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Debieu M, Huard-Chauveau C, Genissel A, Roux F, Roby D. Quantitative disease resistance to the bacterial pathogen Xanthomonas campestris involves an Arabidopsis immune receptor pair and a gene of unknown function. MOLECULAR PLANT PATHOLOGY 2016; 17:510-520. [PMID: 26212639 PMCID: PMC6638543 DOI: 10.1111/mpp.12298] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Although quantitative disease resistance (QDR) is a durable and broad-spectrum form of resistance in plants, the identification of the genes underlying QDR is still in its infancy. RKS1 (Resistance related KinaSe1) has been reported recently to confer QDR in Arabidopsis thaliana to most but not all races of the bacterial pathogen Xanthomonas campestris pv. campestris (Xcc). We therefore explored the genetic bases of QDR in A. thaliana to diverse races of X. campestris (Xc). A nested genome-wide association mapping approach was used to finely map the genomic regions associated with QDR to Xcc12824 (race 2) and XccCFBP6943 (race 6). To identify the gene(s) implicated in QDR, insertional mutants (T-DNA) were selected for the candidate genes and phenotyped in response to Xc. We identified two major QTLs that confer resistance specifically to Xcc12824 and XccCFBP6943. Although QDR to Xcc12824 is conferred by At5g22540 encoding for a protein of unknown function, QDR to XccCFBP6943 involves the well-known immune receptor pair RRS1/RPS4. In addition to RKS1, this study reveals that three genes are involved in resistance to Xc with strikingly different ranges of specificity, suggesting that QDR to Xc involves a complex network integrating multiple response pathways triggered by distinct pathogen molecular determinants.
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Affiliation(s)
- Marilyne Debieu
- Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille-Lille 1, Villeneuve d'Ascq cedex, F-59655, France
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Carine Huard-Chauveau
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Anne Genissel
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Fabrice Roux
- Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille-Lille 1, Villeneuve d'Ascq cedex, F-59655, France
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Dominique Roby
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
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Mohan V, Gupta S, Thomas S, Mickey H, Charakana C, Chauhan VS, Sharma K, Kumar R, Tyagi K, Sarma S, Gupta SK, Kilambi HV, Nongmaithem S, Kumari A, Gupta P, Sreelakshmi Y, Sharma R. Tomato Fruits Show Wide Phenomic Diversity but Fruit Developmental Genes Show Low Genomic Diversity. PLoS One 2016; 11:e0152907. [PMID: 27077652 PMCID: PMC4831840 DOI: 10.1371/journal.pone.0152907] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/21/2016] [Indexed: 01/23/2023] Open
Abstract
Domestication of tomato has resulted in large diversity in fruit phenotypes. An intensive phenotyping of 127 tomato accessions from 20 countries revealed extensive morphological diversity in fruit traits. The diversity in fruit traits clustered the accessions into nine classes and identified certain promising lines having desirable traits pertaining to total soluble salts (TSS), carotenoids, ripening index, weight and shape. Factor analysis of the morphometric data from Tomato Analyzer showed that the fruit shape is a complex trait shared by several factors. The 100% variance between round and flat fruit shapes was explained by one discriminant function having a canonical correlation of 0.874 by stepwise discriminant analysis. A set of 10 genes (ACS2, COP1, CYC-B, RIN, MSH2, NAC-NOR, PHOT1, PHYA, PHYB and PSY1) involved in various plant developmental processes were screened for SNP polymorphism by EcoTILLING. The genetic diversity in these genes revealed a total of 36 non-synonymous and 18 synonymous changes leading to the identification of 28 haplotypes. The average frequency of polymorphism across the genes was 0.038/Kb. Significant negative Tajima’D statistic in two of the genes, ACS2 and PHOT1 indicated the presence of rare alleles in low frequency. Our study indicates that while there is low polymorphic diversity in the genes regulating plant development, the population shows wider phenotype diversity. Nonetheless, morphological and genetic diversity of the present collection can be further exploited as potential resources in future.
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Affiliation(s)
- Vijee Mohan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Soni Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sherinmol Thomas
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Hanjabam Mickey
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Chaitanya Charakana
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Vineeta Singh Chauhan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kapil Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rakesh Kumar
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kamal Tyagi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Supriya Sarma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Suresh Kumar Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Himabindu Vasuki Kilambi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sapana Nongmaithem
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Alka Kumari
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- * E-mail: (RS); (YS)
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- * E-mail: (RS); (YS)
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Tello J, Torres-Pérez R, Grimplet J, Ibáñez J. Association analysis of grapevine bunch traits using a comprehensive approach. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:227-42. [PMID: 26536891 DOI: 10.1007/s00122-015-2623-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/17/2015] [Indexed: 05/09/2023]
Abstract
KEY MESSAGE A set of SNP markers associated to bunch compactness and related traits were identified in grapevine. ABSTRACT Bunch compactness plays an important role in the sanitary status and perceived quality of table and wine grapes, being influenced by cultural practices and by environmental and genetic factors, which are mostly unknown. In this work, we took advantage of genetic, genomic and bioinformatic advances to analyze part of its molecular basis through a combination of transcriptomic and association analyses. Results from different transcriptomic comparisons between loose and compact grapevine clones were analyzed to select a set of candidate genes likely involved in the observed variation for bunch compactness. Up to 183 genes were sequenced in a grapevine collection, and 7032 single nucleotide polymorphisms (SNPs) were detected in more than 100 varieties with a frequency of the minor allele over 5%. They were used to test their association in three consecutive seasons with bunch compactness and two of its most influencing factors: total berry number and length of the first ramification of the rachis. Only one SNP was associated with berry number in two seasons, suggesting the high sensitiveness of this trait to seasonal environmental changes. On the other hand, we found a set of SNPs associated with both the first ramification length and bunch compactness in various seasons, in several genes which had not previously related to bunch compactness or bunch compactness-related traits. They are proposed as interesting candidates for further functional analyses aimed to verify the results obtained in this work, as a previous step to their inclusion in marker-assisted selection strategies.
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Affiliation(s)
- Javier Tello
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (ICVV, CSIC-Universidad de La Rioja-Gobierno de La Rioja), Carretera de Burgos km 6. Finca La Grajera, 26007, Logroño, Spain
| | - Rafael Torres-Pérez
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (ICVV, CSIC-Universidad de La Rioja-Gobierno de La Rioja), Carretera de Burgos km 6. Finca La Grajera, 26007, Logroño, Spain
| | - Jérôme Grimplet
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (ICVV, CSIC-Universidad de La Rioja-Gobierno de La Rioja), Carretera de Burgos km 6. Finca La Grajera, 26007, Logroño, Spain
| | - Javier Ibáñez
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (ICVV, CSIC-Universidad de La Rioja-Gobierno de La Rioja), Carretera de Burgos km 6. Finca La Grajera, 26007, Logroño, Spain.
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Barabaschi D, Tondelli A, Desiderio F, Volante A, Vaccino P, Valè G, Cattivelli L. Next generation breeding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:3-13. [PMID: 26566820 DOI: 10.1016/j.plantsci.2015.07.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/10/2015] [Accepted: 07/11/2015] [Indexed: 05/18/2023]
Abstract
The genomic revolution of the past decade has greatly improved our understanding of the genetic make-up of living organisms. The sequencing of crop genomes has completely changed our vision and interpretation of genome organization and evolution. Re-sequencing allows the identification of an unlimited number of markers as well as the analysis of germplasm allelic diversity based on allele mining approaches. High throughput marker technologies coupled with advanced phenotyping platforms provide new opportunities for discovering marker-trait associations which can sustain genomic-assisted breeding. The availability of genome sequencing information is enabling genome editing (site-specific mutagenesis), to obtain gene sequences desired by breeders. This review illustrates how next generation sequencing-derived information can be used to tailor genomic tools for different breeders' needs to revolutionize crop improvement.
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Affiliation(s)
- Delfina Barabaschi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Alessandro Tondelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Andrea Volante
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Rice Research Unit, SS 11 to Torino Km 2.5, 13100 Vercelli, Italy
| | - Patrizia Vaccino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Research Unit for Cereal Selection in Continental areas, via R. Forlani, e, 26866 S. Angelo Lodigiano, Italy
| | - Giampiero Valè
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Rice Research Unit, SS 11 to Torino Km 2.5, 13100 Vercelli, Italy
| | - Luigi Cattivelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy.
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Chen X, Yuan L, Ludewig U. Natural Genetic Variation of Seed Micronutrients of Arabidopsis thaliana Grown in Zinc-Deficient and Zinc-Amended Soil. FRONTIERS IN PLANT SCIENCE 2016; 7:1070. [PMID: 27507976 PMCID: PMC4960235 DOI: 10.3389/fpls.2016.01070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/07/2016] [Indexed: 05/03/2023]
Abstract
The quality of edible seeds for human and animal nutrition is crucially dependent on high zinc (Zn) and iron (Fe) seed concentrations. The micronutrient bioavailability is strongly reduced by seed phytate that forms complexes with seed cations. Superior genotypes with increased seed Zn concentrations had been identified, but low micronutrient seed levels often prevail when the plants are grown in Zn-deficient soils, which are globally widespread and correlate with human Zn-deficiency. Here, seed Zn concentrations of Arabidopsis accessions grown in Zn-deficient and Zn-amended conditions were measured together with seed Fe and manganese (Mn), in a panel of 108 accessions. By applying genome-wide association, de novo candidate genes potentially involved in the seed micronutrient accumulation were identified. However, a candidate inositol 1,3,4-trisphosphate 5/6-kinase 3 gene (ITPK3), located close to a significant nucleotide polymorphism associated with relative Zn seed concentrations, was dispensable for seed micronutrients accumulation in Col-0. Loss of this gene in itpk3-1 did neither affect phytate seed levels, nor seed Zn, Fe, and Mn. It is concluded that large natural variance of micronutrient seed levels is identified in the population and several accessions maintain high seed Zn despite growth in Zn-deficient conditions.
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Affiliation(s)
- Xiaochao Chen
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, StuttgartGermany
| | - Lixing Yuan
- Key Laboratory of Plant-Soil Interaction, Ministry of Education, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, BeijingChina
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, StuttgartGermany
- *Correspondence: Uwe Ludewig,
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Malyshev AV, Arfin Khan MAS, Beierkuhnlein C, Steinbauer MJ, Henry HAL, Jentsch A, Dengler J, Willner E, Kreyling J. Plant responses to climatic extremes: within-species variation equals among-species variation. GLOBAL CHANGE BIOLOGY 2016; 22:449-464. [PMID: 26426898 DOI: 10.1111/gcb.13114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 09/07/2015] [Indexed: 06/05/2023]
Abstract
Within-species and among-species differences in growth responses to a changing climate have been well documented, yet the relative magnitude of within-species vs. among-species variation has remained largely unexplored. This missing comparison impedes our ability to make general predictions of biodiversity change and to project future species distributions using models. We present a direct comparison of among- versus within-species variation in response to three of the main stresses anticipated with climate change: drought, warming, and frost. Two earlier experiments had experimentally induced (i) summer drought and (ii) spring frost for four common European grass species and their ecotypes from across Europe. To supplement existing data, a third experiment was carried out, to compare variation among species from different functional groups to within-species variation. Here, we simulated (iii) winter warming plus frost for four grasses, two nonleguminous, and two leguminous forbs, in addition to eleven European ecotypes of the widespread grass Arrhenatherum elatius. For each experiment, we measured: (i) C/N ratio and biomass, (ii) chlorophyll content and biomass, and (iii) plant greenness, root (15) N uptake, and live and dead tissue mass. Using coefficients of variation (CVs) for each experiment and response parameter, a total of 156 within- vs. among-species comparisons were conducted, comparing within-species variation in each of four species with among-species variation for each seed origin (five countries). Of the six significant differences, within-species CVs were higher than among-species CVs in four cases. Partitioning of variance within each treatment in two of the three experiments showed that within-species variability (ecotypes) could explain an additional 9% of response variation after accounting for the among-species variation. Our observation that within-species variation was generally as high as among-species variation emphasizes the importance of including both within- and among-species variability in ecological theory (e.g., the insurance hypothesis) and for practical applications (e.g., biodiversity conservation).
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Affiliation(s)
- Andrey V Malyshev
- Experimental Plant Ecology, Institute of Botany and Landscape Ecology, Greifswald University, Soldmannstrasse 15, Greifswald, 17487, Germany
| | - Mohammed A S Arfin Khan
- Disturbance Ecology, BayCEER, University of Bayreuth, Bayreuth, 95440, Germany
- Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | | | | | - Hugh A L Henry
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Anke Jentsch
- Disturbance Ecology, BayCEER, University of Bayreuth, Bayreuth, 95440, Germany
| | - Jürgen Dengler
- Plant Ecology, BayCEER, University of Bayreuth, Bayreuth, 95440, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Evelin Willner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Satellite Collections North, Malchow/Poel, 23999, Germany
| | - Juergen Kreyling
- Experimental Plant Ecology, Institute of Botany and Landscape Ecology, Greifswald University, Soldmannstrasse 15, Greifswald, 17487, Germany
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Fujino K, Obara M, Shimizu T, Koyanagi KO, Ikegaya T. Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region. BREEDING SCIENCE 2015; 65:403-10. [PMID: 26719743 PMCID: PMC4671701 DOI: 10.1270/jsbbs.65.403] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/07/2015] [Indexed: 05/20/2023]
Abstract
Plant breeding programs in local regions may generate genetic variations that are desirable to local populations and shape adaptability during the establishment of local populations. To elucidate genetic bases for this process, we proposed a new approach for identifying the genetic bases for the traits improved during rice breeding programs; association mapping focusing on a local population. In the present study, we performed association mapping focusing on a local rice population, consisting of 63 varieties, in Hokkaido, the northernmost region of Japan and one of the northern limits of rice cultivation worldwide. Six and seventeen QTLs were identified for heading date and low temperature germinability, respectively. Of these, 13 were novel QTLs in this population and 10 corresponded to the QTLs previously reported based on QTL mapping. The identification of QTLs for traits in local populations including elite varieties may lead to a better understanding of the genetic bases of elite traits. This is of direct relevance for plant breeding programs in local regions.
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Affiliation(s)
- Kenji Fujino
- NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
- Corresponding author (e-mail: )
| | - Mari Obara
- NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
| | - Toshiaki Shimizu
- Laboratory of Genome Sciences, Graduate School of Information Science and Technology, Hokkaido University,
Sapporo, Hokkaido 060-0814,
Japan
| | - Kanako O. Koyanagi
- Laboratory of Genome Sciences, Graduate School of Information Science and Technology, Hokkaido University,
Sapporo, Hokkaido 060-0814,
Japan
| | - Tomohito Ikegaya
- NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
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Borrill P, Adamski N, Uauy C. Genomics as the key to unlocking the polyploid potential of wheat. THE NEW PHYTOLOGIST 2015; 208:1008-22. [PMID: 26108556 DOI: 10.1111/nph.13533] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/31/2015] [Indexed: 05/19/2023]
Abstract
Polyploidy has played a central role in plant genome evolution and in the formation of new species such as tetraploid pasta wheat and hexaploid bread wheat. Until recently, the high sequence conservation between homoeologous genes, together with the large genome size of polyploid wheat, had hindered genomic analyses in this important crop species. In the past 5 yr, however, the advent of next-generation sequencing has radically changed the wheat genomics landscape. Here, we review a series of advances in genomic resources and tools for functional genomics that are shifting the paradigm of what is possible in wheat molecular genetics and breeding. We discuss how understanding the relationship between homoeologues can inform approaches to modulate the response of quantitative traits in polyploid wheat; we also argue that functional redundancy has 'locked up' a wide range of phenotypic variation in wheat. We explore how genomics provides key tools to inform targeted manipulation of multiple homoeologues, thereby allowing researchers and plant breeders to unlock the full polyploid potential of wheat.
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Affiliation(s)
| | - Nikolai Adamski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Chen G, Wang X, Hao J, Yan J, Ding J. Genome-Wide Association Implicates Candidate Genes Conferring Resistance to Maize Rough Dwarf Disease in Maize. PLoS One 2015; 10:e0142001. [PMID: 26529245 PMCID: PMC4631334 DOI: 10.1371/journal.pone.0142001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/15/2015] [Indexed: 11/18/2022] Open
Abstract
Maize rough dwarf disease (MRDD) is a destructive viral disease in China, which results in 20-30% of the maize yield losses in affected areas and even as high as 100% in severely infected fields. Understanding the genetic basis of resistance will provide important insights for maize breeding program. In this study, a diverse maize population comprising of 527 inbred lines was evaluated in four environments and a genome-wide association study (GWAS) was undertaken with over 556000 SNP markers. Fifteen candidate genes associated with MRDD resistance were identified, including ten genes with annotated protein encoding functions. The homologous of nine candidate genes were predicted to relate to plant defense in different species based on published results. Significant correlation (R2 = 0.79) between the MRDD severity and the number of resistance alleles was observed. Consequently, we have broadened the resistant germplasm to MRDD and identified a number of resistance alleles by GWAS. The results in present study also imply the candidate genes in defense pathway play an important role in resistance to MRDD in maize.
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Affiliation(s)
- Gengshen Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoming Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Junjie Hao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junqiang Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
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Zhang J, Mason AS, Wu J, Liu S, Zhang X, Luo T, Redden R, Batley J, Hu L, Yan G. Identification of Putative Candidate Genes for Water Stress Tolerance in Canola (Brassica napus). FRONTIERS IN PLANT SCIENCE 2015; 6:1058. [PMID: 26640475 PMCID: PMC4661274 DOI: 10.3389/fpls.2015.01058] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/13/2015] [Indexed: 05/20/2023]
Abstract
Drought stress can directly inhibit seedling establishment in canola (Brassica napus), resulting in lower plant densities and reduced yields. To dissect this complex trait, 140 B. napus accessions were phenotyped under normal (0.0 MPa, S0) and water-stressed conditions simulated by polyethylene glycol (PEG) 6000 (-0.5 MPa, S5) in a hydroponic system. Phenotypic variation and heritability indicated that the root to shoot length ratio was a reliable indicator for water stress tolerance. Thereafter, 66 accessions (16 water stress tolerant, 34 moderate and 16 sensitive lines) were genotyped using 25,495 Brassica single nucleotide polymorphisms (SNPs). Genome-wide association studies (GWAS) identified 16 loci significantly associated with water stress response. Two B. napus accessions were used for RNA sequencing, with differentially-expressed genes under normal and water-stressed conditions examined. By combining differentially-expressed genes detected by RNA sequencing with significantly associated loci from GWAS, 79 candidate genes were identified, of which eight were putatively associated with drought tolerance based on gene ontology of Arabidopsis. Functional validation of these genes may confirm key drought-related genes for selection and breeding in B. napus. Our results provide insight into the genetic basis of water stress tolerance in canola.
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Affiliation(s)
- Jing Zhang
- Ministry of Agriculture (MOA) Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Annaliese S. Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of QueenslandBrisbane, QLD, Australia
| | - Jian Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Sheng Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xuechen Zhang
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Tao Luo
- Ministry of Agriculture (MOA) Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Robert Redden
- Australian Grains Genebank, Department of Economic Development Jobs Transport and ResourcesHorsham, VIC, Australia
| | - Jacqueline Batley
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of QueenslandBrisbane, QLD, Australia
| | - Liyong Hu
- Ministry of Agriculture (MOA) Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Liyong Hu
| | - Guijun Yan
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
- Guijun Yan
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