Population Structure and Genetic Diversity of the 175 Soybean Breeding Lines and Varieties Cultivated in West Siberia and Other Regions of Russia
Abstract
:1. Introduction
2. Material and Methods
2.1. Russian Soybean Varieties
2.2. Genotyping
2.3. Soybean Dataset from SoyBase
2.4. Data Quality Control
2.5. Population Genetic Analysis
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
- FAOSTAT. Databases: Soybean Production in 2021, Crops/World Regions/Production Quantity (from Pick Lists); United Nations, Food and Agriculture Organization, Statistics Division, FAOSTAT: Rome, Italy, 2021; Available online: https://www.fao.org/faostat/en/#data/QCL (accessed on 8 September 2023).
- Avinc, O.; Yavas, A. Soybean: For Textile Applications and Its Printing [Internet]. Soybean-The Basis of Yield, Biomass and Productivity; InTech: Nappanee, IN, USA, 2017. [Google Scholar] [CrossRef]
- Milanović, T.; Popović, V.; Vučković, S.; Rakaščan, N.; Popović, S.; Petković, Z. Analysis of Soybean Production and Biogas Yield to Improve Eco-Marketing and Circular Economy. Ekon. Poljopr. 2020, 67, 141–156. [Google Scholar] [CrossRef]
- Zhang, J.; Mungara, P.; Jane, J. Mechanical and thermal properties of extruded soy protein sheets. Polymer 2001, 42, 2569–2578. [Google Scholar] [CrossRef]
- Liu, Z.; Li, H.; Wen, Z.; Fan, X.; Li, Y.; Guan, R.; Guo, Y.; Wang, S.; Wang, D.; Qiu, L. Comparison of Genetic Diversity between Chinese and American Soybean (Glycine max (L.)) Accessions Revealed by High-Density SNPs. Front. Plant Sci. 2017, 8, 2014. [Google Scholar] [CrossRef]
- Dong, L.; Fang, C.; Cheng, Q.; Su, T.; Kou, K.; Kong, L.; Zhang, C.; Li, H.; Hou, Z.; Zhang, Y.; et al. Genetic Basis and Adaptation Trajectory of Soybean from Its Temperate Origin to Tropics. Nat. Commun. 2021, 12, 5445. [Google Scholar] [CrossRef] [PubMed]
- Maldonado Dos Santos, J.V.; Sant’Ana, G.C.; Wysmierski, P.T.; Todeschini, M.H.; Garcia, A.; Meda, A.R. Genetic Relationships and Genome Selection Signatures between Soybean Cultivars from Brazil and United States after Decades of Breeding. Sci. Rep. 2022, 12, 10663. [Google Scholar] [CrossRef] [PubMed]
- Naflath, T.V.; Rajendra, P.S.; Ravikumar, R.L. Population Structure and Genetic Diversity Characterization of Soybean for Seed Longevity. PLoS ONE 2022, 17, e0278631. [Google Scholar] [CrossRef]
- Deriglazova, G. Current Trends in Soybean Cultivation in Russia. Agric. Lifestock Technol. 2022, 5, 1–10. [Google Scholar] [CrossRef]
- Bayer, P.E.; Valliyodan, B.; Hu, H.; Marsh, J.I.; Yuan, Y.; Vuong, T.D.; Patil, G.; Song, Q.; Batley, J.; Varshney, R.K.; et al. Sequencing the USDA Core Soybean Collection Reveals Gene Loss during Domestication and Breeding. Plant Genome 2022, 15, e20109. [Google Scholar] [CrossRef]
- Kim, M.-S.; Lozano, R.; Kim, J.H.; Bae, D.N.; Kim, S.-T.; Park, J.-H.; Choi, M.S.; Kim, J.; Ok, H.-C.; Park, S.-K.; et al. The Patterns of Deleterious Mutations during the Domestication of Soybean. Nat. Commun. 2021, 12, 97. [Google Scholar] [CrossRef]
- Valliyodan, B.; Brown, A.V.; Wang, J.; Patil, G.; Liu, Y.; Otyama, P.I.; Nelson, R.T.; Vuong, T.; Song, Q.; Musket, T.A.; et al. Genetic Variation among 481 Diverse Soybean Accessions, Inferred from Genomic Re-Sequencing. Sci. Data 2021, 8, 50. [Google Scholar] [CrossRef]
- Liu, N.; Niu, Y.; Zhang, G.; Feng, Z.; Bo, Y.; Lian, J.; Wang, B.; Gong, Y. Genome Sequencing and Population Resequencing Provide Insights into the Genetic Basis of Domestication and Diversity of Vegetable Soybean. Hortic. Res. 2022, 9, uhab052. [Google Scholar] [CrossRef] [PubMed]
- Yang, C.; Yan, J.; Jiang, S.; Li, X.; Min, H.; Wang, X.; Hao, D. Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks. Genom. Proteom. Bioinform. 2022, 20, 29–41. [Google Scholar] [CrossRef] [PubMed]
- Hyten, D.L.; Song, Q.; Zhu, Y.; Choi, I.-Y.; Nelson, R.L.; Costa, J.M.; Specht, J.E.; Shoemaker, R.C.; Cregan, P.B. Impacts of Genetic Bottlenecks on Soybean Genome Diversity. Proc. Natl. Acad. Sci. USA 2006, 103, 16666–16671. [Google Scholar] [CrossRef] [PubMed]
- Lee, J.-D.; Vuong, T.D.; Moon, H.; Yu, J.-K.; Nelson, R.L.; Nguyen, H.T.; Shannon, J.G. Genetic Diversity and Population Structure of Korean and Chinese Soybean [Glycine max (L.) Merr.] Accessions. Crop Sci. 2011, 51, 1080–1088. [Google Scholar] [CrossRef]
- Jo, H.; Lee, J.Y.; Cho, H.; Choi, H.J.; Son, C.K.; Bae, J.S.; Bilyeu, K.; Song, J.T.; Lee, J.-D. Genetic Diversity of Soybeans (Glycine max (L.) Merr.) with Black Seed Coats and Green Cotyledons in Korean Germplasm. Agronomy 2021, 11, 581. [Google Scholar] [CrossRef]
- Nei, M.; Li, W.H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 1979, 76, 5269–5273. [Google Scholar] [CrossRef]
- Watterson, G.A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 1975, 7, 256–276. [Google Scholar] [CrossRef]
- Lewontin, R.C.; Kojima, K. The Evolutionary Dynamics of Complex Polymorphisms. Evolution 1960, 14, 458–472. [Google Scholar]
- Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123, 585–595. [Google Scholar] [CrossRef]
- Song, Q.; Hyten, D.L.; Jia, G.; Quigley, C.V.; Fickus, E.W.; Nelson, R.L.; Cregan, P.B. Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean. PLoS ONE 2013, 8, e54985. [Google Scholar] [CrossRef]
- Wen, Z.; Boyse, J.F.; Song, Q.; Cregan, P.B.; Wang, D. Genomic Consequences of Selection and Genome-Wide Association Mapping in Soybean. BMC Genom. 2015, 16, 671. [Google Scholar] [CrossRef] [PubMed]
- Zhang, J.; Song, Q.; Cregan, P.B.; Nelson, R.L.; Wang, X.; Wu, J.; Jiang, G.-L. Genome-Wide Association Study for Flowering Time, Maturity Dates and Plant Height in Early Maturing Soybean (Glycine max) Germplasm. BMC Genom. 2015, 16, 217. [Google Scholar] [CrossRef] [PubMed]
- Zhang, H.; Song, Q.; Griffin, J.D.; Song, B.-H. Genetic Architecture of Wild Soybean (Glycine soja) Response to Soybean Cyst Nematode (Heterodera glycines). Mol. Genet. Genom. 2017, 292, 1257–1265. [Google Scholar] [CrossRef] [PubMed]
- Perfil’ev, R.; Shcherban, A.; Potapov, D.; Maksimenko, K.; Kiryukhin, S.; Gurinovich, S.; Panarina, V.; Polyudina, R.; Salina, E. Impact of Allelic Variation in Maturity Genes E1–E4 on Soybean Adaptation to Central and West Siberian Regions of Russia. Agriculture 2023, 13, 1251. [Google Scholar] [CrossRef]
- Rogers, S.O.; Bendich, A.J. Extraction of DNA from Milligram Amounts of Fresh, Herbarium and Mummified Plant Tissues. Plant. Mol. Biol. 1985, 5, 69–76. [Google Scholar] [CrossRef]
- Song, Q.; Hyten, D.L.; Jia, G.; Quigley, C.V.; Fickus, E.W.; Nelson, R.L.; Cregan, P.B. Fingerprinting Soybean Germplasm and Its Utility in Genomic Research. G3 Genes Genomes Genet. 2015, 5, 1999–2006. [Google Scholar] [CrossRef]
- Chang, C.C.; Chow, C.C.; Tellier, L.C.; Vattikuti, S.; Purcell, S.M.; Lee, J.J. Second-Generation PLINK: Rising to the Challenge of Larger and Richer Datasets. GigaSci 2015, 4, 7. [Google Scholar] [CrossRef]
- Alexander, D.H.; Novembre, J.; Lange, K. Fast Model-Based Estimation of Ancestry in Unrelated Individuals. Genome Res. 2009, 19, 1655–1664. [Google Scholar] [CrossRef]
- Bradbury, P.J.; Zhang, Z.; Kroon, D.E.; Casstevens, T.M.; Ramdoss, Y.; Buckler, E.S. TASSEL: Software for Association Mapping of Complex Traits in Diverse Samples. Bioinformatics 2007, 23, 2633–2635. [Google Scholar] [CrossRef]
- Remington, D.L.; Thornsberry, J.M.; Matsuoka, Y.; Wilson, L.M.; Whitt, S.R.; Doebley, J.; Kresovich, S.; Goodman, M.M.; Buckler, E.S. Structure of Linkage Disequilibrium and Phenotypic Associations in the Maize Genome. Proc. Natl. Acad. Sci. USA 2001, 98, 11479–11484. [Google Scholar] [CrossRef]
- Bandillo, N.; Jarquin, D.; Song, Q.; Nelson, R.; Cregan, P.; Specht, J.; Lorenz, A. A Population Structure and Genome-Wide Association Analysis on the USDA Soybean Germplasm Collection. Plant Genome 2015, 8, 1–13. [Google Scholar] [CrossRef] [PubMed]
- Zhou, Z.; Jiang, Y.; Wang, Z.; Gou, Z.; Lyu, J.; Li, W.; Yu, Y.; Shu, L.; Zhao, Y.; Ma, Y.; et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 2015, 33, 408–414. [Google Scholar] [CrossRef] [PubMed]
- Jeong, S.-C.; Moon, J.-K.; Park, S.-K.; Kim, M.-S.; Lee, K.; Lee, S.R.; Jeong, N.; Choi, M.S.; Kim, N.; Kang, S.-T.; et al. Genetic Diversity Patterns and Domestication Origin of Soybean. Theor. Appl. Genet 2019, 132, 1179–1193. [Google Scholar] [CrossRef] [PubMed]
- Sedivy, E.J.; Wu, F.; Hanzawa, Y. Soybean Domestication: The Origin, Genetic Architecture and Molecular Bases. New Phytol. 2017, 214, 539–553. [Google Scholar] [CrossRef]
- Fomenko, N.D.; Sinegovskaya, V.T.; Slobodyanik, N.S.; Kletkina, O.O.; Belyaeva, G.N.; Melnikova, E.N.; Ala, A.Y. Catalogue of Soybean Sorts of Selection of All-Russian Sri of Soybean: Collective Scientific Monograph; FSBSI All-Russian SRI of Soybean; Printing Company «ODEON»: Blagoveshchensk, Russia, 2015; 96p, Available online: http://vniisoi.ru/wp-content/uploads/2017/02/Katalog-sortov-soi-Vserossiyskogo-NII-soi.pdf (accessed on 25 September 2023).
- Rozhanskaya, O.A.; Polyudina, R.I. A New Soybean Variety Sibniik 9 for Siberia, Ural and Middle Volga Regions. Sib. Her. Agric. Sci. 2017, 47, 14–20. (In Russian) [Google Scholar]
- Jiang, B.; Zhang, S.; Song, W.; Khan, M.A.A.; Sun, S.; Zhang, C.; Wu, T.; Wu, C.; Han, T. Natural Variations of FT Family Genes in Soybean Varieties Covering a Wide Range of Maturity Groups. BMC Genom. 2019, 20, 230. [Google Scholar] [CrossRef]
- Contreras-Soto, R.I.; De Oliveira, M.B.; Costenaro-da-Silva, D.; Scapim, C.A.; Schuster, I. Population Structure, Genetic Relatedness and Linkage Disequilibrium Blocks in Cultivars of Tropical Soybean (Glycine Max). Euphytica 2017, 213, 173. [Google Scholar] [CrossRef]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Potapova, N.A.; Zlobin, A.S.; Perfil’ev, R.N.; Vasiliev, G.V.; Salina, E.A.; Tsepilov, Y.A. Population Structure and Genetic Diversity of the 175 Soybean Breeding Lines and Varieties Cultivated in West Siberia and Other Regions of Russia. Plants 2023, 12, 3490. https://doi.org/10.3390/plants12193490
Potapova NA, Zlobin AS, Perfil’ev RN, Vasiliev GV, Salina EA, Tsepilov YA. Population Structure and Genetic Diversity of the 175 Soybean Breeding Lines and Varieties Cultivated in West Siberia and Other Regions of Russia. Plants. 2023; 12(19):3490. https://doi.org/10.3390/plants12193490
Chicago/Turabian StylePotapova, Nadezhda A., Alexander S. Zlobin, Roman N. Perfil’ev, Gennady V. Vasiliev, Elena A. Salina, and Yakov A. Tsepilov. 2023. "Population Structure and Genetic Diversity of the 175 Soybean Breeding Lines and Varieties Cultivated in West Siberia and Other Regions of Russia" Plants 12, no. 19: 3490. https://doi.org/10.3390/plants12193490