Genomic and evolutionary relationships among wild and cultivated blueberry species
Abstract Background Blueberries (Vaccinium section Cyanococcus) are an economically important fruit crop in the United States. Understanding genetic structure and relationships in blueberries is essential to advance the genetic improvement of horticulturally important traits. In the present study, w...
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| Format: | Article |
| Language: | English |
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BMC
2023-03-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-023-04124-y |
| _version_ | 1827984781081575424 |
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| author | Byron R. Manzanero Krishnanand P. Kulkarni Nicholi Vorsa Umesh K. Reddy Purushothaman Natarajan Sathya Elavarthi Massimo Iorizzo Kalpalatha Melmaiee |
| author_facet | Byron R. Manzanero Krishnanand P. Kulkarni Nicholi Vorsa Umesh K. Reddy Purushothaman Natarajan Sathya Elavarthi Massimo Iorizzo Kalpalatha Melmaiee |
| author_sort | Byron R. Manzanero |
| collection | DOAJ |
| description | Abstract Background Blueberries (Vaccinium section Cyanococcus) are an economically important fruit crop in the United States. Understanding genetic structure and relationships in blueberries is essential to advance the genetic improvement of horticulturally important traits. In the present study, we investigated the genomic and evolutionary relationships in 195 blueberry accessions from five species (comprising 33 V. corymbosum, 14 V. boreale, 81 V. darrowii, 29 V. myrsinites, and 38 V. tenellum) using single nucleotide polymorphisms (SNPs) mined from genotyping-by-sequencing (GBS) data. Results GBS generated ~ 751 million raw reads, of which 79.7% were mapped to the reference genome V. corymbosum cv. Draper v1.0. After filtering (read depth > 3, minor allele frequency > 0.05, and call rate > 0.9), 60,518 SNPs were identified and used in further analyses. The 195 blueberry accessions formed three major clusters on the principal component (PC) analysis plot, in which the first two PCs accounted for 29.2% of the total genetic variance. Nucleotide diversity (π) was highest for V. tenellum and V. boreale (0.023 each), and lowest for V. darrowii (0.012). Using TreeMix analysis, we identified four migration events and deciphered gene flow among the selected species. In addition, we detected a strong V. boreale lineage in cultivated blueberry species. Pairwise SweeD analysis identified a wide sweep (encompassing 32 genes) as a strong signature of domestication on the scaffold VaccDscaff 12. From this region, five genes encoded topoisomerases, six genes encoded CAP-gly domain linker (which regulates the dynamics of the microtubule cytoskeleton), and three genes coded for GSL8 (involved in the synthesis of the cell wall component callose). One of the genes, augustus_masked-VaccDscaff12-processed-gene-172.10, is a homolog of Arabidopsis AT2G25010 and encodes the protein MAINTENANCE OF MERISTEMS-like involved in root and shoot growth. Additional genomic stratification by admixture analysis identified genetic lineages and species boundaries in blueberry accessions. The results from this study indicate that V. boreale is a genetically distant outgroup, while V. darrowii, V. myrsinites, and V. tenellum are closely related. Conclusion Our study provides new insights into the evolution and genetic architecture of cultivated blueberries. |
| first_indexed | 2024-04-09T23:04:18Z |
| format | Article |
| id | doaj.art-9f541d94479e4aaf937d3185504a6d7c |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-09T23:04:18Z |
| publishDate | 2023-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-9f541d94479e4aaf937d3185504a6d7c2023-03-22T10:50:09ZengBMCBMC Plant Biology1471-22292023-03-0123111410.1186/s12870-023-04124-yGenomic and evolutionary relationships among wild and cultivated blueberry speciesByron R. Manzanero0Krishnanand P. Kulkarni1Nicholi Vorsa2Umesh K. Reddy3Purushothaman Natarajan4Sathya Elavarthi5Massimo Iorizzo6Kalpalatha Melmaiee7Department of Agriculture and Natural Resources, Delaware State UniversityDepartment of Agriculture and Natural Resources, Delaware State UniversityDepartment of Plant Biology, Rutgers UniversityDepartment of Biology, West Virginia State UniversityDepartment of Biology, West Virginia State UniversityDepartment of Agriculture and Natural Resources, Delaware State UniversityDepartment of Horticultural Science and Plants for Human Health Institute, NC State UniversityDepartment of Agriculture and Natural Resources, Delaware State UniversityAbstract Background Blueberries (Vaccinium section Cyanococcus) are an economically important fruit crop in the United States. Understanding genetic structure and relationships in blueberries is essential to advance the genetic improvement of horticulturally important traits. In the present study, we investigated the genomic and evolutionary relationships in 195 blueberry accessions from five species (comprising 33 V. corymbosum, 14 V. boreale, 81 V. darrowii, 29 V. myrsinites, and 38 V. tenellum) using single nucleotide polymorphisms (SNPs) mined from genotyping-by-sequencing (GBS) data. Results GBS generated ~ 751 million raw reads, of which 79.7% were mapped to the reference genome V. corymbosum cv. Draper v1.0. After filtering (read depth > 3, minor allele frequency > 0.05, and call rate > 0.9), 60,518 SNPs were identified and used in further analyses. The 195 blueberry accessions formed three major clusters on the principal component (PC) analysis plot, in which the first two PCs accounted for 29.2% of the total genetic variance. Nucleotide diversity (π) was highest for V. tenellum and V. boreale (0.023 each), and lowest for V. darrowii (0.012). Using TreeMix analysis, we identified four migration events and deciphered gene flow among the selected species. In addition, we detected a strong V. boreale lineage in cultivated blueberry species. Pairwise SweeD analysis identified a wide sweep (encompassing 32 genes) as a strong signature of domestication on the scaffold VaccDscaff 12. From this region, five genes encoded topoisomerases, six genes encoded CAP-gly domain linker (which regulates the dynamics of the microtubule cytoskeleton), and three genes coded for GSL8 (involved in the synthesis of the cell wall component callose). One of the genes, augustus_masked-VaccDscaff12-processed-gene-172.10, is a homolog of Arabidopsis AT2G25010 and encodes the protein MAINTENANCE OF MERISTEMS-like involved in root and shoot growth. Additional genomic stratification by admixture analysis identified genetic lineages and species boundaries in blueberry accessions. The results from this study indicate that V. boreale is a genetically distant outgroup, while V. darrowii, V. myrsinites, and V. tenellum are closely related. Conclusion Our study provides new insights into the evolution and genetic architecture of cultivated blueberries.https://doi.org/10.1186/s12870-023-04124-yBlueberryGenotyping-by-sequencingSingle nucleotide polymorphismsPrincipal component analysisAdmixture analysisDomestication |
| spellingShingle | Byron R. Manzanero Krishnanand P. Kulkarni Nicholi Vorsa Umesh K. Reddy Purushothaman Natarajan Sathya Elavarthi Massimo Iorizzo Kalpalatha Melmaiee Genomic and evolutionary relationships among wild and cultivated blueberry species BMC Plant Biology Blueberry Genotyping-by-sequencing Single nucleotide polymorphisms Principal component analysis Admixture analysis Domestication |
| title | Genomic and evolutionary relationships among wild and cultivated blueberry species |
| title_full | Genomic and evolutionary relationships among wild and cultivated blueberry species |
| title_fullStr | Genomic and evolutionary relationships among wild and cultivated blueberry species |
| title_full_unstemmed | Genomic and evolutionary relationships among wild and cultivated blueberry species |
| title_short | Genomic and evolutionary relationships among wild and cultivated blueberry species |
| title_sort | genomic and evolutionary relationships among wild and cultivated blueberry species |
| topic | Blueberry Genotyping-by-sequencing Single nucleotide polymorphisms Principal component analysis Admixture analysis Domestication |
| url | https://doi.org/10.1186/s12870-023-04124-y |
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