ArticleBMC genomics2016
Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 65 citations in OpenAlex.
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- Genetic relationships and genome selection signatures between soybean cultivars from Brazil and United States after decades of breeding.Scientific reports · 2022Article
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- Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology.BMC biology · 2022Article
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- Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars.Frontiers in plant science · 2022Article
- Genome-Wide Variation Analysis of Four Vegetable Soybean Cultivars Based on Re-Sequencing.Plants (Basel, Switzerland) · 2021Article
- The pan-genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content.Plant biotechnology journal · 2021Article
- Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean).Genomics & informatics · 2021Article
- Genome-wide association study for resistance to the Meloidogyne javanica causing root-knot nematode in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Soybean (Glycine max) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics.Plant biotechnology journal · 2021Article
- The soybean gene GmHsp22.4 is involved in the resistance response to Meloidogyne javanica in Arabidopsis thaliana.BMC plant biology · 2020Article
- Plant Genome Editing and the Relevance of Off-Target Changes.Plant physiology · 2020Article
- A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice.BMC biology · 2020Article
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSoybean [Glycine max (L.) Merrill] is one of the most important legumes cultivated worldwide, and Brazil is one of the main producers of this crop. Since the sequencing of its reference genome, interest in structural and allelic variations of cultivated and wild soybean germplasm has grown. To investigate the genetics of the Brazilian soybean germplasm, we selected soybean cultivars based on the year of commercialization, geographical region and maturity group and resequenced their genomes.
resultsWe resequenced the genomes of 28 Brazilian soybean cultivars with an average genome coverage of 14.8X. A total of 5,835,185 single nucleotide polymorphisms (SNPs) and 1,329,844 InDels were identified across the 20 soybean chromosomes, with 541,762 SNPs, 98,922 InDels and 1,093 CNVs that were exclusive to the 28 Brazilian cultivars. In addition, 668 allelic variations of 327 genes were shared among all of the Brazilian cultivars, including genes related to DNA-dependent transcription-elongation, photosynthesis, ATP synthesis-coupled electron transport, cellular respiration, and precursors of metabolite generation and energy. A very homogeneous structure was also observed for the Brazilian soybean germplasm, and we observed 41 regions putatively influenced by positive selection. Finally, we detected 3,880 regions with copy-number variations (CNVs) that could help to explain the divergence among the accessions evaluated.
conclusionsThe large number of allelic and structural variations identified in this study can be used in marker-assisted selection programs to detect unique SNPs for cultivar fingerprinting. The results presented here suggest that despite the diversification of modern Brazilian cultivars, the soybean germplasm remains very narrow because of the large number of genome regions that exhibit low diversity. These results emphasize the need to introduce new alleles to increase the genetic diversity of the Brazilian germplasm.
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