Identification of candidate phosphorus stress induced genes in Phaseolus vulgaris through clustering analysis across several plant species
Michelle A. Graham A , Mario Ramírez B , Oswaldo Valdés-López B , Miguel Lara B , Mesfin Tesfaye C , Carroll P. Vance D E and Georgina Hernandez B E FA USDA–ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50010, USA.
B Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A Cuernavaca, Mor. México.
C Department of Plant Pathology, University of Minnesota, St Paul, MN 55108, USA.
D USDA–ARS, Plant Research Unit, St Paul, MN 55108, USA.
E Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, USA.
F Corresponding author. Email: gina@ccg.unam.mx
G This paper originates from a presentation at the Third International Conference on Legume Genomics and Genetics, Brisbane, Queensland, Australia, April 2006.
Functional Plant Biology 33(8) 789-797 https://doi.org/10.1071/FP06101
Submitted: 26 April 2006 Accepted: 6 July 2006 Published: 2 August 2006
Abstract
Common bean (Phaseolus vulgaris L.) is the world’s most important grain legume for direct human consumption. However, the soils in which common bean predominate are frequently limited by the availability of phosphorus (P). Improving bean yield and quality requires an understanding of the genes controlling P acquisition and use, ultimately utilising these genes for crop improvement. Here we report an in silico approach for the identification of genes involved in adaptation of P. vulgaris and other legumes to P-deficiency. Some 22 groups of genes from four legume species and Arabidopsis thaliana, encoding diverse functions, were identified as statistically over-represented in EST contigs from P-stressed tissues. By combining bioinformatics analysis with available micro / macroarray technologies and clustering results across five species, we identified 52 P. vulgaris candidate genes belonging to 19 categories as induced by P-stress response. Transport-related, stress (defence and regulation) signal transduction genes are abundantly represented. Manipulating these genes through traditional breeding methodologies and / or biotechnology approaches may allow us to improve crop P-nutrition.
Keywords: ESTs sequences, genomics, legumes, phosphorus deficiency, stress.
Acknowledgments
This work was supported in part by USA Department of Agriculture, Agricultural Research Service CRIS 3640-21000-019-00D ‘Improved Nitrogen and Phosphorus Acquisition and Use in Legumes,’ and CRIS 3625-21220-003-00D, ‘Functional and Structural Genetic Analysis of Soybean.’ GH received a sabbatical fellowship from DGAPA-UNAM.
Altschul SF,
Madden TL,
Schaffer AA,
Zhang J,
Zhang Z,
Miller W, Lipman DJ
(1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25, 3389–3402.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Apweiler R,
Bairoch A,
Wu CH,
Barker WC, Boeckmann B , et al.
(2004) UniProt: the universal protein knowledgebase. Nucleic Acids Research 32, D115–D119.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Bartoz G
(1997) Oxidative stress in plants. Acta Physiologiae Plantarum 19, 47–64.
Broughton WJ,
Hernandez G,
Blair M,
Beebe S,
Gepts P, Vanderleyden J
(2003) Beans (Phaseolus spp.) — model food legumes. Plant and Soil 252, 55–128.
| Crossref | GoogleScholarGoogle Scholar |
Chiou TJ,
Aung K,
Lin SI,
Wu CC,
Chiang SF, Su CL
(2006) Regulation of phosphate homeostasis by MicroRNA in Arabidopsis. The Plant Cell 18, 412–421.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Ge Z,
Rubio G, Lynch JP
(2000) The importance of root gravitropism for inter-root competition and phosphorus acquisition efficiency: results from a geometric simulation model. Plant and Soil 218, 159–171.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Graham MA,
Silverstein KAT,
Cannon SB, VandenBosch KA
(2004) Computational identification and characterization of novel genes from legumes. Plant Physiology 135, 1179–1197.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Graham PH
(1981) Some problems in nodulation and symbiotic nitrogen fixation in Phaseolus vulgaris: a review. Field Crops Research 4, 93–112.
| Crossref | GoogleScholarGoogle Scholar |
Graham PH,
Rosas JC,
Estevez de Jensen C,
Peralta E,
Tlusty B,
Acosta-Gallegos J, Arraes Pereira PA
(2003) Addressing edaphic constraints to bean production: the bean / cowpea CRSP project in perspective. Field Crops Research 82, 179–192.
| Crossref | GoogleScholarGoogle Scholar |
Juszczuk I,
Malusa E, Rychter AM
(2001) Oxidative stress during phosphate deficiency in roots of bean plants (Phaseolus vulgaris L.). Journal of Plant Physiology 158, 1299–1305.
| Crossref | GoogleScholarGoogle Scholar |
López-Bucio J,
Cruz-Ramírez A, Herrera-Estrella L
(2003) The role of nutrient availability in regulating root architecture. Current Opinion in Plant Biology 6, 280–287.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Lynch JP, Brown KM
(2001) Topsoil foraging — an architectural adaptation of plants to low phosphorus availability. Plant and Soil 237, 225–237.
| Crossref | GoogleScholarGoogle Scholar |
Melotto M,
Montenegro-Vitorello CB,
Bruschi A, Camargo LEA
(2005) Comparative bioinformatics analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings. Genome 48, 562–570.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Misson J,
Raghothama KG,
Jain A,
Jouhet J, Block MA , et al.
(2005) A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proceedings of the National Academy of Sciences USA 102, 11 934–11 939.
| Crossref | GoogleScholarGoogle Scholar |
Miura K,
Rus A,
Sharkhuu A,
Yokoi S, Karthikeyan AS , et al.
(2005) The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses. Proceedings of the National Academy of Sciences USA 102, 7760–7765.
| Crossref | GoogleScholarGoogle Scholar |
Raghothama KG
(1999) Phosphate acquisition. Annual Review of Plant Physiology and Plant Molecular Biology 50, 665–693.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Ramírez M,
Graham MA,
Blanco-López L,
Silvente S,
Medrano-Soto A,
Blair MW,
Herrnández G,
Vance CP, Lara M
(2005) Sequencing analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiology 137, 1211–1227.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Reuter DJ,
Elliott DE,
Reddy GD, Abbott RJ
(1997) Phosphorus nutrition of spring wheat (Triticum aestivum L.). Effects of phosphorus supply on plant symptoms, yield, components of yield and plant phosphorus uptake. Australian Journal of Agricultural Research 48, 855–868.
| Crossref | GoogleScholarGoogle Scholar |
Rubio V,
Linhares F,
Solano R,
Martín AC,
Iglesias J,
Leyva A, Paz-Ares J
(2001) A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes & Development 15, 2122–2133.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Smith FW
(2001) Sulphur and phosphorus transport systems in plants. Plant and Soil 232, 109–118.
| Crossref | GoogleScholarGoogle Scholar |
Uhde-Stone C,
Zinn KE,
Ramírez-Yañez M,
Li A,
Vance CP, Allan DL
(2003) Nylon filter arrays reveal different gene expression in proteoid roots of white lupin in response to phosphorus deficiency. Plant Physiology 131, 1064–1079.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Utriainen J, Holopainen T
(2001) Influence of nitrogen and phosphorus availability and ozone stress on Norway spruce seedlings. Tree Physiology 7, 447–456.
