Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial ...closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
913 I. 913 II. 915 III. 917 IV. 919 V. 922 VI. 926 927 References 927 SUMMARY: Barley (Hordeum vulgare ssp. vulgare) is an excellent model for understanding agricultural responses to climate change. ...Its initial domestication over 10 millennia ago and subsequent wide migration provide striking evidence of adaptation to different environments, agro‐ecologies and uses. A bottleneck in the selection of modern varieties has resulted in a reduction in total genetic diversity and a loss of specific alleles relevant to climate‐smart agriculture. However, extensive and well‐curated collections of landraces, wild barley accessions (H. vulgare ssp. spontaneum) and other Hordeum species exist and are important new allele sources. A wide range of genomic and analytical tools have entered the public domain for exploring and capturing this variation, and specialized populations, mutant stocks and transgenics facilitate the connection between genetic diversity and heritable phenotypes. These lay the biological, technological and informational foundations for developing climate‐resilient crops tailored to specific environments that are supported by extensive environmental and geographical databases, new methods for climate modelling and trait/environment association analyses, and decentralized participatory improvement methods. Case studies of important climate‐related traits and their constituent genes – including examples that are indicative of the complexities involved in designing appropriate responses – are presented, and key developments for the future highlighted.
Elite cultivated crop gene pools of the Triticeae tribe (wheat, barley and rye) exhibit limited genetic diversity, raising concerns about our ability to increase or simply sustain crop yield and ...quality in the face of dynamic environmental and biotic threats. Although exploiting their wild relatives as a source of novel alleles is challenging, it has provided notable successes in cereal improvement for >100 years. Increasingly facile gene discovery, improved enabling technologies for genetics and breeding and a better understanding of the factors limiting practical exploitation of exotic germplasm promise to transform existing, and accelerate the development of new, strategies for efficient and directed germplasm utilization.
High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for ...barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation. Markers from an existing and widely used barley 9k Infinium iSelect array were carried over onto the 50k chip for backward compatibility. The array design featured 49,267 SNP markers that converted into 44,040 working assays, of which 43,461 were scorable in GenomeStudio. Of the working assays, 6,251 are from the 9k iSelect platform. We validated the SNPs by comparing the genotype calls from the new array to legacy datasets. Rates of agreement averaged 98.1 and 93.9% respectively for the legacy 9k iSelect SNP set (Comadran et al., 2012) and the exome capture SNPs. To test the utility of the 50k chip for genetic mapping, we genotyped a segregating population derived from a Golden Promise × Morex cross (Liu et al., 2014) and mapped over 14,000 SNPs to genetic positions which showed a near exact correspondence to their known physical positions. Manual adjustment of the cluster files used by the interpreting software for genotype scoring improved results substantially, but migration of cluster files between sites led to a deterioration of results, suggesting that local adjustment of cluster files is required on a site-per-site basis. Information relating to the markers on the chip is available online at https://ics.hutton.ac.uk/50k.
As early farming spread from the Fertile Crescent in the Near East around 10,000 years before the present, domesticated crops encountered considerable ecological and environmental change. Spring-sown ...crops that flowered without the need for an extended period of cold to promote flowering and day length-insensitive crops able to exploit the longer, cooler days of higher latitudes emerged and became established. To investigate the genetic consequences of adaptation to these new environments, we identified signatures of divergent selection in the highly differentiated modern-day spring and winter barleys. In one genetically divergent region, we identify a natural variant of the barley homolog of Antirrhinum CENTRORADIALIS (HvCEN) as a contributor to successful environmental adaptation. The distribution of HvCEN alleles in a large collection of wild and landrace accessions indicates that this involved selection and enrichment of preexisting genetic variants rather than the acquisition of mutations after domestication.
Barley (Hordeum vulgare) is a crop of global significance. However, a third of the genes of barley are largely inaccessible to conventional breeding programmes as crossovers are localised to the ends ...of the chromosomes. This work examines whether crossovers can be shifted to more proximal regions simply by elevating growth temperature.
We utilised a genome-wide marker set for linkage analysis combined with cytological mapping of crossover events to examine the recombination landscape of plants grown at different temperatures.
We found that barley shows heterochiasmy, that is, differences between female and male recombination frequencies. In addition, we found that elevated temperature significantly changes patterns of recombination in male meiosis only, with a repositioning of Class I crossovers determined by cytological mapping of HvMLH3 foci. We show that the length of synaptonemal complexes in male meiocytes increases in response to temperature.
The results demonstrate that the distribution of crossover events are malleable and can be shifted to proximal regions by altering the growth temperature. The shift in recombination is the result of altering the distribution of Class I crossovers, but the higher recombination at elevated temperatures is potentially not the result of an increase in Class I events.
Abstract
A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between ...roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the
QRMC-3HS
, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at
QRMC-3HS
and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (
NLR
) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant’s capacity of shaping rhizosphere microbes.
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we ...derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.
Soil salinity imposes an agricultural and economic burden that may be alleviated by identifying the components of salinity tolerance in barley, a major crop and the most salt tolerant cereal. To ...improve our understanding of these components, we evaluated a diversity panel of 377 two-row spring barley cultivars during both the vegetative, in a controlled environment, and the reproductive stages, in the field. In the controlled environment, a high-throughput phenotyping platform was used to assess the growth-related traits under both control and saline conditions. In the field, the agronomic traits were measured from plots irrigated with either fresh or saline water. Association mapping for the different components of salinity tolerance enabled us to detect previously known associations, such as HvHKT1;5. Using an “interaction model”, which took into account the interaction between treatment (control and salt) and genetic markers, we identified several loci associated with yield components related to salinity tolerance. We also observed that the two developmental stages did not share genetic regions associated with the components of salinity tolerance, suggesting that different mechanisms play distinct roles throughout the barley life cycle. Our association analysis revealed that genetically defined regions containing known flowering genes (Vrn-H3, Vrn-H1, and HvNAM-1) were responsive to salt stress. We identified a salt-responsive locus (7H, 128.35 cM) that was associated with grain number per ear, and suggest a gene encoding a vacuolar H+-translocating pyrophosphatase, HVP1, as a candidate. We also found a new QTL on chromosome 3H (139.22 cM), which was significant for ear number per plant, and a locus on chromosome 2H (141.87 cM), previously identified using a nested association mapping population, which associated with a yield component and interacted with salinity stress. Our study is the first to evaluate a barley diversity panel for salinity stress under both controlled and field conditions, allowing us to identify contributions from new components of salinity tolerance which could be used for marker-assisted selection when breeding for marginal and saline regions.
The cereal grass barley was domesticated about 10,000 years before the present in the Fertile Crescent and became a founder crop of Neolithic agriculture. Here we report the genome sequences of five ...6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole-exome sequence data from a diversity panel of present-day barley accessions showed the close affinity of ancient samples to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel have not experienced major lineage turnover over the past six millennia, although there is evidence for gene flow between cultivated and sympatric wild populations. We demonstrate the usefulness of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species.
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