Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut
Abstract
:1. Introduction
2. Materials and Methods
2.1. Phenotyping RIL Population for Yield and Quality Traits
2.1.1. Phenotyping for Yield-Related Traits
2.1.2. Phenotyping for Physiological Traits
2.1.3. Phenotyping for Oil Content, Fatty Acids, and Protein Content
2.2. Phenotypic Analysis
2.3. DNA Isolation and Sequencing
2.4. SNP Calling and Filtering
2.5. Construction of Genetic Linkage Map and QTL Analysis
2.6. Identification of Candidate Genes from Identified QTL Regions and Expression Analysis
2.7. Identification of Epistatic (Q × Q) Effect
3. Results
3.1. Phenotypic Data Analysis
3.2. Identification of Marker Polymorphism and Genotyping
3.3. Construction of Genetic Linkage Map
3.4. QTLs for Yield and Quality Traits
3.4.1. QTLs for Yield-Related and Physiological Traits
3.4.2. QTLs for Oil Content, Fatty Acids, and Protein Content
3.5. Epistatic (QTL × QTL) Interaction for Yield- and Quality-Related Traits
3.5.1. Digenic Interaction
3.5.2. Trigenic Interaction
3.6. Identification of Candidate Genomic Regions for HSW and SP
4. Discussion
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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Trait/Source of Variation | Mean Sum of Squares | ||||
---|---|---|---|---|---|
Environment | Replication | Genotypes | G × E | Pooled Error | |
Degrees of freedom | 1 | 1 | 143 | 143 | 286 |
Pod yield (kg ha−1) | 9,047,419.28 * | 207,621.32 | 40,307.69 | 61,125.05 *** | 27,562.89 |
Haulm yield (kg ha−1) | 38,793,685.30 * | 227,604.46 | 56,512.90 * | 55,332.65 | 36,921.52 |
HPW (g) | 680.68 | 1676.18 | 120.94 | 107.35 *** | 66.61 |
HSW (g) | 1040.53 | 665.70 | 31.87 | 31.657 *** | 17.71 |
SP | 7696.37 | 2031.01 | 53.69 | 66.38 *** | 39.92 |
SCMR | 1948.92 | 439.82 | 46.98 | 44.46 *** | 24.82 |
Oil content (%) | 470.49 | 1130.28 | 31.43 *** | 12.79 | 9.51 |
Protein content (%) | 2.08 | 194.32 | 5.22 *** | 2.68 | 1.48 |
Linoleic acid (%) | 23.66 | 77.20 | 99.13 *** | 26.02 | 17.11 |
Oleic acid (%) | 526.32 | 867.12 | 137.77 *** | 30.62 | 18.65 |
Traits | Environment | Parental Means | CD (5%) | Recombinant Inbred Lines | |||||
---|---|---|---|---|---|---|---|---|---|
JUG-03 | Valencia-C | RIL | Range | PCV | GCV | H2 | |||
Mean | |||||||||
Pod yield | E1 | 580.00 | 890.00 | 266.72 | 675.24 | 580–960 | 25.73 | 16.20 | 39.67 |
E2 | 299.16 | 690.75 | 371.78 | 420.84 | 121.75–725.16 | 51.37 | 25.29 | 24.25 | |
Haulm yield | E1 | 465.07 | 297.90 | 171.44 | 434.71 | 229.67–608.5 | 24.98 | 15.03 | 36.20 |
E2 | 991.50 | 654.5 | 509.05 | 953.75 | 646.5–1418 | 9.22 | 28.53 | 10.45 | |
HPW | E1 | 66.61 | 94.62 | 22.09 | 78.09 | 61.62–102.06 | 16.37 | 7.95 | 23.57 |
E2 | 74.50 | 82.00 | 6.14 | 75.93 | 73–86 | 5.50 | 3.67 | 44.56 | |
HSW | E1 | 30.00 | 39.50 | 11.69 | 34.48 | 28–44 | 20.23 | 10.74 | 28.15 |
E2 | 30.05 | 32.60 | 1.33 | 31.79 | 29.9–33.2 | 2.78 | 1.79 | 41.58 | |
SP | E1 | 47.00 | 58.49 | 14.63 | 53.07 | 45.5–63.11 | 15.28 | 6.23 | 16.61 |
E2 | 52.11 | 66.85 | 9.79 | 60.41 | 50.87–71.5 | 9.54 | 4.86 | 26.03 | |
SCMR | E1 | 42.50 | 55.35 | 11.44 | 45.32 | 37.5–59.2 | 15.39 | 8.59 | 31.13 |
E2 | 37.60 | 46.15 | 7.94 | 41.64 | 34.9–48.35 | 11.23 | 5.75 | 26.24 | |
Oil content | E1 | 46.23 | 42.47 | 7.62 | 44.26 | 38.41–48.94 | 10.11 | 5.14 | 25.87 |
E2 | 49.28 | 40.41 | 5.73 | 46.08 | 39.21–55.33 | 8.04 | 5.00 | 38.66 | |
Protein content | E1 | 30.50 | 25.98 | 2.52 | 28.91 | 23.03–31 | 5.04 | 2.43 | 23.21 |
E2 | 30.22 | 25.75 | 2.27 | 28.78 | 23.03–30.22 | 5.08 | 3.13 | 38.08 | |
Linoleic acid | E1 | 24.47 | 33.10 | 9.46 | 27.91 | 17.01–36.23 | 20.35 | 10.96 | 29.02 |
E2 | 22.55 | 30.73 | 9.94 | 27.84 | 12.05–34.59 | 24.74 | 16.9 | 46.65 | |
Oleic acid | E1 | 42.21 | 52.92 | 11.98 | 49.15 | 38.51–60.86 | 14.3 | 7.24 | 25.65 |
E2 | 44.14 | 50.32 | 12.9 | 47.24 | 35.59–60.15 | 17.39 | 10.56 | 36.92 |
Chromosome | Mapped Loci | Map Distance (cM) | Inter-Marker Distance (cM) | Map Density (loci/cM) |
---|---|---|---|---|
A01 | 58 | 99.50 | 1.72 | 0.58 |
A02 | 42 | 134.70 | 3.21 | 0.31 |
A03 | 82 | 142.69 | 1.74 | 0.57 |
A04 | 61 | 88.70 | 1.45 | 0.69 |
A05 | 67 | 129.80 | 1.94 | 0.52 |
A06 | 42 | 75.30 | 1.79 | 0.56 |
A07 | 22 | 55.00 | 2.50 | 0.40 |
A08 | 45 | 167.12 | 3.71 | 0.27 |
A09 | 47 | 87.30 | 1.86 | 0.54 |
A10 | 92 | 99.36 | 1.08 | 0.93 |
B01 | 51 | 112.02 | 2.20 | 0.46 |
B02 | 99 | 137.54 | 1.39 | 0.72 |
B03 | 89 | 101.21 | 1.14 | 0.88 |
B04 | 61 | 71.10 | 1.17 | 0.86 |
B05 | 124 | 74.85 | 0.60 | 1.66 |
B06 | 91 | 126.80 | 1.39 | 0.72 |
B07 | 98 | 119.96 | 1.22 | 0.82 |
B08 | 21 | 74.00 | 3.52 | 0.28 |
B09 | 20 | 72.50 | 3.63 | 0.28 |
B10 | 111 | 70.28 | 0.63 | 1.58 |
Grand Total | 1323 | 2003.13 | 1.89 |
QTLs | Traits | Env. | Chr. | Pos. (cM) | Marker Interval | LOD | PVE (%) | Additive Effect |
---|---|---|---|---|---|---|---|---|
qPODYLD18E1 | Pod yield | E1 | B08 | 28.17 | S18_51822496-S18_134813874 | 4.88 | 6.87 | −155.85 |
qPODYLD12.2E2 | Pod yield | E2 | B02 | 99.71 | S12_93246314-S12_100066236 | 4.6 | 6.27 | −65.62 |
qPODYLD12.3E2 | Pod yield | E2 | B02 | 106.01 | S12_110782372-S12_112245066 | 4.78 | 6.53 | −65.04 |
qHAULMYLD18E1 | Haulm yield | E1 | B08 | 28.61 | S18_51822496-S18_134813874 | 4.34 | 6.09 | −64.16 |
qHAULMYLD6E1 | Haulm yield | E1 | A06 | 29.16 | S6_1562649-S6_1630272 | 3.64 | 9.55 | 149.88 |
qHSW12E1 | HSW | E1 | B02 | 57.21 | S12_42838843-S12_73270208 | 4.06 | 5.89 | 9.39 |
qHSW16E1 | HSW | E1 | B06 | 120.57 | S16_2332048-S16_8231918 | 6.65 | 14.65 | −5.38 |
qHSW16E2 | HSW | E2 | B06 | 120.55 | S16_2332048-S16_8231918 | 6.11 | 13.87 | −3.31 |
qSP12E1 | SP | E1 | B02 | 57.23 | S12_42838843-S12_73270208 | 4.36 | 10.98 | 13.95 |
qSP12E2 | SP | E2 | B02 | 57.21 | S12_42838843-S12_73270208 | 4.43 | 11.65 | 5.44 |
qSCMR17E2 | SCMR | E2 | B07 | 22.21 | S17_32203546-S17_66864943 | 4.27 | 5.9 | −6.28 |
qOIL12E1 | Oil content | E1 | B02 | 57.21 | S12_42838843-S12_73270208 | 3.05 | 4.49 | 10.65 |
qOIL12E2 | Oil content | E2 | B02 | 57.23 | S12_42838843-S12_73270208 | 3.02 | 4.46 | 10.67 |
qPROTEIN12E2 | Protein content | E2 | B02 | 57.21 | S12_42838843-S12_73270208 | 3.15 | 4.66 | 6.79 |
qLINOLEIC12E2 | Linoleic acid | E2 | B02 | 64.11 | S12_36421620-S12_118023921 | 3.43 | 5.15 | −3.41 |
qOLEIC17E1 | Oleic acid | E1 | B07 | 22.21 | S17_32203546-S17_66864943 | 5.76 | 8.09 | −9.09 |
qOLEIC17E2 | Oleic acid | E2 | B07 | 22.21 | S17_32203546-S17_66864943 | 6.14 | 8.5 | −9.16 |
Traits | No. of QTLs | LOD Range | PVE % |
---|---|---|---|
Pod yield | 9 | 3.08–4.18 | 24.96–38.48 |
Haulm yield | 15 | 3.00–5.97 | 11.86–54.84 |
HSW | 4 | 3.04–4.17 | 9.31–20.48 |
SP | 14 | 3.00–5.72 | 11.72–72.61 |
SCMR | 8 | 3.00–4.10 | 11.85–22.85 |
Oil content | 7 | 3.04–4.77 | 11.63–28.23 |
Protein content | 11 | 8.54–19.99 | 48.31–61.59 |
Linoleic acid | 2 | 3.02–3.30 | 18.75–26.73 |
Oleic acid | 7 | 3.08–4.38 | 13.07–50.08 |
Traits | QTL Name | Gene Location | Gene Model | Nearest SNP (bp) | Functional Annotation |
---|---|---|---|---|---|
SP | qSP12E1 and qSP12E2 | Araip.B02 | Araip.6MG4Z | 67,500,914 | Disease resistance protein |
Araip.DH675 | 42,817,549 | Serine/threonine-protein phosphatase | |||
Araip.5HJ7H | 67,500,914 | Protein MIZU-KUSSEI 1 | |||
Araip.7QC0C | 42,817,549 | Actin-related protein | |||
HSW | qHSW16E1 and qHSW16E2 | Araip.B06 | Araip.49T7Y | 8,393,784 | Protein kinase superfamily protein |
Araip.5E3CZ | 1,562,649 | Transcription factor bHLH68 | |||
Araip.CXF88 | 271,015 | CBS domain-containing protein | |||
Araip.GWR7V | 2,818,988 | Seed maturation protein | |||
Araip.LE5CL | 1,562,649 | Ethylene-responsive transcription factor | |||
Araip.UY42T | 2,697,960 | Isopentenyltransferase 3 | |||
Araip.WM0UU | 7,821,084 | Cytochrome P450 superfamily protein | |||
Araip.60J6J | 2,818,988 | GTP binding elongation factor | |||
Araip.CY9QC | 8,393,784 | Ribosomal protein L19e family protein | |||
Araip.SKT5W | 1,562,649 | NAD+ ADP-ribosyltransferase |
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Joshi, P.; Soni, P.; Sharma, V.; Manohar, S.S.; Kumar, S.; Sharma, S.; Pasupuleti, J.; Vadez, V.; Varshney, R.K.; Pandey, M.K.; et al. Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut. Genes 2024, 15, 140. https://doi.org/10.3390/genes15020140
Joshi P, Soni P, Sharma V, Manohar SS, Kumar S, Sharma S, Pasupuleti J, Vadez V, Varshney RK, Pandey MK, et al. Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut. Genes. 2024; 15(2):140. https://doi.org/10.3390/genes15020140
Chicago/Turabian StyleJoshi, Pushpesh, Pooja Soni, Vinay Sharma, Surendra S. Manohar, Sampath Kumar, Shailendra Sharma, Janila Pasupuleti, Vincent Vadez, Rajeev K. Varshney, Manish K. Pandey, and et al. 2024. "Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut" Genes 15, no. 2: 140. https://doi.org/10.3390/genes15020140
APA StyleJoshi, P., Soni, P., Sharma, V., Manohar, S. S., Kumar, S., Sharma, S., Pasupuleti, J., Vadez, V., Varshney, R. K., Pandey, M. K., & Puppala, N. (2024). Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut. Genes, 15(2), 140. https://doi.org/10.3390/genes15020140