Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation

Abstract

After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of environmental adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical adaptation, but many factors key to regional success remain unidentified.

Climatic adaptation and ecological descriptors of wild beans from Mexico

“…For example, P. esperanzae was located in a subtropical arid semihot climatic type near Ciudad Victoria, Tamaulipas (northeastern Mexico); P. maculatus was detected near Tepatlaxco de Hidalgo, Puebla (central highlands), in a subtropical subhumid temperate climate; and P. xanthotrichus was found growing in a tropical subhumid semihot climate in Teopisca, Chiapas (southeastern Mexico). These findings are preliminary due to the low number of samples analyzed, although they provide valuable information for future and more intensive collections (Gil & Lobo, 2012; Pliscoff & Fuentes‐Castillo, 2011; Ramírez‐Villegas et al., 2010; Russell et al., 2016). …”

Adding Complexity to Complexity: Gene Family Evolution in Polyploids

“…Such approaches, for example, have been successfully applied to investigating R-gene variation in crop plants (Jupe et al, 2012(Jupe et al, , 2013Andolfo et al, 2014;Giolai et al, 2016;Russell et al, 2016;Van Weymers et al, 2016). Whole genome resequencing approaches could be useful for setting the genomic context and fate of duplications, but there are still substantial challenges to resolve in distinguishing loss of copies from lack of coverage or lack of assembly to the reference due to high sequence divergence.…”

Towards the Genomic Basis of Local Adaptation in Landraces

“…When at least a reference transcriptome is available, exome sequencing, also known as whole-exome sequencing, may represent an affordable option for analyzing a well-characterized adaptive trait or very large plant populations [97], because of its reduced running cost when probes are already available. For instance, an investigation of the barley genomic variability related to environmental conditions was carried out starting from the exome sequencing data of more than 250 georeferenced landraces and wild accessions [97].…”

“…For instance, an investigation of the barley genomic variability related to environmental conditions was carried out starting from the exome sequencing data of more than 250 georeferenced landraces and wild accessions [97].…”

“…This approach is popular especially for GWA studies in crops because it can be also employed on plant species with complex and large genomes, including polyploids. A GbS-based survey of nucleotide diversity in soybean landraces revealed selective sweeps around starch metabolism genes; GWAS also provided insights into the origin and spread of haplotypes linked to agro-climatic traits [96].When at least a reference transcriptome is available, exome sequencing, also known as whole-exome sequencing, may represent an affordable option for analyzing a well-characterized adaptive trait or very large plant populations [97], because of its reduced running cost when probes Diversity 2017, 9, 51 6 of 12 are already available. For instance, an investigation of the barley genomic variability related to environmental conditions was carried out starting from the exome sequencing data of more than 250 georeferenced landraces and wild accessions [97].…”