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      Harnessing Novel Diversity From Landraces to Improve an Elite Barley Variety

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          Abstract

          The Spanish Barley Core Collection (SBCC) is a source of genetic variability of potential interest for breeding, particularly for adaptation to Mediterranean environments. Two backcross populations (BC 2F 5) were developed using the elite cultivar Cierzo as the recurrent parent. The donor parents, namely SBCC042 and SBCC073, were selected from the SBCC lines due to their outstanding yield in drought environments. Flowering time, yield and drought-related traits were evaluated in two field trials in Zaragoza (Spain) during the 2014–15 and 2015–16 seasons and validated in the 2017–18 season. Two hundred sixty-four lines of each population were genotyped with the Barley Illumina iSelect 50k SNP chip. Genetic maps for each population were generated. The map for SBCC042 × Cierzo contains 12,893 SNPs distributed in 9 linkage groups. The map for SBCC073 × Cierzo includes 12,026 SNPs in 7 linkage groups. Both populations shared two QTL hotspots. There are QTLs for flowering time, thousand-kernel weight (TKW), and hectoliter weight on a segment of 23 Mb at ~515 Mb on chromosome 1H, which encompasses the HvFT3 gene. In both populations, flowering was accelerated by the landrace allele, which also increased the TKW. In the same region, better soil coverage was contributed by SBCC042 but coincident with a lower hectoliter weight. The second large hotspot was on chromosome 6H and contained QTLs with wide intervals for grain yield, plant height and TKW. Landrace alleles contributed to increased plant height and TKW and reduced grain yield. Only SBCC042 contributed favorable alleles for “green area,” with three significant QTLs that increased ground coverage after winter, which might be exploited as an adaptive trait of this landrace. Some genes of interest found in or very close to the peaks of the QTLs are highlighted. Strategies to deploy the QTLs found for breeding and pre-breeding are proposed.

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          A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase.

           Min Shi,  Zhen Zhu,  Xian Song (2007)
          Grain weight is one of the most important components of grain yield and is controlled by quantitative trait loci (QTLs) derived from natural variations in crops. However, the molecular roles of QTLs in the regulation of grain weight have not been fully elucidated. Here, we report the cloning and characterization of GW2, a new QTL that controls rice grain width and weight. Our data show that GW2 encodes a previously unknown RING-type protein with E3 ubiquitin ligase activity, which is known to function in the degradation by the ubiquitin-proteasome pathway. Loss of GW2 function increased cell numbers, resulting in a larger (wider) spikelet hull, and it accelerated the grain milk filling rate, resulting in enhanced grain width, weight and yield. Our results suggest that GW2 negatively regulates cell division by targeting its substrate(s) to proteasomes for regulated proteolysis. The functional characterization of GW2 provides insight into the mechanism of seed development and is a potential tool for improving grain yield in crops.
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            The rate of cell differentiation controls the Arabidopsis root meristem growth phase.

            Upon seed germination, apical meristems grow as cell division prevails over differentiation and reach their final size when division and differentiation reach a balance. In the Arabidopsis root meristem, this balance results from the interaction between cytokinin (promoting differentiation) and auxin (promoting division) through a regulatory circuit whereby the ARR1 cytokinin-responsive transcription factor activates the gene SHY2, which negatively regulates the PIN genes encoding auxin transport facilitators. However, it remains unknown how the final meristem size is set, i.e., how a change in the relative rates of cell division and differentiation is brought about to cause meristem growth to stop. Here, we show that during meristem growth, expression of SHY2 is driven by another cytokinin-response factor, ARR12, and that completion of growth is brought about by the upregulation of SHY2 caused by both ARR12 and ARR1: this leads to an increase in cell differentiation rate that balances it with division, thus setting root meristem size. We also show that gibberellins selectively repress expression of ARR1 at early stages of meristem development, and that the DELLA protein REPRESSOR OF GA 1-3 (RGA) mediates this negative control. Copyright 2010 Elsevier Ltd. All rights reserved.
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              Flapjack—graphical genotype visualization

              Summary: New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide polymorphism (SNP) platforms, genotyping-by-sequencing and other comparable genotyping technologies. Flapjack has been developed to facilitate analysis of these data, providing real time rendering with rapid navigation and comparisons between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features. Availability: Flapjack is freely available for Microsoft Windows, Mac OS X, Linux and Solaris, and can be downloaded from http://bioinf.scri.ac.uk/flapjack Contact: flapjack@scri.ac.uk
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                11 April 2019
                2019
                : 10
                Affiliations
                1Aula Dei Experimental Station (EEAD-CSIC) , Zaragoza, Spain
                2Fundación ARAID , Zaragoza, Spain
                Author notes

                Edited by: Dragan Perovic, Julius Kühn-Institut, Germany

                Reviewed by: Ravi Koppolu, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Germany; Manoj Prasad, National Institute of Plant Genome Research (NIPGR), India

                *Correspondence: Ernesto Igartua igartua@ 123456eead.csic.es

                This article was submitted to Plant Breeding, a section of the journal Frontiers in Plant Science

                †Present Address: Carlos P. Cantalapiedra, Centro de Biotecnología y Genómica de Plantas UPM–INIA (CBGP), Pozuelo de Alarcón, Spain

                Bruno Contreras-Moreira, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom

                Article
                10.3389/fpls.2019.00434
                6470277
                Copyright © 2019 Monteagudo, Casas, Cantalapiedra, Contreras-Moreira, Gracia and Igartua.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 3, Tables: 6, Equations: 0, References: 98, Pages: 17, Words: 14559
                Funding
                Funded by: Ministerio de Economía, Industria y Competitividad, Gobierno de España 10.13039/501100010198
                Award ID: AGL2013-48756-R
                Award ID: AGL2016-80967-R
                Award ID: BES-2014-069266
                Funded by: Ministerio de Agricultura y Pesca, Alimentación y Medio Ambiente 10.13039/501100009599
                Award ID: RFP2012-00015-00-00
                Award ID: RFP2015 00006-00-00
                Award ID: RTA2012-00033-C03-02
                Categories
                Plant Science
                Original Research

                Plant science & Botany

                barley, landrace, qtl, adaptation, 50k

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