Theoretical and Applied Genetics

, Volume 120, Issue 7, pp 1393–1404

Cloning and genetic diversity analysis of a new P5CS gene from common bean (Phaseolus vulgaris L.)

Original Paper

Abstract

Δ1-pyrroline-5-carboxylate synthetase (P5CS) is the rate-limiting enzyme involved in the biosynthesis of proline in plants. By the 3′ rapid amplification of cDNA ends (3′-RACE) approach, a 2,246-bp cDNA sequence was obtained from common bean (Phaseolus vulgaris L.), denominated PvP5CS2 differing from another P5CS gene that we cloned previously from common bean (PvP5CS). The predicted amino acid sequence of PvP5CS2 has an overall 93.2% identity GmP5CS (Glycine max L. P5CS). However, PvP5CS2 shows only 83.7% identity in amino acid sequence to PvP5CS, suggesting PvP5CS2 represents a homolog of the soybean P5CS gene. Abundant indel (insertion and deletion events) and SNP (single nucleotide polymorphisms) were found in the cloned PvP5CS2 genome sequence when comparing 24 cultivated and 3 wild common bean accessions and these in turn reflected aspects of common bean evolution. Sequence alignment showed that genotypes from the same gene pool had similar nucleotide variation, while genotypes from different gene pools had distinctly different nucleotide variation for PvP5CS2. Furthermore, diversity along the gene sequence was not evenly distributed, being low in the glutamic-g-semialdehyde dehydrogenase catalyzing region, moderate in the Glu-5-kinase catalyzing region and high in the intervening region. Neutrality tests showed that PvP5CS2 was a conserved gene undergoing negative selection. A new marker (Pv97) was developed for genetic mapping of PvP5CS2 based on an indel between DOR364 and G19833 sequences and the gene was located between markers Bng126 and BMd045 on chromosome b01. The relationship of PvP5CS2 and a previously cloned pyrroline-5-carboxylate synthetase gene as well as the implications of this work on selecting for drought tolerance in common bean are discussed.

Supplementary material

122_2010_1263_MOESM1_ESM.doc (73 kb)
Supplementary Table (DOC 73 kb)

References

  1. Afanador L, Haley S, Kelly JD (1993) Adoption of a mini-prep DNA extraction method for RAPD marker analysis in common bean (Phaseolus vulgaris L). Bean Improv Coop 36:10–11Google Scholar
  2. Armengaud P, Buhot LTN, Grenier-de March G, Savoure A (2004) Transcriptional regulation of proline biosynthesis in Medicago truncatula reveals developmental and environmental specific features. Physiol Plant 120:442–450CrossRefPubMedGoogle Scholar
  3. Balasubramanian S, Harrison P, Hegyi H, Bertone P, Luscombe N, Echols N, McGarvey P, Zhang Z, Gerstein M (2002) SNPs on human chromosomes 21 and 22—analysis in terms of protein features and pseudogenes. Pharmacogenomics 3(3):393–402CrossRefPubMedGoogle Scholar
  4. Barbazuk BW, Emrich S, Schnable PS (2007) SNP mining from maize 454 EST sequences. CSH protocols. doi:10.1101/pdb.prot4786
  5. Beebe SE, Gaitan RE, Duque MC, Tohme J (2001) Diversity and origin of Andean landraces of common bean. Crop Sci 41:854–862Google Scholar
  6. Bhattramakki D, Dolan M, Hanafey M et al (2002) Insertion–deletion polymorphisms in 39 regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol 48:539–547CrossRefPubMedGoogle Scholar
  7. Blair MW, Pedraza F, Buendia HF, Gaitán-Solís E, Beebe SE, Gepts P, Tohme J (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107:1362–1374CrossRefPubMedGoogle Scholar
  8. Blair MW, Giraldo MC, Buendia HF, Tovar E, Duque MC, Beebe SE (2006) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 113:100–109CrossRefPubMedGoogle Scholar
  9. Blair MW, Rodriguez LM, Pedraza F, Morales F, Beebe SE (2007) Genetic mapping of the bean golden yellow mosaic geminivirus resistance gene bgm-1 and linkage with potyvirus resistance in common bean (Phaseolus vulgaris L.). Theor Appl Genet 114:261–271CrossRefPubMedGoogle Scholar
  10. Bohnert HJ, Jensen RG (1996) Strategies for engineering water stress tolerance in plants. Trends Biotechnol 14:89–97CrossRefGoogle Scholar
  11. Broughton WJ, Hernández G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.)—model food legume. Plant Soil 252:55–128CrossRefGoogle Scholar
  12. Bundock PC, Henry RJ (2004) Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley. Theor Appl Genet 109:543–551CrossRefPubMedGoogle Scholar
  13. Chen JB, Wang SM, Jing RL, Mao XG (2009) Cloning the PvP5CS gene from common bean (Phaseolus vulgaris) and its expression patterns under abiotic stresses. J Plant Physiol 166:12–19CrossRefPubMedGoogle Scholar
  14. Delauney AJ, Verma DPS (1993) Proline biosynthesis and osmoregulation in plants. Plant J 4:215–223CrossRefGoogle Scholar
  15. Dombrowski JE, Baldwin JC, Martin RC (2008) Cloning and characterization of a salt stress-inducible small GTPase gene from the model grass species Lolium temulentum. J Plant Physiol 165:651–661CrossRefPubMedGoogle Scholar
  16. Duran LA, Blair MW, Giraldo MC, Machiavelli R, Prophete E, Nin JC, Beaver JS (2005) Morphological and molecular characterization of common bean (Phaseolus vulgaris L.) landraces from the Caribbean. Crop Sci 45:1320–1328Google Scholar
  17. Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS (1998) Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci USA 95:4441–4446CrossRefPubMedGoogle Scholar
  18. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709PubMedGoogle Scholar
  19. Fu D, Huang B, Xiao Y, Muthukrishnan S, Liang GH (2007) Overexpression of barley hva1 gene in creeping bent grass for improving drought tolerance. Plant Cell Rep 26(4):467–477CrossRefPubMedGoogle Scholar
  20. Fujita T, Maggio A, Garcia-Rios M, Bressan RA, Csonka LN (1998) Comparative analysis of the regulation of expression and structures of two evolutionarily divergent genes for Δ1-pyrroline-5-carboxylate synthetase from tomato. Plant Physiol 118:661–674CrossRefPubMedGoogle Scholar
  21. Garcia-Rios M, Fujita T, Larosa PC, Locyi RD, Clithero JM, Bressan RA, Csonka LN (1997) Cloning of a polycistronic cDNA from tomato encoding γ-glutamyl kinase and γ-glutamyl phosphate reductase. Proc Natl Acad Sci 94:8249–8254CrossRefPubMedGoogle Scholar
  22. Gepts P (1998) Origin and evolution of common bean: past events and recent trends. Hortic Sci 33:1124–1130Google Scholar
  23. Griffin TJ, Smith LM (2000) Single-nucleotide polymorphism analysis by MALDI-TOF mass spectrometry. Trends Biotechnol 18:77–84CrossRefPubMedGoogle Scholar
  24. Hartl DL, Clark AG (1997) Principles of population genetics, 3rd edn. Sinauer Associates, Sunderland, MAGoogle Scholar
  25. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231CrossRefGoogle Scholar
  26. Hong Z, Lakkineni K, Zhang Z, Verma DPS (2000) Removal of feedback inhibition of Δ1-pyrroline-5-carboxylate synthetase results in increased proline accumulation and protection of plants from osmotic stress. Plant Physiol 122:1129–1136CrossRefPubMedGoogle Scholar
  27. Hu CAA, Delauney AJ, Verma DPS (1992) A bifunctional enzyme (Δ1-pyrroline-5-carboxylate synthetase) catalyzes the first two steps in proline biosynthesis in plants. Proc Natl Acad Sci 89:9354–9358CrossRefPubMedGoogle Scholar
  28. Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147–164PubMedGoogle Scholar
  29. Igarashi Y, Yoshika Y, Sanada Y, Yamaguchi-Shinozaki K, Wada K, Shinozaki K (1997) Characterization of the gene for Δ1-pyrroline-5-carboxylate synthetase and correlation between the expression of the gene and salt tolerance in Oryza sativa L. Plant Mol Biol 33:857–865CrossRefPubMedGoogle Scholar
  30. Ik-Young Choi, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY, Yi SI, Young ND, Shoemaker RC, Tassell CP, Specht JE, Cregan PB (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685–696CrossRefGoogle Scholar
  31. Kanazin V, Talbert H, See D et al (2002) Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare). Plant Mol Biol 48:529–537CrossRefPubMedGoogle Scholar
  32. Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A (2005) LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics 21(12):2814–2820CrossRefPubMedGoogle Scholar
  33. Kavi Kishor PB, Sangam S, Amrutha RN, Laxmi PS, Naidu KR, Rao KRSS, Rao S, Reddy KJ, Theriappan P, Sreenivasulu N (2005) Regulation of proline biosynthesis, degradation, uptake and transport in higher plants: its implications in plant growth and abiotic stress tolerance. Curr Sci 88:424–438Google Scholar
  34. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge, MACrossRefGoogle Scholar
  35. Kwak M, Velasco D, Gepts P (2008) Mapping homologous sequences for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris). J Hered 99(3):283–291CrossRefPubMedGoogle Scholar
  36. McClean P, Kami J, Gepts P (2004a) Genomic and genetic diversity in common bean. In: Wilson RF, Stalker HT, Brummer EC (eds) Legume crop genomics. AOCS Press, Champaign, IL, pp 60–82Google Scholar
  37. McClean PE, Lee RK, Miklas PN (2004b) Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean. Genome 47:266–280PubMedCrossRefGoogle Scholar
  38. Morrell PL, Toleno DM, Lundy KE, Clegg MT (2005) Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. PNAS 102:2442–2447CrossRefPubMedGoogle Scholar
  39. Murray MG, Thompson WR (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325CrossRefPubMedGoogle Scholar
  40. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York, NYGoogle Scholar
  41. Nordborg M, Charlesworth B, Charlesworth D (1996) Increased levels of polymorphism surrounding selectively maintained sites in highly selfing species. Proc R Soc Lond Ser B 263:1033–1039CrossRefGoogle Scholar
  42. Olsen KM, Womack A, Garrett AR, Suddith JI, Purugganan MD (2002) Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway. Genetics 160:1641–1650PubMedGoogle Scholar
  43. Pollak E (1987) On the theory of partially inbreeding finite populations I. Partial selfing. Genetics 117:353–360PubMedGoogle Scholar
  44. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100CrossRefPubMedGoogle Scholar
  45. Rafalski A, Morgante M (2004) Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet 20:103–111CrossRefPubMedGoogle Scholar
  46. Ramírez M, Graham MA, Blanco-Lopez L, Silvente S, Medrano-Soto A, Blair MW, Hernandez G, Vance CLP, Lara M (2005) Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol 137:1211–1227CrossRefPubMedGoogle Scholar
  47. Rickert AM, Kim JH, Meyer S, Nagel A, Ballvora A, Oefner PJ, Gebhardt C (2003) First-generation SNP/indel markers tagging loci for pathogen resistance in the potato genome. Plant Biotechnol J 1:399–410CrossRefPubMedGoogle Scholar
  48. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497CrossRefPubMedGoogle Scholar
  49. Schmid KJ, Sorensen TR, Stracke R et al (2003) Large-scale identification and analysis of genomewide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res 13:1250–1257CrossRefPubMedGoogle Scholar
  50. Soleimani VD, Baum BR, Johnson DA (2003) Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR, with an example from barley. Plant Mol Biol Report 21:281–288CrossRefGoogle Scholar
  51. Strizhov N, Abraham E, Okresz L et al (1997) Differential expression of two P5CS genes controlling proline accumulation during salt stress requires ABA and is regulated by ABA1, ABI1 and AXR2 in Arabidopsis. Plant J 12:557–569CrossRefPubMedGoogle Scholar
  52. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMedGoogle Scholar
  53. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98:9161–9166CrossRefPubMedGoogle Scholar
  54. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680CrossRefPubMedGoogle Scholar
  55. Verslues PE, Agarwal M, Katiyar-Agarwal S, Zhu JH, Zhu J-K (2006) Methods and concepts in quantifying resistance to drought, salt and freezing, abiotic stresses that affect plant water status. Plant J 45:523–539CrossRefPubMedGoogle Scholar
  56. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276CrossRefPubMedGoogle Scholar
  57. Yoshiba Y, Takeshi Katagiri TK, Ueda H, Mizoguchi Y, Shinozaki KY, Wada K, Harada Y, Shinozaki K (1995) Correlation between the induction of a gene for Δ1-pyrroline-5-carboxylate synthetase and the accumulation of proline in Arabidopsis thaliana under osmotic stress. Plant J 7(5):751–760CrossRefPubMedGoogle Scholar
  58. Zhang CS, Liu Q, Verma DPS (1997) Characterization of Δ1-pyrroline-5-carboxylate synthetase gene promoter in transgenic Arabidopsis thaliana subjected to water stress. Plant Sci 129(1):81–89CrossRefGoogle Scholar
  59. Zhang X, Blair MW, Wang S (2008) Genetic diversity of Chinese common bean (Phaseolus vulgaris L.) landraces assessed with simple sequence repeat (SSR) markers. Theor Appl Genet 117:629–640CrossRefPubMedGoogle Scholar
  60. Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single nucleotide polymorphisms in soybean. Genetics 163:1123–1134PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  1. 1.National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop SciencesThe Chinese Academy of Agricultural Sciences, Ministry of AgricultureBeijingChina
  2. 2.Nanyang Normal UniversityNanyangChina
  3. 3.International Center for Tropical Agriculture (CIAT)CaliColombia
  4. 4.Institute of VegetablesQingdao Academy of Agricultural SciencesQingdaoChina

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