Please cite: Jamie A O'Rourke, Luis P Iniguez, Fengli Fu, Bruna Bucciarelli, Susan S Miller, Scott A Jackson, Philip E McClean, Jun Li, Xinbin Dai, Patrick X Zhao, Georgina Hernandez and Carroll P Vance. An RNA-Seq based gene expression atlas of the common bean. BMC Genomics 2014, 15:866.
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A Common Bean Gene Expression Atlas    
 
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Phaseolus vulgaris L., or common bean, is an important source of proteins, micronutrients and calories for over three hundred million people worldwide. The high levels of dietary protein in bean seeds (between 20 and 25%) and micronutrients complement the high carbohydrates found in maize and cassava (Broughton et al., 2003). In addition to their important contribution to human health, legumes are also important contributors to biological Nitrogen (N), contributing approximately 21 million metric tons of N into agricultural lands each year (Herridge et al., 2008) . Despite the international importance of common bean, both in terms of economics and consumption, genetic resources for this species have been lacking.

This atlas presents the gene expression patterns of 24 unique samples collected from seven distinct tissues of Phaseolus vulgaris cv. negro jamapa; roots, nodules, leaves, stems, flowers, seeds, and pods. Samples were collected at developmentally important time-points spanning the processes of symbiosis, seed and pod development. Plants were either provided with nutrients via fertilizer or inoculated with either effective or ineffective rhizobium. Plants inoculated with ineffective rhizobium formed nodules, but did not fix N2, resulting in N deficient plants.

This suite of expression data provides a platform for common bean functional genomics, including:

  • YL- Fully expanded 2nd trifoliate leaf tissue from plants provided with fertilizer
  • L5- Leaf tissue collected 5 days after plants were inoculated with effective rhizoubium
  • LF- Leaf tissue from fertilized plants collected at the same time of LE and LI
  • LE- Leaf tissue collected 21 days after plants were inoculated with effective rhizobium
  • LI- Leaf tissue collected 21 days after plants were inoculated with ineffective rhizobium
  • YS- All stem internodes above the cotyledon collected at the 2nd trifoliate stage
  • ST- Shoot tip, including the apical meristem, collected at the 2nd trifoliate stage
  • FY- Young flowers, collected prior to floral emergence
  • PY- Young pods, collected 1 to 4 days after floral senescence. Samples contain developing embryos at globular stage
  • PH- Pods approximately 9cm long, associated with seeds at heart stage (pod only)
  • P1- Pods between 10 and 11 cm long, associated with stage 1 seeds (pod only)
  • P2- Pods between 12 and 13 cm long associated with stage 2 seeds (pod only)
  • SH- Heart stage seeds, between 3 and 4 mm across and approximately 7 mg
  • S1- Stage 1 seeds, between 6 and 7 mm across and approximately 50 mg
  • S2- Stage 2 seeds, between 8 and 10 mm across and between 140 and 150 mg
  • RT- Root tips, 0.5 cm of tissue, collected from fertilized plants at 2nd trifoliate stage of development.
  • YR- Whole roots, including root tips, collected at the 2nd trifoliate stage of development
  • R5- Whole roots separated from 5 day old pre-fixing nodules
  • RF- Whole roots from fertilized plants collected at the same time as RE and RI
  • RE- Whole roots separated from fix+ nodules collected 21 days after inoculation
  • RI- Whole roots separated from fix- nodules collected 21 days after inoculation
  • N5- Pre-fixing (effective) nodules collected 5 days after inoculation
  • NE- Effectively fixing nodules collected 21 days after inoculation
  • NI- Ineffectively fixing nodules collected 21 days after inoculation




Data & bioinformatic resources were generated by the laboratory of Dr. Carroll P. Vance, USDA-ARS, St. Paul, MN, Dr. Patrick X. Zhao at the Samuel Roberts Noble Foundation, and many international collaborators.