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Investigation of genetic markers for intramuscular fat in the hybrid Wagyu cattle with bulked segregant analysis. Sci Rep 2021; 11:11530. [PMID: 34075159 PMCID: PMC8169923 DOI: 10.1038/s41598-021-91101-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/20/2021] [Indexed: 11/08/2022] Open
Abstract
ulked Segregant Analysis (BSA) is a rapid strategy for identifying genetic markers in specific regions of the phenotypical population and it has been widely used for QTLs mapping in smaller mixed F2 and F3 populations. We applied a modified BSA method to assessed genome-wide homozygous and heterozygous linkage patterns in the Chinese Wagyu Beef Cattle F2/F3 mixed population. Two overlapped regions from F2 and F3 populations on autosomes were found with high-density heterozygote alleles between high and low intramuscular fat groups. Regions from 24.8 M ~ 29.6 M of chromosome 23 were identified as most significantly correlated to the intramuscular fat in our samples. We also identified other 4 potential loci on chromosomes 5, 9, 15, and 21 correlated with Intramuscular fat. This study provided a novel low-cost method for QTLs mapping and identify molecular markers of phenotypical changes in a small mixed population.
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Tan C, Liu Z, Huang S, Feng H. Mapping of the male sterile mutant gene ftms in Brassica rapa L. ssp. pekinensis via BSR-Seq combined with whole-genome resequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:355-370. [PMID: 30382313 DOI: 10.1007/s00122-018-3223-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/25/2018] [Indexed: 05/19/2023]
Abstract
A male sterile mutant was created by 60Co γ-rays of microspores isolated from Chinese cabbage DH line 'FT'. A candidate gene for the male sterile trait was identified as Bra010198. Male sterility is used for hybrid seed production in Chinese cabbage. In this study, we derived a male sterile mutant (ftms) from Chinese cabbage DH line 'FT' by irradiating microspores with 60Co γ-rays and realized the rapid trait transformation from male fertility to sterility for creating valuable breeding materials. Genetic analysis indicated that the male sterile trait is controlled by a single recessive nuclear gene, ftms. Microspore development in mutant ftms was aborted at the tetrad stage and associated with severely retarded degeneration and vacuolation of tapetum. Using BSR-seq analysis, the candidate region for ftms was mapped on chromosome A05. A large F2 population was created, and the region was narrowed to approximately 1.7-Mb between markers Indel20 and Indel14 via linkage analysis. The recombination frequency was extremely suppressed because the region was located on the chromosome A05 centromere. Whole-genome resequencing of mutant ftms and wild-type 'FT' aligned only one nonsynonymous SNP to Bra010198; this gene is a homolog of Arabidopsis KNS4/UPEX1, which encodes a putative β-(1,3)-galactosyltransferase that controls pollen exine development. Comparative sequencing verified the SNP position on the fifth exon of Bra010198 in mutant ftms. Further genotyping revealed that the male sterile phenotype was fully co-segregated with this SNP. Quantitative real-time PCR indicated that Bra0101918 specifically expressed in stamen. The data presented herein suggested that Bra010198 is a strong candidate gene for ftms. Hence, we developed a male sterile line for potential application in breeding and expanded the knowledge about the molecular mechanism underlying male sterility in Chinese cabbage.
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Affiliation(s)
- Chong Tan
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Zhiyong Liu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Shengnan Huang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
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Delventhal R, Rajaraman J, Stefanato FL, Rehman S, Aghnoum R, McGrann GRD, Bolger M, Usadel B, Hedley PE, Boyd L, Niks RE, Schweizer P, Schaffrath U. A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley. BMC PLANT BIOLOGY 2017; 17:232. [PMID: 29202692 PMCID: PMC5715502 DOI: 10.1186/s12870-017-1178-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/15/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Nonhost resistance (NHR) protects plants against a vast number of non-adapted pathogens which implicates a potential exploitation as source for novel disease resistance strategies. Aiming at a fundamental understanding of NHR a global analysis of transcriptome reprogramming in the economically important Triticeae cereals wheat and barley, comparing host and nonhost interactions in three major fungal pathosystems responsible for powdery mildew (Blumeria graminis ff. ssp.), cereal blast (Magnaporthe sp.) and leaf rust (Puccinia sp.) diseases, was performed. RESULTS In each pathosystem a significant transcriptome reprogramming by adapted- or non-adapted pathogen isolates was observed, with considerable overlap between Blumeria, Magnaporthe and Puccinia. Small subsets of these general pathogen-regulated genes were identified as differentially regulated between host and corresponding nonhost interactions, indicating a fine-tuning of the general pathogen response during the course of co-evolution. Additionally, the host- or nonhost-related responses were rather specific for each pair of adapted and non-adapted isolates, indicating that the nonhost resistance-related responses were to a great extent pathosystem-specific. This pathosystem-specific reprogramming may reflect different resistance mechanisms operating against non-adapted pathogens with different lifestyles, or equally, different co-option of the hosts by the adapted isolates to create an optimal environment for infection. To compare the transcriptional reprogramming between wheat and barley, putative orthologues were identified. Within the wheat and barley general pathogen-regulated genes, temporal expression profiles of orthologues looked similar, indicating conserved general responses in Triticeae against fungal attack. However, the comparison of orthologues differentially expressed between host and nonhost interactions revealed fewer commonalities between wheat and barley, but rather suggested different host or nonhost responses in the two cereal species. CONCLUSIONS Taken together, our results suggest independent co-evolutionary forces acting on host pathosystems mirrored by barley- or wheat-specific nonhost responses. As a result of evolutionary processes, at least for the pathosystems investigated, NHR appears to rely on rather specific plant responses.
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Affiliation(s)
- Rhoda Delventhal
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - Jeyaraman Rajaraman
- Leibniz-Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Francesca L. Stefanato
- Department of Disease and Stress Biology, John Innes Centre, Norwich Research Park, Colney Lane, Colney, Norwich, Norfolk, NR4 7UH UK
- Present address: Molecular microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Sajid Rehman
- Plant Breeding, Graduate School for Experimental Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
- Present address: Biodiversity and Integrated Gene Management Program (BIGM), International Center for Agriculture Research in the Dry Areas, Rabat, Morocco
| | - Reza Aghnoum
- Plant Breeding, Graduate School for Experimental Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
- Present address: Seed and Plant Improvement Research Department, Khorasan Razavi Agricultural and Natural Resources Research and Education Center, AREEO, Mashhad, Iran
| | - Graham R. D. McGrann
- Department of Disease and Stress Biology, John Innes Centre, Norwich Research Park, Colney Lane, Colney, Norwich, Norfolk, NR4 7UH UK
| | - Marie Bolger
- Institute of Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52056 Aachen, Germany
| | - Björn Usadel
- Institute of Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52056 Aachen, Germany
| | - Pete E. Hedley
- The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA UK
| | - Lesley Boyd
- NIAB, Huntingdon Road, Cambridge, CB3 0LE UK
| | - Rients E. Niks
- Plant Breeding, Graduate School for Experimental Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Patrick Schweizer
- Leibniz-Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
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Chowdhury J, Lück S, Rajaraman J, Douchkov D, Shirley NJ, Schwerdt JG, Schweizer P, Fincher GB, Burton RA, Little A. Altered Expression of Genes Implicated in Xylan Biosynthesis Affects Penetration Resistance against Powdery Mildew. FRONTIERS IN PLANT SCIENCE 2017; 8:445. [PMID: 28408913 PMCID: PMC5374208 DOI: 10.3389/fpls.2017.00445] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/14/2017] [Indexed: 05/27/2023]
Abstract
Heteroxylan has recently been identified as an important component of papillae, which are formed during powdery mildew infection of barley leaves. Deposition of heteroxylan near the sites of attempted fungal penetration in the epidermal cell wall is believed to enhance the physical resistance to the fungal penetration peg and hence to improve pre-invasion resistance. Several glycosyltransferase (GT) families are implicated in the assembly of heteroxylan in the plant cell wall, and are likely to work together in a multi-enzyme complex. Members of key GT families reported to be involved in heteroxylan biosynthesis are up-regulated in the epidermal layer of barley leaves during powdery mildew infection. Modulation of their expression leads to altered susceptibility levels, suggesting that these genes are important for penetration resistance. The highest level of resistance was achieved when a GT43 gene was co-expressed with a GT47 candidate gene, both of which have been predicted to be involved in xylan backbone biosynthesis. Altering the expression level of several candidate heteroxylan synthesis genes can significantly alter disease susceptibility. This is predicted to occur through changes in the amount and structure of heteroxylan in barley papillae.
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Affiliation(s)
- Jamil Chowdhury
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of AdelaideGlen Osmond, SA, Australia
| | - Stefanie Lück
- Pathogen-Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
| | - Jeyaraman Rajaraman
- Pathogen-Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
| | - Dimitar Douchkov
- Pathogen-Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
| | - Neil J. Shirley
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of AdelaideGlen Osmond, SA, Australia
| | - Julian G. Schwerdt
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of AdelaideGlen Osmond, SA, Australia
| | - Patrick Schweizer
- Pathogen-Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
| | - Geoffrey B. Fincher
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of AdelaideGlen Osmond, SA, Australia
| | - Rachel A. Burton
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of AdelaideGlen Osmond, SA, Australia
| | - Alan Little
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of AdelaideGlen Osmond, SA, Australia
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Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis. GENETICS RESEARCH INTERNATIONAL 2016; 2016:7052323. [PMID: 27340568 PMCID: PMC4908241 DOI: 10.1155/2016/7052323] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022]
Abstract
Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.
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Rajaraman J, Douchkov D, Hensel G, Stefanato FL, Gordon A, Ereful N, Caldararu OF, Petrescu AJ, Kumlehn J, Boyd LA, Schweizer P. An LRR/Malectin Receptor-Like Kinase Mediates Resistance to Non-adapted and Adapted Powdery Mildew Fungi in Barley and Wheat. FRONTIERS IN PLANT SCIENCE 2016; 7:1836. [PMID: 28018377 PMCID: PMC5156707 DOI: 10.3389/fpls.2016.01836] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/21/2016] [Indexed: 05/04/2023]
Abstract
Pattern recognition receptors (PRRs) belonging to the multigene family of receptor-like kinases (RLKs) are the sensing devices of plants for microbe- or pathogen-associated molecular patterns released from microbial organisms. Here we describe Rnr8 (for Required for non-host resistance 8) encoding HvLEMK1, a LRR-malectin domain-containing transmembrane RLK that mediates non-host resistance of barley to the non-adapted wheat powdery mildew fungus Blumeria graminis f.sp. tritici. Transgenic barley lines with silenced HvLEMK1 allow entry and colony growth of the non-adapted pathogen, although sporulation was reduced and final colony size did not reach that of the adapted barley powdery mildew fungus B. graminis f.sp. hordei. Transient expression of the barley or wheat LEMK1 genes enhanced resistance in wheat to the adapted wheat powdery mildew fungus while expression of the same genes did not protect barley from attack by the barley powdery mildew fungus. The results suggest that HvLEMK1 is a factor mediating non-host resistance in barley and quantitative host resistance in wheat to the wheat powdery mildew fungus.
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Affiliation(s)
- Jeyaraman Rajaraman
- Pathogen-Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
| | - Dimitar Douchkov
- Pathogen-Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
| | - Götz Hensel
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
| | | | - Anna Gordon
- National Institute of Agricultural BotanyCambridge, UK
| | - Nelzo Ereful
- National Institute of Agricultural BotanyCambridge, UK
| | - Octav F. Caldararu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian AcademyBucharest, Romania
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian AcademyBucharest, Romania
| | - Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
| | | | - Patrick Schweizer
- Pathogen-Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
- *Correspondence: Patrick Schweizer,
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Douchkov D, Lück S, Johrde A, Nowara D, Himmelbach A, Rajaraman J, Stein N, Sharma R, Kilian B, Schweizer P. Discovery of genes affecting resistance of barley to adapted and non-adapted powdery mildew fungi. Genome Biol 2015; 15:518. [PMID: 25476012 PMCID: PMC4302706 DOI: 10.1186/s13059-014-0518-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 01/01/2023] Open
Abstract
Background Non-host resistance, NHR, to non-adapted pathogens and quantitative host resistance, QR, confer durable protection to plants and are important for securing yield in a longer perspective. However, a more targeted exploitation of the trait usually possessing a complex mode of inheritance by many quantitative trait loci, QTLs, will require a better understanding of the most important genes and alleles. Results Here we present results from a transient-induced gene silencing, TIGS, approach of candidate genes for NHR and QR in barley against the powdery mildew fungus Blumeria graminis. Genes were selected based on transcript regulation, multigene-family membership or genetic map position. Out of 1,144 tested RNAi-target genes, 96 significantly affected resistance to the non-adapted wheat- or the compatible barley powdery mildew fungus, with an overlap of four genes. TIGS results for QR were combined with transcript regulation data, allele-trait associations, QTL co-localization and copy number variation resulting in a meta-dataset of 51 strong candidate genes with convergent evidence for a role in QR. Conclusions This study represents an initial, functional inventory of approximately 3% of the barley transcriptome for a role in NHR or QR against the powdery mildew pathogen. The discovered candidate genes support the idea that QR in this Triticeae host is primarily based on pathogen-associated molecular pattern-triggered immunity, which is compromised by effector molecules produced by the compatible pathogen. The overlap of four genes with significant TIGS effects both in the NHR and QR screens also indicates shared components for both forms of durable pathogen resistance. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0518-8) contains supplementary material, which is available to authorized users.
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Malacarne G, Costantini L, Coller E, Battilana J, Velasco R, Vrhovsek U, Grando MS, Moser C. Regulation of flavonol content and composition in (Syrah×Pinot Noir) mature grapes: integration of transcriptional profiling and metabolic quantitative trait locus analyses. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4441-53. [PMID: 26071529 PMCID: PMC4507773 DOI: 10.1093/jxb/erv243] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Flavonols are a ubiquitous class of flavonoids that accumulate preferentially in flowers and mature berries. Besides their photo-protective function, they play a fundamental role during winemaking, stabilizing the colour by co-pigmentation with anthocyanins and contributing to organoleptic characteristics. Although the general flavonol pathway has been genetically and biochemically elucidated, the genetic control of flavonol content and composition at harvest is still not clear. To this purpose, the grapes of 170 segregating F1 individuals from a 'Syrah'×'Pinot Noir' population were evaluated at the mature stage for the content of six flavonol aglycons in four seasons. Metabolic data in combination with genetic data enabled the identification of 16 mQTLs (metabolic quantitative trait loci). For the first time, major genetic control by the linkage group 2 (LG 2)/MYBA region on flavonol variation, in particular of tri-hydroxylated flavonols, is demonstrated. Moreover, seven regions specifically associated with the fine control of flavonol biosynthesis are identified. Gene expression profiling of two groups of individuals significantly divergent for their skin flavonol content identified a large set of differentially modulated transcripts. Among these, the transcripts coding for MYB and bZIP transcription factors, methyltranferases, and glucosyltranferases specific for flavonols, proteins, and factors belonging to the UV-B signalling pathway and co-localizing with the QTL regions are proposed as candidate genes for the fine regulation of flavonol content and composition in mature grapes.
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Affiliation(s)
- Giulia Malacarne
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Laura Costantini
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Emanuela Coller
- Computational Biology Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Juri Battilana
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Riccardo Velasco
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Urska Vrhovsek
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Maria Stella Grando
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Claudio Moser
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
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Zivy M, Wienkoop S, Renaut J, Pinheiro C, Goulas E, Carpentier S. The quest for tolerant varieties: the importance of integrating "omics" techniques to phenotyping. FRONTIERS IN PLANT SCIENCE 2015; 6:448. [PMID: 26217344 PMCID: PMC4496562 DOI: 10.3389/fpls.2015.00448] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/31/2015] [Indexed: 05/19/2023]
Abstract
The primary objective of crop breeding is to improve yield and/or harvest quality while minimizing inputs. Global climate change and the increase in world population are significant challenges for agriculture and call for further improvements to crops and the development of new tools for research. Significant progress has been made in the molecular and genetic analysis of model plants. However, is science generating false expectations? Are 'omic techniques generating valuable information that can be translated into the field? The exploration of crop biodiversity and the correlation of cellular responses to stress tolerance at the plant level is currently a challenge. This viewpoint reviews concisely the problems one encounters when working on a crop and provides an outline of possible workflows when initiating cellular phenotyping via "-omic" techniques (transcriptomics, proteomics, metabolomics).
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Affiliation(s)
- Michel Zivy
- Department Génétique Quantitative et Évolution, Le Moulon INRA, CNRS, AgroParisTech, Plateforme PAPPSO, Université Paris-Sud, Gif-sur-Yvette, France
| | - Stefanie Wienkoop
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Jenny Renaut
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Carla Pinheiro
- Instituto de Tecnologia Química e Biológica, New University of Lisbon, Oeiras, Portugal
- Faculdade de Ciências e Tecnologia, New University of Lisbon, Caparica, Portugal
| | - Estelle Goulas
- Department of Sciences et Technologies, CNRS/Université Lille, Villeneuve d’Ascq, France
| | - Sebastien Carpentier
- Department of Biosystems, University of Leuven, Leuven, Belgium
- SYBIOMA, University of Leuven, Leuven, Belgium
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Identification and characterization of microsatellites in expressed sequence tags and their cross transferability in different plants. Int J Genomics 2014; 2014:863948. [PMID: 25389527 PMCID: PMC4217358 DOI: 10.1155/2014/863948] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/31/2014] [Accepted: 09/22/2014] [Indexed: 12/20/2022] Open
Abstract
Expressed sequence tags (EST) are potential source for the development of genic microsatellite markers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4% frequency). Analysis revealed that trinucleotide repeats (47.52%) were most abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through homology search and gene ontology, and 35 EST-SSRs were selected. Primer pairs were designed for evaluation of cross transferability and polymorphism among 11 plants belonging to five different families. Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75. The cross transferability ranged from 34.84% to 98.06% in different plants, with an average of 67.86%. Thus, the validation study of annotated 35 EST-SSR markers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants.
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Schnaithmann F, Kopahnke D, Pillen K. A first step toward the development of a barley NAM population and its utilization to detect QTLs conferring leaf rust seedling resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1513-1525. [PMID: 24797143 DOI: 10.1007/s00122-014-2315-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/15/2014] [Indexed: 06/03/2023]
Abstract
We suggest multi-parental nested association mapping as a valuable innovation in barley genetics, which increases the power to map quantitative trait loci and assists in extending genetic diversity of the elite barley gene pool. Plant genetic resources are a key asset to further improve crop species. The nested association mapping (NAM) approach was introduced to identify favorable genes in multi-parental populations. Here, we report toward the development of the first explorative barley NAM population and demonstrate its usefulness in a study on mapping quantitative trait loci (QTLs) for leaf rust resistance. The NAM population HEB-5 was developed from crossing and backcrossing five exotic barley donors with the elite barley cultivar 'Barke,' resulting in 295 NAM lines in generation BC1S1. HEB-5 was genetically characterized with 1,536 barley SNPs. Across HEB-5 and within the NAM families, no deviation from the expected genotype and allele frequencies was detected. Genetic similarity between 'Barke' and the NAM families ranged from 78.6 to 83.1 %, confirming the backcrossing step during population development. To explore its usefulness, a screen for leaf rust (Puccinia hordei) seedling resistance was conducted. Resistance QTLs were mapped to six barley chromosomes, applying a mixed model genome-wide association study. In total, four leaf rust QTLs were detected across HEB-5 and four QTLs within family HEB-F23. Favorable exotic QTL alleles reduced leaf rust symptoms on two chromosomes by 33.3 and 36.2 %, respectively. The located QTLs may represent new resistance loci or correspond to new alleles of known resistance genes. We conclude that the exploratory population HEB-5 can be applied to mapping and utilizing exotic QTL alleles of agronomic importance. The NAM concept will foster the evaluation of the genetic diversity, which is present in our primary barley gene pool.
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Affiliation(s)
- Florian Schnaithmann
- Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle, Germany
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Satovic Z, Avila CM, Cruz-Izquierdo S, Díaz-Ruíz R, García-Ruíz GM, Palomino C, Gutiérrez N, Vitale S, Ocaña-Moral S, Gutiérrez MV, Cubero JI, Torres AM. A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.). BMC Genomics 2013; 14:932. [PMID: 24377374 PMCID: PMC3880837 DOI: 10.1186/1471-2164-14-932] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/12/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. RESULTS A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. CONCLUSION We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications.
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Affiliation(s)
- Zlatko Satovic
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Present addresses: Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Carmen M Avila
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Serafin Cruz-Izquierdo
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Colegio de Postgraduados, Recursos Genéticos y Productividad – Genética, Campus Montecillo, Km 36.5 Carretera México-Texcoco, C.P., Texcoco, Edo. de México 56230, México
| | - Ramón Díaz-Ruíz
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Colegio de Postgraduados, Campus Puebla, Km 125.5 Carretera México-Puebla, C.P., Puebla, Pue 72760, México
| | - Gloria M García-Ruíz
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Carmen Palomino
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Natalia Gutiérrez
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Stefania Vitale
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Sara Ocaña-Moral
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - María Victoria Gutiérrez
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - José I Cubero
- Departamento de Mejora Genética, IAS-CSIC, Apdo. 4084, Córdoba 14080, Spain
| | - Ana M Torres
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
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Sun M, Hua W, Liu J, Huang S, Wang X, Liu G, Wang H. Design of new genome- and gene-sourced primers and identification of QTL for seed oil content in a specially high-oil Brassica napus cultivar. PLoS One 2012; 7:e47037. [PMID: 23077542 PMCID: PMC3470593 DOI: 10.1371/journal.pone.0047037] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 09/10/2012] [Indexed: 11/18/2022] Open
Abstract
Rapeseed (Brassica napus L.) is one of most important oilseed crops in the world. There are now various rapeseed cultivars in nature that differ in their seed oil content because they vary in oil-content alleles and there are high-oil alleles among the high-oil rapeseed cultivars. For these experiments, we generated doubled haploid (DH) lines derived from the cross between the specially high-oil cultivar zy036 whose seed oil content is approximately 50% and the specially low-oil cultivar 51070 whose seed oil content is approximately 36%. First, to address the deficiency in polymorphic markers, we designed 5944 pairs of newly developed genome-sourced primers and 443 pairs of newly developed primers related to oil-content genes to complement the 2244 pairs of publicly available primers. Second, we constructed a new DH genetic linkage map using 527 molecular markers, consisting of 181 publicly available markers, 298 newly developed genome-sourced markers and 48 newly developed markers related to oil-content genes. The map contained 19 linkage groups, covering a total length of 2,265.54 cM with an average distance between markers of 4.30 cM. Third, we identified quantitative trait loci (QTL) for seed oil content using field data collected at three sites over 3 years, and found a total of 12 QTL. Of the 12 QTL associated with seed oil content identified, 9 were high-oil QTL which derived from the specially high-oil cultivar zy036. Two high-oil QTL on chromosomes A2 and C9 co-localized in two out of three trials. By QTL mapping for seed oil content, we found four candidate genes for seed oil content related to four gene markers: GSNP39, GSSR161, GIFLP106 and GIFLP046. This information will be useful for cloning functional genes correlated with seed oil content in the future.
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Affiliation(s)
- Meiyu Sun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Shunmou Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
- * E-mail:
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Prohens J. Plant Breeding: A Success Story to be Continued Thanks to the Advances in Genomics. FRONTIERS IN PLANT SCIENCE 2011; 2:51. [PMID: 22645539 PMCID: PMC3355770 DOI: 10.3389/fpls.2011.00051] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 08/29/2011] [Indexed: 05/24/2023]
Affiliation(s)
- Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
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Spies A, Korzun V, Bayles R, Rajaraman J, Himmelbach A, Hedley PE, Schweizer P. Allele mining in barley genetic resources reveals genes of race-non-specific powdery mildew resistance. FRONTIERS IN PLANT SCIENCE 2011; 2:113. [PMID: 22629270 PMCID: PMC3355509 DOI: 10.3389/fpls.2011.00113] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 12/22/2011] [Indexed: 05/18/2023]
Abstract
Race-non-specific, or quantitative, pathogen resistance is of high importance to plant breeders due to its expected durability. However, it is usually controlled by multiple quantitative trait loci (QTL) and therefore difficult to handle in practice. Knowing the genes that underlie race-non-specific resistance (NR) would allow its exploitation in a more targeted manner. Here, we performed an association-genetic study in a customized worldwide collection of spring barley accessions for candidate genes of race-NR to the powdery mildew fungus Blumeria graminis f. sp. hordei (Bgh) and combined data with results from QTL mapping as well as functional-genomics approaches. This led to the identification of 11 associated genes with converging evidence for an important role in race-NR in the presence of the Mlo gene for basal susceptibility. Outstanding in this respect was the gene encoding the transcription factor WRKY2. The results suggest that unlocking plant genetic resources and integrating functional-genomic with genetic approaches can accelerate the discovery of genes underlying race-NR in barley and other crop plants.
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Affiliation(s)
- Annika Spies
- Leibniz-Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | | | | | - Jeyaraman Rajaraman
- Leibniz-Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Axel Himmelbach
- Leibniz-Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | | | - Patrick Schweizer
- Leibniz-Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
- *Correspondence: Patrick Schweizer, Leibniz-Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany. e-mail:
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