 | 10.5–15.3 | 3.05–4.54 | |
2017 | 6 | 2, 3, 5, 11, 13, 15 | 8.0–9.7 | 3.2–3.93 | |
C20:1 | 2015 | 5 | 1, 7, 8, 10, 13 | 9.5–10.2 | 3.05–3.31 |
2016 | 9 | 4, 7, 9, 10, 11, 13, 15 | 10.5–15.4 | 3.02–4.57 | |
2017 | 2 | 1, 11 | 7.7–8.1 | 3.09–3.27 |
Trait | QTL | Start | End | Length (cM) | Year | LOD | PVE (%) | Marker | Cross Type | CL53 (♀) | CL81 (♂) | Genotype | Individual Numbers | Phenotype Means(%) | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2015 | 2016 | 2017 | ||||||||||||||
RKS2 | RKS2-q4 | 135.721 | 138.501 | 2.78 | 2016 | 4.48 | 15.1 | Chr04_77743434 | lm × ll | GT | GG | GG | 101 | 59.70 | 62.05 | |
2017 | 3.01 | 7.5 | GT | 76 | 58.24 | 60.33 | ||||||||||
- | 3 | 57.78 | 61.94 | |||||||||||||
RKS2-q6-1 | 50.723 | 64.534 | 13.811 | 2015 | 5.57 | 16.6 | Chr06_142599472 | lm × ll | GA | GG | GG | 97 | 59.25 | 61.07 | ||
2017 | 3.66 | 9.0 | GA | 81 | 59.12 | 61.56 | ||||||||||
- | 1 | 62.77 | 62.97 | |||||||||||||
Chr06_112292496 | lm × ll | GA | GG | GG | 97 | 59.31 | 61.22 | |||||||||
GA | 80 | 59.33 | 61.58 | |||||||||||||
- | 3 | 54.52 | 56.69 | |||||||||||||
Chr06_88890750 | lm × ll | CT | CC | CC | 100 | 59.57 | 61.35 | |||||||||
CT | 77 | 58.85 | 61.29 | |||||||||||||
- | 3 | 56.83 | 60.14 | |||||||||||||
Chr06_25329856 | hk × hk | AG | AG | AA | 35 | 57.95 | 61.19 | |||||||||
AG | 96 | 59.58 | 61.24 | |||||||||||||
GG | 30 | 59.01 | 61.50 | |||||||||||||
- | 19 | 59.93 | 61.57 | |||||||||||||
Chr06_111554923 | lm × ll | GA | GG | GG | 91 | 59.44 | 61.36 | |||||||||
GA | 86 | 58.87 | 61.20 | |||||||||||||
- | 3 | 61.85 | 62.65 | |||||||||||||
RSK1 | RKS1-q4-2 | 135.721 | 138.501 | 2.78 | 2016 | 4.27 | 14.5 | Chr04_77743434 | lm × ll | GT | GG | GG | 101 | 64.78 | 67.21 | |
2017 | 3.28 | 8.1 | GT | 76 | 64.65 | 66.97 | ||||||||||
- | 3 | 63.40 | 67.17 | |||||||||||||
RKS1-q6-1 | 54.072 | 64.534 | 10.462 | 2015 | 4.71 | 14.3 | Chr06_142599472 | lm × ll | GA | GG | GG | 97 | 65.67 | 64.48 | ||
2016 | 3.37 | 11.6 | GA | 81 | 66.71 | 65.26 | ||||||||||
- | 1 | 69.27 | 68.23 | |||||||||||||
Chr06_112292496 | lm × ll | GA | GG | GG | 97 | 66.14 | 64.75 | |||||||||
GA | 80 | 66.23 | 64.72 | |||||||||||||
- | 3 | 62.76 | 61.66 | |||||||||||||
Chr06_88890750 | lm × ll | CT | CC | CC | 100 | 66.31 | 65.23 | |||||||||
CT | 77 | 65.99 | 64.04 | |||||||||||||
- | 3 | 62.91 | 61.79 | |||||||||||||
Chr06_25329856 | hk × hk | AG | AG | AA | 35 | 65.24 | 63.62 | |||||||||
AG | 96 | 66.25 | 65.11 | |||||||||||||
GG | 30 | 66.19 | 64.90 | |||||||||||||
- | 19 | 66.77 | 64.22 | |||||||||||||
C18:3 | C18:3-q11-2 | 84.52 | 85.695 | 1.175 | 2015 | 3.16 | 9.8 | Chr11_27083024 | nn × np | CC | CT | CC | 86 | 22.24 | 24.45 | |
2017 | 3.93 | 9.7 | CT | 92 | 22.23 | 24.53 | ||||||||||
- | 1 | 31.47 | 33.96 | |||||||||||||
C18:2 | C18:2-q11-1 | 162.869 | 166.196 | 3.327 | 2015 | 3.07 | 9.6 | Chr11_114235680 | nn × np | CC | CT | CC | 98 | 6.54 | 7.96 | |
2017 | 3.02 | 7.5 | CT | 80 | 6.90 | 8.05 | ||||||||||
- | 2 | 6.23 | 9.21 | |||||||||||||
Chr11_65073730 | lm × ll | AG | AA | AA | 78 | 6.78 | 8.08 | |||||||||
AG | 98 | 6.59 | 7.91 | |||||||||||||
- | 4 | 8.16 | 9.35 | |||||||||||||
C18:2-q5-1 | 104.487 | 105.646 | 1.159 | 2015 | 3.5 | 10.8 | Chr05_107820202 | lm × ll | AG | GG | GG | 95 | 6.84 | 8.22 | ||
2017 | 3.0 | 7.5 | AG | 79 | 6.55 | 7.76 | ||||||||||
- | 4 | 7.00 | 7.62 | |||||||||||||
Chr05_93231328 | hk × hk | TC | TC | TT | 56 | 6.75 | 7.88 | |||||||||
TC | 67 | 6.87 | 8.13 | |||||||||||||
CC | 32 | 6.37 | 8.15 | |||||||||||||
- | 25 | 6.58 | 7.84 | |||||||||||||
C16:0 | C16:0-q11-3 | 164.001 | 169.537 | 5.536 | 2015 | 3.73 | 11.5 | Chr11_39972487 | lm × ll | AG | AA | AA | 84 | 6.87 | 8.37 | |
2017 | 4.2 | 10.3 | AG | 94 | 7.02 | 8.39 | ||||||||||
- | 2 | 6.68 | 8.10 | |||||||||||||
Chr11_39972501 | lm × ll | AG | AA | AA | 83 | 6.85 | 8.35 | |||||||||
AG | 95 | 7.03 | 8.41 | |||||||||||||
- | 2 | 6.68 | 8.10 | |||||||||||||
Chr11_39972457 | lm × ll | CA | CC | CC | 82 | 6.85 | 8.35 | |||||||||
CA | 96 | 7.03 | 8.40 | |||||||||||||
- | 2 | 6.68 | 8.10 | |||||||||||||
Chr11_128763300 | nn × np | TT | TA | TT | 98 | 6.88 | 8.33 | |||||||||
TA | 79 | 7.04 | 8.44 | |||||||||||||
- | 3 | 6.47 | 8.37 | |||||||||||||
Chr11_10782110 | nn × np | GG | GA | GG | 78 | 6.95 | 8.38 | |||||||||
GA | 100 | 6.95 | 8.38 | |||||||||||||
- | 2 | 6.34 | 8.36 | |||||||||||||
Chr11_64280835 | nn × np | CC | CT | CC | 99 | 6.96 | 8.38 | |||||||||
CT | 78 | 6.93 | 8.37 | |||||||||||||
- | 3 | 6.68 | 8.46 | |||||||||||||
Chr11_146396217 | lm × ll | GA | GG | GG | 79 | 6.91 | 8.37 | |||||||||
GA | 100 | 6.97 | 8.38 | |||||||||||||
- | 1 | 6.84 | 8.44 | |||||||||||||
C18:0 | C18:0-q2 | 78.596 | 82.114 | 3.518 | 2015 | 3.13 | 9.7 | Chr02_116850822 | lm × ll | AG | GG | GG | 99 | 1.85 | 2.13 | |
2017 | 3.44 | 8.5 | GA | 76 | 1.87 | 2.17 | ||||||||||
- | 5 | 1.75 | 1.94 | |||||||||||||
Chr02_98558620 | hk × hk | AG | AG | GG | 41 | 1.79 | 2.11 | |||||||||
GA | 86 | 1.89 | 2.14 | |||||||||||||
AA | 39 | 1.85 | 2.15 | |||||||||||||
- | 14 | 1.81 | 2.21 |
Trait | SNP | 2a 1 | d 2 | d/a | Frequency 3 | a4 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2015 | 2016 | 2017 | 2015 | 2016 | 2017 | 2015 | 2016 | 2017 | 2015 | 2016 | 2017 | ||||
RKS2 | Chr06_25329856 | 1.06 | 0.93 | 0.31 | 1.10 | 0.95 | −0.11 | 2.08 | 2.05 | −0.68 | 0.48 | (G) | −0.76 | −0.51 | 0.04 |
RKS1 | Chr06_25329856 | 0.95 | 1.28 | 0.34 | 0.53 | 0.85 | 0.04 | 1.13 | 1.33 | 0.24 | 0.48 | (G) | −0.42 | −0.46 | −0.07 |
C18:2 | Chr05_93231328 | 0.38 | 0.16 | 0.27 | 0.31 | 0.37 | 0.12 | 1.63 | 4.62 | 0.85 | 0.42 | (C) | −0.11 | −0.17 | −0.02 |
C18:0 | Chr02_98558620 | 0.06 | 0.14 | 0.04 | 0.07 | −0.06 | 0.01 | 2.33 | −0.86 | 0.50 | 0.49 | (A) | −0.03 | 0.04 | −0.01 |
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Lin, P.; Chai, J.; Wang, A.; Zhong, H.; Wang, K. High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing. Int. J. Mol. Sci. 2024, 25, 8840. https://doi.org/10.3390/ijms25168840
Lin P, Chai J, Wang A, Zhong H, Wang K. High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing. International Journal of Molecular Sciences. 2024; 25(16):8840. https://doi.org/10.3390/ijms25168840
Chicago/Turabian StyleLin, Ping, Jingyu Chai, Anni Wang, Huiqi Zhong, and Kailiang Wang. 2024. "High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing" International Journal of Molecular Sciences 25, no. 16: 8840. https://doi.org/10.3390/ijms25168840