title: A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit.
abstract: BACKGROUND
  Melon fruit flesh color is primarily controlled by the "golden" single nucleotide polymorhism of the "Orange" gene, CmOr, which dominantly triggers the accumulation of the pro-vitamin A molecule, β-carotene, in the fruit mesocarp. The mechanism by which CmOr operates is not fully understood. To identify cellular and metabolic processes associated with CmOr allelic variation, we compared the transcriptome of bulks of developing fruit of homozygous orange and green fruited F3 families derived from a cross between orange and green fruited parental lines.
  
  
  RESULTS
  Pooling together F3 families that share same fruit flesh color and thus the same CmOr allelic variation, normalized traits unrelated to CmOr allelic variation. RNA sequencing analysis of these bulks enabled the identification of differentially expressed genes. These genes were clustered into functional groups. The relatively enriched functional groups were those involved in photosynthesis, RNA and protein regulation, and response to stress.
  
  
  CONCLUSIONS
  The differentially expressed genes and the enriched processes identified here by bulk segregant RNA sequencing analysis are likely part of the regulatory network of CmOr. Our study demonstrates the resolution power of bulk segregant RNA sequencing in identifying genes related to commercially important traits and provides a useful tool for better understanding the mode of action of CmOr gene in the mediation of carotenoid accumulation.
authors.affiliation: Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel. noamchayut@gmail.com.|Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel. noamchayut@gmail.com.
authors.forename: Noam
authors.initials: N
authors.lastname: Chayut
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA. hy442@cornell.edu.
authors.forename: Hui
authors.initials: H
authors.lastname: Yuan
authors.affiliation: Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel. shachar@volcani.agri.gov.il.
authors.forename: Shachar
authors.initials: S
authors.lastname: Ohali
authors.affiliation: Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel. meira@volcani.agri.gov.il.
authors.forename: Ayala
authors.initials: A
authors.lastname: Meir
authors.affiliation: Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O.B. 6, Bet-Dagan, 50250, ISRAEL. yeselsonlena@yahoo.com.
authors.forename: Yelena
authors.initials: Y
authors.lastname: Yeselson
authors.affiliation: Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel. portnoyv@agri.gov.il.
authors.forename: Vitaly
authors.initials: V
authors.lastname: Portnoy
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA. yz357@cornell.edu.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA. zf25@cornell.edu.
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.affiliation: Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel. twefraim@volcani.agri.gov.il.
authors.forename: Efraim
authors.initials: E
authors.lastname: Lewinsohn
authors.affiliation: Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel. katzirn@volcani.agri.gov.il.
authors.forename: Nurit
authors.initials: N
authors.lastname: Katzir
authors.affiliation: Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O.B. 6, Bet-Dagan, 50250, ISRAEL. vcaris@volcani.agri.gov.il.
authors.forename: Arthur A
authors.initials: AA
authors.lastname: Schaffer
authors.affiliation: Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel. gepstein@tx.technion.ac.il.
authors.forename: Shimon
authors.initials: S
authors.lastname: Gepstein
authors.affiliation: Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel. burgery@volcani.agri.gov.il.
authors.forename: Joseph
authors.initials: J
authors.lastname: Burger
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA. ll37@cornell.edu.|US Department of Agriculture-Agricultural Research Service, Robert W Holly Center for Agriculture and Health, Cornell University, Ithaca, NY, 14853, USA. ll37@cornell.edu.
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.affiliation: Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel. tadmory@agri.gov.il.
authors.forename: Yaakov
authors.initials: Y
authors.lastname: Tadmor
mesh_terms: D028463:Cucumis melo / Q000235:genetics* / Q000378:metabolism; D005638:Fruit / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D059467:Transcriptome; D019207:beta Carotene / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D019207:beta Carotene