Barley systematics and taxonomy foreseen by seed morphometric variation.

Since its Neolithic domestication in the Fertile Crescent, barley has spread to all continents and represents a major cereal in many modern agrarian systems. Current barley diversity includes thousands of varieties divided into four main categories corresponding to 2-row and 6-row subspecies and naked and hulled types, each of them with winter and spring varieties. This diversity is associated to different uses and allow cultivation in diverse environments.

Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection.

There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production. To address these challenges, new and innovative knowledge, resources, tools, and methods to facilitate breeding are needed. This starts with the development of high throughput genomic tools including single nucleotide polymorphism (SNP) arrays, high density molecular marker maps, and full genome sequences.

Association between SNP Markers and 11 Vitamin Contents in Grains of a Worldwide Bread Wheat Core Collection.

The metabolomic profiling analyses of 11 vitamins' statuses of wheat grain in a subsample of 167 accessions from the INRAE worldwide bread wheat core collection planted in two contrasting environments in France (Le Moulon and Clermont-Ferrand) have been evaluated using a high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS) procedure. This has allowed us to perform a genome-wide association study (GWAS) for these nutritional traits of interest combining the phenotypic data with the genotypic data derived from the TaBW280K SNP chip. Considering both thresholds ( < 0.

Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats.

Structural variations (SVs) such as copy number and presence-absence variations are polymorphisms that are known to impact genome composition at the species level and are associated with phenotypic variations. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent production of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild accessions.

Worldwide phylogeography and history of wheat genetic diversity.

Since its domestication in the Fertile Crescent ~8000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation, and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4506 landraces and cultivars originating from 105 different countries genotyped with a high-density single-nucleotide polymorphism array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the appearance of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.

Tracing the ancestry of modern bread wheats.

For more than 10,000 years, the selection of plant and animal traits that are better tailored for human use has shaped the development of civilizations. During this period, bread wheat (Triticum aestivum) emerged as one of the world's most important crops. We use exome sequencing of a worldwide panel of almost 500 genotypes selected from across the geographical range of the wheat species complex to explore how 10,000 years of hybridization, selection, adaptation and plant breeding has shaped the genetic makeup of modern bread wheats.

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism.

During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat ( L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry ∼60-70% of the genes.

Exploiting the Repetitive Fraction of the Wheat Genome for High-Throughput Single-Nucleotide Polymorphism Discovery and Genotyping.

Transposable elements (TEs) account for more than 80% of the wheat genome. Although they represent a major obstacle for genomic studies, TEs are also a source of polymorphism and consequently of molecular markers such as insertion site-based polymorphism (ISBP) markers. Insertion site-based polymorphisms have been found to be a great source of genome-specific single-nucleotide polymorphism (SNPs) in the hexaploid wheat ( L.

Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model.

Prediction of wheat phenology facilitates the selection of cultivars with specific adaptations to a particular environment. However, while QTL analysis for heading date can identify major genes controlling phenology, the results are limited to the environments and genotypes tested. Moreover, while ecophysiological models allow accurate predictions in new environments, they may require substantial phenotypic data to parameterize each genotype.

Structural and functional partitioning of bread wheat chromosome 3B.

We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination.

Association study of wheat grain protein composition reveals that gliadin and glutenin composition are trans-regulated by different chromosome regions.

Wheat grain storage protein (GSP) content and composition are the main determinants of the end-use value of bread wheat (Triticum aestivum L.) grain. The accumulation of glutenins and gliadins, the two main classes of GSP in wheat, is believed to be mainly controlled at the transcriptional level through a network of transcription factors.

Rht-1 and Ppd-D1 associations with height, GA sensitivity, and days to heading in a worldwide bread wheat collection.

Reduced height (Rht)-1 and Photoperiod (Ppd) have major effects on the adaptability of bread wheat (Triticum aestivum) to specific environments. Ppd-D1a is a photoperiod insensitive allele that reduces time to flowering. The gibberellin (GA) insensitive alleles Rht-B1b and Rht-D1b shorten plant stature and were important components of the 'green revolution'.

Haplotype dictionary for the Rht-1 loci in wheat.

The introduction of Reduced height (Rht)-B1b and Rht-D1b into bread wheat (Triticum aestivum) varieties was a key component of the 'green revolution' and today these alleles are the primary sources of semi-dwarfism in wheat. The Rht-1 loci encode DELLA proteins, which are transcription factors that affect plant growth and stress tolerance. In bread wheat, Rht-D1b and Rht-B1b influence resistance to the disease Fusarium Head Blight.

Genomic regions associated with the nitrogen limitation response revealed in a global wheat core collection.

Modern wheat (Triticum aestivum L.) varieties in Western Europe have mainly been bred, and selected in conditions where high levels of nitrogen-rich fertilizer are applied. However, high input crop management has greatly increased the risk of nitrates leaching into groundwater with negative impacts on the environment.

Association mapping and haplotype analysis of a 3.1-Mb genomic region involved in Fusarium head blight resistance on wheat chromosome 3BS.

A previous study provided an in-depth understanding of molecular population genetics of European and Asian wheat gene pools using a sequenced 3.1-Mb contig (ctg954) on chromosome 3BS. This region is believed to carry the Fhb1 gene for response to Fusarium head blight.

Strong presence of the high grain protein content allele of NAM-B1 in Fennoscandian wheat.

Grain protein content in wheat has been shown to be affected by the NAM-B1 gene where the wildtype allele confers high levels of protein and micronutrients but can reduce yield. Two known non-functional alleles instead increase yield but lead to lower levels of protein and micronutrients. The wildtype allele in hexaploid bread wheat is so far mainly known from historical specimens and a few lines with an emmer wheat introgression.

Application of direct calibration in multivariate image analysis of heterogeneous materials.

Many scientific instruments produce multivariate images characterized by three-way tables, an element of which represents the intensity value at a spatial location for a given spectral channel. A problem frequently encountered is to attempt estimating the contributions of some compounds at each location of these images. Usual regression methods of calibration, such as PLS, require having a matrix of calibration X (n×p) and the corresponding vector y of the dependent variable (n×1).

Genome-wide association analysis to identify chromosomal regions determining components of earliness in wheat.

The modification of flowering date is considered an important way to escape the current or future climatic constraints that affect wheat crops. A better understanding of its genetic bases would enable a more efficient and rapid modification through breeding. The objective of this study was to identify chromosomal regions associated with earliness in wheat.

Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.).

Earliness is very important for the adaptation of wheat to environmental conditions and the achievement of high grain yield. A detailed knowledge of key genetic components of the life cycle would enable an easier control by the breeders. The objective of the study was to investigate the effect of candidate genes on flowering time.

Variation in crossover rates across a 3-Mb contig of bread wheat (Triticum aestivum) reveals the presence of a meiotic recombination hotspot.

In bread wheat (Triticum aestivum L.), initial studies using deletion lines indicated that crossover (CO) events occur mainly in the telomeric regions of the chromosomes with a possible correlation with the presence of genes. However, little is known about the distribution of COs at the sequence level.

Genetic diversity and linkage disequilibrium studies on a 3.1-Mb genomic region of chromosome 3B in European and Asian bread wheat (Triticum aestivum L.) populations.

Genetic diversity and linkage disequilibrium (LD) were investigated in 376 Asian and European accessions of bread wheat (Triticum aestivum L.). After a first and rapid screening about diversity and genetic structure at the whole genome scale using 70 simple sequence repeats (SSRs), we focused on a sequenced contig (ctg954) of 3.

Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat.

In wheat, the deployment of marker-assisted selection has long been hampered by the lack of markers compatible with high-throughput cost-effective genotyping techniques. Recently, insertion site-based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studies in hexaploid wheat. To demonstrate their possible use in wheat breeding programmes, we assessed their potential to meet the five main requirements for utilization in MAS: flexible and high-throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material.

[Genetic differentiation of hexaploid wheat inferred from analysis of microsatellite loci].

Landraces of wheat can serve as important potential sources for extending the genetic basis of selection cultivars. Analysis of microsatellites and typing of polymorphism in a representative sample of 347 genotypes, including landraces and selection cultivars, was performed using a set of 38 selected oligonucleotide primer pairs. Classification of genotypes with respect to the level of their similarity was performed using cluster analysis.

Evaluation of the genetic variability of homoeologous group 3 SSRs in bread wheat.

Thorough characterization of the genetic variability in bread wheat (Triticum aestivum L.) is important for a better improvement of this key crop and to increase cereal yield in the context of sustainable agriculture to face human needs in the next decades. To study the genetic variability of SSRs on wheat homoeologous group 3 chromosomes, we characterized 38 hexaploid and two tetraploid wheat lines using a set of 165 microsatellites that we cytogenetically assigned to the 17 deletion bins for chromosomes group 3.