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Review

Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics

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Pages 759-787 | Received 17 Feb 2021, Accepted 19 Apr 2021, Published online: 21 May 2021

References

  • Alexandratos N, Bruinsma J. World agriculture towards 2030/2050: the 2012 revision. 2012.
  • Beebe SE, Rao IM, Mukankusi CM, et al. Improving resource use efficiency and reducing risk of common bean production in Africa, Latin America, and the Caribbean. Centro Internacional de Agricultura Tropical (CIAT). 2012.
  • Akibode CS, Maredia MK. Global and regional trends in production, trade and consumption of food legume crops (No. 1099-2016-89132). 2011.
  • Yeken MZ, Kantar F, Çancı H, et al. Breeding of dry bean cultivars using Phaseolus vulgaris landraces in Turkey. Int J Agric Wildl Sci. 2018;4(1):45–54.
  • Aydin MF, Baloch FS. Exploring the genetic diversity and population structure of Turkish common bean germplasm by the iPBS-retrotransposons markers. Legum Res. 2019;42(1):18–24.
  • Nadeem MA, Habyarimana E, Çiftçi V, et al. Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information. PLoS ONE. 2018;13(10):e0205363.
  • Nadeem MA, Gündoğdu M, Ercişli S, et al. Uncovering phenotypic diversity and DArTseq marker loci associated with antioxidant activity in common bean. Genes. 2020;11(1):36.
  • Nadeem MA, Karaköy T, Yeken MZ, et al. Phenotypic characterization of 183 Turkish common bean accessions for agronomic, trading, and consumer-preferred plant characteristics for breeding purposes. Agronomy. 2020;10(2):272.
  • Nadeem MA, Çilesiz Y, Ali F, et al. Investigation of quality and cooking traits diversity in a global common bean germplasm. Glob J Bot Sci. 2020;8(1):21–29.
  • McConnell M, Mamidi S, Lee R, et al. Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean. Theor Appl Genet. 2010;121(6):1103–1116.
  • Broughton WJ, Hernandez G, Blair M, et al. Beans (Phaseolus spp.)–model food legumes. Plant Soil. 2003;252(1):55–128.
  • Freytag GF, Debouck DG. Taxonomy, Distribution, and Ecology of the Genus Phaseolus (Leguminosae-Papilionodeae) in North America, Mexico and Central America. Taxonomía, distribución y ecología del género Phaseolus (Leguminosae-Papilionodeae) en Norteamérica, México y Centroaméric. SIDA, Botanical Miscellany. 2002.
  • WHO. [cited on 2021 Feb 14]. 2020.
  • Schmutz J, McClean PE, Mamidi S, et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet. 2014;46(7):707–713.
  • Stefanović S, Pfeil BE, Palmer JD, et al. Relationships among phaseoloid legumes based on sequences from eight chloroplast regions. Syst Bot. 2009;34(1):115–128.
  • Bellucci E, Bitocchi E, Rau D, et al. Genomics of origin, domestication and evolution of Phaseolus vulgaris. In: Tuberosa R, Graner A, Frison E, editors. Genomics of plant genetic resources. Dordrecht: Springer; 2014. p. 483–507.
  • Lavin M, Herendeen PS, Wojciechowski MF. Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst Biol. 2005;54(4):575–594.
  • Galeano CH, Fernández AC, Gómez M, et al. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.). BMC Genom. 2009;10(1):614–629.
  • Delgado-Salinas A, Bibler R, Lavin M. Phylogeny of the genus Phaseolus (Leguminosae): a recent diversification in an ancient landscape. Syst Bot 2006;31(4):779–791.
  • Bitocchi E, Nanni L, Bellucci E, et al. Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proc Natl Acad Sci USA. 2012;109(14):E788–E796.
  • Debouck DG, Toro O, Paredes OM, et al. Genetic diversity and ecological distribution of Phaseolus vulgaris (Fabaceae) in northwestern South America. Econ Bot. 1993;47(4):408–423.
  • Kami J, Velásquez VB, Debouck DG, et al. Identification of presumed ancestral DNA sequences of phaseolin in Phaseolus vulgaris. Proc Natl Acad Sci USA. 1995;92(4):1101–1104.
  • Di Vittori V, Bellucci E, Bitocchi E, et al. Domestication and crop history. In de la Vega MP, Santalla M, Marsolais F, editors. The common bean genome. Cham: Springer; 2017. p. 21–55.
  • Gepts P, Papa R. Evolution during domestication. 2003. 10.1038/npg.els.0003071
  • Kwak M, Gepts P. Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor Appl Genet. 2009;118(5):979–992.
  • Papa R, Gepts P. Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica. Theor Appl Genet. 2003;106(2):239–250.
  • Rossi M, Bitocchi E, Bellucci E, et al. Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol Appl. 2009;2(4):504–522.
  • Acosta-Gallegos JA, Kelly JD, Gepts P. Prebreeding in common bean and use of genetic diversity from wild germplasm. Crop Sci 2007;47:S-44.
  • Angioi SA, Desiderio F, Rau D, et al. Development and use of chloroplast microsatellites in Phaseolus spp. and other legumes. Plant Biol (Stuttg)). 2009;11(4):598–612.
  • Papa R, Nanni L, Sicard D, et al. The evolution of genetic diversity in Phaseolus vulgaris L. New approaches to the origins, evolution and conservation of crops. In: Motley TJ, Zerega N, and Cross H, editors. Darwin’s harvest. New York (NY): Columbia University Press; 2006. p. 121–142.
  • Bitocchi E, Bellucci E, Giardini A, et al. Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes. New Phytol. 2013;197(1):300–313.
  • Nanni L, Bitocchi E, Bellucci E, et al. Nucleotide diversity of a genomic sequence similar to SHATTERPROOF (PvSHP1) in domesticated and wild common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2011;123(8):1341–1357.
  • Bellucci E, Bitocchi E, Ferrarini A, et al. Decreased nucleotide and expression diversity and modified coexpression patterns characterize domestication in the common bean. Plant Cell. 2014;26(5):1901–1912.
  • Trucchi E, Benazzo A, Lari M, et al. Ancient genomes reveal early Andean farmers selected common beans while preserving diversity. Nat Plants. 20217:1–6.
  • Angioi SA, Rau D, Attene G, et al. Beans in Europe: origin and structure of the European landraces of Phaseolus vulgaris L. Theor Appl Genet. 2010;121(5):829–843.
  • Burle ML, Fonseca JR, Kami JA, et al. Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity. Theor Appl Genet. 2010;121(5):801–813.
  • Zhang X, Blair MW, Wang S. Genetic diversity of Chinese common bean (Phaseolus vulgaris L.) landraces assessed with simple sequence repeat markers. Theor Appl Genet. 2008;117(4):629–640.
  • Blair MW, González LF, Kimani PM, et al. Genetic diversity, inter-gene pool introgression and nutritional quality of common beans. Theor Appl Genet. 2010;121(2):237–248.
  • Gepts P, Aragão FJ, De Barros E, et al. Genomics of Phaseolus beans, a major source of dietary protein and micronutrients in the tropics. In: Moore PH, Mong R, editors. Genomics of Tropical Crop Plants. New York (NY): Springer; 2008. p. 113–143
  • Blair MW, Pedraza F, Buendia HF, et al. Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2003;107(8):1362–1374.
  • Freyre R, Skroch PW, Geffroy V, et al. Towards an integrated linkage map of common bean. 4. Development of a core linkage map and alignment of RFLP maps. Theor Appl Genet. 1998;97(5-6):847–856.
  • Nodari RO, Koinange EMK, Kelly JD, et al. Towards an integrated linkage map of common bean : 1. Development of genomic DNA probes and levels of restriction fragment length polymorphism. Theor Appl Genet. 1992;84(1–2):186–192.
  • Beaver JS, Osorno JM. Achievements and limitations of contemporary common bean breeding using conventional and molecular approaches. Euphytica. 2009;168(2):145–175.
  • Şen K, Koca AS, Kacar G. Importance, Biology, Damage and Management of Bean Weevil Acanthoscelides obtectus Say (Coleoptera: Chrysomelidae). J Inst Sci Technol. 2020;10(3):1518–1527.
  • Brunner BR, Beaver JS. Estimation of outcrossing of the common bean in Puerto Rico. HortScience. 1989;24(4):669–671.
  • Ibarra-Perez FJ, Ehdaie B, Waines JG. Estimation of outcrossing rate in common bean. Crop Sci. 1997;37(1):60–65.
  • Kelly JD, Cichy KA. Dry bean breeding and production technologies. In: Siddiq M, Uebersax MA, editors. Dry beans and pulses: production, processing, and nutrition. Chichester (UK): Wiley-Blackwell; 2013. p. 23–54.
  • Urrea CA, Singh SP. Comparison of mass, F2-derived family, and single-seed-descent selection methods in an interracial population of common bean. Can J Plant Sci. 1994;74(3):461–464.
  • Kelly JD, Vallejo VA. A comprehensive review of the major genes conditioning resistance to anthracnose in common bean. HortScience. 2004;39(6):1196–1207.
  • Kelly JD, Adams MW. Phenotypic recurrent selection in ideotype breeding of pinto beans. Euphytica. 1987;36(1):69–80.
  • Kelly JD, Adams MW, Saettler AW, et al. Registration of ‘Sierra’pinto bean. Crop Sci. 1990;30(3):745–746.
  • Kelly JD, Varner GV, Hosfield GL, et al. Registration of ‘Sedona’pink bean. Crop Sci. 2006;46(6):2707–2708.
  • Hosfield GL, Varner GV, Uebersax MA, et al. Registration of’Merlot’small red bean. Crop Sci. 2004;44(1):351–353.
  • Kelly JD, Hosfield GL, Varner GV, et al. Registration of ‘Matterhorn’great northern bean. Crop Sci. 1999;39(2):589–590.
  • Singh SP. Gamete selection for simultaneous improvement of multiple traits in common bean. Crop Sci. 1994;34(2):352–355.
  • Singh SP. Integrated genetic improvement. In: Singh SP, editor. Common bean improvement in the twenty-first century. Dordrecht: Springer; 1999. p. 133–165.
  • Singh SP. Production and utilization. In: Singh SP, editor. Common bean improvement in the twenty-first century. Dordrecht: Springer; 1999. p. 1–24.
  • Terán H, Lema M, Webster D, et al. 75 years of breeding pinto bean for resistance to diseases in the United States. Euphytica. 2009;167(3):341–351.
  • Velez JJ, Bassett MJ, Beaver JS, et al. Inheritance of resistance to bean golden mosaic virus in common bean. J Am Soc Hortic Sci. 1998;123(4):628–631.
  • Blair MW, Giraldo MC, Buendia HF, et al. Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2006;113(1):100–109.
  • Román-Avilés B, Kelly JD. Identification of quantitative trait loci conditioning resistance to Fusarium root rot in common bean. Crop Sci. 2005;45(5):1881–1890.
  • Haghighi KR, Ascher PD. Fertile, intermediate hybrids between Phaseolus vulgaris and P. acutifolius from congruity backcrossing. Sex Plant Reprod. 1988;1(1):51–58.
  • Mejía-Jiménez A, Muñoz C, Jacobsen HJ, et al. Interspecific hybridization between common and tepary beans: increased hybrid embryo growth, fertility, and efficiency of hybridization through recurrent and congruity backcrossing. Theor Appl Genet. 1994;88(3–4):324–331.
  • Singh SP, Urrea CA. Inter-and intraracial hybridization and selection for seed yield in early generations of common bean, Phaseolus vulgaris L. Euphytica. 1995;81(2):131–137.
  • Nadeem MA, Nawaz MA, Shahid MQ, et al. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol Biotechnol Equip. 2018;32(2):261–285.
  • Nodari RO, Tsai SM, Guzman P, et al. Toward an integrated linkage map of common bean. III. Mapping genetic factors controlling host-bacteria interactions. Genetics. 1993;134(1):341–350.
  • Adam-Blondon AF, Sévignac M, Bannerot H, et al. SCAR, RAPD and RFLP markers linked to a dominant gene (Are) conferring resistance to anthracnose in common bean. Theor Appl Genet. 1994;88(6–7):865–870.
  • Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, 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. 2016;17(1):1–18.
  • Vallejos CE, Sakiyama NS, Chase CD. A molecular marker-based linkage map of Phaseolus vulgaris L. Genetics. 1992;131(3):733–740.
  • Yu K, Park SJ, Poysa V. Abundance and variation of microsatellite DNA sequences in beans (Phaseolus and Vigna). Genome. 1999;42(1):27–34.
  • Yu K, Park SJ, Poysa V, et al. Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.). J Hered. 2000;91(6):429–434.
  • Guerra-Sanz JM. New SSR markers of Phaseolus vulgaris from sequence databases. Plant Breed. 2004;123(1):87–89.
  • Garcia RA, Rangel PN, Brondani C, et al. The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris. BMC Genet. 2011;12(1):41–14.
  • Hanai LR, De Campos T, Camargo LEA, et al. Development, characterization, and comparative analysis of polymorphism at common bean SSR loci isolated from genic and genomic sources. Genome. 2007;50(3):266–277.
  • Caixeta ET, Borém A, Kelly JD. Development of microsatellite markers based on BAC common bean clones. Crop Breed Appl Biotechnol. 2005;5(2):125–133.
  • Ragupathy R, Rathinavelu R, Cloutier S. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. BMC Genom. 2011;12(1):1–17.
  • Schlueter JA, Goicoechea JL, Collura K, et al. BAC-end sequence analysis and a draft physical map of the common bean (Phaseolus vulgaris L.) genome. Trop Plant Biol. 2008;1(1):40–48.
  • Yu K. Bacterial artificial chromosome libraries of pulse crops: characteristics and applications. J Biomed Biotechnol. 2012;2012:1–8.
  • Phan NT, Sim SC. Genomic tools and their implications for vegetable breeding. Hortic Sci Technol. 2017;35(2):149–164.
  • Chung YS, Choi SC, Jun TH, et al. Genotyping-by-sequencing: a promising tool for plant genetics research and breeding. Hortic Environ Biotechnol. 2017;58(5):425–431.
  • Blair MW, Cortés AJ, Penmetsa RV, et al. A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2013;126(2):535–548.
  • Song Q, Jia G, Hyten DL, et al. SNP assay development for linkage map construction, anchoring whole-genome sequence, and other genetic and genomic applications in common bean. G3 Genes Genomes Genet. 2015;5(11):2285–2290.
  • Cichy KA, Wiesinger JA, Mendoza FA. Genetic diversity and genome-wide association analysis of cooking time in dry bean (Phaseolus vulgaris L.). Theor Appl Genet. 2015;128(8):1555–1567.
  • Cichy KA, Porch TG, Beaver JS, et al. A Phaseolus vulgaris diversity panel for Andean bean improvement. Crop Sci. 2015;55(5):2149–2160.
  • Kamfwa K, Cichy KA, Kelly JD. Genome-wide association study of agronomic traits in common bean. Plant Genome, 2015;8(2), 1–12.
  • Hart JP, Griffiths PD. Genotyping-by-sequencing enabled mapping and marker development for the By-2 potyvirus resistance allele in common bean. Plant Genome. 2015;8(1):plantgenome2014-09.
  • Diaz LM, Ricaurte J, Tovar E, et al. QTL analyses for tolerance to abiotic stresses in a common bean (Phaseolus vulgaris L.) population. PLoS ONE. 2018;13(8):e0202342.
  • Miklas PN, Delorme R, Stone V, et al. Bacterial, fungal, and viral disease resistance loci mapped in a recombinant inbred common bean population (Dorado’/XAN 176). J Am Soc Hortic Sci. 2000;125(4):476–481.
  • Miklas PN, Johnson WC, Delorme R, et al. QTL conditioning physiological resistance and avoidance to white mold in dry bean. Crop Sci. 2001;41(2):309–315.
  • Miklas PN, Coyne DP, Grafton KF, et al. A major QTL for common bacterial blight resistance derives from the common bean great northern landrace cultivar Montana. Euphytica. 2003;131(1):137–146.
  • Park SO, Coyne DP, Steadman JR, et al. Mapping of QTL for resistance to white mold disease in common bean. Crop Sci. 2001;41(4):1253–1262.
  • McClean PE, Lee RK, Otto C, et al. Molecular and phenotypic mapping of genes controlling seed coat pattern and color in common bean (Phaseolus vulgaris L.). J Hered. 2002;93(2):148–152.
  • Kelly JD, Gepts P, Miklas PN, et al. Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crops Res. 2003;82(2–3):135–154.
  • Kolkman JM, Kelly JD. QTL conferring resistance and avoidance to white mold in common bean. Crop Sci. 2003;43(2):539–548.
  • López CE, Acosta IF, Jara C, et al. Identifying resistance gene analogs associated with resistances to different pathogens in common bean. Phytopathology. 2003;93(1):88–95.
  • Papa R, Acosta J, Delgado-Salinas A, et al. A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica. Theor Appl Genet. 2005;111(6):1147–1158.
  • Papa R, Bellucci E, Rossi M, et al. Tagging the signatures of domestication in common bean (Phaseolus vulgaris) by means of pooled DNA samples. Ann Bot. 2007;100(5):1039–1051.
  • Felicetti E, Song Q, Jia G, et al. Simple sequence repeats linked with slow darkening trait in pinto bean discovered by single nucleotide polymorphism assay and whole genome sequencing. Crop Sci. 2012;52(4):1600–1608.
  • Goretti D, Bitocchi E, Bellucci E, et al. Development of single nucleotide polymorphisms in Phaseolus vulgaris and related Phaseolus spp. Mol Breed. 2014;33(3):531–544.
  • Hyten DL, Song Q, Fickus EW, et al. High-throughput SNP discovery and assay development in common bean. BMC Genom. 2010;11(1):475–478.
  • Zou X, Shi C, Austin RS, et al. Genome-wide single nucleotide polymorphism and insertion-deletion discovery through next-generation sequencing of reduced representation libraries in common bean. Mol Breed. 2014;33(4):769–778.
  • De Ron AM, Papa R, Bitocchi E, et al. Common bean. In De Ron AM, editor. Grain legumes. New York (NY): Springer; 2015. p. 1–36
  • Assefa T, Mahama AA, Brown AV, et al. A review of breeding objectives, genomic resources, and marker-assisted methods in common bean. Mol Breed. 2019;39(2):20.
  • Singh SP, Schwartz HF. Breeding common bean for resistance to diseases: a review. Crop Sci. 2010;50(6):2199–2223.
  • Palacioglu G, Bayraktar H, Ozer G. Genetic variability of Colletotrichum lindemuthianum isolates from Turkey and resistance of Turkish bean cultivars. Span J Agric Res. 2020;18(3):e1005.
  • Palacioglu G, Şanli İ, Bayraktar H, et al. Determination of Resistance Sources to BCMV and BCMNV in Some Common Bean (Phaseolus vulgaris L.) Cultivars Grown in Turkey. Int J Agric Wildl Sci. 2020;6(3):453–460.
  • Yeken MZ, Özer G, ÇeliK A, et al. Identification of genes related to resistance for bean common mosaic virus and bean common mosaic necrosis virus in commercial common bean cultivars in Turkey. Turk J Agric Nat Sci. 2018;5(4):613–619.
  • Ender M, Kelly JD. Identification of QTL associated with white mold resistance in common bean. Crop Sci. 2005;45(6):2482–2490.
  • Mkwaila W, Terpstra KA, Ender M, et al. Identification of QTL for agronomic traits and resistance to white mold in wild and landrace germplasm of common bean. Plant Breed. 2011;130(6):665–672.
  • Soule M, Porter L, Medina J, et al. Comparative QTL map for white mold resistance in common bean, and characterization of partial resistance in dry bean lines VA19 and I9365-3. Crop Sci. 2011;51(1):123–139.
  • Oblessuc PR, Baroni RM, Garcia AAF, et al. Mapping of angular leaf spot resistance QTL in common bean (Phaseolus vulgaris L.) under different environments. BMC Genet. 2012;13(1):50–59.
  • Keller B, Manzanares C, Jara C, et al. Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean. Theor Appl Genet. 2015;128(5):813–826.
  • Wang W, Jacobs JL, Chilvers MI, et al. QTL analysis of Fusarium root rot resistance in an Andean × middle American common bean RIL population. Crop Sci. 2018;58(3):1166–1180.
  • Frei A, Blair MW, Cardona C, et al. QTL mapping of resistance to Thrips palmi Karny in common bean. Crop Sci. 2005;45(1):cropsci2005.0379-387.
  • Kamfwa K, Beaver JS, Cichy KA, et al. QTL mapping of resistance to bean weevil in common bean. Crop Sci. 2018;58(6), 2370–2378.
  • Dramadri IO, Nkalubo ST, Kelly JD. Identification of QTL associated with drought tolerance in Andean common bean. Crop Sci. 2019;59(3):1007–1020.
  • Sedlar A, Zupin M, Maras M, et al. QTL mapping for drought-responsive agronomic traits associated with physiology, phenology, and yield in an andean intra-gene pool common bean population. Agronomy. 2020;10(2):225.
  • Vallejo V, Kelly JD. 2002. The use of AFLP analysis to tag the Co-12 gene conditioning resistance to bean anthracnose In Proceedings of the X conference on plant and animal genome. http://www.intl-pag.org/pag/10/abstracts/PAGX_P233.html.
  • Young RA, Melotto M, Nodari RO, et al. Marker-assisted dissection of the oligogenic anthracnose resistance in the common bean cultivar,’G2333. Theor Appl Genet. 1998;96(1):87–94.
  • Trabanco N, Campa A, Ferreira JJ. Identification of a new chromosomal region involved in the genetic control of resistance to anthracnose in common bean. Plant Genome. 2015;8(2);plantgenome2014-10.
  • Pérez-Vega E, Pañeda A, Rodríguez-Suárez C, et al. Mapping of QTLs for morpho-agronomic and seed quality traits in a RIL population of common bean. Theor Appl Genet. 2010;120(7):1367–1380.
  • Méndez-Vigo B, Rodríguez-Suárez C, Paneda A, et al. Molecular markers and allelic relationships of anthracnose resistance gene cluster B4 in common bean. Euphytica. 2005;141(3):237–245.
  • De Queiroz VT, De Sousa CS, Costa MR, et al. Development of SCAR markers linked to common bean angular leaf spot resistance genes. Annu Rep Bean Improv Coop. 2004;47:237–238.
  • Awale HE, Kelly JD. Development of SCAR markers linked to Co-4^ 2 gene in common bean. Annual Report-Bean Improvement Cooperative, 44, 119–120. 2001.
  • Campa A, Giraldez R, Ferreira JJ. Genetic dissection of the resistance to nine anthracnose races in the common bean differential cultivars MDRK and TU. Theor Appl Genet. 2009;119(1):1–11.
  • Young RA, Kelly JD. RAPD markers linked to three major anthracnose resistance genes in common bean. Crop Sci. 1997;37(3):940–946.
  • Campa A, Rodríguez-Suárez C, Pañeda A, et al. The bean anthracnose resistance gene Co-5, is located in linkage group B7. Annu Rep Bean Improv Coop. 2005;48:68.
  • Geffroy V, Sicard D, de Oliveira JC, et al. Identification of an ancestral resistance gene cluster involved in the coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum. Mol Plant Microbe Interact. 1999;12(9):774–784.
  • Alzate-Marin AL, Costa MR, Arruda KM, et al. Characterization of the anthracnose resistance gene present in Ouro Negro (Honduras 35) common bean cultivar. Euphytica. 2003;133(2):165–169.
  • Melotto M, Kelly J. SCAR markers linked to major disease resistance genes in common bean. Annu Rep Bean Improv Coop. 1998;41:64–65.
  • Haley SD, Afanador LK, Miklas PN, et al. Heterogeneous inbred populations are useful as sources of near-isogenic lines for RAPD marker localization. Theor Appl Genet. 1994;88(3):337–342.
  • Miklas PN. Marker-assisted selection for disease resistance in common bean. Annu Rep Bean Improv Coop. 2002;45:1–3.
  • Park SO, Coyne DP, Steadman JR. Confirmation of the Ur-6 location in Phaseolus vulgaris L. Annu Rep Bean Improv Coop. 2004;47:265–266.
  • Park SO, Coyne DP, Steadman JR, et al. Mapping of the Ur-7 gene for specific resistance to rust in common bean. Crop Sci. 2003;43(4):1470–1476.
  • Jung G, Coyne DP, Bokosi J, et al. Mapping genes for specific and adult plant resistance to rust and abaxial leaf pubescence and their genetic relationships using randomly amplified polymorphic DNA (RAPD) markers in common bean. J Am Soc Hort Sci. 1998;123(5):859–863.
  • Park SO, Coyne DP, Bokosi JM, et al. Molecular markers linked to genes for specific rust resistance and indeterminate growth habit in common bean. Euphytica. 1999;105(2):133–141.
  • Awale HE, Safeena MI, Vallejo VA, et al. Sq4 Scar Marker Linked To The Co-2 Gene On Bll Appears To Be Linked To The Ur-11 Gene. 2008.
  • Johnson E, Miklas PN, Stavely JR, et al. Coupling-and repulsion-phase RAPDs for marker-assisted selection of PI 181996 rust resistance in common bean. Theor Appl Genet. 1995;90(5):659–664.
  • Mienie CMS, Liebenberg MM, Pretorius ZA, et al. SCAR markers linked to the common bean rust resistance gene Ur-13. Theor Appl Genet. 2005;111(5):972–979.
  • Melotto M, Afanador L, Kelly JD. Development of a SCAR marker linked to the I gene in common bean. Genome. 1996;39(6):1216–1219.
  • Strausbaugh CA, Myers JR, Forster RL, et al. bc-1 and bc-u—two loci controlling bean common mosaic virus resistance in common bean are linked. J Am Soc Hortic Sci. 1999;124(6):644–648.
  • Johnson WC, Guzmán P, Mandala D, et al. Molecular tagging of the bc-3 gene for introgression into Andean common bean. Crop Sci. 1997;37(1):248–254.
  • Mukeshimana G, Paneda A, Rodríguez-Suárez C, et al. Markers linked to the bc-3 gene conditioning resistance to bean common mosaic potyviruses in common bean. Euphytica. 2005;144(3):291–299.
  • Urrea CA, Miklas PN, Beaver JS, et al. A codominant randomly amplified polymorphic DNA (RAPD) marker useful for indirect selection of bean golden mosaic virus resistance in common bean. J Am Soc Hortic Sci. 1996;121(6):1035–1039.
  • Blair MW, Beaver JS, Nin JC, et al. Registration of PR9745-232 and RMC-3 red-mottled dry bean germplasm lines with resistance to Bean golden yellow mosaic virus. Crop Sci. 2006;46(2):1000–1002.
  • Chen J, Zhang X, Jing R, et al. Cloning and genetic diversity analysis of a new P5CS gene from common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2010;120(7):1393–1404.
  • Blair MW, Galeano CH, Tovar E, et al. Development of a Mesoamerican intra-genepool genetic map for quantitative trait loci detection in a drought tolerant × susceptible common bean (Phaseolus vulgaris L.) cross. Mol Breed. 2012;29(1):71–88.
  • Johannsen W. The genotype conception of heredity. Am Nat. 1911;45(531):129–159.
  • Motto M, Soressi GP, Salamini F. Seed size inheritance in a cross between wild and cultivated common beans (Phaseolus vulgaris L.). Genetica. 1978;49(1):31–36.
  • Vallejos CE, Chase CD. Linkage between isozyme markers and a locus affecting seed size in Phaseolus vulgaris L. Theor Appl Genet. 1991;81(3):413–419.
  • Blair MW, Izquierdo P. Use of the advanced backcross-QTL method to transfer seed mineral accumulation nutrition traits from wild to Andean cultivated common beans. Theor Appl Genet. 2012;125(5):1015–1031.
  • Koinange EM, Singh SP, Gepts P. Genetic control of the domestication syndrome in common bean. Crop Sci. 1996;36(4):1037–1045.
  • Tar’an B, Michaels TE, Pauls KP. Genetic mapping of agronomic traits in common bean. Crop Sci. 2002;42(2):544–556.
  • Checa OE, Blair MW. Mapping QTL for climbing ability and component traits in common bean (Phaseolus vulgaris L.). Mol Breed. 2008;22(2):201–215.
  • Garcia RAV, Rangel PN, Bassinello PZ, et al. QTL mapping for the cooking time of common beans. Euphytica. 2012;186(3):779–792.
  • Park SO, Coyne DP, Jung G, et al. Mapping of QTL for seed size and shape traits in common bean. J Am Soc Horti Sci. 2000;125(4):466–475.
  • Beebe SE, Rojas-Pierce M, Yan X, et al. Quantitative trait loci for root architecture traits correlated with phosphorus acquisition in common bean. Crop Sci. 2006;46(1):413–423.
  • Hoyos-Villegas V, Song Q, Wright EM, et al. Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations. Crop Sci. 2016;56(5):2546–2563.
  • Bhakta MS, Gezan SA, Clavijo Michelangeli JA, et al. A predictive model for time-to-flowering in the common bean based on QTL and environmental variables. G3 (Bethesda). 2017;7(12):3901–3912.
  • Sandhu KS, You FM, Conner RL, et al. Genetic analysis and QTL mapping of the seed hardness trait in a black common bean (Phaseolus vulgaris) recombinant inbred line (RIL) population. Mol Breed. 2018;38(3):1–13.
  • Lei L, Wang L, Wang S, et al. Marker-trait association analysis of seed traits in accessions of common bean (Phaseolus vulgaris L.) in China. Front Genet. 2020;11:698.
  • Geravandi M, Cheghamirza K, Farshadfar E, et al. QTL analysis of seed size and yield-related traits in an inter-genepool population of common bean (Phaseolus vulgaris L.). Sci Hortic. 2020;274:109678.
  • Blair MW, Knewtson SJ, Astudillo C, et al. Variation and inheritance of iron reductase activity in the roots of common bean (Phaseolus vulgaris L.) and association with seed iron accumulation QTL. BMC Plant Biol. 2010;10(1):215–212.
  • Nemli S, Asciogul TK, Ates D, Esiyok, et al. SNP identification through genotyping by sequencing and genome-wide association study (GWAS) of pod traits in common bean. In International Plant and Animal Genome Conference, Paper. 2016; Vol. 19798).
  • Moghaddam SM, Mamidi S, Osorno JM, et al. Genome-wide association study identifies candidate loci underlying agronomic traits in a Middle American diversity panel of common bean. Plant Genome. 2016;9(3):1–21.
  • Perseguini JMKC, Oblessuc PR, Rosa JRBF, et al. Genome-wide association studies of anthracnose and angular leaf spot resistance in common bean (Phaseolus vulgaris L.). PLoS ONE. 2016;11(3):e0150506.
  • Ferreira JJ, Murube E, Campa A. Introgressed genomic regions in a set of near-isogenic lines of common bean revealed by genotyping-by-sequencing. Plant Genome. 2016;10(1):plantgenome2016-08.
  • Berny Mier Y, Teran JC, Konzen ER, et al. Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L. Ann Bot. 2019;124(6):917–932.
  • Emiliano VP, González-Chavira Mario M, Patricia GC, et al. Identification of novel drought-tolerant-associated SNPs in common bean (Phaseolus vulgaris). Front Plant Sci. 2015;6:546.
  • Hoyos-Villegas V, Song Q, Kelly JD. Genome-wide association analysis for drought tolerance and associated traits in common bean. Plant Genome. 2017;10(1):1–17.
  • Wu L, Chang Y, Wang L, et al. Genetic dissection of drought resistance based on root traits at the bud stage in common bean. Theor Appl Genet. 2021;134:1–15.
  • Leitão ST, Bicho MC, Pereira P, et al. Common bean SNP alleles and candidate genes affecting photosynthesis under contrasting water regimes. Hortic Res. 2021;8(1):1–14.
  • Nemli S, Asciogul TK, Kaya HB, et al. Association mapping for five agronomic traits in the common bean (Phaseolus vulgaris L.). J Sci Food Agric. 2014;94(15):3141–3151.
  • Zuiderveen GH, Padder BA, Kamfwa K, et al. Genome-wide association study of anthracnose resistance in Andean beans (Phaseolus vulgaris). PLoS ONE. 2016;11(6):e0156391.]
  • Tock AJ, Fourie D, Walley PG, 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. 2017;8:1170.
  • Wu C, Chen Z, Dardalhon V, et al. The transcription factor musculin promotes the unidirectional development of peripheral Treg cells by suppressing the TH2 transcriptional program. Nat Immunol. 2017;18(3):344–353.
  • Wu J, Chen J, Wang L, et al. Genome-wide investigation of WRKY transcription factors involved in terminal drought stress response in common bean. Front Plant Sci. 2017;8:380.
  • Ates D, Asciogul TK, Nemli S, et al. Association mapping of days to flowering in common bean (Phaseolus vulgaris L.) revealed by DArT markers. Mol Breed. 2018;38(9):113.
  • Katuuramu DN, Hart JP, Porch TG, et al. Genome-wide association analysis of nutritional composition-related traits and iron bioavailability in cooked dry beans (Phaseolus vulgaris L.). Mol Breed. 2018;38(4):44.
  • Nascimento M, Nascimento ACC, Silva FFE, et al. Quantile regression for genome-wide association study of flowering time-related traits in common bean. PLoS ONE. 2018;13(1):e0190303.
  • Oladzad A, Porch T, Rosas JC, et al. Single and multi-trait GWAS identify genetic factors associated with production traits in common bean under abiotic stress environments. G3 (Bethesda)). 2019;9(6):1881–1892.
  • Tigist SG, Melis R, Sibiya J, et al. Population structure and genome-wide association analysis of bruchid resistance in Ethiopian common bean genotypes. Crop Sci. 2019;59(4):1504–1515.
  • Raggi L, Caproni L, Carboni A, et al. Genome-wide association study reveals candidate genes for flowering time variation in common bean (Phaseolus vulgaris L.). Front Plant Sci. 2019;10:962.
  • Jain S, Poromarto S, Osorno JM, et al. Genome wide association study discovers genomic regions involved in resistance to soybean cyst nematode (Heterodera glycines) in common bean. PLoS ONE. 2019;14(2):e0212140.
  • Wu D, Hought J, Baseggio M, et al. Genomic characterization of the native seeds/search common bean (Phaseolus vulgaris L.) Collection and its seed coat patterns. Genet Resour Crop Evol. 2019;66(7):1469–1482.
  • Wen L, Chang HX, Brown PJ, et al. Genome-wide association and genomic prediction identifies soybean cyst nematode resistance in common bean including a syntenic region to soybean Rhg1 locus. Hortic Res. 2019;6(1):9–12.
  • Ojwang PPO, Eldridge T, Corredor-Moreno P, et al. Genome-wide association study of resistance to bean fly and population structure of market classes of common bean. BioRxiv, 633545. 2019.
  • López-Hernández F, Cortés AJ. Last-generation genome-environment associations reveal the genetic basis of heat tolerance in common bean (Phaseolus vulgaris L.). Front Genet. 2019;10:954.
  • Myers JR, Wallace LT, Mafi Moghaddam S, et al. Improving the health benefits of snap bean: genome-wide association studies of total phenolic content. Nutrients. 2019;11(10):2509.
  • Caproni L, Raggi L, Talsma EF, et al. European landrace diversity for common bean biofortification: a genome-wide association study. Sci Rep. 2020;10(1):1–13.
  • Erdogmus S, Ates D, Nemli S, et al. Genome-wide association studies of Ca and Mn in the seeds of the common bean (Phaseolus vulgaris L.). Genomics. 2020;112(6):4536–4546.
  • Banoo A, Nabi A, Rasool RS, et al. North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study. Front Plant Sci. 2020;11:1459.
  • Vidigal Filho PS, Gonçalves-Vidigal MC, Vaz Bisneta M, et al. Genome-wide association study of resistance to anthracnose and angular leaf spot in Brazilian Mesoamerican and Andean common bean cultivars. Crop Sci. 2020;60(6):2931–2950.
  • Campa A, García-Fernández C, Ferreira JJ. Genome-wide association study (GWAS) for resistance to Sclerotinia sclerotiorum in common bean. Genes. 2020;11(12):1496.
  • Dramadri IO, Amongi W, Kelly JD, et al. Genome-wide association analysis of resistance to Pythium ultimum in common bean (Phaseolus vulgaris. Plant Breed. 2020;139(6):1168–1180.
  • Maldonado-Mota CR, Moghaddam SM, Schröder S, et al. Genomic regions associated with resistance to anthracnose in the Guatemalan climbing bean (Phaseolus vulgaris L.) germplasm collection. Genet Resour Crop Evol. 2020;68:1–11.
  • Costa LC, Nalin RS, Dias MA, et al. Different loci control resistance to different isolates of the same race of Colletotrichum lindemuthianum in common bean. Theor Appl Genet. 2021;1–14.
  • Semagn K, Babu R, Hearne S, et al. Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed. 2014;33(1):1–14.
  • Steele KA, Quinton-Tulloch MJ, Amgai RB, et al. Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice. Mol Breed. 2018;38(4):38–13.
  • Hurtado-Gonzales OP, Valentini G, Gilio TAS, et al. Fine mapping of genes conferring resistance to rust and anthracnose of common bean. Annu Rep Bean Improv Coop. 2017;61:27–28.
  • Gilio TAS, Hurtado-Gonzales OP, Gonçalves-Vidigal MC, et al. Fine mapping of an anthracnose-resistance locus in Andean common bean cultivar Amendoim Cavalo. PLoS ONE. 2020;15(10):e0239763.
  • Libault M, Dickstein R. Advances in functional genomics in legumes. In: Gupta S, Nadarajan N, Gupta DS, editors. Legumes in the Omic Era. New York (NY): Springer; 2014. p. 15–39.
  • Wang X, Elling AA, Li X, et al. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell. 2009;21(4):1053–1069.
  • Hatey F, Tosser-Klopp G, Clouscard-Martinato C, et al. Expressed sequence tags for genes: a review. Genet Sel Evol. 1998;30(6):521–541.
  • Asamizu E, Nakamura Y, Sato S, et al. Characteristics of the Lotus japonicus gene repertoire deduced from large-scale expressed sequence tag (EST) analysis. Plant Mol Biol. 2004;54(3):405–414.
  • Blair MW, Fernandez AC, Ishitani M, et al. Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.). BMC Plant Biol. 2011;11(1):171–115.
  • Cheung F, Haas BJ, Goldberg SM, et al. Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genom. 2006;7(1):1–10.
  • Vodkin LO, Khanna A, Shealy R, et al. Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC Genom. 2004;5(1):73–18.
  • Blair MW, Torres MM, Giraldo MC, et al. Development and diversity of Andean-derived, gene-based microsatellites for common bean (Phaseolus vulgaris L.). BMC Plant Biol. 2009;9(1):100–114.
  • Melotto M, Monteiro-Vitorello CB, Bruschi AG, et al. Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings. Genome. 2005;48(3):562–570.
  • Ramírez M, Graham MA, Blanco-López L, et al. Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol. 2005;137(4):1211–1227.
  • Tian J, Venkatachalam P, Liao H, et al. Molecular cloning and characterization of phosphorus starvation responsive genes in common bean (Phaseolus vulgaris L.). Planta. 2007;227(1):151–165.
  • McClean PE, Mamidi S, McConnell M, et al. Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genom. 2010;11(1):184–110.
  • Blair MW, Hurtado N, Chavarro CM, et al. Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series. BMC Plant Biol. 2011;11(1):50–10.
  • Thibivilliers S, Joshi T, Campbell KB, et al. Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection. BMC Plant Biol. 2009;9(1):46–13.
  • Kalavacharla V, Liu Z, Meyers BC, et al. Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing. BMC Plant Biol. 2011;11(1):135–118.
  • Kavas M, Kizildogan A, Gökdemir G, et al. Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean. EXCLI J. 2015;14:1187–1206.
  • Kavas M, Baloğlu MC, Atabay ES, et al. Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration. Mol Genet Genom. 2016;291(1):129–143.
  • Büyük İ . Inal B, Ilhan E, Tanriseven M, Aras S, Erayman M. Genome-wide identification of salinity responsive HSP70s in common bean. Mol Biol Rep. 2016;43(11):1251–1266.
  • Wu J, Wang L, Wang S. Comprehensive analysis and discovery of drought-related NAC transcription factors in common bean. BMC Plant Biol. 2016;16(1):1–13.
  • İnal B, Büyük İ, İlhan E, et al. Genome-wide analysis of Phaseolus vulgaris C2C2-YABBY transcription factors under salt stress conditions. 3 Biotech. 2017;7(5):302.
  • Ilhan E. Genome-Wide Characterization and Analysis of Sbp Transcription Factor Family in Common Bean (Phaseolus vulgaris L. Appl Ecol Env Res. 2018;16(5):5467–5480.
  • Buyuk I, Inal B, Ilhan E, et al. Common Bean (Phaseolus vulgaris L.) Dof Transcription Factors Differentially Expressed Under Salt Stress. Commun Fac Sci Univ Ankara Ser C Biol. 2019;28(1):43–66.
  • Gökdemir FS. Genome-Wide Identification and Characterization of Whirly and Arr-B Genes in Common Bean (Phaseolus vulgaris L.) and Assessment of Their Possible Role in Biotic Stress Response at Gene Expression Level, Ph.D. Thesis, Ankara University, Graduate School of Natural and Applied Science, Department of Biology. 2019.
  • Zhang Q, Li WJ, Zhang WJ, et al. PvB3s: genome-wide and transcriptome-wide identification and analysis reveals the B3 family regulate auxin to resist salt stress at the sprout stage in common bean (P. vulgaris L.). 2020. https://doi.org/10.21203/rs.3.rs-36056/v1.
  • Silva DAD, Tsai SM, Chiorato AF, et al. Analysis of the common bean (Phaseolus vulgaris L.) transcriptome regarding efficiency of phosphorus use. PLoS ONE. 2019;14(1):e0210428.
  • Hernández G, Ramírez M, Valdés-López O, et al. Phosphorus stress in common bean: root transcript and metabolic responses. Plant Physiol. 2007;144(2):752–767.
  • Bliss FA, Brown JW. Breeding common bean for improved quantity and quality of seed protein. In: Janick J, editor. Plant breeding reviews. Boston (MA): Springer; 1983. p. 59–102.
  • FAO. Food and Agriculture Organization of the United Nations. 2013. Available from http://www.fao.org/faostat/en/#data/TP.
  • Vitale A, Bollini R. Legume storage proteins. In: Kigel J, Gad G, editors. Seed Development and Germination. Boca Raton: Routledge; 1995. p. 73–102.
  • Mühling M, Gilroy J, Croy RR. Legumin proteins from seeds of Phaseolus vulgaris L. J Plant Physiol. 1997;150(4):489–492.
  • Gepts P, Bliss FA. Enhanced available methionine concentration associated with higher phaseolin levels in common bean seeds. Theor Appl Genet. 1984;69(1):47–53.
  • Osborn TC, Bliss FA. Effects of genetically removing lectin seed protein on horticultural and seed characteristics of common bean. J Am Soc Hortic Sci. 1985;110:484–488.
  • Voelker TA, Staswick P, Chrispeels MJ. Molecular analysis of two phytohemagglutinin genes and their expression in Phaseolus vulgaris cv. Pinto, a lectin-deficient cultivar of the bean. Embo J. 1986;5(12):3075–3082.
  • Bollini R, Ceriotti A, Daminati MG, et al. Glycosylation is not needed for the intracellular transport of phytohemagglutinin in developing Phaseolus vulgaris cotyledons and for the maintenance of its biological activities. Physiol Plant. 1985;65(1):15–22.
  • De La Fuente M, Borrajo A, Bermúdez J, et al. 2-DE-based proteomic analysis of common bean (Phaseolus vulgaris L.) seeds. J Proteom. 2011;74(2):262–267.
  • Robison FM, Heuberger AL, Brick MA, et al. Proteome characterization of leaves in common bean. Proteomes. 2015;3(3):236–248.
  • Torres NL, Cho K, Shibato J, et al. Gel-based proteomics reveals potential novel protein markers of ozone stress in leaves of cultivated bean and maize species of Panama. Electrophoresis. 2007;28(23):4369–4381.
  • Zadražnik T, Hollung K, Egge-Jacobsen W, et al. Differential proteomic analysis of drought stress response in leaves of common bean (Phaseolus vulgaris L.). J Proteomics. 2013;78:254–272.
  • Parreira JR, Bouraada J, Fitzpatrick MA, et al. Differential proteomics reveals the hallmarks of seed development in common bean (Phaseolus vulgaris L.). J Proteomics. 2016;143:188–198.
  • Badowiec A, Weidner S. Proteomic changes in the roots of germinating Phaseolus vulgaris seeds in response to chilling stress and post-stress recovery. J Plant Physiol. 2014;171(6):389–398.
  • Salavati A, Taleei A, Akbar Shahnejat Bushehri A, et al. Analysis of the proteome of common bean (Phaseolus vulgaris L.) roots after inoculation with Rhizobium etli. Protein Pept Lett. 2012;19(8):880–889.
  • Lee J, Feng J, Campbell KB, et al. Quantitative proteomic analysis of bean plants infected by a virulent and avirulent obligate rust fungus. Mol Cell Proteom. 2009;8(1):19–31.
  • Natarajan SS, Pastor-Corrales MA, Khan FH, et al. Proteomic analysis of common bean (Phaseolus vulgaris L.) by two-dimensional gel electrophoresis and mass spectrometry. J Basic Appl Sci. 2013;9:424–437.
  • López-Pedrouso M, Alonso J, Zapata C. Evidence for phosphorylation of the major seed storage protein of the common bean and its phosphorylation-dependent degradation during germination. Plant Mol Biol. 2014;84(4–5):415–428.
  • Mensack MM, Fitzgerald VK, Ryan EP, et al. Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of domestication using’omics’ technologies. BMC Genom. 2010;11(1):1–11.
  • Lei Z, Dai X, Watson BS, et al. A legume specific protein database (LegProt) improves the number of identified peptides, confidence scores and overall protein identification success rates for legume proteomics. Phytochemistry. 2011;72(10):1020–1027.
  • El-Gebali S, Mistry J, Bateman A, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47(D1):D427–D432.
  • Guo AY, Zhu QH, Chen X, et al. GSDS: a gene structure display server. Yi Chuan. 2007;29(8):1023–1026.
  • Bailey TL, Williams N, Misleh C, et al. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006;34(Web Server issue):W369–W373.
  • Horton P, Park KJ, Obayashi T, et al. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 2007;35(Web Server issue):W585–W587.
  • Emanuelsson O, Brunak S, Von Heijne G, et al. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc. 2007;2(4):953–971.
  • Zhang Y. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res. 2005;33(Web Server issue):W701–W704.
  • Conesa A, Götz S, García-Gómez JM, et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674–3676.
  • Lee TH, Tang H, Wang X, et al. PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res. 2013;41(Database issue):D1152–D1158.
  • Zheng Y, Jiao C, Sun H, et al. iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Mol Plant. 2016;9(12):1667–1670.
  • Kelley LA, Mezulis S, Yates CM, et al. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015;10(6):845–858.
  • Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006;34(Web Server issue):W609–W612.
  • Gautam B, & Bonthala VS, Gajula MP. PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes. DATABASE-OXFORD. 2016;2016:baw114.
  • Caldas DGG, Konzen ER, Recchia GH, et al. Functional genomics of biotic and abiotic stresses in Phaseolus vulgaris. In: Shanker AK, Shanker C, editor. Abiotic and biotic stress in plants-recent advances and future perspectives. London: IntechOpen; 2016. p. 121–150.
  • Amugune NO, Anyango B, Mukiama TK. Arobacterium-mediated transformation of common bean. Afr Crop Sci J. 2011;19(3):137–147.
  • Aragão FJ, Vianna GR, Albino MM, et al. Transgenic dry bean tolerant to the herbicide glufosinate ammonium. Crop Sci. 2002;42(4):1298–1302.
  • Dillen W, Engler G, Van Montagu M, et al. Electroporation-mediated DNA delivery to seedling tissues of Phaseolus vulgaris L.(common bean). Plant Cell Rep. 1995;15(1–2):119–124.
  • Kim JW, Minamikawa T. Transformation and regeneration of French bean plants by the particle bombardment process. Plant Sci. 1996;117(1–2):131–138.
  • Rech EL, Vianna GR, Aragao FJ. High-efficiency transformation by biolistics of soybean, common bean and cotton transgenic plants. Nat Protoc. 2008;3(3):410–418.
  • Aragão FJ, de Sa MFG, Davey MR, et al. Factors influencing transient gene expression in bean (Phaseolus vulgaris L.) using an electrical particle acceleration device. Plant Cell Rep. 1993;12(9):483–490.
  • Russell DR, Wallace KM, Bathe JH, et al. Stable transformation of Phaseolus vulgaris via electric-discharge mediated particle acceleration. Plant Cell Rep. 1993;12(3):165–169.
  • Aragão FJL, Barros LMG, Brasileiro ACM, et al. Inheritance of foreign genes in transgenic bean (Phaseolus vulgaris L.) co-transformed via particle bombardment. Theor Appl Genet. 1996;93(1–2):142–150.
  • Aragão FJ, Rech EL. Morphological factors influencing recovery of transgenic bean plants (Phaseolus vulgaris L.) of a carioca cultivar. Int J Plant Sci. 1997;158(2):157–163.
  • Aragão FJL, Barros LMG, De Sousa MV, et al. Expression of a methionine-rich storage albumin from the Brazil nut (Bertholletia excelsa HBK, Lecythidaceae) in transgenic bean plants (Phaseolus vulgaris L., Fabaceae). Genet Mol Biol. 1999;22(3):445–449.
  • Faria JC, Albino MM, Dias BB, et al. Partial resistance to Bean golden mosaic virus in a transgenic common bean (Phaseolus vulgaris L.) line expressing a mutated rep gene. Plant Sci. 2006;171(5):565–571.
  • Bonfim K, Faria JC, Nogueira EO, et al. RNAi-mediated resistance to Bean golden mosaic virus in genetically engineered common bean (Phaseolus vulgaris). Mol Plant Microbe Interact. 2007;20(6):717–726.
  • Aragão FJ, Nogueira EO, Tinoco MLP, et al. Molecular characterization of the first commercial transgenic common bean immune to the Bean golden mosaic virus. J Biotechnol. 2013;166(1–2):42–50.
  • Aragão FJL, Ribeiro SG, Barros LMG, et al. Transgenic beans (Phaseolus vulgaris L.) engineered to express viral antisense RNAs show delayed and attenuated symptoms to bean golden mosaic geminivirus. Mol Breed. 1998;4(6):491–499.
  • Franklin CI, Trieu TN, Cassidy BG, et al. Genetic transformation of green bean callus via Agrobacterium mediated DNA transfer. Plant Cell Rep. 1993;12(2):74–79.
  • Zhang Z, Coyne DP, Mitra A. Factors affecting Agrobacterium-mediated transformation of common bean. J Am Soc Hortic Sci. 1997;122(3):300–305.
  • Arellano J, Fuentes SI, Castillo-Espana P, et al. Regeneration of different cultivars of common bean (Phaseolus vulgaris L.) via indirect organogenesis. Plant Cell Tiss Organ Cult. 2009;96(1):11–18.
  • Colpaert N, Tilleman S, Van Montagu M, et al. Composite Phaseolus vulgaris plants with transgenic roots as research tool. Afr J Biotechnol. 2008;7(4).
  • Genga AM, Allavena A, Ceriotti A, et al. Genetic transformation in Phaseolus species by high-velocity microprojectiles. In Vitro Culture, XXIII IHC. 1990;300:309–314.
  • McClean P, Chee P, Held B, et al. Susceptibility of dry bean (Phaseolus vulgaris L.) to Agrobacterium infection: transformation of cotyledonary and hypocotyl tissues. Plant Cell Tiss Organ Cult. 1991;24(2):131–138.
  • Lewis ME, Bliss FA. Tumor formation and β-glucuronidase expression in Phaseolus vulgaris inoculated with Agrobacterium tumefaciens. J Am Soc Hortic Sci. 1994;119(2):361–366.
  • Kapila J, De Rycke R, Van Montagu M, et al. An Agrobacterium-mediated transient gene expression system for intact leaves. Plant Sci. 1997;122(1):101–108.
  • Mukeshimana G, Ma Y, Walworth AE, et al. Factors influencing regeneration and Agrobacterium tumefaciens-mediated transformation of common bean (Phaseolus vulgaris L.). Plant Biotechnol Rep. 2013;7(1):59–70.
  • Estrada-Navarrete G, Alvarado-Affantranger X, Olivares JE, et al. Agrobacterium rhizogenes transformation of the Phaseolus spp.: a tool for functional genomics. Mol Plant Microbe Interact. 2006;19(12):1385–1393.
  • Estrada-Navarrete G, Alvarado-Affantranger X, Olivares JE, et al. Fast, efficient and reproducible genetic transformation of Phaseolus spp. by Agrobacterium rhizogenes. Nat Protoc. 2007;2(7):1819–1824.
  • Xue R, Wu X, Wang Y, et al. Hairy root transgene expression analysis of a secretory peroxidase (PvPOX1) from common bean infected by Fusarium wilt. Plant Sci. 2017;260:1–7.
  • Liu Z, Park BJ, Kanno A, et al. The novel use of a combination of sonication and vacuum infiltration in Agrobacterium-mediated transformation of kidney bean (Phaseolus vulgaris L.) with lea gene. Mol Breed. 2005;16(3):189–197.
  • Espinosa-Huerta E, Quintero-Jiménez A, Cabrera-Becerra K, et al. Stable and efficient Agrobacterium tumefaciens mediated transformation of Phaseolus vulgaris. Agrociencia. 2013;47(4):319–333.
  • Dang W, Wei ZM. High frequency plant regeneration from the cotyledonary node of common bean. Biol Plant. 2009;53(2):312–316.
  • Thảo NT, Thảo NT, Hassan F, Jacobsen HJ, et al. In vitro propagation of common bean (Phaseolus vulgaris L.). J Sci Dev. 2013;11:868–876.
  • Castillo BM, Rodríguez de la O JL, Gallardo JOM, et al. In vitro plants of common bean (Phaseolus vulgaris L.) obtained by direct organogenesis. JAS. 2015;7(11):169.
  • Quintero-Jiménez A, Espinosa-Huerta E, Acosta-Gallegos JA, et al. Enhanced shoot organogenesis and regeneration in the common bean (Phaseolus vulgaris L.). Plant Cell Tiss Organ Cult. 2010;102(3):381–386.
  • Veltcheva M, Svetleva D. In vitro regeneration of Phaseolus vulgaris L. via organogenesis from petiole explants. J Cent Eur Agric. 2005;6(1):53–58.
  • Sabzikar R, Sticklen MB, Kelly JD. In vitro regeneration and morphogenesis studies in common bean. Plant Cell, Tissue Organ Cult. 2010;100(1):97–105.
  • Souter JR, Gurusamy V, Porch TG, et al. Successful introgression of abiotic stress tolerance from wild tepary bean to common bean. Crop Sci. 2017;57(3):1160–1171.
  • Melotto M, Kelly JD. An allelic series at the Co-1 locus conditioning resistance to anthracnose in common bean of Andean origin. Euphytica. 2000;116(2):143–149.
  • You MP, Colmer TD, Barbetti MJ. Salinity drives host reaction in Phaseolus vulgaris (common bean) to Macrophomina phaseolina. Funct Plant Biol. 2011;38(12):984–992.