Genome diversity in wild grasses under environmental stress

Abstract

Patterns of diversity distribution in the Isa defense locus in wild-barley populations suggest adaptive selection at this locus. The extent to which environmental selection may act at additional nuclear-encoded defense loci and within the whole chloroplast genome has now been examined by analyses in two grass species. Analysis of genetic diversity in wild barley ( Hordeum spontaneum ) defense genes revealed much greater variation in biotic stress-related genes than abiotic stress-related genes. Genetic diversity at the Isa defense locus in wild populations of weeping ricegrass [ Microlaena stipoides (Labill.) R. Br.], a very distant wild-rice relative, was more diverse in samples from relatively hotter and drier environments, a phenomenon that reflects observations in wild barley populations. Whole-chloroplast genome sequences of bulked weeping ricegrass individuals sourced from contrasting environments showed higher levels of diversity in the drier environment in both coding and noncoding portions of the genome. Increased genetic diversity may be important in allowing plant populations to adapt to greater environmental variation in warmer and drier climatic conditions.

Analysis of adaptive ribosomal gene diversity in wild plant populations from contrasting climatic environments

“…[3][4][5] While the SNP distribution for an individual plant follows the expected pattern of being higher within the ITS than the RNA coding region, the number of SNP is far higher than previously reported within an individual for this locus. This is likely the result of utilizing whole genome shotgun massively parallel sequencing which can identify a far greater amount of intra-individual ribosomal diversity as it is not restricted by the limitations of PCR and detects very low frequency alleles in a population of sequences far beyond that which could be captured by cloning.…”

“…2 Chloroplast genome diversity also exhibited a similar variation with environment. 3 We now report analysis of nuclear ribosomal genes from the same wild population. Two contrasting environments did not show significant differences in the level of diversity.…”

High-Throughput Sequencing and Mutagenesis to Accelerate the Domestication of Microlaena stipoides as a New Food Crop

“…This locus is reported as a small single copy gene with no introns in rice, barley and wild barley ( Hordeum ) species. Sequence diversity within this gene has been positively correlated with increasing environmental variability [34], [51]. Only two of the five SNPs identified in the Isa gene of the wild populations were putatively functional, and neither would necessarily cause a loss of function [34].…”

Advances in DNA sequencing enabling more rapid development of improved biomass and biofuel conversion technologies

“…Sequencing of plant genomes at the level of the plant population or community will eventually provide the insights required to improve plant performance in marginal environments or more difficult climates supporting biofuel crop development [12]. Sequencing of plant pathogens is providing important advances in understanding of the biology of these organisms and contributes to control of pests and diseases in biofuel crop production.…”