Genome-wide association analysis of symbiotic nitrogen fixation in common bean

Theoretical and Applied Genetics

Volumn 128, Issue 10, 2015, Pages 1999-2017

  Kamfwa, Kelvin ^a   Cichy, Karen A ^a   Kelly, James D ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHROMOSOMES; GENES; NITROGEN; SIGNAL TRANSDUCTION;

COMMON BEAN (PHASEOLUS VULGARIS); GENETIC IMPROVEMENTS; GENOME-WIDE ASSOCIATION; GENOME-WIDE ASSOCIATION STUDIES; LEUCINE-RICH REPEAT RECEPTORS; MARKER-ASSISTED BREEDING; POPULATION STRUCTURES; SYMBIOTIC NITROGEN FIXATION;

NITROGEN FIXATION;

GENETIC ASSOCIATION; GENETICS; GENOTYPE; NITROGEN FIXATION; PHASEOLUS; PHENOTYPE; PHYSIOLOGY; PLANT CHROMOSOME; PLANT GENE; PLANT SEED; POPULATION GENETICS; SHOOT; SINGLE NUCLEOTIDE POLYMORPHISM; SYMBIOSIS;

CHROMOSOMES, PLANT; GENES, PLANT; GENETIC ASSOCIATION STUDIES; GENETICS, POPULATION; GENOTYPE; NITROGEN FIXATION; PHASEOLUS; PHENOTYPE; PLANT SHOOTS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEEDS; SYMBIOSIS;

EID: 84942195169     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-015-2562-5     Document Type: Article

References (61)

1. Akibode CS, Maredia M (2012) Global and regional trends in production, trade and consumption of food legume crops. Staff Paper 2012–10. Department of Agricultural, Food and Resource Economics, Michigan State University
2. Beebe S (2012) Common bean breeding in the tropics. Plant Breed Rev 36:357–426
3. Bliss FA (1993) Breeding common bean for improved biological nitrogen fixation. Plant Soil 152:71–79
4. Bliss F, Pereira P, Araujo R (1989) Registration of five high nitrogen fixing common bean germplasm lines. Crop Sci 29:240–241
5. Boddey RM, Alves BJR, de Henrique B, Soares L, Jantalia CP, Urquiaga S (2009) Biological nitrogen fixation and the mitigation of greenhouse gas emissions. In: Emerich DW, Krishnan HB (eds) Nitrogen fixation in crop production. Crop Science Society of America, Madison, pp 387–413
6. Bradbury P, Zhang D, Kroon T, Casstevens Y, Ramdoss Y, Buckler E (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
7. Broughton WJ, Dilworth MJ (1970) Plant nutrient solutions. In: Somasegaran P, Hoben HJ (eds) Methods in legume-Rhizobium technology handbook for rhizobia niftal project. Univ of Hawaii, Hawaii, pp 245–249
8. Broughton WJ, Hernandez G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.)—model food legumes. Plant Soil 252:55–128
9. Buttery BR, Park SJ, Pv Berkum (1997) Effects of common bean (Phaseolus vulgaris L.) cultivar and Rhizobium strain on plant growth, seed yield and nitrogen content. Can J Plant Sci 77:347–351
10. 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 (2015) A Phaseolus vulgaris diversity panel for Andean bean improvement. Crop Sci. doi:10.2135/cropsci2014.09.0653
11. Ehrhardt DW, Wais R, Long SR (1996) Calcium spiking in plant root hairs responding to Rhizobium nodulation signals. Cell 85:673–681
12. 2) fixation in common bean (Phaseolus vulgaris L.). Field Crops Res 62:119–128
13. Gage DJ (2009) Nodule development in legumes. In: Emerich DW, Krishnan HB (eds) Nitrogen fixation in crop production. Crop Science Society of America, Madison, pp 1–24
14. Giller KE (2001) Nitrogen fixation in tropical cropping systems, 2nd edn. CABI, New York
15. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:1178–1186
16. Graham PH (1981) Some problems of nodulation and symbiotic nitrogen fixation in Phaseolus vulgaris L.: a review. Field Crops Res 4:93–112
17. Graham PH (2009) Soil biology with an emphasis on symbiotic nitrogen fixation. In: Emerich DW, Krishnan HB (eds) Nitrogen fixation in crop production. Crop Science Society of America, Madison, pp 171–209
18. Graham P, Rosas J (1977) Growth and development of indeterminate bush and climbing cultivars of Phaseolus vulgaris L. inoculated with Rhizobium. J Agric Sci 88:503–508
19. Graham P, Rosas J, Estevez de Jensen C, Peralta E, Tlusty B, Acosta-Gallegos J, Arraes Pereira P (2003) Addressing edaphic constraints to bean production: the bean/cowpea CRSP project in perspective. Field Crops Res 82:179–192
20. Hardarson G, Bliss FA, Cigales-Rivero M, Henson RA, Kipe-Nolt JA, Longeri L, Manrique A, Pena-Cabriales J, Pereira PAA, Sanabria C, Tsai SM (1993) Genotypic variation in biological nitrogen fixation by common bean. Plant Soil 521:59–70
21. Hardy RWF, Havelka UD (1976) Photosynthate as a major factor limiting nitrogen fixation by field grown legumes with emphasis on soybeans. In: Nutman PS (ed) Symbiotic nitrogen fixation in plants. Cambridge University Press, London, pp 421–439
22. Herridge DF, Redden RJ (1999) Evaluation of genotypes of navy and culinary bean (Phaseolus vulgaris L.) selected for superior growth and nitrogen fixation. Aust J Exp Agric 39:975–980
23. Holland JB (2006) Estimating genotypic correlations and their standard errors using multivariate restricted maximum likelihood estimation with SAS Proc MIXED. Crop Sci 46:642–654
24. Hyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor-Corrales MA, Cregan PB (2010) High throughput SNP discovery and assay development in common bean. BMC Genom 11:475
25. 2 fixation in agriculture benefit the environment? Plant Soil 252:177–186
26. Kamfwa K, Cichy KA, Kelly JD (2015) Genome-wide association study of agronomic traits in common bean. Plant Genome. doi:10.3835/plantgenome2014.09.0059
27. 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
28. Levy J, Bres C, Geurts R, Chalhoub B, Kulikova O, Duc G, Journet EP, Ane JM, Lauber E, Bisseling T, Denarie J, Rosenberg C, Debelle F (2004) A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science 303:1361–1364
29. Mafongoya PL, Mpepereki S, Mudyazhezha S (2009) The importance of biological nitrogen fixation in cropping systems in nonindustrialized nations. In: Emerich DW, Krishnan HB (eds) Nitrogen fixation in crop production. Crop Science Society of America, Madison, pp 329–348
30. Mitra RM, Gleason CA, Edwards A, Hadfield J, Downie JA, Oldroyd GE, Long SR (2004) A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: gene identification by transcript-based cloning. Proc Natl Acad Sci USA 101:4701–4705
31. Nodari RO, Tsai SM, Guzmán P, Gilbertson RL, Gepts P (1993) Toward an integrated linkage map of common bean. III. Mapping genetic factors controlling host-bacteria interactions. Genetics 134:341–350
32. Peoples MB, Hauggaard-Nielsen H, Jensen ES (2009a) The potential environmental benefits and risks derived from legumes in rotations. In: Emerich DW, Krishnan HB (eds) Nitrogen fixation in crop production. Crop Science Society of America, Madison, pp 349–385
33. Peoples MB, Unkovich MJ, Herridge DF (2009b) Measuring symbiotic nitrogen fixation by legumes. In: Emerich DW, Krishnan HB (eds) Nitrogen fixation in crop production. Crop Science Society of America, Madison, pp 125–170
34. Pereira PAA, Miranda BD, Attewell JR, Kmiecik KA, Bliss FA (1993) Selection for increased nodule number in common bean (Phaseolus vulgaris L.). Plant Soil 148:203–209
35. Price A, Patterson N, Plenge R, Weinblatt M, Shadick N, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909
36. Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
37. Ramaekers L, Galeano CH, Garzon N, Vanderleyden J, Blair MW (2013) Identifying quantitative trait loci for symbiotic nitrogen fixation capacity and related traits in common bean. Mol Breed 31:163–180
38. 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
39. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31:224–228
40. Riely BK, Ané J-M, Penmetsa RV, Cook DR (2004) Genetic and genomic analysis in model legumes bring Nod-factor signaling to center stage. Curr Opin Plant Biol 7:408–413
41. Sanchez-Lopez R, Jauregui D, Nava N, Alvarado-Affantranger X, Montiel J, Santana O, Sanchez F, Quinto C (2011) Down-regulation of SymRK correlates with a deficiency in vascular bundle development in Phaseolus vulgaris nodules. Plant, Cell Environ 34:2109–2121
42. Sanchez-Lopez R, Jauregui D, Quinto C (2012) SymRK and the nodule vascular system: an underground connection. Plant Signal Behav 7:691–693
43. Santos MA, Geraldi IO, Garcia AAF, Bortolatto N, Schiavon A, Hungria M (2013) Mapping of QTLs associated with biological nitrogen fixation traits in soybean. Hereditas 150:17–25
44. SAS Institute (2011) SAS version 9.3. SAS Institute Inc, Cary
45. 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 M, 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 46:707–713
46. 15N abundance. Funct Plant Biol 13:699–756
47. Singh SP, Gutiérrez JA (1984) Geographical distribution of the DL1 and DL2 genes causing hybrid dwarfism in Phaseolus vulgaris L., their association with seed size, and their significance to breeding. Euphytica 33:337–345
48. Souza AA, Boscariol RL, Moon DH, Camargo LE, Tsai SM (2000) Effects of Phaseolus vulgaris QTL in controlling host-bacteria interactions under two levels of nitrogen fertilization. Genetics Mol Biol 23:155–161
49. Stacey G, Libault M, Brechenmacher L, Wan J, May GD (2006) Genetics and functional genomics of legume nodulation. Curr Opin Plant Biol 9:110–121
50. Stracke S, Kistner C, Yoshida S, Mulder L, Sato S, Kaneko T, Tabata S, Sandal N, Stougaard J, Szczyglowski K (2002) A plant receptor-like kinase required for both bacterial and fungal symbiosis. Nature 417:959–962
51. Strodtman KN, Emerich DW (2009) Nodule metabolism. In: Emerich DW, Krishnan HB (eds) Nitrogen fixation in crop production. Crop Science Society of America, Madison, pp 95–124
52. Tsai SM, Da Silva PM, Cabezas WL, Bonetti R (1993) Variability in nitrogen fixation of common bean (Phaseolus vulgaris L.) intercropped with maize. Plant Soil 152:93–101
53. Tsai S, Nodari R, Moon D, Camargo L, Vencovsky R, Gepts P (1998) QTL mapping for nodule number and common bacterial blight in Phaseolus vulgaris L. Plant Soil 204:135–145
54. Uddling J, Gelang-Alfredsson J, Piikki K, Pleijel H (2007) Evaluating the relationship between leaf chlorophyll concentration and SPAD-502 chlorophyll meter readings. Photosynth Res 91:37–46
55. 2 fixation by annual legumes. Field Crops Res 65:211–228
56. van Kessel C, Hartley C (2000) Agricultural management of grain legumes: has it led to an increase in nitrogen fixation? Field Crops Res 65:165–181
57. Vance CP (2001) Symbiotic nitrogen fixation and phosphorus acquisition. Plant nutrition in a world of declining renewable resources. Plant Physiol 127:390–397
58. Vandemark GJ, Brick MA, Osorno JM, Kelly JD, Urrea CA (2014) Edible grain legumes. In: Smith S, Diers B, Specht J, Carver B (eds) Yield gains in major US field crops. CSSA Spec. Publ. 33. Crop Science Society of America, Madison, pp 87–124
59. Vincent JM (1970) A manual for practical study of root nodule bacteria. IBP Handbook No 15. Blackwell, Oxford
60. Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203–214
61. Zhang Z, Ersoz E, Lai C, Todhunter R, Tiwari H, Gore M, Bradbury P, Yu J, Arnett D, Ordovas J (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42:355–360