Brachypodium, a model grass genus for bioenergy: perenniality, abiotic stress tolerances and plant-microbe interactions
Our understanding of the control of biomass partitioning is strongly influenced by current model annual plants, which constitute nearly all reference and most crop plant species. By contrast, cellulosic biofuel crops are predominantly perennial. The extent to which perennial plants invest in harvestable vegetative biomass is a critical determinant of the success of biofuel crops. We propose to leverage the substantial genomic resources of the annual grass Brachypodium distachyon to elucidate the genetic control of transitions to perenniality, and its interaction with the environment, in the genus Brachypodium. Variation in life history strategy and environmental tolerances in this genus represents an untapped resource for deepening our understanding of key aspects of cellulosic biofuel improvement. Progress is currently limited, however, by the lack of genomic and microbiome meta-genomic resources in the genus beyond B. distachyon.
We propose four objectives to develop the genus Brachypodium as the pre-eminent system for functional genomic analysis of perenniality:
1. Comparative grade de novo sequencing of whole genomes and transcriptomes of three perennial Brachypodium species: B.mexicanum, B.arbuscula, B.sylvaticum. These species have evolved short-rhizomatous versus long-rhizomatous behavior independently. Independent derivation of perennial habits in this genus makes it theoretically possible to identify the underlying genetic basis of perenniality. DNA sequencing of mapping populations of autogamous B.mexicanum and allogamous B.arbuscula and B.sylvaticum lines will be used for the genome assembly and genomic annotation. Transcriptome sequences will be generated from RNA isolated from different tissues. Transcriptome sequences will be leveraged to develop Gene Atlases for each species and to annotate the genome sequences. We will also define a pan-genome for the genus, allowing us to identify genes which are present across all the species and gene families which show copy-number turnover among species.
2. Large-scale resequencing of flagship perennial B.sylvaticum. We will use the B.sylvaticum genome to aid in constructing a pangenome for this species. The pangenome will characterize the core and dispensable genes within this perennial and cold-adapted/sensitive species and allow comparison of the recently described pangenome of the annual grass B.distachyon. This approach notably revealed up to 24,368 genes not present in the B.distachyon Bd21 reference genome. Many of these genes presumably confer resistance to biotic and abiotic stress and adaptation to specific environments.
3. Assessment of regulatory control of stress response in perennial and annual species. We will grow replicates of each of the annual and perennial species from seed under controlled greenhouse conditions. Pre-flowering plants will be subjected to soil drying and RNA and DNA will be harvested from the leaves of control and treatment plants. We will perform bisulfite DNA sequencing to assess genome-wide methylation patterns in control and stressed plants, and to assess legacy effects of stress in second-year perennials. These data will be analyzed in conjunction with RNASeq transcript counts for differential gene expression (DGE) analysis. DGE data will be used along with the genome sequences to perform and ENCODE-style analysis to identify non-coding elements which modulate constitutive and stress-inducible transcript abundance.
4. Plant microbiomes of flagship perennial B.sylvaticum. Current comparative plant microbiome metagenomic analysis is being conducted in populations of the annuals B.distachyon and B.hybridum. The goals of this investigation are to contribute to understand the mechanisms by which microbial-plant interactions might enable perennial vs annual life-cycle habit and their respective mesic-cold vs xeric climate adaptations.
Acronym:
Proposal 1941 - CSP 2016 Proposal
Author:
Contreras Moreira (on leave since 30/09/2018) , Bruno
Our understanding of the control of biomass partitioning is strongly influenced by current model annual plants, which constitute nearly all reference and most crop plant species. By contrast, cellulosic biofuel crops are predominantly perennial. The extent to which perennial plants invest in harvestable vegetative biomass is a critical determinant of the success of biofuel crops. We propose to leverage the substantial genomic resources of the annual grass Brachypodium distachyon to elucidate the genetic control of transitions to perenniality, and its interaction with the environment, in the genus Brachypodium. Variation in life history strategy and environmental tolerances in this genus represents an untapped resource for deepening our understanding of key aspects of cellulosic biofuel improvement. Progress is currently limited, however, by the lack of genomic and microbiome meta-genomic resources in the genus beyond B. distachyon.
We propose four objectives to develop the genus Brachypodium as the pre-eminent system for functional genomic analysis of perenniality:
1. Comparative grade de novo sequencing of whole genomes and transcriptomes of three perennial Brachypodium species: B.mexicanum, B.arbuscula, B.sylvaticum. These species have evolved short-rhizomatous versus long-rhizomatous behavior independently. Independent derivation of perennial habits in this genus makes it theoretically possible to identify the underlying genetic basis of perenniality. DNA sequencing of mapping populations of autogamous B.mexicanum and allogamous B.arbuscula and B.sylvaticum lines will be used for the genome assembly and genomic annotation. Transcriptome sequences will be generated from RNA isolated from different tissues. Transcriptome sequences will be leveraged to develop Gene Atlases for each species and to annotate the genome sequences. We will also define a pan-genome for the genus, allowing us to identify genes which are present across all the species and gene families which show copy-number turnover among species.
2. Large-scale resequencing of flagship perennial B.sylvaticum. We will use the B.sylvaticum genome to aid in constructing a pangenome for this species. The pangenome will characterize the core and dispensable genes within this perennial and cold-adapted/sensitive species and allow comparison of the recently described pangenome of the annual grass B.distachyon. This approach notably revealed up to 24,368 genes not present in the B.distachyon Bd21 reference genome. Many of these genes presumably confer resistance to biotic and abiotic stress and adaptation to specific environments.
3. Assessment of regulatory control of stress response in perennial and annual species. We will grow replicates of each of the annual and perennial species from seed under controlled greenhouse conditions. Pre-flowering plants will be subjected to soil drying and RNA and DNA will be harvested from the leaves of control and treatment plants. We will perform bisulfite DNA sequencing to assess genome-wide methylation patterns in control and stressed plants, and to assess legacy effects of stress in second-year perennials. These data will be analyzed in conjunction with RNASeq transcript counts for differential gene expression (DGE) analysis. DGE data will be used along with the genome sequences to perform and ENCODE-style analysis to identify non-coding elements which modulate constitutive and stress-inducible transcript abundance.
4. Plant microbiomes of flagship perennial B.sylvaticum. Current comparative plant microbiome metagenomic analysis is being conducted in populations of the annuals B.distachyon and B.hybridum. The goals of this investigation are to contribute to understand the mechanisms by which microbial-plant interactions might enable perennial vs annual life-cycle habit and their respective mesic-cold vs xeric climate adaptations.