Whole-genome resequencing of common bean elite breeding lines
Abstract The expansion of bean genome technologies has prompted new perspectives on generating resources and knowledge essential to research and implementing biotechnological tools for the practical operations of plant breeding programs. This study aimed to resequence the entire genome (whole genome...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-39399-6 |
| _version_ | 1827634627193339904 |
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| author | Isabela Pavanelli de Souza Beatriz Rosa de Azevedo Alexandre Siqueira Guedes Coelho Thiago Lívio Pessoa Oliveira de Souza Paula Arielle Mendes Ribeiro Valdisser Lucas Matias Gomes-Messias Breno Osvaldo Funicheli Claudio Brondani Rosana Pereira Vianello |
| author_facet | Isabela Pavanelli de Souza Beatriz Rosa de Azevedo Alexandre Siqueira Guedes Coelho Thiago Lívio Pessoa Oliveira de Souza Paula Arielle Mendes Ribeiro Valdisser Lucas Matias Gomes-Messias Breno Osvaldo Funicheli Claudio Brondani Rosana Pereira Vianello |
| author_sort | Isabela Pavanelli de Souza |
| collection | DOAJ |
| description | Abstract The expansion of bean genome technologies has prompted new perspectives on generating resources and knowledge essential to research and implementing biotechnological tools for the practical operations of plant breeding programs. This study aimed to resequence the entire genome (whole genome sequencing—WGS) of 40 bean genotypes selected based on their significance in breeding programs worldwide, with the objective of generating an extensive database for the identification of single nucleotide polymorphisms (SNPs). Over 6 million SNPs were identified, distributed across the 11 bean chromosomes. After quality variant filtering, 420,509 high-quality SNPs were established, with an average of 38,228 SNPs per chromosome. These variants were categorized based on their predicted effects, revealing that the majority exerted a modifier impact on non-coding genome regions (94.68%). Notably, a significant proportion of SNPs occurred in intergenic regions (62.89%) and at least one SNP was identified in 58.63% of the genes annotated in the bean genome. Of particular interest, 7841 SNPs were identified in 85% of the putative plant disease defense-related genes, presenting a valuable resource for crop breeding efforts. These findings provide a foundation for the development of innovative and broadly applicable technologies for the routine selection of superior genotypes in global bean improvement and germplasm characterization programs. |
| first_indexed | 2024-03-09T15:15:58Z |
| format | Article |
| id | doaj.art-c9443058ac214897b5d9241d0974ede9 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T15:15:58Z |
| publishDate | 2023-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-c9443058ac214897b5d9241d0974ede92023-11-26T13:06:27ZengNature PortfolioScientific Reports2045-23222023-08-0113111510.1038/s41598-023-39399-6Whole-genome resequencing of common bean elite breeding linesIsabela Pavanelli de Souza0Beatriz Rosa de Azevedo1Alexandre Siqueira Guedes Coelho2Thiago Lívio Pessoa Oliveira de Souza3Paula Arielle Mendes Ribeiro Valdisser4Lucas Matias Gomes-Messias5Breno Osvaldo Funicheli6Claudio Brondani7Rosana Pereira Vianello8Genetics and Plant Breeding, Brazilian Agricultural Research CorporationBiotechnology, Scientific Initiation Scholarship, Brazilian Agricultural Research CorporationPlant Breeding, Universidade Federal de GoiásPlant Breeding, Brazilian Agricultural Research CorporationGenetics and Molecular Biology, Brazilian Agricultural Research CorporationGenetics and Plant Breeding, Universidade Federal de GoiásComputer Science, Universidade Federal de São CarlosMolecular Biology, Brazilian Agricultural Research CorporationMolecular Biology, Brazilian Agricultural Research CorporationAbstract The expansion of bean genome technologies has prompted new perspectives on generating resources and knowledge essential to research and implementing biotechnological tools for the practical operations of plant breeding programs. This study aimed to resequence the entire genome (whole genome sequencing—WGS) of 40 bean genotypes selected based on their significance in breeding programs worldwide, with the objective of generating an extensive database for the identification of single nucleotide polymorphisms (SNPs). Over 6 million SNPs were identified, distributed across the 11 bean chromosomes. After quality variant filtering, 420,509 high-quality SNPs were established, with an average of 38,228 SNPs per chromosome. These variants were categorized based on their predicted effects, revealing that the majority exerted a modifier impact on non-coding genome regions (94.68%). Notably, a significant proportion of SNPs occurred in intergenic regions (62.89%) and at least one SNP was identified in 58.63% of the genes annotated in the bean genome. Of particular interest, 7841 SNPs were identified in 85% of the putative plant disease defense-related genes, presenting a valuable resource for crop breeding efforts. These findings provide a foundation for the development of innovative and broadly applicable technologies for the routine selection of superior genotypes in global bean improvement and germplasm characterization programs.https://doi.org/10.1038/s41598-023-39399-6 |
| spellingShingle | Isabela Pavanelli de Souza Beatriz Rosa de Azevedo Alexandre Siqueira Guedes Coelho Thiago Lívio Pessoa Oliveira de Souza Paula Arielle Mendes Ribeiro Valdisser Lucas Matias Gomes-Messias Breno Osvaldo Funicheli Claudio Brondani Rosana Pereira Vianello Whole-genome resequencing of common bean elite breeding lines Scientific Reports |
| title | Whole-genome resequencing of common bean elite breeding lines |
| title_full | Whole-genome resequencing of common bean elite breeding lines |
| title_fullStr | Whole-genome resequencing of common bean elite breeding lines |
| title_full_unstemmed | Whole-genome resequencing of common bean elite breeding lines |
| title_short | Whole-genome resequencing of common bean elite breeding lines |
| title_sort | whole genome resequencing of common bean elite breeding lines |
| url | https://doi.org/10.1038/s41598-023-39399-6 |
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