Abstract
BackgroundLandrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift.ResultsHere we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize landraces of Chiapas, Mexico. We collected landraces from three distinct elevational zones and planted them in a midland common garden. Early season leaf tissue was collected for RNA-seq and we performed weighted gene co-expression network analysis (WGCNA). We then used association analysis between landrace co-expression module expression values and environmental parameters of landrace origin to elucidate genes and gene networks potentially shaped by environmental factors along our study gradient. Elevation of landrace origin affected the transcriptome profiles. Two co-expression modules were highly correlated with temperature parameters of landrace origin and queries into their ‘hub’ genes suggested that temperature may have led to differentiation among landraces in hormone biosynthesis/signaling and abiotic and biotic stress responses. We identified several ‘hub’ transcription factors and kinases as candidates for the regulation of these responses.ConclusionsThese findings indicate that natural selection may influence the transcriptomes of crop landraces along an elevational gradient in a major diversity center, and provide a foundation for exploring the genetic basis of local adaptation. While we cannot rule out the role of neutral evolutionary forces in the patterns we have identified, combining whole transcriptome sequencing technologies, established bioinformatics techniques, and common garden experimentation can powerfully elucidate structure of adaptive diversity across a varied landscape. Ultimately, gaining such understanding can facilitate the conservation and strategic utilization of crop genetic diversity in a time of climate change.
Highlights
Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated
By independently mapping the preprocessed reads from each library to the maize reference genome, we found that between 70 and 80% of the initial raw reads from each library uniquely mapped to the maize genome when allowing a two base pair mismatch (except for lowland landrace 6 with 66%; calculated from Additional file 5; uniquely mapped reads/raw reads)
Here, we have presented a novel approach of using RNAseq in combination with WCGNA that can be employed to understand how genetic diversity shaped by natural selection is distributed across the landscape
Summary
Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. (ii) gene flow between wild teosinte species and maize landrace populations [7,8,9]; (iii) diverse selection previously imposed by ecological and environmental heterogeneity [10, 11]; and (iv) the cultural diversity present among Mexican maize landrace farmers [7, 11, 12]. These factors, along with neutral evolutionary processes, have shaped the morphological, phenological, and physiological characteristics of maize throughout Mexico [13], as well as the genetic diversity underlying these traits. They maintain upwards of 20 races of maize, 11 of which are common [14], and three are dominant [15]
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