Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico

BMC Genomics

Research Article

Matthew A. Kost¹  Eric Stockinger¹  Kristin L. Mercer²  Hugo R. Perales³  Saranga Wijeratne⁴  Asela J. Wijeratne⁵ 

[1] Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA;Department of Horticulture and Crop Sciences, The Ohio State University, Columbus, OH, USA;El Colegio de la Frontera Sur, Departmento de Agroecología, San Cristóbal de Las Casas, Chiapas, Mexico;Molecular Cellular and Imagining Center, The Ohio State University/OARDC, Wooster, OH, USA;Molecular Cellular and Imagining Center, The Ohio State University/OARDC, Wooster, OH, USA;Department of Biological Sciences, Arkansas State University, AR, Jonesboro, USA;

关键词: Maize;    Landraces;    Transcriptomics;    WGCNA;    RNA-seq;    Chiapas;    Adaptation;   

DOI  :  10.1186/s12864-017-4005-y

 received in 2016-04-29, accepted in 2017-08-02,  发布年份 2017

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2017