Identification of Multiple Genetic Loci and Candidate Genes Determining Seed Size and Weight in Soybean
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Phenotyping
2.2. DNA Extraction and Sequencing
2.3. Analysis of Genomic Variants between the Two Parents
2.4. BSA-Seq Data Analysis
2.5. Naming Principle for QTLs
2.6. RNA Extraction and Sequencing
2.7. Transcriptome Data Analysis
2.8. RT-qPCR Assay
2.9. InDel/CAPS Marker Design and Linkage Mapping
3. Results
3.1. Phenotype Distribution and Correlations among Different Seed Traits in the Segregating Populations
3.2. Identification of Genetic Loci for Seed Traits through BSA-Seq
3.3. Linkage Mapping of Stable QTLs
3.4. Gene Expression Difference and Genetic Variation in Candidate Genes within qSS4-1, qSS20-1, and qSW14-1
4. Discussion
4.1. Identification of Novel QTLs for Seed Size and Weight in Soybean
4.2. The Pleiotropic Loci for Soybean Seed Size and Weight
4.3. Prediction of Candidate Genes in qSS4-1, qSS20-1, and qSW14-1
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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QTL | Chr | Traits | LOD | PVE(%) a | Left Marker | Right Marker | Position (bp) b |
---|---|---|---|---|---|---|---|
qSS4-1 | 4 | SL | 7.37 | 15.04 | Caps4-1 | Caps4-2 | 3,294,059–4,511,350 |
SW | 6.14 | 12.51 | Caps4-1 | Caps4-2 | 3,294,059–4,511,350 | ||
HSW | 5.24 | 10.75 | Caps4-1 | Caps4-2 | 3,294,059–4,511,350 | ||
qSS20-1 | 20 | SL | 10.37 | 19.87 | Marker20-4 | Marker20-5 | 37,158,491–38,379,617 |
SW | 4.04 | 13.73 | Marker20-4 | Marker20-5 | 37,158,491–38,379,617 | ||
ST | 3.33 | 6.86 | Marker20-4 | Marker20-5 | 37,158,491–38,379,617 | ||
HSW | 10.39 | 19.84 | Marker20-4 | Marker20-5 | 37,158,491–38,379,617 | ||
qSW14-1 | 14 | SW | 20.31 | 8.64 | Marker14-4 | Marker14-6 | 14,344,083–28,212,214 |
QTL | ID | At Locus | Name a | DEG b | Variation |
---|---|---|---|---|---|
qSS4-1 | Glyma.04G042000 | AT4G34160 | CYCD3;1 | ||
Glyma.04G045500 | AT4G37630 | CYCD5;1 | R3 pods | ||
Glyma.04G046600 | AT4G33800 | T16L1.290 | |||
Glyma.04G047900 | AT4G37750 | ANT | R5 seeds | ||
Glyma.04G055600 | AT5G21482 | CKX7 | |||
qSW14-1 | Glyma.14G128400 | AT1G15550 | GA3OX1 | NA | upstream/downstream |
Glyma.14G132500 | AT3G49600 | SUP32 | intron/upstream/downstream | ||
Glyma.14G138700 | AT2G24400 | SAUR37 | NA | upstream/downstream | |
Glyma.14G144200 | AT1G10010 | AAP8 | R5 seeds | intron | |
Glyma.14G144400 | AT1G10010 | AAP8 | NA | upstream | |
Glyma.14G144700 | AT1G10010 | AAP8 | 3′-UTR/upstream/downstream | ||
qSS20-1 | Glyma.20G135400 | AT1G70210 | CYCD1;1 | intron/upstream/downstream | |
Glyma.20G135700 | AT3G49780 | PSK4 | R3 pods | synonymous | |
Glyma.20G136400 | AT5G60440 | AGL62 | NA | ||
Glyma.20G136500 | AT5G60440 | AGL62 | NA | ||
Glyma.20G136600 | AT5G60440 | AGL62 | upstream | ||
Glyma.20G136700 | AT5G60440 | AGL62 | NA | synonymous/upstream/downstream | |
Glyma.20G136800 | AT2G24840 | AGL61 | NA | missense (Asn-Ser)/intron/upstream/downstream |
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Wang, M.; Ding, X.; Zeng, Y.; Xie, G.; Yu, J.; Jin, M.; Liu, L.; Li, P.; Zhao, N.; Dong, Q.; et al. Identification of Multiple Genetic Loci and Candidate Genes Determining Seed Size and Weight in Soybean. Agronomy 2024, 14, 1957. https://doi.org/10.3390/agronomy14091957
Wang M, Ding X, Zeng Y, Xie G, Yu J, Jin M, Liu L, Li P, Zhao N, Dong Q, et al. Identification of Multiple Genetic Loci and Candidate Genes Determining Seed Size and Weight in Soybean. Agronomy. 2024; 14(9):1957. https://doi.org/10.3390/agronomy14091957
Chicago/Turabian StyleWang, Meng, Xiaoyang Ding, Yong Zeng, Gang Xie, Jiaxin Yu, Meiyu Jin, Liu Liu, Peiyuan Li, Na Zhao, Qianli Dong, and et al. 2024. "Identification of Multiple Genetic Loci and Candidate Genes Determining Seed Size and Weight in Soybean" Agronomy 14, no. 9: 1957. https://doi.org/10.3390/agronomy14091957