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      Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL- hotspot” region for drought tolerance in chickpea

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          Abstract

          To enhance the marker density in the “ QTL- hotspot” region, harboring several QTLs for drought tolerance-related traits identified on linkage group 04 (CaLG04) in chickpea recombinant inbred line (RIL) mapping population ICC 4958 × ICC 1882, a genotyping-by-sequencing approach was adopted. In total, 6.24 Gb data from ICC 4958, 5.65 Gb data from ICC 1882 and 59.03 Gb data from RILs were generated, which identified 828 novel single-nucleotide polymorphisms (SNPs) for genetic mapping. Together with these new markers, a high-density intra-specific genetic map was developed that comprised 1,007 marker loci spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data for 20 traits collected over one to seven seasons identified 49 SNP markers in the “ QTL- hotspot” region. These efforts have refined the “ QTL- hotspot” region to 14 cM. In total, 164 main-effect QTLs including 24 novel QTLs were identified. In addition, 49 SNPs integrated in the “ QTL- hotspot” region were converted into cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers which can be used in marker-assisted breeding.

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          The online version of this article (doi:10.1007/s00438-014-0932-3) contains supplementary material, which is available to authorized users.

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

          Xian-Jun Song, Wei Huang, Min Shi … (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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            Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis.

            Qiang Liu, Mie Kasuga, Yoh Sakuma … (1998)
            Plant growth is greatly affected by drought and low temperature. Expression of a number of genes is induced by both drought and low temperature, although these stresses are quite different. Previous experiments have established that a cis-acting element named DRE (for dehydration-responsive element) plays an important role in both dehydration- and low-temperature-induced gene expression in Arabidopsis. Two cDNA clones that encode DRE binding proteins, DREB1A and DREB2A, were isolated by using the yeast one-hybrid screening technique. The two cDNA libraries were prepared from dehydrated and cold-treated rosette plants, respectively. The deduced amino acid sequences of DREB1A and DREB2A showed no significant sequence similarity, except in the conserved DNA binding domains found in the EREBP and APETALA2 proteins that function in ethylene-responsive expression and floral morphogenesis, respectively. Both the DREB1A and DREB2A proteins specifically bound to the DRE sequence in vitro and activated the transcription of the b-glucuronidase reporter gene driven by the DRE sequence in Arabidopsis leaf protoplasts. Expression of the DREB1A gene and its two homologs was induced by low-temperature stress, whereas expression of the DREB2A gene and its single homolog was induced by dehydration. Overexpression of the DREB1A cDNA in transgenic Arabidopsis plants not only induced strong expression of the target genes under unstressed conditions but also caused dwarfed phenotypes in the transgenic plants. These transgenic plants also revealed freezing and dehydration tolerance. In contrast, overexpression of the DREB2A cDNA induced weak expression of the target genes under unstressed conditions and caused growth retardation of the transgenic plants. These results indicate that two independent families of DREB proteins, DREB1 and DREB2, function as trans-acting factors in two separate signal transduction pathways under low-temperature and dehydration conditions, respectively.
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              An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping

              Humira Sonah, Maxime Bastien, Elmer Iquira … (2013)
              Highly parallel SNP genotyping platforms have been developed for some important crop species, but these platforms typically carry a high cost per sample for first-time or small-scale users. In contrast, recently developed genotyping by sequencing (GBS) approaches offer a highly cost effective alternative for simultaneous SNP discovery and genotyping. In the present investigation, we have explored the use of GBS in soybean. In addition to developing a novel analysis pipeline to call SNPs and indels from the resulting sequence reads, we have devised a modified library preparation protocol to alter the degree of complexity reduction. We used a set of eight diverse soybean genotypes to conduct a pilot scale test of the protocol and pipeline. Using ApeKI for GBS library preparation and sequencing on an Illumina GAIIx machine, we obtained 5.5 M reads and these were processed using our pipeline. A total of 10,120 high quality SNPs were obtained and the distribution of these SNPs mirrored closely the distribution of gene-rich regions in the soybean genome. A total of 39.5% of the SNPs were present in genic regions and 52.5% of these were located in the coding sequence. Validation of over 400 genotypes at a set of randomly selected SNPs using Sanger sequencing showed a 98% success rate. We then explored the use of selective primers to achieve a greater complexity reduction during GBS library preparation. The number of SNP calls could be increased by almost 40% and their depth of coverage was more than doubled, thus opening the door to an increase in the throughput and a significant decrease in the per sample cost. The approach to obtain high quality SNPs developed here will be helpful for marker assisted genomics as well as assessment of available genetic resources for effective utilisation in a wide number of species.
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                Author and article information

                Contributors
                Rajeev K. Varshney: 0091 40 30713305 , r.k.varshney@cgiar.org
                Journal
                Journal ID (nlm-ta): Mol Genet Genomics
                Journal ID (iso-abbrev): Mol. Genet. Genomics
                Title: Molecular Genetics and Genomics
                Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )
                ISSN (Print): 1617-4615
                ISSN (Electronic): 1617-4623
                Publication date (Electronic): 25 October 2014
                Publication date PMC-release: 25 October 2014
                Publication date (Print): 2015
                Volume: 290
                Issue: 2
                Pages: 559-571
                Affiliations
                [ ]International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
                [ ]Osmania University, Hyderabad, India
                [ ]National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO USA
                [ ]Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064 Australia
                [ ]School of Plant Biology and the Institute of Agriculture, The University of Western Australia (UWA), Crawley, WA Australia
                Author notes

                Communicated by S. Hohmann.

                Article
                Publisher ID: 932
                DOI: 10.1007/s00438-014-0932-3
                PMC ID: 4361754
                PubMed ID: 25344290
                SO-VID: d8acbe7d-b1a3-4077-a0ed-0d4c36edc25f
                Copyright © © The Author(s) 2014
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.

                History
                Date received : 25 July 2014
                Date accepted : 23 September 2014
                Categories
                Subject: Original Paper
                Custom metadata
                issue-copyright-statement © Springer-Verlag Berlin Heidelberg 2015

                ScienceOpen disciplines: Genetics
                Keywords: chickpea,drought tolerance,genotyping-by-sequencing,“qtl-hotspot”,fine mapping,candidate genes,caps/dcaps,marker-assisted breeding
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: chickpea, drought tolerance, genotyping-by-sequencing, “qtl-hotspot”, fine mapping, candidate genes, caps/dcaps, marker-assisted breeding

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