title: Transcriptome analysis of secondary cell wall development in Medicago truncatula.
abstract: BACKGROUND
  Legumes are important to humans by providing food, feed and raw materials for industrial utilizations. Some legumes, such as alfalfa, are potential bioenergy crops due to their high biomass productivity. Global transcriptional profiling has been successfully used to identify genes and regulatory pathways in secondary cell wall thickening in Arabidopsis, but such transcriptome data is lacking in legumes.
  
  
  RESULTS
  A systematic microarray assay and high through-put real time PCR analysis of secondary cell wall development were performed along stem maturation in Medicago truncatula. More than 11,000 genes were differentially expressed during stem maturation, and were categorized into 10 expression clusters. Among these, 279 transcription factor genes were correlated with lignin/cellulose biosynthesis, therefore representing putative regulators of secondary wall development. The b-ZIP, NAC, WRKY, C2H2 zinc finger (ZF), homeobox, and HSF gene families were over-represented. Gene co-expression network analysis was employed to identify transcription factors that may regulate the biosynthesis of lignin, cellulose and hemicellulose. As a complementary approach to microarray, real-time PCR analysis was used to characterize the expression of 1,045 transcription factors in the stem samples, and 64 of these were upregulated more than 5-fold during stem maturation. Reverse genetics characterization of a cellulose synthase gene in cluster 10 confirmed its function in xylem development.
  
  
  CONCLUSIONS
  This study provides a useful transcriptome and expression resource for understanding cell wall development, which is pivotal to enhance biomass production in legumes.
authors.affiliation: Department of Plant Science and Landscape Architecture, University of Connecticut, 1390 Storrs Rd., Storrs, CT, 06269, USA. huanzhong.wang@uconn.edu.
authors.forename: Huanzhong
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Plant Science and Landscape Architecture, University of Connecticut, 1390 Storrs Rd., Storrs, CT, 06269, USA. jung.yang@uconn.edu.
authors.forename: Jung Hyun
authors.initials: JH
authors.lastname: Yang
authors.affiliation: Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA. Fang.Chen@unt.edu.|Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA. Fang.Chen@unt.edu.
authors.forename: Fang
authors.initials: F
authors.lastname: Chen
authors.affiliation: Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA. itjerez@noble.org.
authors.forename: Ivone
authors.initials: I
authors.lastname: Torres-Jerez
authors.affiliation: Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA. ytang@noble.org.
authors.forename: Yuhong
authors.initials: Y
authors.lastname: Tang
authors.affiliation: Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA. mingy.wang@gmail.com.
authors.forename: Mingyi
authors.initials: M
authors.lastname: Wang
authors.affiliation: Department of Plant Science and Landscape Architecture, University of Connecticut, 1390 Storrs Rd., Storrs, CT, 06269, USA. qian.du@uconn.edu.
authors.forename: Qian
authors.initials: Q
authors.lastname: Du
authors.affiliation: Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA. xcheng@noble.org.
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA. jwen@noble.org.
authors.forename: Jiangqi
authors.initials: J
authors.lastname: Wen
authors.affiliation: Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA. Richard.Dixon@unt.edu.|Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA. Richard.Dixon@unt.edu.
authors.forename: Richard
authors.initials: R
authors.lastname: Dixon
mesh_terms: D002473:Cell Wall / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks / Q000235:genetics; D005964:Glucosyltransferases / Q000096:biosynthesis* / Q000235:genetics; D008031:Lignin / Q000096:biosynthesis / Q000235:genetics; D046913:Medicago truncatula / Q000235:genetics* / Q000254:growth & development; D018547:Plant Stems / Q000235:genetics; D014157:Transcription Factors / Q000096:biosynthesis / Q000235:genetics
chemical_list: D014157:Transcription Factors; D008031:Lignin; D005964:Glucosyltransferases; C478648:cellulose synthase