Genetic architecture of inter-specific and -generic grass hybrids by network analysis on multi-omics data.

Background: Understanding the mechanisms underlining forage production and its biomass nutritive quality at the omics level is crucial for boosting the output of high-quality dry matter per unit of land. Despite the advent of multiple omics integration for the study of biological systems in major crops, investigations on forage species are still scarce.

Results: Our results identified substantial changes in gene co-expression and metabolite-metabolite network topologies as a result of genetic perturbation by hybridizing L.

Leveraging spatiotemporal genomic breeding value estimates of dry matter yield and herbage quality in ryegrass via random regression models.

Joint modeling of correlated multienvironment and multiharvest data of perennial crop species may offer advantages in prediction schemes and a better understanding of the underlying dynamics in space and time. The goal of the present study was to investigate the relevance of incorporating the longitudinal dimension of within-season multiple measurements of forage perennial ryegrass (Lolium perenne L.) traits in a reaction-norm model setup that additionally accounts for genotype × environment (G × E) interactions.

Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass.

The growing demand for food and feed crops in the world because of growing population and more extreme weather events requires high-yielding and resilient crops. Many agriculturally important traits are polygenic, controlled by multiple regulatory layers, and with a strong interaction with the environment. In this study, 120 F families of perennial ryegrass (Lolium perenne L.

Transcriptional and Metabolomic Analyses Indicate that Cell Wall Properties are Associated with Drought Tolerance in .

is an established model for drought tolerance. We previously identified accessions exhibiting high tolerance, susceptibility and intermediate tolerance to drought; respectively, ABR8, KOZ1 and ABR4. Transcriptomics and metabolomic approaches were used to define tolerance mechanisms.

Genomic Prediction in Tetraploid Ryegrass Using Allele Frequencies Based on Genotyping by Sequencing.

Perennial ryegrass is an outbreeding forage species and is one of the most widely used forage grasses in temperate regions. The aim of this study was to investigate the possibility of implementing genomic prediction in tetraploid perennial ryegrass, to study the effects of different sequencing depth when using genotyping-by-sequencing (GBS), and to determine optimal number of single-nucleotide polymorphism (SNP) markers and sequencing depth for GBS data when applied in tetraploids. A total of 1,515 F tetraploid ryegrass families were included in the study and phenotypes and genotypes were scored on family-pools.

Optimized Use of Low-Depth Genotyping-by-Sequencing for Genomic Prediction Among Multi-Parental Family Pools and Single Plants in Perennial Ryegrass ( L.).

Ryegrass single plants, bi-parental family pools, and multi-parental family pools are often genotyped, based on allele-frequencies using genotyping-by-sequencing (GBS) assays. GBS assays can be performed at low-coverage depth to reduce costs. However, reducing the coverage depth leads to a higher proportion of missing data, and leads to a reduction in accuracy when identifying the allele-frequency at each locus.

Evidence for Active Uptake and Deposition of Si-based Defenses in Tall Fescue.

Silicon (Si) is taken up from the soil as monosilicic acid by plant roots, transported to leaves and deposited as phytoliths, amorphous silica (SiO) bodies, which are a key component of anti-herbivore defense in grasses. Silicon transporters have been identified in many plant species, but the mechanisms underpinning Si transport remain poorly understood. Specifically, the extent to which Si uptake is a passive process, driven primarily by transpiration, or has both passive and active components remains disputed.

Accuracy of Genomic Prediction in a Commercial Perennial Ryegrass Breeding Program.

The implementation of genomic selection (GS) in plant breeding, so far, has been mainly evaluated in crops farmed as homogeneous varieties, and the results have been generally positive. Fewer results are available for species, such as forage grasses, that are grown as heterogenous families (developed from multiparent crosses) in which the control of the genetic variation is far more complex. Here we test the potential for implementing GS in the breeding of perennial ryegrass ( L.

Genomic dissection and prediction of heading date in perennial ryegrass.

Background: Genomic selection (GS) has become a commonly used technology in animal breeding. In crops, it is expected to significantly improve the genetic gains per unit of time. So far, its implementation in plant breeding has been mainly investigated in species farmed as homogeneous varieties.

Estimating genomic heritabilities at the level of family-pool samples of perennial ryegrass using genotyping-by-sequencing.

By using the genotyping-by-sequencing method, it is feasible to characterize genomic relationships directly at the level of family pools and to estimate genomic heritabilities from phenotypes scored on family-pools in outbreeding species. Genotyping-by-sequencing (GBS) has recently become a promising approach for characterizing plant genetic diversity on a genome-wide scale. We use GBS to extend the concept of heritability beyond individuals by genotyping family-pool samples by GBS and computing genomic relationship matrices (GRMs) and genomic heritabilities directly at the level of family-pools from pool-frequencies obtained by sequencing.

Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice.

Vernalization, a period of low temperature to induce transition from vegetative to reproductive state, is an important environmental stimulus for many cool season grasses. A key gene in the vernalization pathway in grasses is the VRN1 gene. The objective of this study was to identify causative polymorphism(s) at the VRN1 locus in perennial ryegrass (Lolium perenne) for variation in vernalization requirement.

Genetic variation, population structure, and linkage disequilibrium in European elite germplasm of perennial ryegrass.

Perennial ryegrass (Lolium perenne L.) is a highly valued temperate climate grass species grown as forage crop and for amenity uses. Due to its outbreeding nature and recent domestication, a high degree of genetic diversity is expected among cultivars.

Nucleotide diversity and linkage disequilibrium of nine genes with putative effects on flowering time in perennial ryegrass (Lolium perenne L.).

Optimization of flowering is an important breeding goal in forage and turf grasses, such as perennial ryegrass (Lolium perenne L.). Nine floral control genes including Lolium perenne CONSTANS (LpCO), SISTER OF FLOWERING LOCUS T (LpSFT), TERMINAL FLOWER1 (LpTFL1), VERNALIZATION1 (LpVRN1, identical to LpMADS1) and five additional MADS-box genes, were analyzed for nucleotide diversity and linkage disequilibrium (LD).

Comparative analysis of transgenic tall fescue (Festuca arundinacea Schreb.) plants obtained by Agrobacterium-mediated transformation and particle bombardment.

Agrobacterium-mediated transformation and particle bombardment are the two most widely used methods for genetically modifying grasses. Here, these two systems are compared for transformation efficiency, transgene integration and transgene expression when used to transform tall fescue (Festuca arundinacea Schreb.).

A high-throughput Agrobacterium-mediated transformation system for the grass model species Brachypodium distachyon L.

In the ongoing process of developing Brachypodium distachyon as a model plant for temperate cereals and forage grasses, we have developed a high-throughput Agrobacterium-mediated transformation system for a diploid accession. Embryogenic callus, derived from immature embryos of the accession BDR018, were transformed with Agrobacterium tumefaciens strain AGL1 carrying two T-DNA plasmids, pDM805 and pWBV-Ds-Ubi-bar-Ds. Transient and stable transformation efficiencies were optimised by varying the pre-cultivation period, which had a strong effect on stable transformation efficiency.

Functional characterization of tobacco transcription factor TGA2.1.

Activation sequence-1 (as-1)-like regulatory cis elements mediate transcriptional activation in response to increased levels of plant signalling molecules auxin and salicylic acid (SA). Our earlier work has shown that tobacco cellular as-1-binding complex SARP (salicylic acid responsive protein) is primarily comprised of bZIP protein TGA2.2 and of minor amounts of a protein that cross-reacts with an antibody directed against related bZIP factor TGA2.