What is PpdH2 doing in winter varieties?

1 .pdf copy (A3) of the original poster presented by the Authors.Temperatures during barley growing season have been on the rise in the Mediterranean basin over the last 40 years. Under these circumstances, winter cereal farmers are exposed to a difficult choice of cultivars for autumn sowing, from spring cultivars in warm areas to strictly winter cultivars. The choice must take into account frost probability for the region. The most common process found in winter cereals to achieve frost tolerance is vernalization, although high frost tolerance can also be attained in cultivars almost devoid of vernalization requirement. We have carried out an experiment with winter barley subjected to insufficient vernalization to test the influence of allelic diversity at genes HvFT1 (VrnH3) and HvFT3 (PpdH2) on development. The experiment used selected plants of the population Esterel x SBCC016, grown in growth chambers. Three F4 lines of each of the four haplotypes determined by HvFT1 and HvFT3, selected with markers, were tested under three different day lengths, 8, 12 and 16h light. The plants were deliberately chosen to be strictly winter types). They were partially vernalized (45 days) before being transferred to the day length chambers, to test the performance of the haplotypes under conditions close to the natural target of the study. The plants showed a large range of duration of development and other phenotypic traits in response to day length, but also between the genetic haplotypes tested. The relationship of the phenotypic development with the expression levels of genes HvFT1, HvFT3, VrnH1 and VrnH2 will be presented and discussed, together with possible agronomic implications. Flowering time is closely related to HvFT1 expression, which seems controlled by a balance between its positive regulator VrnH1 and its well-known repressor VrnH2, but also by an epistatic interaction between VrnH2 and HvFT3, with further implications on tillering.Peer reviewe

Natural variation in FLOWERING LOCUS T, HvFT1

1 .pdf copy (A3) of the original poster presented by the Authors.The barley ortholog of FLOWERING LOCUS T, HvFT1, also called VrnH3, is the main integrator of the photoperiod and vernalization signals leading to the transition from the vegetative to the reproductive stage. Results gathered by us and other groups for the last years have repeatedly identified variation in this gene related with flowering time QTL in mapping populations and also in genome wide association studies. Differences in the promoter, SNPs in the first intron and also copy number variation have all being associated with phenotypic and expression differences, resulting in earlier or later heading. The first reports found that mutations in the HvFT1 first intron differentiated plants with dominant and recessive alleles, with large phenotypic effect on time to flowering. The catalog of polymorphisms at this gene with potential phenotypic effect has been enlarged with copy number variation and sequence variation at the promoter. There is variation in the number of copies of the HvFT1 gene, apparently related to growth habit. A large set of winter genotypes, with a functional VrnH2 allele, has one copy of VrnH3, whereas variable number (1-5), was found in also a large set of spring or facultative barleys (without VrnH2). The dominant VrnH3 allele, which overrides the vernalization requirement of winter VrnH1 and VrnH2 alleles, is found only in Nordic barleys and carries a particular structure of the gene, with one promoter and variable number of transcribed regions. Using two indels from the promoter region and allele-specific markers for two SNPs in the first intron, we were able to classify four VrnH3 haplotypes, which showed differences in heading time among Spanish landraces. We will present results from several mapping populations and association analyses to contribute to describe the different polymorphisms that should be taken into consideration when analyzing this gene and its phenotypic effects.Peer reviewe

Joint analysis for heading date QTL in small interconnected barley populations

42 Pag., 5 Tabl., 4 Fig. The definitive version is available at: http://www.springer.com/life+sciences/plant+sciences/journal/11032The purpose of the present work is to validate the effect of the main QTL determining heading date in a set of 281 doubled haploid lines of barley, derived from 17 small interconnected populations, whose parents are cultivars commonly used in the Spanish barley breeding program. We used 72 molecular markers distributed across the seven chromosomes, particularly in regions known to contain flowering time genes or QTL. A combined linkage map over the 17 populations was constructed. The lines were evaluated in four field trials: two autumn sowings and two winter sowings, and in two treatments at a greenhouse trial, under controlled conditions of photoperiod and temperature. We have found that it is possible to carry out QTL detection in a complex germplasm set, representative of the materials used in an active breeding programme. In most cases two alleles per QTL were detected, though polymorphism of flanking markers was notably higher. The results revealed that there is a set of QTL that accounts for an important percentage of the phenotypic variation, suitable for marker assisted selection. Also, the role of the regions carrying the photoperiod response genes Ppd-H1 and Ppd-H2, the vernalization response genes Vrn-H1 and Vrn-H2, and the earliness per se locus Eam6, of which allele-specific or closely linked markers were available, was confirmed. These results support the use of this kind of approach for the validation of QTL found in single cross population studies, or to survey allelic diversity in plant breeding sets of materials.This work was supported by the Spanish Ministry of Education and Research (Projects AGL2001-2289, including a scholarship granted to Mr. Alfonso Cuesta-Marcos, and AGL2004-05311) and by the European Regional Development Fund.Peer reviewe

Expression analysis of vernalization and day-length response genes in barley (Hordeum vulgare L.) indicates that VRNH2 is a repressor of PPDH2 (HvFT3) under long days

38 Pag., 1 Tabl., 6 Fig.The response to vernalization and the expression of genes associated with responses to vernalization (VRNH1, VRNH2, and VRNH3) and photoperiod (PPDH1 and PPDH2) were analysed in four barley (Hordeum vulgare L.) lines: ‘Alexis’ (spring), ‘Plaisant’ (winter), SBCC058, and SBCC106 (Spanish inbred lines), grown under conditions of vernalization and short days (VSD) or no vernalization and long days (NVLD). The four genotypes differ in VRNH1. Their growth habits and responses to vernalization correlated with the level of expression of VRNH1 and the length of intron 1. ‘Alexis’ and ‘Plaisant’ behaved as expected. SBCC058 and SBCC106 showed an intermediate growth habit and flowered relatively late in the absence of vernalization. VRNH1 expression was induced by cold for all genotypes. Under VSD, VRNH1 expression was detected in the SBCC genotypes later than in ‘Alexis’ but earlier than in ‘Plaisant’. VRNH2 was repressed under short days while VRNH1 expression increased in parallel. VRNH3 was detected only in ‘Alexis’ under NVLD, whereas it was not expressed in plants with the active allele of VRNH2 (SBCC058 and ‘Plaisant’). Under VSD, PPDH2 was expressed in ‘Alexis’, SBCC058, and SBCC106, but it was only expressed weakly in ‘Alexis’ under NVLD. Further analysis of PPDH2 expression in two barley doubled haploid populations revealed that, under long days, HvFT3 and VRNH2 expression levels were related inversely. The timing of VRNH2 expression under a long photoperiod suggests that this gene might be involved in repression of PPDH2 and, indirectly, in the regulation of flowering time through an interaction with the day-length pathway.This study was funded by grants AGL2007-63625 and HH2008-0013 from the Spanish Ministry of Science and Technology and by the European Regional Development Fund. Germplasm from the SBCC is maintained with funding from project RFP2004-00015-00-00. MCC was supported by an I3P Predoctoral Fellowship from CSIC.Peer reviewe

Identification of genetic selection footprints in barley landraces in relation to agroclimatic indices

2 .pdf files with the extended abstract and the original Poster from the authors. Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)This study intends to establish relationships between genetic diversity of the Spanish landraces and the climate of their collection sites. A thorough study of a period of 30 years of past climate (1981-2010), extracted agroclimatic variables meaningful for cereal production at the collection sites of 140 barley landraces.Work funded by projects ClimBar (ERA-NET, FACCE-JPI) and RFP2015-000006-00-00 (Spanish Ministry of Industry, Economy and Competitiveness)Peer reviewe

Molecular characterization and genetic diversity of Prunus rootstocks

The definitive version is available at: http://www.sciencedirect.com/science/journal/03044238Twenty microsatellite primer pairs, previously developed in peach, were used to characterize and to explore genetic relationships among 44 clones, representing three groups of rootstocks defined as: (1) Peach-based rootstocks (Prunus dulcis x P. persica, P. persica x P. davidiana); (2) Myrobalan - Marianna plums (P. cerasifera, and interspecific hybrids having P. cerasifera as a parent); and (3) Slow growing plums (P. insititia, P. domestica, and P. domestica x P. spinosa). Eighteen SSR markers, from the 20 initially used, were able to amplify polymorphic products for the Peach-based rootstocks and 13 common markers gave also polymorphism for the Myrobalan-Marianna and Slow growing plums groups. The Dice coefficient of similarity was calculated between all pairs of accessions and their genetic similarity represented by a principal coordinate analysis. The genetic diversity detected among the 44 clones studied divided them in three groups, which are in agreement with their current taxonomic classification and their morphological characteristics. A set of three microsatellites (BPPCT001, CPPCT022 and UDP98-407) can distinguish between all the clones analyzed. The analysis within groups reveal another two sets of three SSR to distinguish between the clones from the peach based rootstocks and the myrobalan-Marianna plums respectively and only a single SSR is needed to distinguish within the clones from the Slow growing plums group. These results demonstrate the high potential of the SSR analysis for peach rootstock identification and studies of diversity in Prunus species.This research was funded by CICYT (Comisión Interministerial de Ciencia y Tecnología AGL 2005-05533), INIA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, RF03-014-C2 and RF2007-00026-C02-01), DGA (Diputación General de Aragón, A44). M. Bouhadida was supported by a fellowship from the AECI (Agencia Española de Cooperación Internacional) of the Spanish Ministry of Foreign Affairs and an I3P-PC2006 contract from the CSIC-FSE for M.J. Gonzalo.Peer reviewe

A new Vrs1 allele identified in 2-row Spanish landraces

1 .pdf copy (A3) of the original poster presented by the Authors.Vrs1, the gene determining the type of spike in barley has been extensively studied. The wild dominant allele encodes a homeodomain-leucine zipper transcription factor whose activity results in a two-rowed spike, whereas the recessive allele produces a six-row phenotype. Phylogenetic analysis of barley cultivars identified two alleles in two-rowed types and at least four different alleles in six-rowed barleys. Previous results genotyping with MWG699, a marker closely linked to Vrs1, suggested different geographic origins for six-row alleles, among them the vrs1.a2 allele originated in the Western Mediterranean. Using this same marker, we showed that a large proportion of Spanish and Moroccan landraces (both 2- and 6-rowed) as well as Moroccan Hordeum spontaneum lines, all shared the same haplotype. We then analyzed the sequence of the Vrs1 gene in those lines. All (11) six-rowed barleys sequenced carried the vrs1.a2 allele, but we found different Vrs1 alleles among 2-rowed types: the material from Morocco, both wild (3) and cultivated (2), carried the Vrs1.b2 allele, which was absent from the Spanish 2-rowed landraces studied. The most common allele among these was Vrs1.b3, in 46 lines out of 53 evaluated. The other seven lines presented a new Vrs1 allele, Vrs1.b5. This new allele contains a ‘T’ insertion in exon 2, originally proposed as the causal mutation giving rise to the 6-row vrs1.a2 allele, but has an additional upstream deletion that results in the change of 15 amino acids and a potentially functional protein. These results add a new hypothesis to the origin of the 6-rowed vrs1.a2 allele, which could result from a mutation either at the Vrs1.b2 allele (classical hypothesis) or at the newly found Vrs1.b5 allele identified in Spanish landraces.Peer reviewe

Analysis of powdery mildew resistance in the Spanish barley core collection

24 Pag., 4 Tabl., 2 Fig. The definitive version is available at: www3.interscience.wiley.comThe Spanish Barley Core Collection, consisting of one hundred and fifty-nine landrace-derived inbred lines and sixteen cultivars, was characterized for resistance to powdery mildew (Blumeria graminis f. sp. hordei) using a set of 27 isolates with a wide spectra of virulences/avirulences on most of the genes expected to occur in Europe. No landrace-derived line and no cultivar were resistant to all the isolates but at least three landraces showed infection types below 2 for 23 isolates. Twenty-two landraces and one cultivar showed resistance against half of the isolates used. Eleven isolates were sufficient to separate the majority of resistance profiles. In total, thirty-four resistance spectra were detected and fourteen resistance genes/alleles were postulated alone or in combination: MlLa, Mlh, Mlg, Mla22, Mla7(Mlu), Mla7(Mlk), Mlk, Mla12, Mla9, Mla3, Mla6(Mla14), Mlra and Mla1. The majority of resistance spectra are composed only by one line. Resistance in twenty-one landrace-derived lines and four cultivars was based on either unidentified genes or combinations of known and unknown genes/alleles. Therefore, the SBCC may be a source for broadening the genetic base of powdery mildew resistance.This research was funded by projects AGL2004-05311 and AGL2007-63625, granted by the Spanish Ministry of Science and Innovation. C.S. holds an I3P-Doc contract from CSIC. C.S. was supported by mobility fellowships from DFG, CSIC and Fundación Caja Inmaculada.Peer reviewe

HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys

29 Pag., 5 Tabl., 4 Fig. The definitive version is available at: http://www.springer.com/life+sciences/plant+sciences/journal/122Flowering time is an important factor in the adaptation of barley varieties to environmental conditions and maximizing yield potential (Boyd et al. 2003; Cockram et al. 2007a; Cuesta-Marcos et al. 2009), by synchronizing the plant cycle to the prevailing environmental conditions. Flowering time is a complex trait that shows an almost continuous variation in cereals. The investigation of the genetic control of flowering time in barley has benefited from the comparative use of floral pathways in Arabidopsis thaliana (Cockram et al. 2007a) and rice, via the identification of candidate genes through orthology. The variation in flowering time is mainly due to variations in genes regulated by day length (photoperiod) or long exposures to low temperature (vernalization) (Laurie et al. 1995; Trevaskis et al. 2003; Dubcovsky et al. 2005). In barley, three genes are responsible for the vernalization requirement: VrnH1 (isolated by map-based cloning in diploid wheat, Yan et al. 2003), VrnH2 (identified by positional cloning, Yan et al. 2004) and VrnH3 (identified by homology to a known gene from Arabidopsis thaliana, Yan et al. 2006). VrnH1 is induced by vernalization and promotes the transition from vegetative to reproductive development. VrnH2 is a floral repressor that delays flowering until the plants are vernalized. The VrnH3 gene seems to be orthologous to the A. thaliana floral pathway integrator FT (FLOWERING LOCUS T) gene (Yan et al. 2006; Faure et al. 2007; Turck et al. 2008; Kikuchi et al. 2009). In A. thaliana, FT expression increases in the leaves when plants are exposed to inductive day length. In barley, expression of orthologous HvFT1 (synonymous to VrnH3) is induced by long day conditions and promotes flowering (Hemming et al. 2008). The winter growth habit of barley requires the presence of a recessive VrnH1 allele, together with an active VrnH2 allele (Cockram et al. 2007b; Hemming et al. 2009). Vernalization induces VrnH1 under both short and long days, which then represses VrnH2. Distelfeld et al. (2009) reported that the interactions among the three vernalization genes generate a feedback regulatory loop that once started, leads to an irreversible induction of flowering. The function of HvFT1 has started to be unraveled only recently. There is now mounting evidence supporting the role of the FT protein in Arabidopsis (and corresponding proteins in other species) as an important part of the florigen (Corbesier et al. 2007; Tamaki et al. 2007). Kikuchi et al. (2009) presented strong evidence suggesting that HvFT1 plays a central role in promoting flowering, integrating the photoperiod and vernalization pathways. HvFT1 expression seems to be regulated by the major photoperiod response genes: PpdH1 under LD conditions and PpdH2 under SD conditions. There are evidences on the adaptive role played by VrnH1, VrnH2 and PpdH1 during the expansion of the crop, facilitating its adaptation to new agroecological niches (Cockram et al. 2007a; Jones et al. 2008). Does VrnH3-HvFT1 also have an adaptive role? We know that the phenotypic effect of HvFT1 on flowering time can be very large (Yan et al. 2006), and therefore may be an important factor for the final determination of barley flowering time. Other open questions on this gene are: to what environmental cue does VrnH3 respond, temperature or photoperiod? What effect does it have on flowering time under natural conditions? To address these questions, we analyzed the polymorphism and the phenotypic effect of this gene on a collection of Spanish barley landraces and its variation at the sequence level, and validated its effect on a segregating population.This work was supported by the Spanish Ministry of Science and Innovation (Projects AGL2007-63625 and RTA01-088-C3) and by the European Regional Development Fund. A Djemel was supported by a fellowship from IAMZ-CIHEAM. S Yahiaoui and L Ponce were supported by fellowships from AECID-Spanish Ministry of Foreign Affairs and Cooperation.Peer reviewe

Genomic Prediction of Grain Yield in a Barley MAGIC Population Modeling Genotype per Environment Interaction

18 Pags.- 7 Figs.- 4 Tabls. © 2021 Puglisi, Delbono, Visioni, Ozkan, Kara, Casas, Igartua, Valè, Piero, Cattivelli, Tondelli and Fricano. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).Multi-parent Advanced Generation Inter-crosses (MAGIC) lines have mosaic genomes that are generated shuffling the genetic material of the founder parents following pre-defined crossing schemes. In cereal crops, these experimental populations have been extensively used to investigate the genetic bases of several traits and dissect the genetic bases of epistasis. In plants, genomic prediction models are usually fitted using either diverse panels of mostly unrelated accessions or individuals of biparental families and several empirical analyses have been conducted to evaluate the predictive ability of models fitted to these populations using different traits. In this paper, we constructed, genotyped and evaluated a barley MAGIC population of 352 individuals developed with a diverse set of eight founder parents showing contrasting phenotypes for grain yield. We combined phenotypic and genotypic information of this MAGIC population to fit several genomic prediction models which were cross-validated to conduct empirical analyses aimed at examining the predictive ability of these models varying the sizes of training populations. Moreover, several methods to optimize the composition of the training population were also applied to this MAGIC population and cross-validated to estimate the resulting predictive ability. Finally, extensive phenotypic data generated in field trials organized across an ample range of water regimes and climatic conditions in the Mediterranean were used to fit and cross-validate multi-environment genomic prediction models including G×E interaction, using both genomic best linear unbiased prediction and reproducing kernel Hilbert space along with a non-linear Gaussian Kernel. Overall, our empirical analyses showed that genomic prediction models trained with a limited number of MAGIC lines can be used to predict grain yield with values of predictive ability that vary from 0.25 to 0.60 and that beyond QTL mapping and analysis of epistatic effects, MAGIC population might be used to successfully fit genomic prediction models. We concluded that for grain yield, the single-environment genomic prediction models examined in this study are equivalent in terms of predictive ability while, in general, multi-environment models that explicitly split marker effects in main and environmental-specific effects outperform simpler multi-environment models.This research was carried out in the framework of the iBarMed project, which has been funded through the ARIMNet2 initiative and the Italian “Ministry of Agricultural, Food and Forestry Policies” under grant agreement “DM n. 20120.” ARIMNet2 has received funding from the EU 7th Framework Programme for research, technological development and demonstration under grant agreement no. 618127. The work was also supported by YSTEMIC_1063 (An integrated approach to the challenge of sustainable food systems: adaptive and mitigatory strategies to address climate change and malnutrition: From cereal diversity to plant breeding), a research project funded by Italian “Ministry of Agricultural, Food and Forestry Policies” in the frame of the Knowledge Hub on Food and Nutrition Security.Peer reviewe