Advertisement

Marker-Assisted Breeding for Economic Traits in Common Bean

  • James D. Kelly
  • Nolan Bornowski
Chapter

Abstract

The common bean (Phaseolus vulgaris L.) is the most widely grown grain legume species that is consumed directly by humans. The crop is grown from the northern regions of Canada to the temperate regions in the Southern Hemisphere including highland tropical regions of Latin America and East Africa where a wide diversity of seed types and growth habits are produced. Local adaptation is critical, and consumers are very selective in the seed types they grow and consume. Despite its broad adaptation, common bean productivity is low compared to cereal crops and is constrained by a wide range of biotic and abiotic stresses. In addition, grower and consumer preferences for specific growth habits, maturity classes, seed types, and quality traits limit improvement to specific regions and seed types. Breeders are challenged with having to maintain separate breeding programs where outcomes are limited to specific seed types. As a community, many of the biotic stresses are similar, and the genetic tools to control them can be shared. The broad area of marker technologies linked to economic traits is one area where the bean community has shared benefits. This chapter summarizes some of the broad advances in marker technologies as they have been applied to improve economic traits controlling both productivity and quality characteristics of common bean.

Keywords

Disease resistance Dry bean Molecular markers Marker-assisted selection MAS Phaseolus vulgaris Plant breeding Quality traits Quantitative trait loci QTL Quality traits 

References

  1. Adam-Blondon AF, Sevignac M, Dron D, Bannerot H (1994) A genetic map of common bean to localize specific resistance genes against anthracnose. Genome 37:915–924CrossRefPubMedGoogle Scholar
  2. Aragão FJ, Faria JC (2009) First transgenic gemini virus-resistant plant in the field. Nat Biotechnol 27:1086–1088CrossRefPubMedGoogle Scholar
  3. Ariani A, Berny Mier y Teran JC, Gepts P (2016) Genome-wide identification of SNPs and copy number variation in common bean (Phaseolus vulgaris L.) using genotyping-by-sequencing (GBS). Mol Breed 36(7):1–11CrossRefGoogle Scholar
  4. Awale H, Ismail SM, Vallejo VA, Kelly JD (2008) SQ4 SCAR marker linked to the Co-2 gene on B11 appears to be linked to the Ur-11 gene. Annu Rep Bean Improv Coop 51:174–175Google Scholar
  5. Balasubramanian P, Slinkard A, Tyler R, Vandenberg A (2000) A modified laboratory canning protocol for quality evaluation of dry bean (Phaseolus vulgaris L). J Sci Food Agric 80(6):732–738CrossRefPubMedGoogle Scholar
  6. Bassett MJ (1996) The margo (mar) seedcoat color gene is a synonym for the joker (j) locus in common bean. J Am Soc Hortic Sci 121(6):1028–1031Google Scholar
  7. Bassett MJ (2007) Genetics of seed coat color and pattern in common bean. In: Janick J (ed) Plant breeding reviews. Hoboken, New Jersey, pp 239–315Google Scholar
  8. Bello MH, Moghaddam SM, Massoudi M, McClean PE, Cregan PB, Miklas PN (2014) Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virus resistance in common bean. BMC Genomics 15:903CrossRefPubMedPubMedCentralGoogle Scholar
  9. Beninger CW, Gu L, Prior RL, Junk–Knievel DC, Vandenberg A, Bett KE (2005) Changes in polyphenols of the seed coat during the after-darkening process in pinto beans (Phaseolus vulgaris L.). J Agric Food Chem 53(20):7777–7782CrossRefPubMedGoogle Scholar
  10. Bitocchi E, Nanni L, Bellucci E, Rossi M, Giardini A, Spagnoletti Zeuli P, Logozzo G, Stougaard J, McClean P, Attene G, Papa R (2012) Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proc Natl Acad Sci USA 109:E788–E796CrossRefPubMedGoogle Scholar
  11. Bitocchi E, Bellucci E, Giardini A, Rau D, Rodriguez M, Biagetti E, Santilocchi R, Spagnoletti Zeuli P, Gioia T, Logozzo G, Attene G, Nanni L, Papa R (2013) Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes. New Phytol 197(1):300–313CrossRefPubMedGoogle Scholar
  12. Blair MW, Astudillo C, Grusak MA, Graham R, Beebe SE (2009) Inheritance of seed iron and zinc concentrations in common bean (Phaseolus vulgaris L.). Mol Breed 23(2):197–207CrossRefGoogle Scholar
  13. Blair MW, Knewtson SJB, Astudillo C, Li C, Fernandez AC, Grusak MA (2010) 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 10(1):215CrossRefPubMedPubMedCentralGoogle Scholar
  14. Blair MW, Astudillo C, Rengifo J, Beebe SE, Graham R (2011) QTL analyses for seed iron and zinc concentrations in an intra-genepool population of Andean common beans (Phaseolus vulgaris L.). Theor Appl Genet 122(3):511–521CrossRefPubMedGoogle Scholar
  15. Bonfim K, Faria JC, Nogueira EOPL, Mendes ÉA, Aragão FJL (2007) RNAi-mediated resistance to bean golden mosaic virus in genetically engineered common bean (Phaseolus vulgaris). Mol Plant-Microbe Interact 20(6):717–726CrossRefPubMedGoogle Scholar
  16. Brick MA, Gul G, Schwartz HF (2000) Morphological features of the seed coat surface of shiny and opaque black bean seed. Annu Rep Bean Improv Coop 43:15–16Google Scholar
  17. Brisco EI, Porch TG, Cregan PB, Kelly JD (2014) Quantitative trait loci associated with resistance to Empoasca in common bean. Crop Sci 54:2509–2519CrossRefGoogle Scholar
  18. Burt AJ, William HM, Perry G, Khanal R, Pauls KP, Kelly JD, Navabi A (2015) Candidate gene identification with SNP marker-based fine mapping of anthracnose resistance gene Co-4 in common bean. PLoS One 10(10):e0139450.  https://doi.org/10.1371/journal.pone.0139450 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Bushey SM, Hosfield GL, Beninger CW (2000) Water uptake and its relationship to pigment leaching in black beans (Phaseolus vulgaris L.). Annu Rep Bean Improv Coop 43:104–105Google Scholar
  20. Bushey SM, Owens S, Hosfield GL (2001) The epicuticular wax layer and water uptake in black beans. Annu Rep Bean Improv Coop 44:159–160Google Scholar
  21. Campa A, Rodríguez-Suárez C, Giraldez R, Ferreira JJ (2014) Genetic analysis of the response to eleven Colletotrichum lindemuthianum races in a RIL population of common bean (Phaseolus vulgaris L.). BMC Plant Biol 14:115CrossRefPubMedPubMedCentralGoogle Scholar
  22. Campion B, Sparvoli F, Doria E, Tagliabue G, Galasso I, Fileppi M, Bollini R, Nielsen E (2009) Isolation and characterisation of an lpa (low phytic acid) mutant in common bean (Phaseolus vulgaris L.). Theor Appl Genet 118(6):1211–1221CrossRefPubMedGoogle Scholar
  23. Chen M, Wu J, Wang L, Mantri N, Zhang X, Zhu Z, Wang S (2017) Mapping and genetic structure analysis of the anthracnose resistance locus Co-1HY in the common bean (Phaseolus vulgaris L.). PLoS One 12:e0169954CrossRefPubMedPubMedCentralGoogle Scholar
  24. Cichy KA, Blair MW, Galeno-Mendoza CH, Snapp SS, Kelly JD (2009a) QTL analysis of root architecture traits and low phosphorus tolerance in an Andean bean population. Crop Sci 49:59–68CrossRefGoogle Scholar
  25. Cichy KA, Caldas GV, Snapp SS, Blair MW (2009b) QTL analysis of seed iron, zinc, and phosphorus levels in an Andean bean population. Crop Sci 49(5):1742–1750CrossRefGoogle Scholar
  26. Cichy KA, Fernandez A, Kilian A, Kelly JD, Galeano CH, Shaw S, Brick MA, Hodkinson D, Troxtell E (2014) QTL analysis of canning quality and color retention in black beans (Phaseolus vulgaris L.). Mol Breed 33(1):139–154CrossRefGoogle Scholar
  27. Cichy KA, Porch TG, Beaver JS, Cregan P, Fourie D, Glahn RP, Grusak MA, Kamfwa K, Katuuramu DN, McClean P, Mndolwa E, Nchimbi-Msolla S, Pastor-Corrales MA, Miklas PN (2015a) A Phaseolus vulgaris diversity panel for Andean bean improvement. Crop Sci 55:2149–2160.  https://doi.org/10.2135/cropsci2014.09.0653 CrossRefGoogle Scholar
  28. Cichy KA, Wiesinger JA, Mendoza FA (2015b) Genetic diversity and genome-wide association analysis of cooking time in dry bean (Phaseolus vulgaris L.). Theor Appl Genet 128(8):1555–1567CrossRefPubMedGoogle Scholar
  29. Coimbra-Gonçalves GK, Gonçalves-Vidigal MC, Coelho RT, Valentini G, Vidigal Filho PS, Lacanallo GF, Sousa LL, Elias HT (2016) Characterization and mapping of anthracnose resistance gene in Mesoamerican common bean cultivar Crioulo 159. Crop Sci 56:2904–2915CrossRefGoogle Scholar
  30. de Lima Castro SA, Gonçalves-Vidigal MC, Gilio TA, Lacanallo GF, Valentini G, Martins VD, Song Q, Galván MZ, Hurtado-Gonzales OP, Pastor-Corrales MA (2017) Genetics and mapping of a new anthracnose resistance locus in Andean common bean Paloma. BMC Genomics 18:306CrossRefPubMedPubMedCentralGoogle Scholar
  31. Elia FM, Hosfield GL, Kelly JD, Uebersax MA (1997) Genetic analysis and interrelationships between traits for cooking time, water absorption, and protein and tannin content of Andean dry beans. J Am Soc Hortic Sci 122(4):512–518Google Scholar
  32. Elsadr HT, Wright LC, Pauls KP, Bett KE (2011) Characterization of seed coat post harvest darkening in common bean (Phaseolus vulgaris L.). Theor Appl Genet 123(8):1467–1472CrossRefPubMedGoogle Scholar
  33. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6(5):1–10CrossRefGoogle Scholar
  34. Faria JC, Valdisser PA, Nogueira EO, Aragão FJ (2014) RNAi-based Bean golden mosaic virus-resistant common bean (Embrapa 5.1) shows simple inheritance for both transgene and disease resistance. Plant Breed 133:649–653CrossRefGoogle Scholar
  35. Felicetti E, Song Q, Jia G, Cregan P, Bett KE, Miklas PN (2012) Simple sequence repeats linked with slow darkening trait in pinto bean discovered by single nucleotide polymorphism assay and whole genome sequencing. Crop Sci 52(4):1600–1608CrossRefGoogle Scholar
  36. Ferreira JJ, Campa A, Kelly JD (2013) Organization of genes conferring resistance to anthracnose in common bean. In: Varshney RK, Tuberosa R (eds) Translational genomics for crop breeding, Volume I: Biotic stresses. Hoboken, New Jersey, pp 151–181Google Scholar
  37. Fileppi M, Galasso I, Tagliabue G, Daminati MG, Campion B, Doria E, Sparvoli F (2010) Characterisation of structural genes involved in phytic acid biosynthesis in common bean (Phaseolus vulgaris L.). Mol Breed 25(3):453–470CrossRefGoogle Scholar
  38. Foyer CH, Lam H-M, Nguyen HT, Siddique KHM, Varshney RK, Colmer TD, Cowling W, Bramley H, Mori TA, Hodgson JM, Cooper JW, Miller AJ, Kunert K, Vorster J, Cullis C, Ozga JA, Wahlqvist ML, Liang Y, Shou H, Shi K, Yu J, Fodor N, Kaiser BN, Wong F-L, Valliyodan B, Considine MJ (2016) Neglecting legumes has compromised human health and sustainable food production. Nat Plants 2(8).  https://doi.org/10.1038/nplants.2016.112
  39. Freixas Coutin JA, Munholland S, Silva A, Subedi S, Lukens L, Crosby WL, Pauls KP, Bozzo GG (2017) Proanthocyanidin accumulation and transcriptional responses in the seed coat of cranberry beans (Phaseolus vulgaris L.) with different susceptibility to postharvest darkening. BMC Plant Biol 17(89):23Google Scholar
  40. Freyre R, Skroch PW, Geffroy V, Adam-Blondon A-F, Shirmohamadali A, Johnson WC, Llaca V, Nodari RO, Pereira PA, Tsai SM, Tohme J, Dron M, Nienhuis J, Vallejos CE, Gepts P (1998) Towards an integrated linkage map of common bean. 4. Development of a core linkage map and alignment of RFLP maps. Theor Appl Genet 97:847–856CrossRefGoogle Scholar
  41. Freytag GF, Debouck DG (2002) 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 Centroamérica. SIDA, Botanical Miscellany.Google Scholar
  42. Frossard E, Bucher M, Mächler F, Mozafar A, Hurrell R (2000) Potential for increasing the content and bioavailability of Fe, Zn and Ca in plants for human nutrition. J Sci Food Agric 80(7):861–879CrossRefGoogle Scholar
  43. Garcia RAV, Rangel PN, Bassinello PZ, Brondani C, Melo LC, Sibov ST, Vianello-Brondani RP (2012) QTL mapping for the cooking time of common beans. Euphytica 186(3):779–792CrossRefGoogle Scholar
  44. Geffroy V, Sévignac M, Billant P, Dron M, Langin T (2008) Resistance to Colletotrichum lindemuthianum in Phaseolus vulgaris: a case study for mapping two independent genes. Theor Appl Genet 116:407–415CrossRefPubMedGoogle Scholar
  45. Ghandilyan A, Vreugdenhil D, Aarts MGM (2006) Progress in the genetic understanding of plant iron and zinc nutrition. Physiol Plant 126(3):407–417CrossRefGoogle Scholar
  46. Gilio TAS, Hurtado-Gonzales OP, Valentini G, Castro SAL, Elias HT, Song Q, Gonçalves-Vidigal M, Pastor-Corrales MA (2016) Fine mapping the broad spectrum anthracnose resistance gene in Amendoim Cavalo. Annu Rep Bean Improv Coop 60:127–128Google Scholar
  47. Gonçalves-Vidigal MC, Cruz AS, Garcia A, Vidigal Filho PS, Sousa LL (2011) Linkage mapping of the Phg-1 and Co-1 4 genes for resistance to angular leaf spot and anthracnose in the common bean cultivar AND 277. Theor Appl Genet 122:893–903CrossRefPubMedGoogle Scholar
  48. Gonçalves-Vidigal MC, Cruz AS, Lacanallo GF, Vidigal Filho PS, Sousa LL, Pacheco CMNA, McClean P, Gepts P, Pastor-Corrales MA (2013) Co-segregation analysis and mapping of the anthracnose Co-10 and angular leaf spot Phg-ON disease-resistance genes in the common bean cultivar Ouro Negro. Theor Appl Genet 126:2245–2255CrossRefPubMedGoogle Scholar
  49. Gonçalves-Vidigal MC, Pacheco CMNA, Vidigal Filho PS, Lacanallo GF, Sousa LL, Martins VSR (2016) Genetic mapping of the anthracnose resistance gene Co-14 in the common bean cultivar Pitanga. Annu Rep Bean Improv Coop 59:55–65Google Scholar
  50. Guzmán-Maldonado SH, Martínez O, Acosta-Gallegos JA, Guevara-Lara F, Paredes-López O (2003) Putative quantitative trait loci for physical and chemical components of common bean. Crop Sci 43(3):1029–1035CrossRefGoogle Scholar
  51. Hart JP, Griffiths PD (2015) Genotyping-by-sequencing enabled mapping and marker development for the potyvirus resistance allele in common bean. Plant Genome 8(1):1–14CrossRefGoogle Scholar
  52. Heilig JA, Beaver JS, Wright EM, Song Q, Kelly JD (2017) QTL analysis of symbiotic nitrogen fixation in a black bean population. Crop Sci 57:118–129.  https://doi.org/10.2135/cropsci2016.05.0348 CrossRefGoogle Scholar
  53. Hnatuszko-Konka K, Kowalczyk T, Gerszberg A, Wiktorek-Smagur A, Kononowicz AK (2014) Phaseolus vulgaris—recalcitrant potential. Biotechnol Adv 32:1205–1215CrossRefPubMedGoogle Scholar
  54. Hosfield GL, Uebersax MA (1980) Variability in physico-chemical properties and nutritional components of tropical and domestic dry bean germplasm. J Am Soc Hortic Sci 105(2):246–252Google Scholar
  55. Hosfield GL, Uebersax MA (1990) Culinary quality in dry bean- can it be improved? Annu Rep Bean Improv Coop 33:17–18Google Scholar
  56. Hosfield GL, Uebersax MA, Isleib TG (1984) Seasonal and genotypic effects on yield and physico-chemical seed characteristics related to food quality in dry, edible beans. J Am Soc Hortic Sci 109(2):182–189Google Scholar
  57. Hosfield GL, Kelly JD, Silbernagel MJ, Stavely JR, Adams MW, Uebersax MA, Varner GV (1995) Eight small-red dry bean germplasm lines with upright architecture, narrow profile, and short vine growth habit. Hortscience 30(7):1479–1482Google Scholar
  58. Hoyos-Villegas V, Mkwaila W, Cregan PB, Kelly JD (2015) QTL analysis of white mold avoidance in pinto bean (Phaseolus vulgaris). Crop Sci 55:2116–2129. https://doi.org/10.2135/cropsci2015.02.0106 CrossRefGoogle Scholar
  59. Hoyos-Villegas V, Song Q, Kelly JD (2016) Genome-wide association analysis for drought tolerance and associated traits in common bean. Plant Genome 9.  https://doi.org/10.3835/plantgenome2015.12.0122
  60. Hurtado-Gonzales OP, Valentini G, Gilio TA, Martins AM, Song Q, Pastor-Corrales MA (2017) Fine mapping of Ur-3, a historically important rust resistance locus in common bean. G3 Genes Genomes Genetics 7:557–569PubMedGoogle Scholar
  61. Jacinto-Hernández C, Azpiroz-Rivero S, Acosta-Gallegos JA, Hernandez-Sanchez H, Bernal-Lugo I (2003) Genetic analysis and random amplified polymorphic DNA markers associated with cooking time in common bean. Crop Sci 43:329–332CrossRefGoogle Scholar
  62. Jackson GM, Varriano-Marston E (1981) Hard-to-cook phenomenon in beans: effects of accelerated storage on water absorption and cooking time. J Food Sci 46(3):799–803CrossRefGoogle Scholar
  63. Junk-Knievel DC, Vandenberg A, Bett KE (2007) An accelerated postharvest seed-coat darkening protocol for pinto beans grown across different environments. Crop Sci 47(2):694–702CrossRefGoogle Scholar
  64. Junk-Knievel DC, Vandenberg A, Bett KE (2008) Slow darkening in pinto bean (Phaseolus vulgaris L.) seed coats is controlled by a single major gene. Crop Sci 48(1):189–193CrossRefGoogle Scholar
  65. Kamfwa K, Cichy KA, Kelly JD (2015a) Genome-wide association study of agronomic traits in common bean. Plant Genome 8.  https://doi.org/10.3835/plantgenome2014.09.0059
  66. Kamfwa K, Cichy KA, Kelly JD (2015b) Genome-wide association analysis of symbiotic nitrogen fixation in common bean. Theor Appl Genet 128:1999–2017.  https://doi.org/10.1007/s00122-015-2562-5 CrossRefPubMedGoogle Scholar
  67. Kami J, Velásquez VB, Debouck DG, Gepts P (1995) Identification of presumed ancestral DNA sequences of phaseolin in Phaseolus vulgaris. Proc Natl Acad Sci U S A 92:1101–1104CrossRefPubMedPubMedCentralGoogle Scholar
  68. Kelly JD (1995) Use of random amplified polymorphic DNA markers in breeding for major gene resistance to plant pathogens. Hortscience 30:461–465Google Scholar
  69. Kelly JD (2001) Remaking bean plant architecture for efficient production. Adv Agron 71:109–143.  https://doi.org/10.1016/S0065-2113(01)71013-9 CrossRefGoogle Scholar
  70. Kelly JD, Miklas PN (1998) The role of RAPD markers in breeding for disease resistance in common bean. Mol Breed 4:1–11CrossRefGoogle Scholar
  71. Kelly JD, Vallejo VA (2004) A comprehensive review of the major genes conditioning resistance to anthracnose in common bean. Hortscience 39:1196–1207Google Scholar
  72. Kelly JD, Vallejo VA (2005) QTL analysis of multigenic disease resistance in plant breeding. In: Tuzun S, Bent E (eds) Multigenic and induced systemic resistance in plants. Springer, New York, pp 21–48Google Scholar
  73. Kelly JD, Gepts P, Miklas PN, Coyne DP (2003) Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crop Res 82:135–154CrossRefGoogle Scholar
  74. Kim S-I, Tai TH (2011) Identification of genes necessary for wild-type levels of seed phytic acid in Arabidopsis thaliana using a reverse genetics approach. Mol Gen Genomics 286(2):119–133CrossRefGoogle Scholar
  75. Konzen ER, Tsai SM (2014) Seed coat shininess in Phaseolus vulgaris: rescuing a neglected trait by its screening on commercial lines and landraces. J Agric Sci 6(8):1–18Google Scholar
  76. Kwak M, Velasco D, Gepts P (2008) Mapping homologous sequences for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris). J Hered 99:283–291.  https://doi.org/10.1093/jhered/esn005 CrossRefPubMedGoogle Scholar
  77. Lacanallo GF, Gonçalves-Vidigal MC (2015) Mapping of an Andean gene for anthracnose resistance (Co-13) in common bean (Phaseolus vulgaris L.) Jalo Listras Pretas landrace. Aust J Crop Sci 9:394–400Google Scholar
  78. Lamprecht H (1951) Die Vererbung der Testafarbe bei Phaseolus vulgaris L. Agric Hortic Genet 9:18–83Google Scholar
  79. Liebenberg MM, Madubanya LA, Mienie CMS, Kelly JD (2009) A closer look at the resistance gene cluster on common bean chromosome 11. Annu Rep Bean Improv Coop 52:80–81Google Scholar
  80. Mamidi S, Rossi M, Moghaddam SM, Annam D, Lee R, Papa R, McClean PE (2013) Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L. Heredity 110:267–276CrossRefPubMedGoogle Scholar
  81. Mamidi S, Miklas PN, Trapp J, Felicetti E, Grimwood J, Schmutz J, Lee R, McClean PE (2016) Sequence-based introgression mapping identifies candidate white mold tolerance genes in common bean. Plant Genome 9(2):1–11CrossRefGoogle Scholar
  82. Martínez-Manrique E, Jacinto-Hernández C, Garza-García R, Campos A, Moreno E, Bernal-Lugo I (2011) Enzymatic changes in pectic polysaccharides related to the beneficial effect of soaking on bean cooking time. J Sci Food Agric 91(13):2394–2398CrossRefPubMedGoogle Scholar
  83. Matella NJ, Mishra DK, Dolan KD (2013) Hydration, blanching and thermal processing of dry beans. In: Siddiq M, Uebersax MA (eds) Dry beans and pulses production, processing and nutrition. Blackwell Publishing Ltd., Oxford, pp 129–154Google Scholar
  84. McClean PE, Lee RK, Otto C, Gepts P, Bassett MJ (2002) Molecular and phenotypic mapping of genes controlling seed coat pattern and color in common bean (Phaseolus vulgaris L.). J Hered 93(2):148–152CrossRefPubMedGoogle Scholar
  85. McClean PE, Mamidi S, McConnell M, Chikara S, Lee R (2010) Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genomics 11:184CrossRefPubMedPubMedCentralGoogle Scholar
  86. McClean PE, Moghaddam SM, Lopéz-Millán A-F, Brick MA, Kelly JD, Miklas PN, Osorno J, Porch TG, Urrea CA, Soltani A, Grusak MA (2017) Phenotypic diversity for seed mineral concentration in North American dry bean germplasm of Middle American Ancestry. Crop Sci 57:3129–3144.  https://doi.org/10.2135/cropsci2017.04.0244 CrossRefGoogle Scholar
  87. Melotto M, Kelly JD (2001) Fine mapping of the Co-4 locus of common bean reveals a resistance gene candidate, COK-4, that encodes for a protein kinase. Theor Appl Genet 103:508–517CrossRefGoogle Scholar
  88. Melotto M, Afanador L, Kelly JD (1996) Development of a SCAR marker linked to the I gene in common bean. Genome 39:1216–1219CrossRefPubMedGoogle Scholar
  89. Meziadi C, Richard MMS, Derquennes A, Thareau V, Blanchet S, Gratias A, Pflieger S, Geffroy V (2016) Development of molecular markers linked to disease resistance genes in common bean based on whole genome sequence. Plant Sci 242:351–357CrossRefPubMedGoogle Scholar
  90. Mienie CM, Liebenberg MM, Pretorius ZA, Miklas PN (2005) SCAR markers linked to the common bean rust resistance gene Ur-13. Theor Appl Genet 111:972–979CrossRefPubMedGoogle Scholar
  91. Miklas PN, Delorme R, Stone V, Daly MJ, Stavely JR, Steadman JR, Bassett MJ, Beaver JS (2000a) Bacterial, fungal, virus disease loci mapped in a recombinant inbred common bean population (‘Dorado’/XAN176). J Am Soc Hortic Sci 125(2):476–481Google Scholar
  92. Miklas PM, Larsen RC, Riley R, Kelly JD (2000b) Potential marker-assisted selection for bc-1 2 resistance to bean common mosaic potyvirus in common bean. Euphytica 116:211–219CrossRefGoogle Scholar
  93. Miklas PN, Pastor-Corrales MA, Jung G, Coyne DP, Kelly JD, McClean PE, Gepts P (2002) Comprehensive linkage map of bean rust resistance genes. Annu Rep Bean Improv Coop 45:125–129Google Scholar
  94. Miklas PN, Kelly JD, Beebe SE, Blair MW (2006) Common bean breeding for resistance against biotic and abiotic stresses: from classical to MAS breeding. Euphytica 147:105–131CrossRefGoogle Scholar
  95. Miklas PN, Porter LD, Kelly JD, Myers JR (2013) Characterization of white mold disease avoidance in common bean. Eur J Plant Pathol 135:525–543.  https://doi.org/10.1007/s10658-012-0153-8 CrossRefGoogle Scholar
  96. Miklas PN, Fourie D, Trapp J, Davis J, Myers JR (2014) New loci including conferring resistance to halo bacterial blight on chromosome Pv04 in common bean. Crop Sci 54:2099–2108CrossRefGoogle Scholar
  97. Moghaddam SM, Stonehouse R, Lee R, Mamidi S, Bello M, Miklas P, McClean PE, Bett KE (2014) Molecular genetic analysis of the Phaseolus vulgaris P locus. Annu Rep Bean Improv Coop 57:15–16Google Scholar
  98. Moghaddam SM, Mamidi S, Osorno JM, Lee R, Brick M, Kelly J, Miklas P, Urrea C, Song Q, Cregan P, Grimwood J, Schmutz J, McClean PE (2016) Genome-wide association study identifies candidate loci underlying agronomic traits in a Middle American diversity panel of common bean. Plant Genome 9(3).  https://doi.org/10.3835/plantgenome2016.02.0012
  99. Mukeshimana G, Butare L, Cregan PB, Blair MW, Kelly JD (2014) Quantitative trait loci associated with drought tolerance in common bean. Crop Sci 54:923–938.  https://doi.org/10.2135/cropsci2013.06.0427 CrossRefGoogle Scholar
  100. Muñoz-Amatriaín M, Mirebrahim H, Xu P, Wanamaker SI, Luo MC, Alhakami H, Alpert M, Atokple I, Batieno BJ, Boukar O, Bozdag S, Cisse N, Drabo I, Ehlers JD, Farmer A, Fatokun C, Gu YQ, Guo YN, Huynh BL, Jackson SA, Kusi F, Lawley CT, Lucas MR, Ma Y, Timko MP, Wu J, You F, Barkley NA, Roberts PA, Lonardi S, Close TJ (2016) Genome resources for climate-resilient cowpea, an essential crop for food security. Plant J 89(5):1042–1054CrossRefGoogle Scholar
  101. Manon M. S. Richard, Stéphanie Pflieger, Mireille Sévignac, Vincent Thareau, Sophie Blanchet, Yupeng Li, Scott A. Jackson, Valérie Geffroy, (2014) Fine mapping of Co-x, an anthracnose resistance gene to a highly virulent strain of Colletotrichum lindemuthianum in common bean. Theoretical and Applied Genetics 127(7):1653–1666CrossRefGoogle Scholar
  102. Oblessuc PR, Baroni RM, da Silva Pereira G, Chioratto AF, Carbonell SAM, Briñez B, Da Costa E Silva L, Garcia AAF, Camargo LEA, Kelly JD, Benchimol-Reis LL (2014) Quantitative analysis of race-specific resistance to Colletotrichum lindemuthianum in common bean. Mol Breed 34:1313–1329.  https://doi.org/10.1007/s11032-014-0118-z CrossRefGoogle Scholar
  103. Oblessuc PR, Francisco C, Melotto M (2015) The Co-4 locus on chromosome Pv08 contains a unique cluster of 18 COK-4 genes and is regulated by immune response in common bean. Theor Appl Genet 128:1193–1208.  https://doi.org/10.1007/s00122-015-2500-6. CrossRefPubMedGoogle Scholar
  104. Panzeri D, Cassani E, Doria E, Tagliabue G, Forti L, Campion B, Bollini R, Brearley CA, Pilu R, Nielsen E, Sparvoli F (2011) A defective ABC transporter of the MRP family, responsible for the bean lpa1 mutation, affects the regulation of the phytic acid pathway, reduces seed myo-inositol and alters ABA sensitivity. New Phytol 191(1):70–83CrossRefPubMedGoogle Scholar
  105. Park SO, Coyne DP, Steadman JR, Crosby KM, Brick MA (2004) RAPD and SCAR markers linked to the Andean gene controlling specific rust resistance in common bean. Crop Sci 44:1799–1807CrossRefGoogle Scholar
  106. Pedrosa-Harand A, Porch T, Gepts P (2008) Standard nomenclature for common bean chromosomes and linkage groups. Annu Rep Bean Improv Coop 51:106–107Google Scholar
  107. Pérez-Vega E, Pañeda A, Rodríguez-Suárez C, Campa A, Giraldez R, Ferreira JJ (2010) Mapping of QTLs for morpho-agronomic and seed quality traits in a RIL population of common bean (Phaseolus vulgaris L.). Theor Appl Genet 120(7):1367–1380CrossRefPubMedGoogle Scholar
  108. Perry G, Dinatale C, Xie W, Navabi A, Reinprecht Y, Crosby W, Yu K, Shi C, Pauls KP (2013) A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes. Front Plant Sci 4:318CrossRefPubMedPubMedCentralGoogle Scholar
  109. Petry N, Boy E, Wirth JP, Hurrell RF (2015) Review: the potential of the common bean (Phaseolus vulgaris) as a vehicle for iron biofortification. Nutrients 7(2):1144–1173CrossRefPubMedPubMedCentralGoogle Scholar
  110. Pilu R, Panzeri D, Gavazzi G, Rasmussen SK, Consonni G, Nielsen E (2003) Phenotypic, genetic and molecular characterization of a maize low phytic acid mutant (lpa241). Theor Appl Genet 107(6):980–987CrossRefPubMedGoogle Scholar
  111. Popelka JC, Gollasch S, Moore A, Molvig L, Higgins TJ (2006) Genetic transformation of cowpea (Vigna unguiculata L.) and stable transmission of the transgenes to progeny. Plant Cell Rep 25:304–312CrossRefPubMedGoogle Scholar
  112. Posa-Macalincag MCT, Hosfield GL, Grafton KF, Uebersax MA, Kelly JD (2002) Quantitative trait loci (QTL) analysis of canning quality traits in kidney bean (Phaseolus vulgaris L.). J Am Soc Hortic Sci 127(4):608–615Google Scholar
  113. Prakken R (1970) Inheritance of colour in Phaseolus vulgaris L. II. A critical review. Meded Landbouwhogeschool Wageningen 23:1–38Google Scholar
  114. Prakken R (1974) Inheritance of colour in Phaseolus vulgaris L. IV. Recombination within the ‘complex locus C'. Meded Landbouwhogeschool Wageningen 74–24:1–36Google Scholar
  115. Raboy V (2007) The ABCs of low-phytate crops. Nat Biotechnol 25(8):874–875CrossRefPubMedGoogle Scholar
  116. Repinski SL, Kwak M, Gepts P (2012) The common bean growth habit gene PvTFL1y is a functional homolog of Arabidopsis TFL1. Theor Appl Genet 124:1539–1547.  https://doi.org/10.1007/s00122-012-1808-8 CrossRefPubMedGoogle Scholar
  117. Reyes-Moreno C, Paredes-López O, Gonzalez E (1993) Hard-to-cook phenomenon in common beans — a review. Crit Rev Food Sci Nutr 33(3):227–286CrossRefPubMedGoogle Scholar
  118. Richard MMS, Pflieger S, Sévignac M, Thareau V, Blanchet S, Li Y, Jackson SA, Geffroy V (2014) Fine mapping of Co-x, an anthracnose resistance gene to a highly virulent strain of Colletotrichum lindemuthianum in common bean. Theor Appl Genet 127: 1653–1666Google Scholar
  119. Richard MMS, Pflieger S, Sévignac M, Thareau V, Blanchet S, Li Y, Jackson SA, Geffroy V (2014) Fine mapping of Co-x, an anthracnose resistance gene to a highly virulent strain of Colletotrichum lindemuthianum in common bean. Theor Appl Genet 127: 1653–1666Google Scholar
  120. Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia B, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MMS, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46:707–713CrossRefPubMedGoogle Scholar
  121. Schreiber F (1940) Die Genetik der Teilfärbung der Bohnensamen (Phaseolus vulgaris). Zeit Abst Vererb 78:59–114Google Scholar
  122. Schröder S, Mamidi S, Lee R, McKain MR, McClean PE, Osorno JM (2016) Optimization of genotyping by sequencing (GBS) data in common bean (Phaseolus vulgaris L.). Mol Breed 36(1):1–9CrossRefGoogle Scholar
  123. Schroeder JI, Delhaize E, Frommer WB, Lou Guerinot M, Harrison MJ, Herrera-Estrella L, Horie T, Kochian LV, Munns R, Nishizawa NK, Tsay Y-F, Sanders D (2013) Using membrane transporters to improve crops for sustainable food production. Nature 497(7447):60–66CrossRefPubMedPubMedCentralGoogle Scholar
  124. Shi J, Wang H, Schellin K, Li B, Faller M, Stoop JM, Meeley RB, Ertl DS, Ranch JP, Glassman K (2007) Embryo-specific silencing of a transporter reduces phytic acid content of maize and soybean seeds. Nat Biotechnol 25(8):930–937CrossRefPubMedGoogle Scholar
  125. Silva DVF, Santos JB (2005) Controle genético da capacidade de cozimento do feijão (Phaseolus vulgaris L.) e identificação de marcadores RAPD e SSR. pp 389–392. In: VIII Congresso Nacional de Pesquisa de FeijãoGoogle Scholar
  126. Soltani A, Bello M, Mndolwa E, Schröder S, Moghaddam SM, Osorno JM, Miklas PN, McClean PE (2016) Targeted analysis of dry bean growth habit: interrelationship among architectural, phenological, and yield components. Crop Sci 56:3005–3015.  https://doi.org/10.2135/cropsci2016.02.0119 CrossRefGoogle Scholar
  127. Song Q, Jia G, Hyten DL, Jenkins J, Hwang E-Y, Schroeder SG, Osorno JM, Schmutz J, Jackson SA, McClean PE, Cregan PB (2015) SNP assay development for linkage map construction, anchoring whole genome sequence and other genetic and genomic applications in common bean. G3 Genes Genomes Genetics 5(11):2285–2290.  https://doi.org/10.1534/g3.115.020594 CrossRefPubMedPubMedCentralGoogle Scholar
  128. Sousa LL, Cruz AS, Vidigal Filho PS, Vallejo VA, Kelly JD, Gonçalves-Vidigal MC (2014) Genetic mapping of the resistance allele Co-52 to Colletotrichum lindemuthianum in the common bean MSU 7-1 line. Aust J Crop Sci 8:317–323Google Scholar
  129. Sousa LL, Gonçalves AO, Gonçalves-Vidigal MC, Lacanallo GF, Fernandez AC, Awale H, Kelly JD (2015) Genetic characterization and mapping of anthracnose resistance of Corinthiano common bean landrace cultivar. Crop Sci 55:1900–1910.  https://doi.org/10.2135/cropsci2014.09.0604 CrossRefGoogle Scholar
  130. Souza TLPO, Gonçalves-Vidigal MC, Raatz B, Mukankusi CM, Abreu ÂFB, Melo LC, Pastor-Corrales MA (2016) Major loci controlling resistance to the angular leaf spot of common bean. Annu Rep Bean Improv Coop 59:xv–xviiiGoogle Scholar
  131. Souza TLPO, Faria JC, Aragão FJL, Del Peloso MJ, Faria LC, Wendland A, Aguiar MS, Quintela ED, Melo CLP, Hungria M, Vianello RP, Pereira HS, Melo LC (2018) Agronomic performance and yield stability of the RNA interference-based Bean golden mosaic virus-resistant common bean. Crop Sci 58(2):579–591CrossRefGoogle Scholar
  132. Stavely JR (1998) Recombination of two major dominant rust resistance genes that are tightly linked in repulsion. Annu Rep Bean Improv Coop 41:17–18Google Scholar
  133. Strausbaugh CA, Myers JR, Forster RL, McClean PE (1999) Bc-1 and Bc-u—two loci controlling bean common mosaic virus resistance in common bean are linked. J Am Soc Hortic Sci 124:644–648Google Scholar
  134. Trabanco N, Campa A, Ferreira JJ (2015) Identification of a new chromosomal region involved in the genetic control of resistance to anthracnose in common bean. Plant Genome 8.  https://doi.org/10.3835/plantgenome2014.10.0079
  135. Valentini G, Gonçalves-Vidigal MC, Hurtado-Gonzales OP, de Lima Castro SA, Cregan PB, Song Q, Pastor-Corrales MA (2017) High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust, anthracnose, and angular leaf spot diseases. Theor Appl Genet:1–18.  https://doi.org/10.1007/s00122-017-2920-6
  136. Vallejo VA, Awale HE, Kelly JD (2003) Characterization of the anthracnose resistance in the Andean bean cultivar Jalo EEP558. Annu Rep Bean Improv Coop 46:179–180Google Scholar
  137. Van Der Poel AFB (1990) Effect of processing on antinutritional factors and protein nutritional value of dry beans (Phaseolus vulgaris L.): a review. Anim Feed Sci Technol 29(3–4):179–208CrossRefGoogle Scholar
  138. Varriano-Marston E, De Omana E (1979) Effects of sodium salt solutions on the chemical composition and morphology of black beans (Phaseolus vulgaris). J Food Sci 44(2):531–536CrossRefGoogle Scholar
  139. Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MTA, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang S-P, Shah T, Saxena KB, Michael T, McCombie WR, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, Jackson SA (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30(1):83–89CrossRefGoogle Scholar
  140. Vasconcellos RCC, Oraguzie OB, Soler A, Arkwazee H, Myers JR, Ferreira JJ, Song Q, McClean PE, Miklas PN (2017) Meta-QTL for resistance to white mold in common bean. PLoS One 12(2):e0171685.  https://doi.org/10.1371/journal.pone.0171685 CrossRefPubMedPubMedCentralGoogle Scholar
  141. Vazin M, Burt AJ, Zarei A, Xie W, Pauls KP, Gillard C, Bett K, Navabi A (2014) Molecular characterization of anthracnose resistance to race 73 in the navy bean variety Bolt. Annu Rep Bean Improv Coop 57:161–162Google Scholar
  142. Veltcheva M, Svetleva D, Petkova S, Perl A (2005) In vitro regeneration and genetic transformation of common bean (Phaseolus vulgaris L.) – problems and progress. Sci Hortic 107:2–10CrossRefGoogle Scholar
  143. Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Álvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R (2016) 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):32.  https://doi.org/10.1186/s13059-016-0883-6 CrossRefPubMedPubMedCentralGoogle Scholar
  144. Vandemark GJ, Brick MA, Osorno JM, Kelly JD, Urrea CA, Smith S, Diers B, Specht J, Carver B (2014) Edible Grain Legumes. In S Smith, B Diers, J Specht, B Carver, eds, Yield Gains in Major U.S. Field Crops. ASA, CSSA, and SSSA, Madison, pp 87–123Google Scholar
  145. Walters KJ, Hosfield GL, Uebersax MA, Kelly JD (1997) Navy bean canning quality: correlations, heritability estimates, and randomly amplified polymorphic DNA markers associated with component traits. J Am Socs Hortic Sci 122(3):338–343Google Scholar
  146. Wassimi NN, Hosfield GL, Uebersax MA (1990) Inheritance of physico-chemical seed characters related to culinary quality in dry bean. J Am Soc Hortic Sci 115(3):492–499Google Scholar
  147. Wright EM, Kelly JD (2011) Mapping QTL for seed yield and canning quality following processing of black bean (Phaseolus vulgaris L.). Euphytica 179(3):471–484CrossRefGoogle Scholar
  148. Wright EW, Awale HE, Kelly JD (2008) Use of TRAP markers to map resistance to a new race of common bean rust in Michigan. Annu Rep Bean Improv Coop 51:210–211Google Scholar
  149. Xu X-H, Zhao H-J, Liu Q-L, Frank T, Engel K-H, An G, Shu Q-Y (2009) Mutations of the multi-drug resistance-associated protein ABC transporter gene 5 result in reduction of phytic acid in rice seeds. Theor Appl Genet 119(1):75–83CrossRefPubMedGoogle Scholar
  150. Young RA, Kelly JD (1996) RAPD marker flanking the are gene for anthracnose resistance in common bean. J Am Soc Hortic Sci 121:37–41Google Scholar
  151. Zou X, Shi C, Austin RS, Merico D, Munholland S, Marsolais F, Navabi A, Crosby WL, Pauls KP, Yu K, Cui Y (2014) Genome-wide single nucleotide polymorphism and insertion-deletion discovery through next-generation sequencing of reduced representation libraries in common bean. Mol Breed 33(4):769–778CrossRefGoogle Scholar
  152. Zuiderveen GH, Padder BA, Kamfwa K, Song Q, Kelly JD (2016) Genome-wide association study of anthracnose resistance in Andean beans. PLoS One 11(6):e0156391.  https://doi.org/10.1371/journal.pone.0156391 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of PlantSoil and Microbial Sciences Michigan State UniversityEast LansingUSA

Personalised recommendations