QTLs and Candidate Genes for Seed Protein Content in Two Recombinant Inbred Line Populations of Soybean
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Variation in the Seed Protein Content
2.2. Linkage Map Construction
2.3. QTL Analysis
2.4. Phenotypic Variation According to the Allele Patterns
2.5. SNP Variation Analysis and Variant Annotation
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. Analysis of Crude Seed Protein Concentrations
4.3. Genomic DNA Extraction and Genotyping
4.4. Genetic Linkage Map Construction and QTL Analysis
4.5. Prediction of Novel Candidate QTL and Genes
4.6. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Population 1 | Marker 2 | Chr 3 | Genetic Position (cM) | Physical Position of Markers (bp) 4 | Year | Gene Name | Gene No. | LOD 5 | PVE 6 (%) | Add 7 | Reference |
---|---|---|---|---|---|---|---|---|---|---|---|
Y × S | qPSD15-1 | 15 | 305 | 7,930,801–8,678,412 | 2020 2021 Average 8 | Glyma.15g101800–Glyma.15g110600 | 89 | 14.0 14.6 12.3 | 17.5 17.1 13.8 | −2.7 −2.1 −1.7 | |
Y × S | qPSD18-1 | 18 | 75 | 46,911,930–47,526,734 | 2022 Average | Glyma.18g193300–Glyma.18g197100 | 39 | 6.7 5.9 | 7.0 5.5 | −0.9 −0.6 | [38,39,40] |
Y × S | qPSD20-1 | 20 | 96 | 31,781,045–31,961,695 | 2020 2021 2022 Average | Glyma.20g085100–Glyma.20g085700 | 7 | 21.1 24.7 20.9 30.6 | 22.5 29.1 24.7 35.4 | −1.8 −1.6 −1.8 −1.6 | [14,24,25] |
S × I | qPSD20-2 | 20 | 68 | 30,395,400–31,781,045 | 2020 2021 2022 Average | Glyma.20g081000–Glyma.20g085450 | 46 | 23.0 48.2 55.0 52.7 | 34.1 59.7 66.0 61.5 | 2.4 2.1 2.4 2.3 | [14,15,19,24,25,41] |
Top 20 RILs with High Protein Content | Genotype of the Marker Linked to the QTLs | Protein Content (%) | Bottom 20 RILs with Low Protein Content | Genotype of the Marker Linked to the QTLs | Protein Content (%) | ||||
---|---|---|---|---|---|---|---|---|---|
qPSD15-1 | qPSD18-1 | qPSD20-1 | qPSD15-1 | qPSD18-1 | qPSD20-1 | ||||
YS-196 | B | B | A | 52.3 | YS-229 | A | B | A | 39.4 |
SI-400 | B | B | B | 52.1 | SI-465 | A | A | A | 39.6 |
YS-068 | B | B | B | 52.1 | YS-111 | A | A | A | 39.8 |
YS-080 | B | A | B | 52.0 | YS-209 | A | A | A | 39.9 |
YS-005 | B | A | B | 52.0 | YS-036 | B | B | A | 40.0 |
SI-317 | A | A | B | 51.9 | YS-037 | A | A | A | 40.3 |
YS-190 | B | A | B | 51.8 | YS-117 | A | A | A | 40.4 |
YS-109 | B | B | B | 51.7 | SI-337 | A | A | A | 40.6 |
YS-199 | B | B | B | 51.6 | YS-043 | B | A | A | 40.8 |
SI-428 | B | B | B | 51.5 | YS-118 | B | A | A | 40.9 |
YS-173 | B | A | B | 51.4 | SI-361 | B | B | A | 41.1 |
SI-423 | B | A | B | 51.4 | YS-063 | A | B | A | 41.1 |
YS-205 | B | A | B | 51.3 | YS-227 | B | A | A | 41.2 |
SI-445 | B | B | B | 51.3 | YS-048 | B | A | A | 41.2 |
YS-090 | B | B | B | 51.3 | SI-473 | B | A | A | 41.2 |
YS-008 | B | A | B | 51.2 | YS-015 | B | A | A | 41.4 |
SI-348 | B | B | B | 51.2 | YS-235 | A | A | A | 41.6 |
YS-202 | B | B | B | 51.2 | YS-100 | B | B | A | 41.6 |
SI-326 | B | B | B | 51.1 | SI-502 | A | A | A | 41.6 |
SI-345 | A | B | B | 51.1 | YS-045 | B | A | A | 41.6 |
Population | Marker | Gene ID | Annotation Description | Biological Process | Reference | SNP Type |
---|---|---|---|---|---|---|
Y × S | qPSD15-1 | Glyma.15g102100 | Alpha/Beta hydrolase domain-containing protein | NA | Stop gain | |
Glyma.15g102202 | Elongation factor Tu GTP binding domain | Translational elongation | Frameshift variant | |||
Glyma.15g102252 | Elongation factor Tu C-terminal domain | Translational elongation | Frameshift variant | |||
Glyma.15g102800 | Mediator of RNA polymerase II transcription subunit 33a | Phenylpropanoid metabolic process | Stop gain | |||
Glyma.15g103100 | Mitochondrial editing factor 18 | RNA modification | Frameshift variant | |||
Glyma.15g107200 | GPI-anchored protein | Biological process | Stop gain | |||
Glyma.15g108000 | Starch/carbohydrate-binding module (family 53) | Starch biosynthetic process | Frameshift variant | |||
Glyma.15g108900 | Glycosyl hydrolases family 17 | Carbohydrate metabolic process | Frameshift variant | |||
Glyma.15g109800 | Peroxisomal membrane protein 2 | Biological process | Frameshift variant | |||
Glyma.15g109900 | F-BOX protein with a domain protein | NA | Frameshift variant | |||
qPSD18-1 | Glyma.18g193300 | Laccase | Iron ion transport | Frameshift variant | ||
Glyma.18g193600 | Fructose-1,6-bisphosphatase, N-terminal domain | Sucrose metabolic process | [38] | Frameshift variant | ||
Glyma.18g194700 | NA | NA | Stop gain | |||
Glyma.18g194900 | NA | NA | Frameshift variant | |||
Glyma.18g195000 | NA | Biological process | Frameshift variant | |||
Glyma.18g195700 | Alpha-carboxyltransferase aCT-1 precursor | Fatty acid biosynthesis | [39,40] | Missense variant | ||
Glyma.18g195900 | Carboxyl transferase domain | Fatty acid biosynthesis | [39,40] | Missense variant | ||
Glyma.18g196000 | Carboxyl transferase domain | Fatty acid biosynthesis | [39,40] | Missense variant | ||
Glyma.18g196600 | NA | NA | Stop gain | |||
Glyma.18g197100 | NA | NA | Frameshift variant | |||
qPSD20-1 | Glyma.20g085100 | POWR1 CCT motif family protein | Biological process | [14,24,25] | Missense variant | |
Glyma.20g085700 | Unknown protein | NA | [15] | Stop gain | ||
S × I | qPSD20-2 | Glyma.20g081500 | Lipase containing protein | Lipid catabolic process | Missense variant | |
Glyma.20g082450 | Ammonium transporter 1 | Ammonium transport | [15] | Missense variant | ||
Glyma.20g082700 | Sugar efflux transporter SWEET52 | Carbohydrate transport | [42,43] | Missense variant | ||
Glyma.20g084000 | Small nuclear ribonucleoprotein F | Spliceosomal snRNP assembly | [15] | Missense variant | ||
Glyma.20g084051 | Far1-relate | Regulation of transcription | [15] | Missense variant | ||
Glyma.20G084500 | WD40 repeat protein | Innate immune response | [15] | Missense variant | ||
Glyma.20g085100 | POWR1 CCT motif family protein | Biological process | [14,24,25] | Missense variant |
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Park, H.R.; Seo, J.H.; Kang, B.K.; Kim, J.H.; Heo, S.V.; Choi, M.S.; Ko, J.Y.; Kim, C.S. QTLs and Candidate Genes for Seed Protein Content in Two Recombinant Inbred Line Populations of Soybean. Plants 2023, 12, 3589. https://doi.org/10.3390/plants12203589
Park HR, Seo JH, Kang BK, Kim JH, Heo SV, Choi MS, Ko JY, Kim CS. QTLs and Candidate Genes for Seed Protein Content in Two Recombinant Inbred Line Populations of Soybean. Plants. 2023; 12(20):3589. https://doi.org/10.3390/plants12203589
Chicago/Turabian StylePark, Hye Rang, Jeong Hyun Seo, Beom Kyu Kang, Jun Hoi Kim, Su Vin Heo, Man Soo Choi, Jee Yeon Ko, and Choon Song Kim. 2023. "QTLs and Candidate Genes for Seed Protein Content in Two Recombinant Inbred Line Populations of Soybean" Plants 12, no. 20: 3589. https://doi.org/10.3390/plants12203589