| Sonstiges: |
- Nachgewiesen in: MEDLINE
- Sprachen: English
- Publication Type: Journal Article; Research Support, Non-U.S. Gov't
- Language: English
- [Sci Rep] 2021 Feb 03; Vol. 11 (1), pp. 2964. <i>Date of Electronic Publication: </i>2021 Feb 03.
- MeSH Terms: Genome, Plant* ; Selection, Genetic* ; Phaseolus / *genetics ; Plant Breeding / *methods ; Brazil ; DNA, Plant ; Domestication ; Gene Frequency ; Gene Pool ; Genetic Variation ; Genome-Wide Association Study ; Genotyping Techniques ; Linkage Disequilibrium ; Polymorphism, Single Nucleotide
- References: Broughton, W. J. et al. Beans (Phaseolus spp.)—model food legumes. Plant Soil 252, 55–128 (2003). (PMID: 10.1023/A:1024146710611) ; FAO, F. and A. O. FAOSTAT: FAO Statistical Databases. http://www.fao.org/faostat/ (2020). ; Kwak, M. & Gepts, P. Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor. Appl. Genet. 118, 979–992 (2009). (PMID: 1913002910.1007/s00122-008-0955-4) ; Bitocchi, E. et al. Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes. New Phytol. 197, 300–313 (2013). (PMID: 2312668310.1111/j.1469-8137.2012.04377.x) ; Schmutz, J. et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet. 46, 707–713 (2014). (PMID: 24908249704869810.1038/ng.3008) ; Vlasova, A. et al. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol. 17, 1–18 (2016). (PMID: 10.1186/s13059-016-0883-6) ; Oladzad, A. et al. Single and multi-trait GWAS identify genetic factors associated with production traits in common bean under abiotic stress environments. G3 Genes Genomes Genet. 9, 1881–1892 (2019). ; Cichy, K. A., Caldas, G. V., Snapp, S. S. & Blair, M. W. QTL analysis of seed iron, zinc, and phosphorus levels in an andean bean population. Crop Sci. 49, 1742–1750 (2009). (PMID: 10.2135/cropsci2008.10.0605) ; Ribeiro, N. D. et al. Evaluation of special grains bean lines for grain yield, cooking time and mineral concentrations. Crop Breed. Appl. Biotechnol. 14, 15–22 (2014). (PMID: 10.1590/S1984-70332014000100003) ; Perseguini, J. M. K. C. et al. Developing a common bean core collection suitable for association mapping studies. Genet. Mol. Biol. 38, 67–78 (2015). (PMID: 2598362710.1590/S1415-475738120140126) ; MAPA, Ministerio da Agricultura Pecuária e Abastecimento. Plano nacional de desenvolvimento da cadeia do feijão e pulses (2018). ; Cheng, J. et al. Development of a SNP array and its application to genetic mapping and diversity assessment in pepper (Capsicum spp.). Sci. Rep. 6, 1–11 (2016). ; He, J. et al. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front. Plant Sci. 5, 484 (2014). (PMID: 25324846417970110.3389/fpls.2014.00484) ; Bhattarai, U. & Subudhi, P. K. Identification of drought responsive QTLs during vegetative growth stage of rice using a saturated GBS-based SNP linkage map. Euphytica 214, 1–17 (2018). (PMID: 10.1007/s10681-018-2117-3) ; Stapley, J. et al. Adaptation genomics: The next generation. Trends Ecol. Evol. 25, 705–712 (2010). (PMID: 2095208810.1016/j.tree.2010.09.002) ; Gujaria-Verma, N. et al. Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping. BMC Genomics 17, 239 (2016). (PMID: 26979462479350710.1186/s12864-016-2499-3) ; Siadjeu, C., Mayland-Quellhorst, E. & Albach, D. C. Genetic diversity and population structure of trifoliate yam (Dioscorea dumetorum Kunth) in Cameroon revealed by genotyping-by-sequencing (GBS). BMC Plant Biol. 18, 1–14 (2018). (PMID: 10.1186/s12870-018-1593-x) ; Ariani, A., Bern y Miery Teran, J. C. & Gepts, P. Genome-wide identification of SNPs and copy number variation in common bean (Phaseolus vulgaris L.) using genotyping-by-sequencing (GBS). Mol. Breed. 36, 87 (2016). (PMID: 10.1007/s11032-016-0512-9) ; Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6, 1–10 (2011). (PMID: 10.1371/journal.pone.0019379) ; Schröder, S. et al. Optimization of genotyping by sequencing (GBS) data in common bean (Phaseolus vulgaris L.). Mol. Breed. 36, 1–9 (2016). (PMID: 10.1007/s11032-015-0431-1) ; Wang, S. et al. Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes. Genome Biol. 16, 108 (2015). (PMID: 26003111446957710.1186/s13059-015-0678-1) ; Burghardt, L. T., Young, N. D. & Tiffin, P. A guide to genome-wide association mapping in plants. Curr. Protoc. Plant Biol. 2, 22–38 (2017). (PMID: 3172597310.1002/cppb.20041) ; Korte, A. & Ashley, F. The advantages and limitations of trait analysis with GWAS: A review Self-fertilisation makes Arabidopsis particularly well suited to GWAS. Plant Methods 9, 29 (2013). (PMID: 23876160375030510.1186/1746-4811-9-29) ; Zhang, D., Bai, G., Zhu, C., Yu, J. & Carver, B. F. Genetic diversity, population structure, and linkage disequilibrium in U.S. elite winter wheat. Plant Genome J. 3, 117 (2010). ; Nicolas, S. D. et al. Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies. BMC Plant Biol. 16, 1–19 (2016). (PMID: 10.1186/s12870-016-0754-z) ; Bhatta, M., Morgounov, A., Belamkar, V., Poland, J. & Baenziger, P. S. Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat. BMC Genomics 19, 1–12 (2018). (PMID: 10.1186/s12864-018-4969-2) ; Eltaher, S. et al. Genetic diversity and population structure of F3:6 Nebraska Winter wheat genotypes using genotyping-by-sequencing. Front. Genet. 9, 1–9 (2018). (PMID: 10.3389/fgene.2018.00076) ; Alipour, H. et al. Genotyping-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and cultivars. Front. Plant Sci. 8, 1–14 (2017). (PMID: 10.3389/fpls.2017.01293) ; Luo, Z. et al. Genetic diversity and population structure of a Camelina sativa spring panel. Front. Plant Sci. 10, 1–12 (2019). (PMID: 10.3389/fpls.2019.00184) ; Pereira-Dias, L., Vilanova, S., Fita, A., Prohens, J. & Rodríguez-Burruezo, A. Genetic diversity, population structure, and relationships in a collection of pepper (Capsicum spp.) landraces from the Spanish centre of diversity revealed by genotyping-by-sequencing (GBS). Hortic. Res. 6, 54 (2019). (PMID: 31044080649149010.1038/s41438-019-0132-8) ; Xu, Q. et al. The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis. BMC Genet. 17, 1–8 (2016). (PMID: 10.1186/s12863-016-0361-x) ; Moghaddam, S. M. et al. Genome-wide association study identifies candidate loci underlying agronomic traits in a middle American diversity panel of common bean. Plant Genome 9, 1–21 (2016). (PMID: 10.3835/plantgenome2016.02.0012) ; Cichy, K. A. et al. A Phaseolus vulgaris diversity panel for Andean bean Improvement. Crop Sci. 55, 2149–2160 (2015). (PMID: 10.2135/cropsci2014.09.0653) ; Campa, A., Murube, E. & Ferreira, J. J. Genetic diversity, population structure, and linkage disequilibrium in a Spanish common bean diversity panel revealed through genotyping-by-sequencing. Genes (Basel) 9, 518 (2018). (PMID: 10.3390/genes9110518) ; Lioi, L., Zuluaga, D. L., Pavan, S. & Sonnante, G. Genotyping-by-sequencing reveals molecular genetic diversity in Italian common bean landraces. Diversity 11, 1–14 (2019). (PMID: 10.3390/d11090154) ; Raggi, L., Caproni, L., Carboni, A. & Negri, V. Genome-wide association study reveals candidate genes for flowering time variation in common bean (Phaseolus vulgaris L.). Front. Plant Sci. 10, 1–14 (2019). (PMID: 10.3389/fpls.2019.00962) ; Perseguini, J. M. K. C. et al. Genome-wide association studies of anthracnose and angular leaf spot resistance in common bean (Phaseolus vulgaris L.). PLoS ONE 11, 1–19 (2016). (PMID: 10.1371/journal.pone.0150506) ; Tock, A. J. et al. Genome-wide linkage and association mapping of halo blight resistance in common bean to race 6 of the globally important bacterial pathogen. Front. Plant Sci. 8, 1–17 (2017). (PMID: 10.3389/fpls.2017.01170) ; Katuuramu, D. N. et al. Genome-wide association analysis of nutritional composition-related traits and iron bioavailability in cooked dry beans (Phaseolus vulgaris L.). Mol. Breed. 38, 44 (2018). (PMID: 10.1007/s11032-018-0798-x) ; Resende, R. T. et al. Genome-wide association and Regional Heritability Mapping of plant architecture, lodging and productivity in Phaseolus vulgaris. G3 Genes Genomes Genet. 8, 2841–2854 (2018). ; Moghaddam, S. M. et al. Genetic architecture of dietary fiber and oligosaccharide content in a middle american panel of edible dry bean. Plant Genome 11, 1–11 (2018). (PMID: 10.3835/plantgenome2017.08.0074) ; Kamfwa, K., Cichy, K. A. & Kelly, J. D. Genome-wide association study of agronomic traits in common bean. Plant Genome 8, 1–12 (2015). (PMID: 10.3835/plantgenome2014.09.0059) ; Cichy, K. A., Wiesinger, J. A. & Mendoza, F. A. Genetic diversity and genome-wide association analysis of cooking time in dry bean (Phaseolus vulgaris L.). Theor. Appl. Genet. 128, 1555–1567 (2015). (PMID: 2600319110.1007/s00122-015-2531-z) ; Kamfwa, K., Cichy, K. A. & Kelly, J. D. Genome-wide association analysis of symbiotic nitrogen fixation in common bean. Theor. Appl. Genet. 128, 1999–2017 (2015). (PMID: 2613373310.1007/s00122-015-2562-5) ; Zuiderveen, G. H., Padder, B. A., Kamfwa, K. & Song, Q. Genome-wide association study of anthracnose resistance in Andean beans (Phaseolus vulgaris). PLoS ONE https://doi.org/10.1371/journal.pone.0156391 (2016). (PMID: 10.1371/journal.pone.0156391272706274894742) ; Soltani, A. et al. Genetic architecture of flooding tolerance in the dry bean middle-American diversity panel. Front. Plant Sci. 8, 1–15 (2017). (PMID: 10.3389/fpls.2017.01183) ; Soltani, A. et al. Genetic analysis of flooding tolerance in an Andean diversity panel of dry bean (Phaseolus vulgaris L.). Front. Plant Sci. 9, 767 (2018). (PMID: 29928287599796810.3389/fpls.2018.00767) ; Valdisser, P. A. et al. Genome-wide association studies detect multiple QTLs for productivity in Mesoamerican diversity panel of common bean under drought stress. Front. Plant Sci. https://doi.org/10.3389/fpls.2020.574674 (2020). (PMID: 10.3389/fpls.2020.574674333435917738703) ; Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14, 2611–2620 (2005). (PMID: 10.1111/j.1365-294X.2005.02553.x15969739) ; Burle, M. L., Fonseca, J. R., Kami, J. A. & Gepts, P. Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity. Theor. Appl. Genet. 121, 801–813 (2010). (PMID: 20502861294043310.1007/s00122-010-1350-5) ; Valdisser, P. A. M. R. et al. In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping. BMC Genomics 18, 1–19 (2017). (PMID: 10.1186/s12864-017-3805-4) ; Gaur, R. et al. High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea. Sci. Rep. 5, 1–11 (2015). (PMID: 10.1038/srep13387) ; Pavan, S. et al. A distinct genetic cluster in cultivated chickpea as revealed by genome-wide marker discovery and genotyping. Plant Genome 10, 1–9 (2017). (PMID: 10.3835/plantgenome2016.11.0115) ; Guo, C. et al. Transversions have larger regulatory effects than transitions. BMC Genomics 18, 1 (2017). (PMID: 10.1186/s12864-017-3785-4) ; Berny Mier y Teran, J. C. et al. Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L.). Ann. Bot. https://doi.org/10.1093/aob/mcy221 (2018). (PMID: 10.1093/aob/mcy2216881220) ; Blair, M. W. et al. Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.). PLoS ONE 13, 1–21 (2018). (PMID: 10.1371/journal.pone.0189597) ; Diniz, A. L. et al. Evidence for strong kinship influence on the extent of linkage disequilibrium in cultivated common beans. Genes (Basel) 10, 1–16 (2019). ; Pipan, B. & Meglič, V. Diversification and genetic structure of the western-to-eastern progression of European Phaseolus vulgaris L. germplasm. BMC Plant Biol. 19, 1–16 (2019). (PMID: 10.1186/s12870-019-2051-0) ; Raatz, B. et al. Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: Diversity, quality control and molecular breeding. Genet. Resour. Crop Evol. 66, 707–722 (2019). (PMID: 30956400642415110.1007/s10722-019-00746-0) ; Valentini, G., Gonçalves-Vidigal, M. C., Elias, J. C. F., Moiana, L. D. & Mindo, N. N. A. Population structure and genetic diversity of common bean accessions from Brazil. Plant Mol. Biol. Rep. 36, 897–906 (2018). (PMID: 10.1007/s11105-018-1129-4) ; Valdisser, P. A. M. R. et al. SNP discovery in common bean by restriction-associated DNA (RAD) sequencing for genetic diversity and population structure analysis. Mol. Genet. Genomics 291, 1277–1291 (2016). (PMID: 2693237210.1007/s00438-016-1182-3) ; Gioia, T., Logozzo, G., Marzario, S., Zeuli, P. S. & Gepts, P. Evolution of SSR diversity from wild types to U.S. Advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris). PLoS ONE 14, 1–21 (2019). (PMID: 10.1371/journal.pone.0211342) ; Delfini, J. et al. Distinctness of Brazilian common bean cultivars with carioca and black grain by means of morphoagronomic and molecular descriptors. PLoS ONE 12, e0188798 (2017). (PMID: 29190665570870010.1371/journal.pone.0188798) ; Delfini, J. et al. Estimation of genetic parameters and prediction of genotypic values in common beans using mixed models. Emirates J. Food Agric. 30, 1026–1035 (2018). ; Cortés, A. J., Chavarro, M. C. & Blair, M. W. SNP marker diversity in common bean (Phaseolus vulgaris L.). Theor. Appl. Genet. 123, 827–845 (2011). (PMID: 2178595110.1007/s00122-011-1630-8) ; Blair, M. W. et al. A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.). Theor. Appl. Genet. 126, 535–548 (2013). (PMID: 2312438910.1007/s00122-012-1999-z) ; Ariani, A., Mier Teran, J. C. B. & Gepts, P. Spatial and temporal scales of range expansion in wild Phaseolus vulgaris. Mol. Biol. Evol. 35, 119–131 (2017). (PMID: 585074510.1093/molbev/msx273) ; 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 213, 173 (2017). (PMID: 10.1007/s10681-017-1966-5) ; Flint-Garcia, S. A., Thornsberry, J. M. & Buckler, E. S. Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 54, 357–374 (2003). (PMID: 1450299510.1146/annurev.arplant.54.031902.134907) ; Glaubitz, J. C. et al. TASSEL-GBS: A high capacity genotyping by sequencing analysis pipeline. PLoS ONE 9, e90346 (2014). (PMID: 24587335393867610.1371/journal.pone.0090346) ; Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010). (PMID: 20080505282810810.1093/bioinformatics/btp698) ; Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011). (PMID: 21653522313721810.1093/bioinformatics/btr330) ; Browning, B. L., Zhou, Y. & Browning, S. R. A one-penny imputed genome from next-generation reference panels. Am. J. Hum. Genet. 103, 338–348 (2018). (PMID: 30100085612830810.1016/j.ajhg.2018.07.015) ; R Core Team. R: A language and environment for statistical computing (2020). ; Hu, Z., Olatoye, M. O., Marla, S. & Morris, G. P. An integrated genotyping-by-sequencing polymorphism map for over 10,000 sorghum genotypes. Plant Genome 12, 180044 (2019). (PMID: 10.3835/plantgenome2018.06.0044) ; Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000). (PMID: 10835412146109610.1093/genetics/155.2.945) ; Chhatre, V. E. & Emerson, K. J. StrAuto: Automation and parallelization of STRUCTURE analysis. BMC Bioinform. 18, 1–5 (2017). (PMID: 10.1186/s12859-017-1593-0) ; Purcell, S. et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007). (PMID: 17701901195083810.1086/519795) ; Zheng, X. et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326–3328 (2012). (PMID: 23060615351945410.1093/bioinformatics/bts606) ; Bradbury, P. J. et al. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635 (2007). (PMID: 10.1093/bioinformatics/btm30817586829) ; Rambaut, A. FigTree v1.4.4 (2018). ; Bardou, P., Mariette, J., Escudié, F., Djemiel, C. & Klopp, C. SOFTWARE Open Access jvenn: An interactive Venn diagram viewer. BMC Bioinform. 15, 1–7 (2014). (PMID: 10.1186/1471-2105-15-293) ; Weir, B. S. & Cockerham, C. C. Estimating F-statistics for the analysis of population structure. Evolution (N.Y.) 38, 1358–1370 (1984). ; Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595 (1989). (PMID: 2513255120383110.1093/genetics/123.3.585) ; Desrousseaux, D., Sandron, F., Siberchicot, A., Cierco-Ayrolles, C. & Mangin, B. LDcorSV: Linkage disequilibrium corrected by the structure and the relatedness. R package version 1.3.2 (2017). ; Endelman, J. B. Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome J. 4, 250 (2011). (PMID: 10.3835/plantgenome2011.08.0024) ; Hill, W. G. & Weir, B. S. Variances and covariances of squared linkage disequilibria in finite populations. Theor. Popul. Biol. 33, 54–78 (1988). (PMID: 337605210.1016/0040-5809(88)90004-4)
- Substance Nomenclature: 0 (DNA, Plant)
- Entry Date(s): Date Created: 20210204 Date Completed: 20211112 Latest Revision: 20230128
- Update Code: 20240513
- PubMed Central ID: PMC7859210
|
