DOI: 10.5061/dryad.gxd2547h1
title: Transcriptional differentiation of UV-B protectant genes in maize landraces spanning an elevational gradient in Chiapas, Mexico

description: Globally, farmers cultivate and maintain crop landraces (i.e., traditional
 varieties). Landraces contain unique diversity shaped in part by natural
 and human-mediated selection and are an indispensable resource to farmers.
 Since environmental conditions change with elevation, crop landraces grown
 along elevational gradients have provided ideal locations to explore
 patterns of local adaptation. To further probe traits underlying this
 differentiation, transcriptome signatures can help provide a foundation
 for understanding the ways in which functional genetic diversity may be
 shaped by environment. In this study, we returned to an elevational
 gradient in Chiapas, Mexico, to assess transcriptional differentiation of
 genes underlying UV-B protection in locally adapted maize landraces from
 multiple elevations. We collected and planted landraces from three
 elevational zones (lowland, approximately 600 m; midland, approximately
 1,550 m; highland approximately 2,100 m) in a common garden at 1,531 m.
 Using RNA-seq data derived from leaf tissue, we performed differential
 expression analysis between maize from these distinct elevations. Highland
 and lowland landraces displayed differential expression in phenylpropanoid
 and flavonoid biosynthesis genes involved in the production of UV-B
 protectants and did so at a rate greater than expected based on observed
 background transcriptional differentiation across the genome. These
 findings provide evidence for the differentiation of suites of genes
 involved in complex ecologically relevant pathways. Thus, while neutral
 evolutionary processes may have played a role in the observed patterns of
 differentiation, UV-B may have also acted as a selective pressure to
 differentiate maize landraces in the region. Studies of the distribution
 of functional crop genetic diversity across variable landscapes can aid us
 in understanding the response of diversity to abiotic/biotic change and,
 ultimately, may facilitate its conservation and utilization.
description: The uploaded data is raw reads from the sequencer, no processing
 has been performed. Following is a brief description of how the data was
 collected. See manuscript for further information.  As
 described in Kost et al. (2017), we performed RNA extractions with Qiagen
 RNeasy Plant Mini Kits and confirmed RNA integrity with the Agilent 2100
 Bioanalyzer. In total, we performed 135 RNA extractions (15 landraces x 9
 individuals per landrace). To aid in RNA-seq library construction, we
 assessed RNA concentrations using Qubit® 2.0 Fluorometer combined with the
 Qubit RNA Assay Kit. Before library construction, we pooled RNA from the
 three individuals sampled per landrace per block, resulting in 45 pooled
 RNA samples – one pooled sample per block x 15 landraces x three blocks.
 We performed RNA-seq library construction using the strand specific
 library preparation method described in Zhong et al., (2011). Since we
 employed a multiplex sequence strategy, we assigned each library a barcode
 during library preparation. We randomized pooled RNA samples before
 library preparation to account for batch effects. Following library
 construction, we analyzed cDNA libraries using the Qubit DNA Assay Kit to
 determine concentration and we used the Agilent 2100 Bioanalyzer to
 determine library size. We sequenced the 45 RNA-seq libraries in four flow cell lanes of the Illumina HiSeq 2500 at the Genomics Resources Core Facility located at the Weill Cornell Medical College. We performed paired end sequencing at 50 bp. Since HiSeq 2500 normally produce ~ 120-130 million paired-end reads per lane, we multiplexed 12 libraries per lane to produce ~ 10-11 million reads per library. In order to ensure balanced sequencing lanes, we ran 12 libraries in each lane. Since we only had 45 libraries, we sequenced one library in all four lanes, bringing the number of libraries in each lane to 12.
description: Following the materials and Methods section of this manuscript
 will allow you to recreate the entire analysis presented in the
 manuscript.