L. Cistué

An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

Recent advances in high‐throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a single nucleotide polymorphism (SNP)‐based genotyping platform was developed and used to genotype 373 individuals in four barley (Hordeum vulgare L.) mapping populations. This led to a 2943 SNP consensus genetic map with 975 unique positions. In this work, we add data from six additional populations and more individuals from one of the original populations to develop an improved consensus map from 1133 individuals. A stringent and systematic analysis of each of the 10 populations was performed to achieve uniformity. This involved reexamination of the four populations included in the previous map. As a consequence, we present a robust consensus genetic map that contains 2994 SNP loci mapped to 1163 unique positions. The map spans 1137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform for gene detection allowed the assignment of 2930 genes to flow‐sorted chromosomes or arms, confirmed the position of 2545 SNP‐mapped loci, added chromosome or arm allocations to an additional 370 SNP loci, and delineated pericentromeric regions for chromosomes 2H to 7H. Marker order has been improved and map resolution has been increased by almost 20%. These increased precision outcomes enable more optimized SNP selection for marker‐assisted breeding and support association genetic analysis and map‐based cloning. It will also improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.

Somatic embryogenesis and plant regeneration from barley cultivars grown in Spain

Abstract Thirty-two barley cultivars grown in Spain, 18 of the two-row type and 14 of the six-row type, were screened for plant regeneration from cultured immature embryos. Although there was much variation in regeneration capacity among the cultivars, plants were obtained from all cultivars except Almunia. No statistical differences were found in the percentage of regeneration between two- and six-row types. The influence of the auxins 2,4-dichlorophenoxyacetic acid, dicamba, and picloram on the induction and maintenance of embryogenesis and regeneration capacity after 3–4 months in culture, were evaluated for cultivars Cobra, Hop and Reinette. Hop had the highest rates of maintenance of embryogenic capacity and plant regeneration. The medium containing dicamba gave the best embryogenic callus induction, maintenance and regeneration. Five regeneration media, differing in growth regulators and micronutrient composition, as well as partial desiccation of the calli before regeneration, were tested. The regeneration medium containing 10 μm copper sulfate gave the best results. Regeneration frequencies after 3–4 months in culture of cultivar Hop were raised from 59.5 to 93.7% in this medium. Silver nitrate and partial desiccation of the calli also enhanced plant regeneration, but the medium containing 10 μm of silver nitrate reduced root formation.

Production of large number of doubled haploid plants from barley anthers pretreated with high concentrations of mannitol.

Pretreatment with increasing concentrations of mannitol, from 0.3 to 0.7 M, was used to induce stress in cultured anthers of barley (Hordeum vulgare L.). Three cultivars with varying degrees of androgenetic ability were studied. A positive linear relationship was found between concentration of mannitol in the pretreatment medium and the number of regenerated green doubled haploid plants in all the cultivars. The pretreatment also resulted in an increasing proportion of embryos to dividing microspores, and in green to albino plantlets. The optimum length of the pretreatment seemed to be genotype dependent. When Ficoll was used as an alternative stress agent a differential genotype response was observed.

Comparison of anther and isolated microspore cultures in barley: effects of culture density and regeneration medium

A comparison of anther and microspore culture efficiency for green doubled haploid plant production was undertaken using 17 F1 crosses with potential agronomic performance. Green doubled haploid plants were produced from all F1 crosses by anther and microspore cultures, although there was a great variation among crosses. On average, anther culture resulted in a production of green plant twice that of isolated microspore culture (30 and 14 greenplants/100 anthers, respectively).The effect of microspore culture density on green plant regeneration was studied with the cultivars Igri, Reinette and Hop which have a high, medium and low androgenic response. The highest number of dividing microspores was obtained at a density of 2.4 ×105 viable microspores/ml for the three cultivars. However, the optimal density for the percentage of embryos/dividing microspores and greenplants/103 microspores depended on the cultivar. The highest number of green plants/103microspores was produced at 1.2 × 105 viable microspores/ml for cv. Igri and 2.4 × 105 for cultivars Reinette and Hop. Percentage of green plants/total plants was raised when the culture density was increased up to 6.0 × 105 viable microspores/ml, especially for cv. Reinette. Six regeneration media differing in maltose concentration, organic nitrogen and type of auxin were assayed with embryos from cultivar Reinette. Media without organic nitrogen containing 31 g l-1maltose and the auxins IAA or NAA produced more vigorous green plants.

Influence of anther pretreatment and culture medium composition on the production of barley doubled haploids from model and low responding cultivars

Different pretreatments were given to anthers of barley before culturing, and their effects assessed on the frequency of embryos and green doubled haploid plants produced. Mannitol pretreatment was better than cold pretreatment for some low responding cultivars. Optimal concentration of mannitol for pretreatment depended on cultivar. Low responding genotypes needed a higher concentration of mannitol than responsive ones. The addition of Ficoll to liquid medium increased the number of embryos and green plants. The influence of the growth regulators 2,4-D and TIBA was assayed using ten cultivars of barley grown in Spain. The anti-auxin TIBA gave good embryo production with some of the low responding cultivars. Two row-type cultivars always produced higher number of embryos and green plantlets than six row-type. The application of these modifications to 10 F1 hybrids with potential agronomic value, allowed the production of almost 1000 doubled haploid plants from only 3500 anthers. Up to two doubled haploid plants per flower were produced from the cross Monlon × Sonja.

Efficient production of androgenic doubled-haploid mutants in barley by the application of sodium azide to anther and microspore cultures

Abstract The aim of this study was to establish a protocol for an efficient production of agronomical and/or physiological mutants from model (cvs. Igri and Cobra) and low-androgenic-responding (cv. Volga) cultivars of barley through the application of a mutagenic agent, sodium azide, to anthers and isolated microspores cultured in vitro. This technology offers the possibilities of screening for recessive mutants in the first generation, selecting for novel genotypes from very large haploid populations, avoiding chimerism and rapidly fixing selected genotypes as fertile true breeding lines. The mutagenic treatment, 10–3–10–5 M sodium azide, was applied during the anther induction pre-treatment or immediately after the microspore isolation procedure. Out of 616 M2 doubled-haploid lines characterised under field conditions, a total of 63 morphological and developmental independent mutant lines were identified. The percentage of M2 doubled-haploid lines carrying mutations per line analysed was 3.8% when 10–4 M sodium azide was applied to anthers from the low-responding cv. Volga; this increased to 8.6% and 15.6% when 10–5 and 10–4 M sodium azide were applied to freshly isolated microspores from model cultivars.

Use of new EST markers to elucidate the genetic differences in grain protein content between European and North American two-rowed malting barleys.

A population comprising 102 doubled haploid lines were produced from a cross between Beka, a barley cultivar widely grown in Spain, and Logan, a north American cultivar with inherently low protein content, a character considered to derive from the cultivar Karl. The intentions were to determine whether low-nitrogen malting barleys could be developed in Spain, and if genetic factors that influenced protein content were similarly expressed in widely diverse environments, i.e. northeastern Spain and eastern Scotland. An extensive map comprising 187 molecular markers was developed. Expressed sequence-tagged-derived markers were used in addition to anonymous simple sequence repeats to determine the potential for identifying candidate genes for quantitative trait loci (QTLs), and 22 such markers were mapped for the first time. There was transgressive segregation for both yield and protein content, and the gene for low protein from Logan was not expressed in the Scottish environment. In 2002, high yield was associated with earlier heading date in Spain, while late heading at the Scottish site was associated with greater lodging and lower thousand-kernel weight. These appeared to be possible pleiotropic effects of a factor detected on chromosome 2H. Using information from a consensus map, it was shown that this locus on 2H was in the region of the photoperiod response gene Eam6. A QTL explaining 18% of the variation in grain protein content was detected on chromosome 5H in a region in which a gene for nitrate reductase was previously observed. No effect on grain protein was associated with chromosome 6H, which has been suggested as the location of the low protein gene from Karl. However, it is likely that Karl contained more than one genetic factor reducing protein, and we postulate that the gene on 6H may have been lost during the breeding of Logan.

Genetic markers for doubled haploid response in barley

In order to analyse the genetic control of anther culture response in barley, a doubled-haploid (DH) population from the cross between a medium responsive cultivar ‘Dobla’ and the model cultivar ‘Igri’ was produced. A linkage map was constructed with 91 markers. A sub-population of 41 lines was characterised for different components of the anther culture response, and was used for quantitative trait loci (QTL) analysis. The vrs1 locus region on chromosome 2H, which determines inflorescence row type, was coincident with the largest putative QTL for number of embryos (nEMB) and albino plants. A region of chromosome 6H was associated with QTLs for nEMB and green plants. QTLs for number and percentage of green plants were located on the long arm of chromosome 5H. Therefore, new QTLs for main components of barley anther culture response were identified on chromosomes 2H, 5H and 6H, indicating that anther culture response in barley could be controlled by relative few genes of large effect. This work is a useful step towards the identification of new regions on the barley genome that could be associated with fundamental biological process implicated in the anther culture response.

Chromosome Doubling in Monocots

The development of efficient chromosome doubling protocols is essential for the useful application of doubled haploid (DH) plants in breeding programs, since frequency of spontaneous doubling is most of the time too low. Chromosome doubling has been traditionally applied to plantlets, being the colchicine the most widely anti-microtubule agent used in vivo and in vitro. However during the last 15 years, protocols have been developed for the incorporation of different anti-microtubule agents during the early stages of androgenesis or gynogenesis. Factors affecting frequencies of spontaneous and induced chromosome doubling are summarized. For a successful chemical induction, a compromise between toxicity (which can result from high concentration and/or long time of application) and genome doubling efficiency should be adopted in order to obtain the highest number of green DH plants.

Linkage map construction involving a reciprocal translocation

This paper is concerned with a novel statistical–genetic approach for the construction of linkage maps in populations obtained from reciprocal translocation heterozygotes of barley (Hordeum vulgare L.). Using standard linkage analysis, translocations usually lead to ‘pseudo-linkage’: the mixing up of markers from the chromosomes involved in the translocation into a single linkage group. Close to the translocation breakpoints recombination is severely suppressed and, as a consequence, ordering markers in those regions is not feasible. The novel strategy presented in this paper is based on (1) disentangling the “pseudo-linkage” using principal coordinate analysis, (2) separating individuals into translocated types and normal types and (3) separating markers into those close to and those more distant from the translocation breakpoints. The methods make use of a consensus map of the species involved. The final product consists of integrated linkage maps of the distal parts of the chromosomes involved in the translocation.