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Guerra D, Morcia C, Badeck F, Rizza F, Delbono S, Francia E, Milc JA, Monostori I, Galiba G, Cattivelli L, Tondelli A. Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:553-569. [PMID: 34757472 PMCID: PMC8866391 DOI: 10.1007/s00122-021-03985-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/26/2021] [Indexed: 05/24/2023]
Abstract
Exome sequencing-based allele mining for frost tolerance suggests HvCBF14 rather than CNV at Fr-H2 locus is the main responsible of frost tolerance in barley. Wild relatives, landraces and old cultivars of barley represent a reservoir of untapped and potentially important genes for crop improvement, and the recent sequencing technologies provide the opportunity to mine the existing genetic diversity and to identify new genes/alleles for the traits of interest. In the present study, we use frost tolerance and vernalization requirement as case studies to demonstrate the power of allele mining carried out on exome sequencing data generated from > 400 barley accessions. New deletions in the first intron of VRN-H1 were identified and linked to a reduced vernalization requirement, while the allelic diversity of HvCBF2a, HvCBF4b and HvCBF14 was investigated by combining the analysis of SNPs and read counts. This approach has proven very effective to identify gene paralogs and copy number variants of HvCBF2 and the HvCBF4b-HvCBF2a segment. A multiple linear regression model which considers allelic variation at these genes suggests a major involvement of HvCBF14, rather than copy number variation of HvCBF4b-HvCBF2a, in controlling frost tolerance in barley. Overall, the present study provides powerful resource and tools to discover novel alleles at relevant genes in barley.
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Affiliation(s)
- Davide Guerra
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy.
| | - Caterina Morcia
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Franz Badeck
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Fulvia Rizza
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Stefano Delbono
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Enrico Francia
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad. Besta, 42122, Reggio Emilia, Italy
| | - Justyna Anna Milc
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad. Besta, 42122, Reggio Emilia, Italy
| | - Istvan Monostori
- Centre for Agricultural Research, Agricultural Institute, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
| | - Gabor Galiba
- Centre for Agricultural Research, Agricultural Institute, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Department of Environmental Sustainability, Festetics Doctoral School, IES, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, 8360, Hungary
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
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Hoseinzadeh P, Zhou R, Mascher M, Himmelbach A, Niks RE, Schweizer P, Stein N. High Resolution Genetic and Physical Mapping of a Major Powdery Mildew Resistance Locus in Barley. FRONTIERS IN PLANT SCIENCE 2019; 10:146. [PMID: 30838011 PMCID: PMC6382739 DOI: 10.3389/fpls.2019.00146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/28/2019] [Indexed: 05/02/2023]
Abstract
Powdery mildew caused by Blumeria graminis f. sp. hordei is a foliar disease with highly negative impact on yield and grain quality in barley. Thus, breeding for powdery mildew resistance is an important goal and requires constantly the discovery of new sources of natural resistance. Here, we report the high resolution genetic and physical mapping of a dominant race-specific powdery mildew resistance locus, originating from an Ethiopian spring barley accession 'HOR2573,' conferring resistance to several modern mildew isolates. High-resolution genetic mapping narrowed down the interval containing the resistance locus to a physical span of 850 kb. Four candidate genes with homology to known disease resistance gene families were identified. The mapped resistance locus coincides with a previously reported resistance locus from Hordeum laevigatum, suggesting allelism at the same locus in two different barley lines. Therefore, we named the newly mapped resistance locus from HOR2573 as MlLa-H. The reported co-segregating and flanking markers may provide new tools for marker-assisted selection of this resistance locus in barley breeding.
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Affiliation(s)
- Parastoo Hoseinzadeh
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Ruonan Zhou
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Martin Mascher
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Axel Himmelbach
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Rients E. Niks
- Department of Plant Science, Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Patrick Schweizer
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Nils Stein
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, University of Göttingen, Göttingen, Germany
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Prodhomme C, Esselink D, Borm T, Visser RGF, van Eck HJ, Vossen JH. Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3. PLANT METHODS 2019; 15:60. [PMID: 31160919 PMCID: PMC6540404 DOI: 10.1186/s13007-019-0445-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/23/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Standard strategies to identify genomic regions involved in a specific trait variation are often limited by time and resource consuming genotyping methods. Other limiting pre-requisites are the phenotyping of large segregating populations or of diversity panels and the availability and quality of a closely related reference genome. To overcome these limitations, we designed efficient Comparative Subsequence Sets Analysis (CoSSA) workflows to identify haplotype specific SNPs linked to a trait of interest from Whole Genome Sequencing data. RESULTS As a model, we used the resistance to Synchytrium endobioticum pathotypes 2, 6 and 18 that co-segregated in a tetraploid full sib population. Genomic DNA from both parents, pedigree genotypes, unrelated potato varieties lacking the wart resistance traits and pools of resistant and susceptible siblings were sequenced. Set algebra and depth filtering of subsequences (k-mers) were used to delete unlinked and common SNPs and to enrich for SNPs from the haplotype(s) harboring the resistance gene(s). Using CoSSA, we identified a major and a minor effect locus. Upon comparison to the reference genome, it was inferred that the major resistance locus, referred to as Sen3, was located on the north arm of chromosome 11 between 1,259,552 and 1,519,485 bp. Furthermore, we could anchor the unanchored superscaffold DMB734 from the potato reference genome to a synthenous interval. CoSSA was also successful in identifying Sen3 in a reference genome independent way thanks to the de novo assembly of paired end reads matching haplotype specific k-mers. The de novo assembly provided more R haplotype specific polymorphisms than the reference genome corresponding region. CoSSA also offers possibilities for pedigree analysis. The origin of Sen3 was traced back until Ora. Finally, the diagnostic power of the haplotype specific markers was shown using a panel of 56 tetraploid varieties. CONCLUSIONS CoSSA is an efficient, robust and versatile set of workflows for the genetic analysis of a trait of interest using WGS data. Because the WGS data are used without intermediate reads mapping, CoSSA does not require the use of a reference genome. This approach allowed the identification of Sen3 and the design of haplotype specific, diagnostic markers.
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Affiliation(s)
- Charlotte Prodhomme
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Danny Esselink
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Theo Borm
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G. F. Visser
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Herman J. van Eck
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jack H. Vossen
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Case AJ, Bhavani S, Macharia G, Steffenson BJ. Genome-wide association study of stem rust resistance in a world collection of cultivated barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:107-126. [PMID: 29177535 DOI: 10.1007/s00122-017-2989-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/19/2017] [Indexed: 05/20/2023]
Abstract
QTL conferring a 14-40% reduction in adult plant stem rust severity to multiple races of Pgt were found on chromosome 5H and will be useful in barley breeding. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt) is an important disease of barley. The resistance gene Rpg1 has protected the crop against stem rust losses for over 70 years in North America, but is not effective against the African Pgt race TTKSK (and its variants) nor the domestic race QCCJB. To identify resistance to these Rpg1-virulent races, the Barley iCore Collection, held by the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection was evaluated for adult plant resistance (APR) and seedling resistance to race TTKSK and APR to race QCCJB and the Pgt TTKSK composite of races TTKSK, TTKST, TTKTK, and TTKTT. Using a genome-wide association study approach based on 6224 single nucleotide polymorphic markers, seven significant loci for stem rust resistance were identified on chromosomes 1H, 2H, 3H, and 5H. The most significant markers detected were 11_11355 and SCRI_RS_177017 at 71-75 cM on chromosome 5H, conferring APR to QCCJB and TTKSK composite. Significant markers were also detected for TTKSK seedling resistance on chromosome 5H. All markers detected on 5H were independent of the rpg4/Rpg5 complex at 152-168 cM. This study verified the importance of the 11_11355 locus in conferring APR to races QCCJB and TTKSK and suggests that it may be effective against other races in the Ug99 lineage.
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Affiliation(s)
- Austin J Case
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Sridhar Bhavani
- Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), Nairobi, Kenya
| | - Godwin Macharia
- Kenya Agriculture Livestock Research Organization (KALRO), Njoro, Kenya
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
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Kochetov AV, Glagoleva AY, Strygina KV, Khlestkina EK, Gerasimova SV, Ibragimova SM, Shatskaya NV, Vasilyev GV, Afonnikov DA, Shmakov NA, Antonova OY, Gavrilenko TA, Alpatyeva NV, Khiutti A, Afanasenko OS. Differential expression of NBS-LRR-encoding genes in the root transcriptomes of two Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis. BMC PLANT BIOLOGY 2017; 17:251. [PMID: 29297325 PMCID: PMC5751396 DOI: 10.1186/s12870-017-1193-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUND The characterization of major resistance genes (R genes) in the potato remains an important task for molecular breeding. However, R genes are rapidly evolving and frequently occur in genomes as clusters with complex structures, and their precise mapping and identification are complicated and time consuming. RESULTS Comparative analysis of root transcriptomes of Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis revealed a number of differentially expressed genes. However, compiling a list of candidate R genes for further segregation analysis was hampered by their scarce annotation. Nevertheless, combination of transcriptomic analysis with data on predicted potato NBS-LRR-encoding genes considerably improved the quality of the results and provided a reasonable number of candidate genes that provide S. phureja with strong resistance to the potato golden cyst nematode. CONCLUSION Combination of comparative analyses of tissue-specific transcriptomes in resistant and susceptible genotypes may be used as an approach for the rapid identification of candidate potato R genes for co-segregation analysis and may be used in parallel with more sophisticated studies based on genome resequencing.
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Affiliation(s)
- Alex V Kochetov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia.
- Novosibirsk State Agrarian University, Novosibirsk, 630039, Russia.
| | - Anastasiya Y Glagoleva
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | - Elena K Khlestkina
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | | | | | | | | | - Nikolay A Shmakov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
| | - Olga Y Antonova
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
| | - Tatyana A Gavrilenko
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
- St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Natalia V Alpatyeva
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
| | - Alexander Khiutti
- All Russian Research Institute for Plant Protection, Saint Petersburg, 196608, Russia
| | - Olga S Afanasenko
- All Russian Research Institute for Plant Protection, Saint Petersburg, 196608, Russia
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Contreras-Moreira B, Cantalapiedra CP, García-Pereira MJ, Gordon SP, Vogel JP, Igartua E, Casas AM, Vinuesa P. Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species. FRONTIERS IN PLANT SCIENCE 2017; 8:184. [PMID: 28261241 PMCID: PMC5306281 DOI: 10.3389/fpls.2017.00184] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/30/2017] [Indexed: 05/22/2023]
Abstract
The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes. The goal was to sample their pan-genomes and classify sequences as core, if detected in all accessions, or accessory, when absent in some of them. The resulting sequence clusters were used to simulate pan-genome growth, and to compile Average Nucleotide Identity matrices that summarize intra-species variation. Although transcripts were found to under-estimate pan-genome size by at least 10%, we concluded that clusters of expressed sequences can recapitulate phylogeny and reproduce two properties observed in A. thaliana gene models: accessory loci show lower expression and higher non-synonymous substitution rates than core genes. Finally, accessory sequences were observed to preferentially encode transposon components in both species, plus disease resistance genes in cultivated barleys, and a variety of protein domains from other families that appear frequently associated with presence/absence variation in the literature. These results demonstrate that pan-genome analyses are useful to explore germplasm diversity.
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Affiliation(s)
- Bruno Contreras-Moreira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones CientíficasZaragoza, Spain; Fundación ARAIDZaragoza, Spain
| | - Carlos P Cantalapiedra
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - María J García-Pereira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | | | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | - Ernesto Igartua
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - Ana M Casas
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
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