QTL Mapping and Candidate Gene Analysis for Pod Shattering Tolerance in Soybean (Glycine max)
Abstract
:1. Introduction
2. Results
2.1. Variation in Pod Shattering Ratios
2.2. Linkage Map Construction
2.3. QTL Analysis
2.4. Phenotypic Variation According to the Allele Patterns
2.5. Identification of Candidate Genes within and Near QTL
3. Discussion
4. Materials and Methods
4.1. Plant Material
4.2. Evaluation of Pod Shattering Tolerance
4.3. Genomic DNA Extraction and Genotyping
4.4. Linkage Map Construction and QTL Mapping
4.5. Prediction of Novel Candidate QTL and Genes
4.6. Gene Expression Analysis of the Candidate Genes
4.7. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Drying Time (Hour) | Year | Pod Shattering Ratio ± SE (%) † | Broad-Sense Heritability | |||||
---|---|---|---|---|---|---|---|---|
Parents | RILs | |||||||
DW | TW | SO | DT | DS | DT | DS | ||
24 | 2016 | 0 | 25 | 100 | 12.1 ± 24.6 | 24.4 ± 33.5 | ||
2017 | 0 | 0 | 100 | 9.9 ± 34.8 | 23.3 ± 33.8 | |||
2018 | 0 | 50 | 100 | 27.8 ± 40.4 | 32.5 ± 32.0 | |||
average | 0 | 25 | 100 | 16.6 ± 19.0c ‡ | 26.7 ± 26.2c | 0.38 | 0.62 | |
48 | 2016 | 0 | 35 | 100 | 27.8 ± 34.7 | 47.7 ± 42.9 | ||
2017 | 0 | 20 | 100 | 38.4 ± 39.6 | 48.0 ± 46.1 | |||
2018 | 0 | 50 | 100 | 44.8 ± 36.4 | 50.5 ± 38.6 | |||
average | 0 | 35 | 100 | 37.0 ± 31.9b | 48.7 ± 39.1b | 0.78 | 0.84 | |
72 | 2016 | 0 | 80 | 100 | 43.6 ± 40.3 | 54.7 ± 43.6 | ||
2017 | 0 | 100 | 100 | 53.5 ± 43.2 | 51.1 ± 46.8 | |||
2018 | 0 | 60 | 100 | 52.0 ± 37.7 | 60.1 ± 37.3 | |||
average | 0 | 80 | 100 | 49.7 ± 37.4a | 55.3 ± 39.0a | 0.88 | 0.82 |
Name of QTL | Chr. (LG) 1 | Year | Drying Time (Hour) | Position (cM) | Physical Interval 2 (bp) | LOD 3 | PVE 4 (%) | Add 5 | No. Candidate Genes | References |
---|---|---|---|---|---|---|---|---|---|---|
qPS-DT02 | 2 (D1b) | 2017 | 24 | 122 | 7,211,739–8,082,789 | 6.0 | 1.9 | −5.9 | 87 | Kang et al. 2009 |
qPS-DT06 | 6 (C2) | 2016 | 48 | 103 | 5,498,397–6,170,213 | 3.6 | 6.1 | −9.0 | 82 | Novel |
qPS-DT11 | 11 (B1) | 2017 | 48 | 92 | 26,717,840–30,547,921 | 17.4 | 13.3 | −20.0 | 189 | Novel |
qPS-DT13 | 13 (F) | 2017 | 24 | 108 | 35,019,516–35,459,889 | 4.3 | 1.3 | −5.0 | 54 | Novel |
qPS-DT14 | 14 (B2) | 2017 | 24 | 11 | 48,063,838–48,101,634 | 33.4 | 16.4 | −17.8 | 2 | Novel |
qPS-DT16-1 | 16 (J) | 2017 | 24 | 63 | 29,532,807–29,809,243 | 7.4 | 2.3 | −6.7 | 21 | qPDH1(nearby) |
2018 | 72 | 29,532,807–29,809,243 | 31.0 | 67.8 | −32.0 | |||||
qPS-DT16-2 | 16 (J) | 2016 | 48 | 64 | 29,913,393–29,972,096 | 13.4 | 26.1 | −19.0 | 5 | qPDH1 (Funatsuki et al. 2008) |
2016 | 72 | 29,913,393–29,972,096 | 23.9 | 48.0 | −29.2 | |||||
2017 | 48 | 29,913,393–29,972,096 | 30.1 | 29.6 | −30.3 | |||||
2017 | 72 | 29,913,393–29,972,096 | 67.1 | 82.8 | −42.0 | |||||
Combined 6 | 24 | 29,913,393–29,972,096 | 13.4 | 33.1 | −11.2 | |||||
Combined | 48 | 29,913,393–29,972,096 | 35.7 | 60.8 | −25.9 | |||||
Combined | 72 | 29,913,393–29,972,096 | 55.4 | 78.7 | −34.6 | |||||
qPS-DT20 | 20 | Combined | 48 | 93 | 2,151,689–2,392,383 | 3.7 | 3.7 | −6.3 | 17 | Novel |
Name of QTL | Chr. (LG) 1 | Year | Drying Time (Hour) | Position (cM) | Physical Interval 2 (bp) | LOD 3 | PVE 4 (%) | Add 5 | No. Candidate Genes | References |
---|---|---|---|---|---|---|---|---|---|---|
qPS-DS16-1 | 16 (J) | Combined 6 | 24 | 61 | 7,325,202–7,760,393 | 5.4 | 11.2 | −7.1 | 41 | Novel |
qPS-DS16-2 | 16 (J) | 2016 | 48 | 45 | 29,857,920–30,146,414 | 19.5 | 44.8 | −28.7 | 20 | qPDH1 (Funatsuki et al. 2008) |
2016 | 72 | 29,857,920–30,146,414 | 18.0 | 42.4 | −28.3 | |||||
2017 | 24 | 29,857,920–30,146,414 | 14.6 | 36.0 | −20.2 | |||||
2017 | 48 | 29,857,920–30,146,414 | 56.0 | 61.2 | −40.9 | |||||
2017 | 72 | 29,857,920–30,146,414 | 60.0 | 63.0 | −41.9 | |||||
Combined | 24 | 29,857,920–30,146,414 | 19.2 | 48.7 | −14.8 | |||||
Combined | 48 | 29,857,920–30,146,414 | 40.9 | 70.3 | −26.8 | |||||
Combined | 72 | 29,857,920–30,146,414 | 40.8 | 71.8 | −26.9 | |||||
qPS-DS16-3 | 16 (J) | 2018 | 24 | 43 | 30,144,267–30,580,464 | 15.2 | 56.8 | −24.4 | 25 | qPDH1 (nearby) |
2018 | 48 | 30,144,267–30,580,464 | 31.8 | 80.1 | −37.0 | |||||
2018 | 72 | 30,144,267–30,580,464 | 27.2 | 76.4 | −34.3 |
Genotype 1 | qPS-DS16-1 | qPS-DT11 | qPS-DT14 | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Major | Minor | 24 h | 48 h | 72 h | 24 h | 48 h | 72 h | 24 h | 48 h | 72 h |
P1 | P1 | 2.5 | 6.5 | 10.9 | 2.6 | 6.5 | 10.7 | 3.5 | 8.1 | 12.7 |
P2 | 6.2 | 12.5 | 18.6 | 4.3 | 10.7 | 15.6 | 3.8 | 9.0 | 13.6 | |
t-value 2 | −1.68 * | −1.50 ns | −1.61 ns | −1.15 ns | −1.45 ns | −1.44 ns | −0.15 ns | −0.29 ns | −0.24 ns | |
P2 | P1 | 24.3 | 60.5 | 76.1 | 37.2 | 70.3 | 82.8 | 32.0 | 65.6 | 81.7 |
P2 | 37.6 | 69.9 | 83.5 | 31.9 | 65.9 | 80.8 | 36.8 | 69.8 | 81.6 | |
t-value | −3.81 ** | −2.07 * | −2.00 * | 1.43 ns | 1.12 ns | 0.73 ns | −1.32 ns | −1.09 ns | 0.04 ns |
Gene Name | Position (bp) | Reference (Williams82) | DW | TW | SO | AA Change | Description |
---|---|---|---|---|---|---|---|
Glyma.16g072700 | 7,335,363 | - | - | 12 bp deletion | 12 bp deletion | Deletion | Myb-like DNA-binding domain, DNA binding |
Glyma.16g073700 | 7,446,096 | A | A | T | T | Tyr/Asn | Unknown |
Glyma.16g076100 | 7,665,996 | C | T | C | C | Glu/Lys | Rho guanyl-nucleotide exchange factor activity |
Glyma.16g076300 | 7,725,602 | A | C | A | A | Met/Leu | GMC oxidoreductase |
Glyma.16g076500 | 7,760,100 | T | C | T | T | Leu/Ser | Adaptin N terminal region |
7,760,393 | A | C | A | A | Ile/Leu | ||
Glyma.16g076600 | 7,775,892 | C | T | C | C | Glu/Lys | Cytochrome P450, |
7,775,945 | T | A | T | T | Lys/Met | (+)-abscisic acid 8′-hydroxylase activity | |
7,775,948 | A | G | A | A | Ile/Thr | ||
7,775,970 | - | 18 bp insertion | - | - | Insertion | ||
7,776,045 | C | T | C | C | Met/Ile | ||
7,777,575 | - | 3 bp deletion | - | - | Asn/- |
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Seo, J.-H.; Kang, B.-K.; Dhungana, S.K.; Oh, J.-H.; Choi, M.-S.; Park, J.-H.; Shin, S.-O.; Kim, H.-S.; Baek, I.-Y.; Sung, J.-S.; et al. QTL Mapping and Candidate Gene Analysis for Pod Shattering Tolerance in Soybean (Glycine max). Plants 2020, 9, 1163. https://doi.org/10.3390/plants9091163
Seo J-H, Kang B-K, Dhungana SK, Oh J-H, Choi M-S, Park J-H, Shin S-O, Kim H-S, Baek I-Y, Sung J-S, et al. QTL Mapping and Candidate Gene Analysis for Pod Shattering Tolerance in Soybean (Glycine max). Plants. 2020; 9(9):1163. https://doi.org/10.3390/plants9091163
Chicago/Turabian StyleSeo, Jeong-Hyun, Beom-Kyu Kang, Sanjeev K. Dhungana, Jae-Hyeon Oh, Man-Soo Choi, Ji-Hee Park, Sang-Ouk Shin, Hong-Sik Kim, In-Youl Baek, Jung-Sook Sung, and et al. 2020. "QTL Mapping and Candidate Gene Analysis for Pod Shattering Tolerance in Soybean (Glycine max)" Plants 9, no. 9: 1163. https://doi.org/10.3390/plants9091163