NASCArrays Information at The BAR

Welcome to NASCArrays information at the BAR. This page hosts meta-information from the NASCArrays service (2002-2013). This information was parsed from text files available on the NASCArrays site. NASCArrays data is on iPlant server. To download experiment data from iPlant, please click on the experiment number. To download the CEL files, please click on the ftp link.

Title:Environmental Genomics of calcicole-calcifuge physiology
Description:Aim To identify genes which are differentially expressed between calcicoles and non- calcicoles.BackgroundGrasslands on the calcareous soils of chalk and other limestones are among the most species-rich plant communities in Europe (Rodwell 1991 et seq.). They have experienced huge losses and remain vulnerable to such impacts as neglect of traditional management, agricultural improvement and global changes in climate, nitrogen depositions and ozone levels. Our understanding of the physiological characteristics of calcicoles and calcifuges remains limited. A detailed understanding of the genetic basis of the mechanisms that enable calcicoles to thrive on calcareous soils is essential to enable us to predict how these plant communities and their constituent species will be affected by environmental change and how the biodiversity of these ecosystems can be sustained.At Lancaster we have been studying calcicole-calcifuge physiology, with particular reference to Ca2+-tolerance, for over fifteen years. Recently, our research has focused on the regulation of apoplastic Ca2+ in Arabidospsis thaliana. We have compared the response of two ecotypes of A. thaliana, the non-calcicole ecotype Columbia (Col-4) and the calcicole ecotype Cal-0, which is a genetically uniform line from an original population collected by Ratcliffe from a rocky limestone slope in 1954, to rhizospheric Ca2+. Our results show that Cal-0, exhibits a markedly higher tolerance to growth on high rhizospheric Ca2+ compared to Col-4.Our hypothesis is that adaptation to a calcareous environment will be reflected in altered gene expression. To test this hypothesis we will grow Col-4 and Cal-0 at low (1 mM) and high (12.5 mM) rhizospheric Ca2+ and compare the patterns of gene expression by microarray analysis. In the first instance, to eliminate any differences in gene expression between the Cal-0 and Col-4 ecotypes, we will compare RNA that will be extracted using the Qiagen RNEasy kits, from plants grown at 16 hour day lengths and will be harvested after 30 days of growth on sand watered with 0.5 X Long Ashton solution containing 1 mM CaCl2.
ftp Link:ftp Link

Slide Information:
Slide IDSlide NameGenetic BackgroundTissueStock CodeCel File
Shirras_1-1_Calcicole_Rep1_ATH1426Whole plant N1063Shirras_1-1_Calcicole_Rep1_ATH1.cel
Shirras_1-2_Calcicole_Rep2_ATH1427Whole plant N1063Shirras_1-2_Calcicole_Rep2_ATH1.cel
Shirras_1-3_Non-Calcicole_Rep1_ATH1428Whole plant N933Shirras_1-3_Non-Calcicole_Rep1_ATH1.cel
Shirras_1-4_Non-Calcicole_Rep2_ATH1429Whole plant N933Shirras_1-4_Non-Calcicole_Rep2_ATH1.cel
Shirras_1-5_Calcicole_Rep3_ATH1562Whole plant N1063Shirras_1-5_Calcicole_Rep3_ATH1.cel
Shirras_1-6_Calcicole_Rep4_ATH1563Whole plant N1063Shirras_1-6_Calcicole_Rep4_ATH1.cel
Shirras_1-7_Non-Calcicole_Rep3_ATH1564Whole plant N933Shirras_1-7_Non-Calcicole_Rep3_ATH1.cel
Shirras_1-8_Non-Calcicole_Rep4_ATH1565Whole plant N933Shirras_1-8_Non-Calcicole_Rep4_ATH1.cel