Genome-Wide Detection of Major and Epistatic Effect QTLs for Seed Protein and Oil Content in Soybean Under Multiple Environments Using High-Density Bin Map
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Analysis of Seed Protein and Oil Content
2.2. QTL Analysis for Seed Protein and Oil Content
2.3. QTL × Environment Interaction Analysis
2.4. Epistatic-Effect QTLs and Epistatic QTL Interactions with the Environment
2.5. Candidate Gene Prediction of the Major Stable QTLs
3. Discussion
4. Materials and Methods
4.1. Plant Material and Experimental Conditions
4.2. Measurement and Analysis of Seed Protein and Oil Contents
4.3. Bin Map Construction
4.4. Mapping of Main- and Epistatic-Effect QTLs
4.5. Identification of Candidate Genes
5. Conclusions
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
Abbreviations
RAD-seq | Restriction site associated DNA sequencing |
QTL | Quantitative trait loci |
RIL | Recombinant inbred line |
R2 | Phenotypic variation explained |
GO | Gene ontology |
RNA-seq | Ribonucleic acid sequencing |
MAS | Marker-assisted selection |
Q × E | QTL and environment interaction |
RCBD | Randomized complete block design |
ANOVA | Analysis of variance |
MSG | Multiplexed shotgun genotyping |
SNP | Single nucleotide polymorphism |
CIM | Composite interval mapping |
MCMC | Markov chain monte carlo |
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QTLs Names a | Chr b | Pos (cM) c | LOD d | R2 (%) e | A f | Confidence Interval (cM) g | Env. h | Ref. i |
---|---|---|---|---|---|---|---|---|
qPro-1-I | 1 | 39.51 | 2.74 | 6.32 | 0.32 | 37.9–44.4 | CE | [18] |
qPro-4-1 | 4 | 37.51 | 2.55 | 5.80 | −0.45 | 27.1–41.4 | YC2014 | New |
qPro-6-1 | 6 | 62.11 | 6.17 | 15.09 | 0.74 | 56.1–65.4 | YC2014 | New |
qPro-6-2 | 6 | 67.41 | 5.08 | 13.23 | 0.69 | 65.4–74.8 | YC2014 | New |
qPro-6-3 | 6 | 168.61 | 3.47 | 11.16 | −2.58 | 163.5–172.7 | JP2012 | New |
qPro-7-1 | 7 | 41.71 | 5.62 | 13.59 | 0.69 | 34.2–44.7 | YC2014 | New |
42.01 | 10.28 | 26.22 | 0.81 | 40.9–42.6 | JP2014 | |||
42.01 | 8.46 | 22.21 | 0.58 | 38.8–43.4 | CE | |||
44.91 | 4.34 | 14.04 | 2.85 | 42.9–46.1 | JP2012 | |||
qPro-7-2 | 7 | 49.21 | 5.30 | 15.01 | 0.64 | 48.8–51.9 | JP2014 | [7] |
49.21 | 4.59 | 13.07 | 0.45 | 48.8–52.0 | CE | |||
qPro-8-1 | 8 | 19.91 | 2.60 | 8.21 | 2.15 | 12.4–25.9 | JP2012 | New |
qPro-9-1 | 9 | 67.41 | 3.51 | 7.70 | 0.46 | 61.6–69.5 | YC2014 | [14] |
qPro-9-2 | 9 | 74.31 | 3.54 | 11.94 | 0.39 | 70.3–81.8 | JP2017 | [14] |
qPro-9-3 | 9 | 97.71 | 2.78 | 6.40 | 0.33 | 91.3–105.4 | CE | [14] |
qPro-10-1 | 10 | 26.11 | 8.93 | 21.52 | 0.76 | 22.3–27.5 | YC2014 | [36] |
26.11 | 6.26 | 15.35 | 0.49 | 23.1–28.4 | CE | |||
qPro-10-2 | 10 | 33.31 | 5.46 | 13.62 | 0.48 | 32.9–33.9 | CE | New |
34.01 | 6.18 | 15.84 | 0.66 | 33.1–35.3 | YC2014 | |||
qPro-10-3 | 10 | 59.51 | 3.66 | 8.10 | 0.46 | 58.0–61.3 | JP2014 | [37] |
qPro-10-4 | 10 | 64.71 | 3.53 | 7.84 | 0.45 | 62.7–70.8 | JP2014 | [37] |
qPro-13-1 | 13 | 0.91 | 3.24 | 10.27 | −2.11 | 0.0–06.6 | JP2013 | [38] |
qPro-13-2 | 13 | 79.91 | 3.05 | 10.78 | −2.50 | 75.6–81.1 | JP2013 | [39] |
qPro-14-1 | 14 | 63.41 | 2.70 | 8.46 | 0.32 | 62.9–67.0 | JP2017 | [40,41] |
qPro-14-2 | 14 | 104.51 | 2.66 | 5.74 | 0.38 | 104.4–105.5 | JP2014 | [42] |
qPro-16-1 | 16 | 94.71 | 3.20 | 6.96 | 0.42 | 89.2–97.2 | JP2014 | New |
qPro-17-1 | 17 | 38.21 | 3.99 | 9.32 | 0.57 | 34.7–39.3 | YC2014 | New |
qPro-18-1 | 18 | 57.51 | 4.52 | 10.09 | 0.50 | 56.4–61.6 | JP2014 | [40] |
qPro-18-2 | 18 | 64.91 | 3.11 | 7.15 | 0.42 | 62.2–69.2 | JP2014 | [14] |
73.51 | 3.57 | 8.33 | 0.47 | 67.5–77.9 | YC2014 | |||
qPro-19-1 | 19 | 11.91 | 3.52 | 8.05 | −0.55 | 10.7–17.2 | YC2014 | [39] |
qPro-20-1 | 20 | 2.01 | 3.34 | 10.71 | 2.49 | 0.0–2.9 | JP2012 | New |
QTLs Names a | Chr b | Pos (cM) c | LOD d | R2 (%) e | A f | Confidence Interval (cM) g | Env. h | Ref. i |
---|---|---|---|---|---|---|---|---|
qOil-1-1 | 1 | 39.31 | 4.88 | 10.58 | −0.29 | 37.4–39.5 | JP2014 | [33] |
40.01 | 4.13 | 10.14 | −0.24 | 37.9–43.3 | YC2014 | |||
qOil-2-1 | 2 | 139.21 | 4.08 | 13.31 | 1.38 | 138.0–149.4 | JP2012 | [43] |
qOil-2-2 | 2 | 114.01 | 3.10 | 7.73 | 0.23 | 110.8–121.9 | JP2013 | [14] |
97.61 | 2.55 | 4.92 | 0.13 | 94.7–110.9 | CE | |||
qOil-3-1 | 3 | 6.11 | 2.83 | 8.96 | 1.09 | 0.9–15.4 | JP2012 | [14] |
qOil-6-1 | 6 | 62.11 | 2.74 | 5.44 | −0.71 | 55.0–75.6 | FY2012 | New |
qOil-8-1 | 8 | 11.41 | 2.77 | 6.03 | 0.14 | 09.7–17.6 | CE | [43] |
qOil-8-2 | 8 | 36.71 | 2.93 | 7.98 | −0.16 | 36.3–37.0 | CE | New |
qOil-8-3 | 8 | 42.81 | 4.08 | 10.49 | −0.24 | 40.7–43.8 | YC2014 | New |
45.51 | 2.88 | 6.19 | −0.21 | 43.8–51.7 | JP2014 | |||
46.91 | 7.91 | 19.37 | −0.25 | 44.2–49.4 | CE | |||
qOil-8-4 | 8 | 51.81 | 4.70 | 12.69 | −0.27 | 50.1–55.2 | YC2014 | [44] |
qOil-10-1 | 10 | 17.61 | 3.54 | 9.64 | −0.23 | 16.1–19.3 | YC2014 | [14] |
19.31 | 2.57 | 7.48 | −0.15 | 17.3–24.8 | JP2017 | |||
qOil-10-2 | 10 | 23.01 | 3.70 | 10.94 | −0.27 | 19.0–26.1 | JP2013 | New |
26.11 | 12.11 | 30.57 | −0.48 | 25.4–27.9 | JP2014 | |||
26.11 | 6.62 | 16.91 | −0.30 | 20.6–28.6 | YC2014 | |||
26.11 | 8.41 | 21.00 | −0.26 | 22.9–28.6 | CE | |||
qOil-10-3 | 10 | 30.41 | 3.70 | 9.90 | −0.29 | 30.4–30.8 | JP2013 | [14,45] |
qOil-10-4 | 10 | 32.91 | 5.66 | 14.50 | −0.32 | 32.2–33.6 | JP2013 | [14] |
33.31 | 6.06 | 15.65 | −0.29 | 32.9–35.3 | YC2014 | |||
33.31 | 7.66 | 19.42 | −0.25 | 32.9–35.6 | CE | |||
33.91 | 10.53 | 27.49 | −0.45 | 33.2–34.7 | JP2014 | |||
qOil-11-1 | 11 | 52.91 | 4.85 | 12.61 | −0.31 | 46.0–55.5 | JP2013 | [43] |
qOil-13-1 | 13 | 38.31 | 3.35 | 10.01 | 0.19 | 32.3–43.1 | JP2017 | [46] |
qOil-16-1 | 16 | 94.71 | 3.92 | 8.69 | −0.17 | 87.7–97.8 | CE | New |
qOil-20-1 | 20 | 4.41 | 3.09 | 9.86 | 1.20 | 0.0–13.8 | JP2012 | [47] |
qOil-20-2 | 20 | 72.41 | 3.15 | 9.27 | 0.17 | 66.3–81.8 | JP2017 | [14] |
qOil-20-3 | 20 | 99.21 | 3.92 | 8.28 | −0.25 | 92.7–102.2 | JP2014 | [14] |
QTL | Chr | Position (cM) | Marker Range | Additive Effect | Additive x Environment Effect | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
A | H2 (%) | AE1 | AE2 | AE3 | AE4 | AE5 | AE6 | H2 (%) | ||||
qOil-8-4 | 8 | 50.23 | bin908-bin909 | −0.21 ** | 7.38 | NS | NS | NS | NS | 0.29 ** | NS | 4.11 |
qOil-10-2 | 10 | 26.12 | bin1134-bin1135 | −0.22 ** | 8.36 | NS | NS | NS | −0.12 * | 0.22 ** | NS | 2.40 |
qOil-11-1 | 11 | 54.01 | bin1274-bin1275 | −0.16 ** | 4.64 | NS | NS | −0.10 * | NS | NS | NS | 2.18 |
qOil-16-1 | 16 | 96.87 | bin1819-bin1820 | −0.14 ** | 3.52 | NS | NS | NS | NS | NS | 0.11 * | 0.47 |
qPro-6-1 | 6 | 57.91 | bin612-bin613 | 0.38 ** | 5.55 | NS | NS | NS | NS | 0.25 * | −0.43 ** | 2.13 |
qPro-7-1 | 7 | 41.68 | bin771-bin772 | 0.59 ** | 13.47 | NS | −0.17 ** | NS | −0.12 * | 0.55 ** | NS | 3.17 |
qPro-10-1 | 10 | 26.12 | bin1134-bin1135 | 0.34 ** | 4.62 | NS | NS | −0.10 * | NS | 0.36 ** | NS | 1.62 |
Trait | QTL | Chr_i | Pos_i | Marker Interval_i | QTL | Chr_j | Pos_j | Marker Interval_j | Epistatic (AA) Effect | Epistatic (AA) x Environment Effect | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
AA | H2 (%) | AAE1 | AAE2 | AAE3 | AAE4 | AAE5 | AAE6 | H2 (%) | |||||||||
Oil | qOil-2-3 | 2 | 36.37 | bin132-bin133 | qOil-13-2 | 13 | 28.91 | bin1429-bin1430 | −0.14 ** | 3.81 | NS | −0.20 ** | NS | NS | NS | 0.12 * | 0.75 |
Protein | qPro-2-1 | 2 | 150.55 | bin223-bin224 | qPro-13-3 | 13 | 57.27 | bin1455-bin1456 | 1.65 ** | 1.06 | NS | NS | NS | NS | 2.33 ** | −2.07 ** | 0.85 |
Protein | qPro-17-2 | 17 | 78.16 | bin1892-bin1893 | qPro-17-3 | 17 | 94.43 | bin1911-bin1912 | 0.37 ** | 0.05 | 0.32 ** | NS | NS | NS | NS | −0.38 ** | 0.03 |
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Karikari, B.; Li, S.; Bhat, J.A.; Cao, Y.; Kong, J.; Yang, J.; Gai, J.; Zhao, T. Genome-Wide Detection of Major and Epistatic Effect QTLs for Seed Protein and Oil Content in Soybean Under Multiple Environments Using High-Density Bin Map. Int. J. Mol. Sci. 2019, 20, 979. https://doi.org/10.3390/ijms20040979
Karikari B, Li S, Bhat JA, Cao Y, Kong J, Yang J, Gai J, Zhao T. Genome-Wide Detection of Major and Epistatic Effect QTLs for Seed Protein and Oil Content in Soybean Under Multiple Environments Using High-Density Bin Map. International Journal of Molecular Sciences. 2019; 20(4):979. https://doi.org/10.3390/ijms20040979
Chicago/Turabian StyleKarikari, Benjamin, Shuguang Li, Javaid Akhter Bhat, Yongce Cao, Jiejie Kong, Jiayin Yang, Junyi Gai, and Tuanjie Zhao. 2019. "Genome-Wide Detection of Major and Epistatic Effect QTLs for Seed Protein and Oil Content in Soybean Under Multiple Environments Using High-Density Bin Map" International Journal of Molecular Sciences 20, no. 4: 979. https://doi.org/10.3390/ijms20040979