Malcolm Macaulay

• James Hutton Institute

In the last century, breeding programs have traditionally favoured yield-related traits, grown under high-input conditions, resulting in a loss of genetic diversity and an increased susceptibility to stresses in crops. Thus, exploiting understudied genetic resources, that potentially harbour tolerance genes, is vital for sustainable agriculture. No...

Using a positional candidate-gene approach we show that semi-sterile desynaptic8 mutants are associated with deletions in or complete knockout of the barley homolog of XRCC2 ( X-Ray Repair Cross Complementing 2 ). In barley XRCC2 mutants, the initial meiotic progression is normal, albeit with a small delay in initiation, with completion of synapsis...

During meiosis, genetic recombination occurs via repair of DNA double-strand breaks (DSBs) as crossovers (COs) resulting in the exchange of parental genetic material (De Muyt et al., 2009). Crossovers are important for chromosome segregation and shuffling genetic variation, but their number and distribution are tightly regulated (Zickler and Kleckn...

Plant breeding relies on the meiotic recombination or crossing over to generate the new combinations of the alleles along and among the chromosomes. However, crossing over is constrained in the crops such as barley by a combination of the low frequency and biased distribution. In this study, we attempted to identify the genes that limit the recombi...

Programmed meiotic DNA double-strand breaks (DSBs), necessary for proper chromosomal segregation and viable gamete formation, are repaired by homologous recombination (HR) as crossovers (COs) or non-crossovers (NCOs). The mechanisms regulating the number and distribution of COs are still poorly understood. The regulator of telomere elongation helic...

In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialized reproductive development program we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytological...

Key message: Historical malting quality data was collated from UK national and recommended list trial data and used in a GWAS. 25 QTL were identified, with the majority from spring barley cultivar sets. In Europe, the most economically significant use of barley is the production of malt for use in the brewing and distilling industries. As such, se...

During plant growth, sodium (Na⁺) in the soil is transported via the xylem from the root to the shoot. While excess Na⁺ is toxic to most plants, non-toxic concentrations have been shown to improve crop yields under certain conditions, such as when soil K⁺ is low. We quantified grain Na⁺ across a barley genome-wide association study panel grown unde...

In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialised reproductive development programme we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologic...

In barley (Hordeum vulgare L.), Agrobacterium-mediated transformation efficiency is highly dependent on genotype with very few cultivars being amenable to transformation. Golden Promise is the cultivar most widely used for barley transformation and developing embryos are the most common donor tissue. We tested whether barley mutants with abnormally...

Gramine is an indole alkaloid found in certain grass species. Results of previous studies have diverged as to whether this compound might cause resistance to aphids or not. In a breeding program aiming to introduce resistance to the cereal pest Rhopalosiphum padi L. in barley, a cultivar has been crossed with the progenitor of cultivated barley, Ho...

We quantified grain sodium (Na+) content across a barley GWAS panel grown under optimal conditions. We identified a strong association with a region containing two low and one high Na+ accumulating haplotypes of a Class 1 HIGH-AFFINITY POTASSIUM TRANSPORTER (HKT1;5) known to be involved in regulating plant Na+ homeostasis. The haplotypes exhibited...

Determining when a barley plant starts and finishes meiosis is not trivial as when the spikelets undergo meiosis, the spike is not visible as it is still well within the leaf sheath on the developing tiller. This is a general constraint for any experiment involving meiosis, such as cytology, RNA extractions, or abiotic stress treatments aiming to t...

In barley (Hordeum vulgare L.), Agrobacterium-mediated transformation efficiency is highly dependent on genotype with very few cultivars being amenable to transformation. Golden Promise is the cultivar most widely used for barley transformation and developing embryos are the most common donor tissue. We tested whether barley mutants with abnormally...

Background: We developed and characterised a highly mutagenised TILLING population of the barley (Hordeum vulgare) cultivar Golden Promise. Golden Promise is the 'reference' genotype for barley transformation and a primary objective of using this cultivar was to be able to genetically complement observed mutations directly in order to prove gene f...

Despite conservation of the process of meiosis, recombination landscapes vary between species, with large genome grasses such as barley (Hordeum vulgare L.) exhibiting a pattern of recombination that is very heavily skewed to the ends of chromosomes. We have been using a collection of semi-sterile desynaptic meiotic mutant lines to help elucidate h...

We compared the performance of two commonly used genotyping platforms, genotyping-by-sequencing (GBS) and single nucleotide polymorphism-arrays (SNP), to investigate the extent and pattern of genetic variation within a collection of 1,000 diverse barley genotypes selected from the German Federal ex situ GenBank hosted at IPK Gatersleben. Each platf...

Key message Association analyses of resistance to Rhynchosporium commune in a collection of European spring barley germplasm detected 17 significant resistance quantitative trait loci. The most significant association was confirmed as Rrs1. Abstract Rhynchosporium commune is a fungal pathogen of barley which causes a highly destructive and economi...

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 cap...

List of the 170 barley lines used for variant discovery.

List of physical positions for the SNP markers on the 50k chip.

Genetic map of the Golden Promise × Morex cross population genotyped with the new 50k chip.

We used the ‘Baronesse’/‘Full Pint’ doubled haploid population to analyse the genetic factors controlling flowering date under South American conditions. Both parents have similar heading dates, but the population shows transgressive segregation. Two genes, eps2S on chromosome 2H and sdw1 on chromosome 3H, explained most of the phenotypic variation...

Key message: Awn length was mapped using a multiparent population derived from cv. Morex and four wild accessions. One QTL was fine mapped and candidate genes were identified in NILs by RNA-seq. Barley awns are photosynthetically active and contribute to grain yield. Awn length is variable among both wild and cultivated barley genotypes and many m...

Although meiosis is evolutionarily conserved, many of the underlying mechanisms show species‐specific differences. These are poorly understood in large genome plant species such as barley ( Hordeum vulgare ) where meiotic recombination is very heavily skewed to the ends of chromosomes. The characterization of mutant lines can help elucidate how rec...

Genetic diversity among rice cultivars from Bangladesh and North East India was assessed using a custom 384-SNP microarray assay. A total of 511 cultivars were obtained from several sources, choosing landraces likely to be from the aus subpopulation and modern improved cultivars from Bangladesh. Cultivars from the OryzaSNP set and Rice Diversity Pa...

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...

The crop management practice of alternate wetting and drying (AWD) is being promoted by IRRI and the national research and extension program in Bangladesh and other parts of the world as a water-saving irrigation practice that reduces the environmental impact of dry season rice production through decreased water usage, and potentially increases yie...

The geographic distribution of genetic diversity can reveal the evolutionary history of a species. For crop plants, phylogeographic patterns also indicate how seed has been exchanged and spread in agrarian communities. Such patterns are, however, easily blurred by the intense seed trade, plant improvement and even genebank conservation during the t...

Waterlogging is a major factor limiting barley grain yield worldwide. Climate change will likely increase this water stress in Northern Europe. Breeding for waterlogging tolerance (WLT), as for other abiotic stresses, is difficult, but identification of genetic markers linked to genes affecting WLT could facilitate the breeding process. To identify...

Author Summary The majority of eukaryotes reproduce via a specialized cell division called meiosis, which generates gametes with half the number of chromosomes. During meiosis, homologous chromosomes pair and undergo a process of reciprocal exchange, called crossing-over (CO), which generates new combinations of genetic variation. The relative cha...

Flow cytometry analysis of I1b QRT1 pollen fluorescence. (A) Schematic diagram showing homologous chromosomes (black lines) heterozygous for cis-linked FTL-eYFP (green triangles) and FTL-DsRed (red triangles) transgenes segregating through meiosis-I and –II in the absence (left) or presence (right) of a crossover (CO) between the transgenes. (B) Mi...

Pollen-typing analysis of 3a. (A) Schematic diagram illustrating pollen-typing strategy. Black lines represent the chromosome with Col and Ler polymorphisms indicated by white or black circles respectively. Nested amplifications using allele-specific primers (arrows) are performed to amplify parental or CO molecules as indicated. (B) Ethidium bromi...

Maps of cM/Mb, gene, repeat and DNA methylation, LND and H3K4me3 densities throughout the A. thaliana genome. The coordinates correspond to those of the merged genetic map. The CEN column indicates whether an interval is located in the pericentromeres (Y) or chromsome arms (N). (XLSX)

Total genetic map length in wild type and met1–3. The upper sub-table shows crossover numbers (COs) observed in wild type and met1–3 recombinants per chromosome and total. The lower sub-table shows the number of double CO pairs (DCOs) observed in each population and the average inter-CO distance (bp) for each chromosome and the whole genome. (DOCX)

MLH1 counts in wild type and met1–3−/−. Summary of MLH1 counts showing number of meiocytes (N) scored for Col and met1–3−/− genotypes at diplotene and diakinesis meiotic stages. The p-value from the model fitted using the R glm function compares Col and met1–3−/− at equivalent stages. The goodness-of-fit of the count data with the Poisson distribut...

Seed scoring data for 420 Col/Col homozygotes. (G+R)/Total = Rf. (1-SQRT(1–2*Rf))*100 = cM. (DOCX)

Supplemental Experimental Procedures. Additional experimental methods for recombination map analysis, flow cytometry of I1b QRT1 FTL pollen, and pollen-typing analysis of the 3a hotspot. (DOCX)

Physical and genetic dimensions of the A. thaliana genome. Gene and repeat annotations were downloaded from the TAIR10 genome release. Genetic map lengths (cM) are from (1) Col×Ler male backcross (Giraut et al., 2011) [21], (2) Col×Ler female backcross (Giraut et al., 2011) [21], (3) sex averaged map (Giraut et al., 2011) [21], and (4) merged genet...

Oligonucleotides used for dCAPs markers and 3a pollen typing. Where relevant the Col/Ler polymorphisms are listed, in addition to being highlighted in the allele-specific PCR primers. Red indicates Col-specific polymorphisms and blue indicates Ler-specific polymorphisms. Green indicates mismatches added to both primer variants and underlined cytosi...

Tetrad scoring data for CEN3 qrt1. NPD = non-parental ditype, T = tetratype. Map distance (cM) = (100 (6N+T))/(2(P+N+T)). Standard error of cM (S.E.) = Sqrt(0.25Var[T/Total]+9Var[N/Total]+3Cov[T/Total,N/Total]). Standard deviation of map distances in each genotype group (S.D.). (DOCX)

Tetrad scoring data for I1b qrt1. NPD = non-parental ditype, T = tetratype. Map distance (cM) = (100 (6N+T))/(2(P+N+T)). Standard error of cM (S.E.) = Sqrt(0.25Var[T/Total]+9Var[N/Total]+3Cov[T/Total,N/Total]). Standard deviation of map distances in each genotype group (S.D.). (DOCX)

Seed scoring data for 420 Col/Ler heterozygotes. Fisher's exact test p-value given for differences between *wild type male and female (Col/Col), **wild type male and female (Col/Ler) and ***wild type male and met1 male (Col/Ler). (DOCX)

Gene, transposon, and cM/Mb frequencies within the 420 interval. (DOCX)

Crossover distributions within 3a identified by pollen-typing. SNP positions highlighted in red are iden tical to polymorphisms used to design 420 interval 8 dCAPs markers 774 and 775. (DOCX)

Meiosis is a specialized eukaryotic cell division that generates haploid gametes required for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover (CO). Meiotic CO frequency varies along the physical length of chromosomes and is determined by hierarchical mechanisms, including ep...

A typical barley (Hordeum vulgare) floret consists of reproductive organs three stamens and a pistil, and non-reproductive organs-lodicules and two floral bracts, abaxial called 'lemma' and adaxial 'palea'. The floret is subtended by two additional bracts called outer or empty glumes. Together these organs form the basic structural unit of the gras...

Traits associated with resistance to R. commune were investigated in a mapping population from a cross between a winter and spring barley. In addition, its ancestral lines were studied using GFP-expressing R. commune isolates and confocal microscopy. Visible disease symptoms were closely associated with independent measures of pathogen growth. Howe...

GenBank staff is unable to verify sequence and/or annotation provided by the submitter.

GenBank staff is unable to verify sequence and/or annotation provided by the submitter.

GenBank staff is unable to verify sequence and/or annotation provided by the submitter.

In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognized as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars, two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In thi...

The genetic basis of several different components of resistance to Rhynchosporium secalis in barley was investigated in a mapping population derived from a cross between winter and spring barley types. Both the severity of visual disease symptoms and amount of R. secalis DNA in leaf tissues were assessed in field trials in Scotland in the 2007/2008...

The domestication of cereals has involved common changes in morphological features, such as seed size, seed retention and modification of vegetative and inflorescence architecture that ultimately contributed to an increase in harvested yield. In barley, this process has resulted in two different cultivated types, two-rowed and six-rowed forms, both...

The identification of genes underlying complex quantitative traits such as grain yield by means of conventional genetic analysis (positional cloning) requires the development of several large mapping populations. However, it is possible that phenotypically related, but more extreme, allelic variants generated by mutational studies could provide a m...

Breeding progress in barley yield in the UK is being sustained at a rate in the order of 1% per annum against a background of declining seed sales. Commercial barley breeders are largely concentrating upon the elite local gene pool but with genotypic evidence suggesting that there is still considerable variation between current recommended cultivar...

We have developed a ’genotyping set’ of 48 SSR-based genetic markers for application in genetical studies of barley. The SSRs are a subset of a collection of approximately 600 SSRs available to the barley research community. They have been specifically chosen according to the following criteria: (1) they are single locus; (2) their product quality...

A total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence repeats. Analysis of the SSRs on 16 barley cultivars revealed variable levels of informativeness but no obvious correlation was found w...

The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeats. The average frequency of SSR...

Simple sequence repeat (SSR)-based genetic markers are being actively developed for the majority of crop plant species. In barley, characterization of 290 dinucleotide repeat-containing clones from SSR-enriched libraries has revealed that a high percentage are associated with cereal retrotransposon-like and other dispersed repetitive elements. Asso...

Eleven microsatellite loci were used to survey 24 barley genotypes representing 23 cultivars and a breeding line in official trials. Three separate combinations of four microsatellites had overall probabilities of identity of less than 1 in 1000 and could distinguish between all 24 barley genotypes. It is shown that the microsatellites could distin...