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Seki K, Toda Y. QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp. FRONTIERS IN PLANT SCIENCE 2022; 13:949470. [PMID: 36311127 PMCID: PMC9606697 DOI: 10.3389/fpls.2022.949470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Wild species of lettuce (Lactuca sp.) are thought to have first been domesticated for oilseed contents to provide seed oil for human consumption. Although seed morphology is an important trait contributing to oilseed in lettuce, the underlying genetic mechanisms remain elusive. Since lettuce seeds are small, a manual phenotypic determination required for a genetic dissection of such traits is challenging. In this study, we built and applied an instance segmentation-based seed morphology quantification pipeline to measure traits in seeds generated from a cross between the domesticated oilseed type cultivar 'Oilseed' and the wild species 'UenoyamaMaruba' in an automated manner. Quantitative trait locus (QTL) mapping following ddRAD-seq revealed 11 QTLs linked to 7 seed traits (area, width, length, length-to-width ratio, eccentricity, perimeter length, and circularity). Remarkably, the three QTLs with the highest LOD scores, qLWR-3.1, qECC-3.1, and qCIR-3.1, for length-to-width ratio, eccentricity, and circularity, respectively, mapped to linkage group 3 (LG3) around 161.5 to 214.6 Mb, a region previously reported to be associated with domestication traits from wild species. These results suggest that the oilseed cultivar harbors genes acquired during domestication to control seed shape in this genomic region. This study also provides genetic evidence that domestication arose, at least in part, by selection for the oilseed type from wild species and demonstrates the effectiveness of image-based phenotyping to accelerate discoveries of the genetic basis for small morphological features such as seed size and shape.
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Affiliation(s)
- Kousuke Seki
- Nagano Vegetable and Ornamental Crops Experiment Station, Shiojiri, Japan
| | - Yosuke Toda
- Phytometrics Co., Ltd., Shizuoka, Japan
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
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Macias-González M, Truco MJ, Han R, Jenni S, Michelmore RW. High-resolution genetic dissection of the major QTL for tipburn resistance in lettuce, Lactuca sativa. G3 (BETHESDA, MD.) 2021; 11:jkab097. [PMID: 33772545 PMCID: PMC8495944 DOI: 10.1093/g3journal/jkab097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/21/2021] [Indexed: 12/13/2022]
Abstract
Tipburn is an important physiological disorder of lettuce, Lactuca sativa L., related to calcium deficiency that can result in leaf necrosis and unmarketable crops. The major quantitative trait locus (QTL), qTPB5.2, can account for up to 70% of the phenotypic variance for tipburn incidence in the field. This QTL was genetically dissected to identify candidate genes for tipburn by creating lines with recombination events within the QTL and assessing their resistance to tipburn. By comparing lines with contrasting haplotypes, the genetic region was narrowed down to ∼877 Kb that was associated with a reduction of tipburn by ∼60%. Analysis of the lettuce reference genome sequence revealed 12 genes in this region, one of which is a calcium transporter with a single nucleotide polymorphism in an exon between haplotypes with contrasting phenotypes. RNA-seq analysis of recombinants revealed two genes that were differentially expressed between contrasting haplotypes consistent with the tipburn phenotype. One encodes a Teosinte branched1/Cycloidea/Proliferating Cell factor transcription factor; however, differential expression of the calcium transporter was detected. The phenotypic data indicated that there is a second region outside of the ∼877 Kb region but within the QTL, at which a haplotype from the susceptible parent decreased tipburn by 10-20%. A recombinant line was identified with beneficial haplotypes in each region from both parents that showed greater tipburn resistance than the resistant parent; this line could be used as the foundation for breeding cultivars with more resistance than is currently available.
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Affiliation(s)
- Miguel Macias-González
- The Genome Center, University of California, Davis, Davis, CA 95616, USA
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Maria Jose Truco
- The Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Rongkui Han
- The Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Sylvie Jenni
- Science and Technology Branch, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
| | - Richard W Michelmore
- The Genome Center, University of California, Davis, Davis, CA 95616, USA
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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Damerum A, Smith HK, Clarkson G, Truco MJ, Michelmore RW, Taylor G. The genetic basis of water-use efficiency and yield in lettuce. BMC PLANT BIOLOGY 2021; 21:237. [PMID: 34044761 PMCID: PMC8157645 DOI: 10.1186/s12870-021-02987-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Water supply limits agricultural productivity of many crops including lettuce. Identifying cultivars within crop species that can maintain productivity with reduced water supply is a significant challenge, but central to developing resilient crops for future water-limited climates. We investigated traits known to be related to water-use efficiency (WUE) and yield in lettuce, a globally important leafy salad crop, in a recombinant inbred line (RIL) lettuce mapping population, produced from a cross between the cultivated Lactuca sativa L. cv. Salinas and its wild progenitor L. serriola L. RESULTS Wild and cultivated lettuce differed in their WUE and we observed transgressive segregation in yield and water-use traits in the RILs. Quantitative trait loci (QTL) analysis identified genomic regions controlling these traits under well-watered and droughted conditions. QTL were detected for carbon isotope discrimination, transpiration, stomatal conductance, leaf temperature and yield, controlling 4-23 % of the phenotypic variation. A QTL hotspot was identified on chromosome 8 that controlled carbon isotope discrimination, stomatal conductance and yield under drought. Several promising candidate genes in this region were associated with WUE, including aquaporins, late embryogenesis abundant proteins, an abscisic acid-responsive element binding protein and glutathione S-transferases involved in redox homeostasis following drought stress were also identified. CONCLUSIONS For the first time, we have characterised the genetic basis of WUE of lettuce, a commercially important and water demanding crop. We have identified promising candidate genomic regions determining WUE and yield under well-watered and water-limiting conditions, providing important pre-breeding data for future lettuce selection and breeding where water productivity will be a key target.
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Affiliation(s)
- Annabelle Damerum
- Department of Plant Sciences, University of California, Davis, 95616, CA, USA
| | - Hazel K Smith
- School of Biological Sciences, University of Southampton, Hampshire, SO17 1BJ, UK
- Present address: Vitacress Salads, Lower Link Farm, St Mary Bourne, SP11 6DB, Hampshire, UK
| | - Gjj Clarkson
- Present address: Vitacress Salads, Lower Link Farm, St Mary Bourne, SP11 6DB, Hampshire, UK
| | - Maria José Truco
- The Genome Centre, University of California, Davis, 95616, CA, USA
| | | | - Gail Taylor
- Department of Plant Sciences, University of California, Davis, 95616, CA, USA.
- School of Biological Sciences, University of Southampton, Hampshire, SO17 1BJ, UK.
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Linkage Map Development by EST-SSR Markers and QTL Analysis for Inflorescence and Leaf Traits in Chrysanthemum ( Chrysanthemum morifolium Ramat.). PLANTS 2020; 9:plants9101342. [PMID: 33050665 PMCID: PMC7600071 DOI: 10.3390/plants9101342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022]
Abstract
Chrysanthemums (Chrysanthemum morifolium Ramat.) are famous ornamental crops with high medicinal and industrial values. The inflorescence and leaf traits are key factors that affect the yield and quality of chrysanthemum. However, the genetic improvement of those traits is slow within chrysanthemum because of its hexaploidy, high heterozygosity and enormous genome. To study the genetic control of the important traits and facilitate marker-assisted selection (MAS) in chrysanthemum, it is desirable to populate the genetic maps with an abundance of transferrable markers such as microsatellites (SSRs). A genetic map was constructed with expressed sequence tag–simple sequence repeat (EST-SSR) markers in an F1 progeny of 192 offspring. A total of 1000 alleles were generated from 223 EST-SSR primer pairs. The preliminary maternal and paternal maps consisted of 265 marker alleles arranged into 49 and 53 linkage groups (LGs), respectively. The recombined parental maps covered 906.3 and 970.1 cM of the genome, respectively. Finally, 264 polymorphic loci were allocated to nine LGs. The integrated map spanned 954.5 cM in length with an average genetic distance of 3.6 cM between two neighbouring loci. Quantitative trait loci (QTLs) analysis was performed using the integrated map for inflorescence diameter (ID), central disc flower diameter (CDFD), number of whorls of ray florets (NWRF), number of ray florets (NRF), number of disc florets (NDF), number of florets (NF), ray floret length (RFL), ray floret width (RFW), ray floret length/width (RFL/W), leaf length (LL), leaf width (LW) and leaf length/width (LL/W). Overall, 36 (21 major) QTLs were identified. The successful mapping of inflorescence and leaf traits QTL demonstrated the utility of the new integrated linkage map. This study is the first report of a genetic map based on EST-SSR markers in chrysanthemum. The EST-SSR markers, genetic map and QTLs reported here could be valuable resources in implementing MAS for chrysanthemums in breeding programs.
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Damerum A, Chapman MA, Taylor G. Innovative breeding technologies in lettuce for improved post-harvest quality. POSTHARVEST BIOLOGY AND TECHNOLOGY 2020; 168:111266. [PMID: 33012992 PMCID: PMC7397847 DOI: 10.1016/j.postharvbio.2020.111266] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Societal awareness of healthy eating is increasing alongside the market for processed bagged salads, which remain as one of the strongest growing food sectors internationally, including most recently from indoor growing systems. Lettuce represents a significant proportion of this ready-to-eat salad market. However, such products typically have a short shelf life, with decay of post-harvest quality occurring through complex biochemical and physiological changes in leaves and resulting in spoilage, food waste and risks to health. We review the functional and quantitative genetic understanding of lettuce post-harvest quality, revealing that few findings have translated into improved cultivar development. We identify (i) phytonutrient status (for enhanced antioxidant and vitamin status, aroma and flavour) (ii) leaf biophysical, cell wall and water relations traits (for longer shelf life) (iii) leaf surface traits (for enhanced food safety and reduced spoilage) and (iv) chlorophyll, other pigments and developmental senescence traits (for appearance and colour), as key targets for future post-harvest breeding. Lettuce is well-placed for rapid future exploitation to address postharvest quality traits with extensive genomic resources including the recent release of the lettuce genome and the development of innovative breeding technologies. Although technologies such as CRISPR/Cas genome editing are paving the way for accelerated crop improvement, other equally important resources available for lettuce include extensive germplasm collections, bi-parental mapping and wide populations with genotyping for genomic selection strategies and extensive multiomic datasets for candidate gene discovery. We discuss current progress towards post-harvest quality breeding for lettuce and how such resources may be utilised for future crop improvement.
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Affiliation(s)
- Annabelle Damerum
- Department of Plant Sciences, University of California, Davis, 95616, USA
| | - Mark A Chapman
- School of Biological Sciences, University of Southampton, Southampton, SO179BJ, UK
| | - Gail Taylor
- Department of Plant Sciences, University of California, Davis, 95616, USA
- School of Biological Sciences, University of Southampton, Southampton, SO179BJ, UK
- Corresponding author at: Department of Plant Sciences, University of California, Davis, 95616, USA.
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Wen G, Dang J, Xie Z, Wang J, Jiang P, Guo Q, Liang G. Molecular karyotypes of loquat ( Eriobotrya japonica) aneuploids can be detected by using SSR markers combined with quantitative PCR irrespective of heterozygosity. PLANT METHODS 2020; 16:22. [PMID: 32123538 PMCID: PMC7041098 DOI: 10.1186/s13007-020-00568-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/13/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Aneuploidy, a condition caused by an imbalance between the relative dosages of chromosomes, generally produces a novel phenotype specific to the molecular karyotype. Few techniques are currently available for detecting the molecular karyotypes of aneuploids in plants. RESULTS Based on this imbalance in chromosome dosage, a new approach (referred to as 'SSR-qPCR') combining simple sequence repeat (SSR) markers and quantitative real-time PCR (qPCR) has been developed and utilized to detect some common aneuploids irrespective of heterozygosity. We screened 17 specific SSR markers covering all loquat linkage groups and redesigned 6 pairs of primers for SSR markers that can detect loquat chromosome aneuploidies. The SSR-qPCR detection results obtained for hybrid progeny and open-pollination progeny of triploid loquat showed diagnostic accuracies of 88.9% and 62.5%, respectively, compared with the chromosome preparation results. CONCLUSION SSR-qPCR can detect loquat aneuploids and be used to construct the entire molecular karyotypes of aneuploid individuals. Therefore, this method offers a novel alternative for the detection of chromosome aneuploidies.
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Affiliation(s)
- Guo Wen
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Jiangbo Dang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Zhongyi Xie
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Jinying Wang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Pengfei Jiang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
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Patella A, Palumbo F, Galla G, Barcaccia G. The Molecular Determination of Hybridity and Homozygosity Estimates in Breeding Populations of Lettuce ( Lactuca sativa L.). Genes (Basel) 2019; 10:E916. [PMID: 31717592 PMCID: PMC6895879 DOI: 10.3390/genes10110916] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/26/2022] Open
Abstract
The development of new varieties of horticultural crops benefits from the integration of conventional and molecular marker-assisted breeding schemes in order to combine phenotyping and genotyping information. In this study, a selected panel of 16 microsatellite markers were used in different steps of a breeding programme of lettuce (Lactuca sativa L., 2 n = 18). Molecular markers were first used to genotype 71 putative parental lines and to plan 89 controlled crosses designed to maximise recombination potentials. The resulting 871 progeny plants were then molecularly screened, and their marker allele profiles were compared with the profiles expected based on the parental lines. The average cross-pollination success rate was 68 ± 33%, so 602 F1 hybrids were completely identified. Unexpected genotypes were detected in 5% of cases, consistent with this species' spontaneous out-pollination rate. Finally, in a later step of the breeding programme, 47 different F3 progenies, selected by phenotyping for a number of morphological descriptors, were characterised in terms of their observed homozygosity and within-population genetic uniformity and stability. Ten of these populations had a median homozygosity above 90% and a median genetic similarity above 95% and are, therefore, particularly suitable for pre-commercial trials. In conclusion, this study shows the synergistic effects and advantages of conventional and molecular methods of selection applied in different steps of a breeding programme aimed at developing new varieties of lettuce.
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Affiliation(s)
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro PD, Italy; (A.P.); (G.G.); (G.B.)
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Macias-González M, Truco MJ, Bertier LD, Jenni S, Simko I, Hayes RJ, Michelmore RW. Genetic architecture of tipburn resistance in lettuce. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2209-2222. [PMID: 31055612 DOI: 10.1007/s00122-019-03349-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/20/2019] [Indexed: 05/16/2023]
Abstract
KEY MESSAGE Two major QTLs for tipburn were identified in LGs 1 and 5 contributing to resistance in cv. Salinas. The findings suggest pleiotropic effects between leaf crinkliness/savoy and tipburn. Tipburn is a physiological disorder in lettuce that is thought to be caused by a localized deficiency of calcium in leaf tissues. To elucidate the genetic architecture of resistance to tipburn in lettuce, seven recombinant inbred line populations were analyzed in multiple environments and years to identify quantitative trait loci (QTLs) for tipburn. Core height, head firmness, head closure, leaf crinkliness, plant fresh weight, and leaf savoy were also analyzed to investigate whether QTLs for these morphological traits collocated with QTLs for tipburn, which would be indicative of pleiotropic effects. Twenty-three major, intermediate, and minor unique QTLs for tipburn were identified in one or more populations scattered throughout the genome. Two major QTLs for tipburn incidence were identified in linkage groups (LGs) 1 and 5, which determined up to 45 and 66% of the phenotypic variance. The major QTL in LG 1 collocated with the head firmness QTL. The major QTL in LG 5 collocated with the QTL for core height, leaf crinkliness, and head firmness. Further research is needed to determine whether these associations are due to pleiotropic effects of the same gene or if the genes determining these traits are tightly linked. The beneficial alleles at the QTLs in LGs 1 and 5 are present in Lactuca sativa cv. Salinas, the genotype sequenced for the reference genome assembly. Therefore, these QTLs are good targets to identify genes causing tipburn as well as regions for marker-assisted selection to improve resistance to tipburn in lettuce.
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Affiliation(s)
- M Macias-González
- The Genome Center, University of California, Davis, CA, 95616, USA
- Enza Zaden North America Research, Inc - San Juan Bautista, 525 Lucy Brown Lane, San Juan Bautista, CA, 95045, USA
| | - M J Truco
- The Genome Center, University of California, Davis, CA, 95616, USA
| | - L D Bertier
- The Genome Center, University of California, Davis, CA, 95616, USA
| | - S Jenni
- Science and Technology Branch, Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-Sur-Richelieu, QC, J3B 3E6, Canada
| | - I Simko
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA, 93905, USA
| | - R J Hayes
- U.S. Department of Agriculture, Agricultural Research Secorrectlyrvice, Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR, 97331-8539, USA
| | - R W Michelmore
- The Genome Center, University of California, Davis, CA, 95616, USA.
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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Bertier LD, Ron M, Huo H, Bradford KJ, Britt AB, Michelmore RW. High-Resolution Analysis of the Efficiency, Heritability, and Editing Outcomes of CRISPR/Cas9-Induced Modifications of NCED4 in Lettuce ( Lactuca sativa). G3 (BETHESDA, MD.) 2018; 8:1513-1521. [PMID: 29511025 PMCID: PMC5940144 DOI: 10.1534/g3.117.300396] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 02/25/2018] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 is a transformative tool for making targeted genetic alterations. In plants, high mutation efficiencies have been reported in primary transformants. However, many of the mutations analyzed were somatic and therefore not heritable. To provide more insights into the efficiency of creating stable homozygous mutants using CRISPR/Cas9, we targeted LsNCED4 (9-cis-EPOXYCAROTENOID DIOXYGENASE4), a gene conditioning thermoinhibition of seed germination in lettuce. Three constructs, each capable of expressing Cas9 and a single gRNA targeting different sites in LsNCED4, were stably transformed into lettuce (Lactuca sativa) cvs. Salinas and Cobham Green. Analysis of 47 primary transformants (T1) and 368 T2 plants by deep amplicon sequencing revealed that 57% of T1 plants contained events at the target site: 28% of plants had germline mutations in one allele indicative of an early editing event (mono-allelic), 8% of plants had germline mutations in both alleles indicative of two early editing events (bi-allelic), and the remaining 21% of plants had multiple low frequency mutations indicative of late events (chimeric plants). Editing efficiency was similar in both genotypes, while the different gRNAs varied in efficiency. Amplicon sequencing of 20 T1 and more than 100 T2 plants for each of the three gRNAs showed that repair outcomes were not random, but reproducible and characteristic for each gRNA. Knockouts of NCED4 resulted in large increases in the maximum temperature for seed germination, with seeds of both cultivars capable of germinating >70% at 37°. Knockouts of NCED4 provide a whole-plant selectable phenotype that has minimal pleiotropic consequences. Targeting NCED4 in a co-editing strategy could therefore be used to enrich for germline-edited events simply by germinating seeds at high temperature.
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Affiliation(s)
| | | | - Heqiang Huo
- Department of Plant Sciences, Seed Biotechnology Center
| | | | | | - Richard W Michelmore
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA 95616
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Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts. 3 Biotech 2018; 8:242. [PMID: 29744274 DOI: 10.1007/s13205-018-1276-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/03/2018] [Indexed: 01/01/2023] Open
Abstract
The eucalypt species, Eucalyptus tereticornis and Eucalyptus camaldulensis, show tolerance to drought and salinity conditions, respectively, and are widely cultivated in arid and semiarid regions of tropical countries. In this study, genetic linkage map was developed for interspecific cross E. tereticornis × E. camaldulensis using pseudo-testcross strategy with simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), and sequence-related amplified polymorphism (SRAP) markers. The consensus genetic map comprised totally 283 markers with 84 SSRs, 94 ISSRs, and 105 SRAP markers on 11 linkage groups spanning 1163.4 cM genetic distance. Blasting the SSR sequences against E. grandis sequences allowed an alignment of 64% and the average ratio of genetic-to-physical distance was 1.7 Mbp/cM, which strengths the evidence that high amount of synteny and colinearity exists among eucalypts genome. Blast searches also revealed that 37% of SSRs had homologies with genes, which could potentially be used in the variety of downstream applications including candidate gene polymorphism. Quantitative trait loci (QTL) analysis for adventitious rooting traits revealed six QTL for rooting percent and root length on five chromosomes with interval and composite interval mapping. All the QTL explained 12.0-14.7% of the phenotypic variance, showing the involvement of major effect QTL on adventitious rooting traits. Increasing the density of markers would facilitate the detection of more number of small-effect QTL and also underpinning the genes involved in rooting process.
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Ates D, Aldemir S, Alsaleh A, Erdogmus S, Nemli S, Kahriman A, Ozkan H, Vandenberg A, Tanyolac B. A consensus linkage map of lentil based on DArT markers from three RIL mapping populations. PLoS One 2018; 13:e0191375. [PMID: 29351563 PMCID: PMC5774769 DOI: 10.1371/journal.pone.0191375] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/03/2018] [Indexed: 12/21/2022] Open
Abstract
Background Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. Materials and methods A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including “CDC Redberry” x “ILL7502” (LR8), “ILL8006” x “CDC Milestone” (LR11) and “PI320937” x “Eston” (LR39). Results The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. Conclusion This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.
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Affiliation(s)
- Duygu Ates
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Secil Aldemir
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Ahmad Alsaleh
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Semih Erdogmus
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Seda Nemli
- Department of Bieoengineering and Genetics, Gumushane University, Gumushane, Turkey
| | - Abdullah Kahriman
- Department of Field Crops, Faculty of Agriculture, Harran University, Sanlı Urfa, Turkey
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Albert Vandenberg
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Bahattin Tanyolac
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
- * E-mail:
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Hunter PJ, Atkinson LD, Vickers L, Lignou S, Oruna-Concha MJ, Pink D, Hand P, Barker G, Wagstaff C, Monaghan JM. Oxidative discolouration in whole-head and cut lettuce: biochemical and environmental influences on a complex phenotype and potential breeding strategies to improve shelf-life. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2017; 213:180. [PMID: 32025042 PMCID: PMC6979504 DOI: 10.1007/s10681-017-1964-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 07/08/2017] [Indexed: 05/28/2023]
Abstract
Lettuce discolouration is a key post-harvest trait. The major enzyme controlling oxidative discolouration has long been considered to be polyphenol oxidase (PPO) however, levels of PPO and subsequent development of discolouration symptoms have not always correlated. The predominance of a latent state of the enzyme in plant tissues combined with substrate activation and contemporaneous suicide inactivation mechanisms are considered as potential explanations for this phenomenon. Leaf tissue physical properties have been associated with subsequent discolouration and these may be influenced by variation in nutrient availability, especially excess nitrogen and head maturity at harvest. Mild calcium and irrigation stress has also been associated with a reduction in subsequent discolouration, although excess irrigation has been linked to increased discolouration potentially through leaf physical properties. These environmental factors, including high temperature and UV light intensities, often have impacts on levels of phenolic compounds linking the environmental responses to the biochemistry of the PPO pathway. Breeding strategies targeting the PAL and PPO pathway biochemistry and environmental response genes are discussed as a more cost-effective method of mitigating oxidative discolouration then either modified atmosphere packaging or post-harvest treatments, although current understanding of the biochemistry means that such programs are likely to be limited in nature and it is likely that they will need to be deployed alongside other methods for the foreseeable future.
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Affiliation(s)
- Paul J. Hunter
- Harper Adams University, Newport, Shropshire TF10 8NB UK
| | | | - Laura Vickers
- Harper Adams University, Newport, Shropshire TF10 8NB UK
| | - Stella Lignou
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, Berkshire RG6 6AH UK
| | - Maria Jose Oruna-Concha
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, Berkshire RG6 6AH UK
| | - David Pink
- Harper Adams University, Newport, Shropshire TF10 8NB UK
| | - Paul Hand
- Harper Adams University, Newport, Shropshire TF10 8NB UK
| | - Guy Barker
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL UK
| | - Carol Wagstaff
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, Berkshire RG6 6AH UK
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13
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Walley PG, Hough G, Moore JD, Carder J, Elliott M, Mead A, Jones J, Teakle G, Barker G, Buchanan-Wollaston V, Hand P, Pink D, Collier R. Towards new sources of resistance to the currant-lettuce aphid ( Nasonovia ribisnigri). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2017; 37:4. [PMID: 28111522 PMCID: PMC5209396 DOI: 10.1007/s11032-016-0606-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/01/2016] [Indexed: 05/28/2023]
Abstract
Domesticated lettuce varieties encompass much morphological variation across a range of crop type groups, with large collections of cultivars and landrace accessions maintained in genebanks. Additional variation not captured during domestication, present in ancestral wild relatives, represents a potentially rich source of alleles that can deliver to sustainable crop production. However, these large collections are difficult and costly to screen for many agronomically important traits. In this paper, we describe the generation of a diversity collection of 96 lettuce and wild species accessions that are amenable to routine phenotypic analysis and their genotypic characterization with a panel of 682 newly developed expressed sequence tag (EST)-linked KASP™ single nucleotide polymorphism (SNP) markers that are anchored to the draft Lactuca sativa genome assembly. To exemplify the utility of these resources, we screened the collection for putative sources of resistance to currant-lettuce aphid (Nasonovia ribisnigri) and carried out association analyses to look for potential SNPs linked to resistance.
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Affiliation(s)
- Peter G. Walley
- Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Gemma Hough
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY UK
| | | | - John Carder
- School of Life Sciences, Warwick Crop Centre, The University of Warwick, Wellesbourne, Warwick, CV35 9EF UK
| | - Marian Elliott
- School of Life Sciences, Warwick Crop Centre, The University of Warwick, Wellesbourne, Warwick, CV35 9EF UK
| | - Andrew Mead
- Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ UK
| | - Julie Jones
- School of Life Sciences, Warwick Crop Centre, The University of Warwick, Wellesbourne, Warwick, CV35 9EF UK
| | - Graham Teakle
- School of Life Sciences, Warwick Crop Centre, The University of Warwick, Wellesbourne, Warwick, CV35 9EF UK
| | - Guy Barker
- School of Life Sciences, Warwick Crop Centre, The University of Warwick, Wellesbourne, Warwick, CV35 9EF UK
| | - Vicky Buchanan-Wollaston
- School of Life Sciences, Warwick Crop Centre, The University of Warwick, Wellesbourne, Warwick, CV35 9EF UK
| | - Paul Hand
- Harper Adams University College, Newport, Shropshire TF10 8NB UK
| | - David Pink
- Harper Adams University College, Newport, Shropshire TF10 8NB UK
| | - Rosemary Collier
- School of Life Sciences, Warwick Crop Centre, The University of Warwick, Wellesbourne, Warwick, CV35 9EF UK
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14
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Monden Y, Tahara M. Genetic linkage analysis using DNA markers in sweetpotato. BREEDING SCIENCE 2017; 67:41-51. [PMID: 28465667 PMCID: PMC5407921 DOI: 10.1270/jsbbs.16142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/03/2016] [Indexed: 05/23/2023]
Abstract
Sweetpotato is one of the most important food crop species in the world, with more than 104,000,000 tons produced each year, and the breeding of superior cultivars with agronomically important traits, such as improved disease resistance, yield, and nutrient richness, is necessary, especially in developing countries. However, as a result of the crop's complex genomic architecture, which results from its hexaploidy (2n = 6× = 90), high heterozygosity, huge genome, and outcrossing nature, the analysis of genetic linkage in sweetpotato has been challenging. In addition, the lack of whole genome sequences or gene annotations for cultivated hexaploids has interrupted the validation of mapped QTL regions and gene cloning. In spite of these technical difficulties, linkage map construction and QTL mapping analysis have been reported. This review summarizes the results of these linkage analyses, which used SSR, AFLP, and retrotransposon-based molecular markers, and describes future directions for the genetic analysis and marker-assisted breeding of this important but genetically complex crop species.
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Affiliation(s)
- Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University,
1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530,
Japan
| | - Makoto Tahara
- Graduate School of Environmental and Life Science, Okayama University,
1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530,
Japan
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15
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Wang Y, Lu H, Hu J. Molecular Mapping of High Resistance to Bacterial Leaf Spot in Lettuce PI 358001-1. PHYTOPATHOLOGY 2016; 106:1319-1325. [PMID: 27454703 DOI: 10.1094/phyto-09-15-0238-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Lettuce (Lactuca sativa L.) is a diploid (2n = 18) with a genome size of 2,600 Mbp, and belongs to the family Compositae. Bacterial leaf spot (BLS), caused by Xanthomonas campestris pv. vitians, is a major disease of lettuce worldwide. Leaf lettuce PI 358001-1 has been characterized as an accession highly resistant to BLS and has white seed. In order to understand inheritance of the high resistance in this germplasm line, an F3 population consisting of 163 families was developed from the cross PI 358001-1 × 'Tall Guzmaine' (a susceptible Romaine lettuce variety with black seed). The segregation ratio of reaction to disease by seedling inoculation with X. campestris pv. vitians L7 strain in the F3 families was shown to be 32:82:48 homozygous resistant/heterozygous/homozygous susceptible, fitting to 1:2:1 (n = 162, χ2 = 3.19, P = 0.20). The segregation ratio of seed color by checking F2 plants was 122:41 black/white, fitting to 3:1 (n = 163, χ2 = 0.002, P = 0.96). The results indicated that both BLS resistance and seed color were inherited as a dominant gene mode. A genetic linkage map based on 124 randomly selected F2 plants was developed to enable molecular mapping of the BLS resistance and the seed color trait. In total, 199 markers, comprising 176 amplified fragment length polymorphisms, 16 simple-sequence repeats, 5 resistant gene candidate markers, and 2 cleaved amplified polymorphic sequences (CAPS) markers were assigned to six linkage groups. The dominant resistance gene to BLS (Xcvr) was mapped on linkage group 2 and the gene locus y for seed color was identified on linkage group 5. Due to the nature of a single gene inheritance, the high-resistance gene should be readily transferred to adapted lettuce cultivars to battle against the devastating disease of lettuce.
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Affiliation(s)
- Yunwen Wang
- First and second authors: Everglades Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences, Belle Glade 33430; and third author: United States Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman 99164
| | - Huangjun Lu
- First and second authors: Everglades Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences, Belle Glade 33430; and third author: United States Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman 99164
| | - Jinguo Hu
- First and second authors: Everglades Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences, Belle Glade 33430; and third author: United States Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman 99164
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16
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Arias M, Hernandez M, Remondegui N, Huvenaars K, van Dijk P, Ritter E. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers. Sci Rep 2016; 6:31031. [PMID: 27488242 PMCID: PMC4973268 DOI: 10.1038/srep31031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/11/2016] [Indexed: 11/09/2022] Open
Abstract
Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.
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Affiliation(s)
- Marina Arias
- Neiker Tecnalia (Granja Modelo de Arkaute), Ctra. N1-Km 355, Arcaute (Alava) CP: 01192, Spain
| | - Monica Hernandez
- Neiker Tecnalia (Granja Modelo de Arkaute), Ctra. N1-Km 355, Arcaute (Alava) CP: 01192, Spain
| | - Naroa Remondegui
- Neiker Tecnalia (Granja Modelo de Arkaute), Ctra. N1-Km 355, Arcaute (Alava) CP: 01192, Spain
| | - Koen Huvenaars
- KeyGene, Agro Business Park 90, Wageningen, 6708 PW, The Netherlands
| | - Peter van Dijk
- KeyGene, Agro Business Park 90, Wageningen, 6708 PW, The Netherlands
| | - Enrique Ritter
- Neiker Tecnalia (Granja Modelo de Arkaute), Ctra. N1-Km 355, Arcaute (Alava) CP: 01192, Spain
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17
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Higashi T, Aoki K, Nagano AJ, Honjo MN, Fukuda H. Circadian Oscillation of the Lettuce Transcriptome under Constant Light and Light-Dark Conditions. FRONTIERS IN PLANT SCIENCE 2016; 7:1114. [PMID: 27512400 PMCID: PMC4961695 DOI: 10.3389/fpls.2016.01114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/13/2016] [Indexed: 05/23/2023]
Abstract
Although, the circadian clock is a universal biological system in plants and it orchestrates important role of plant production such as photosynthesis, floral induction and growth, there are few such studies on cultivated species. Lettuce is one major cultivated species for both open culture and plant factories and there is little information concerning its circadian clock system. In addition, most of the relevant genes have not been identified. In this study, we detected circadian oscillation in the lettuce transcriptome using time-course RNA sequencing (RNA-Seq) data. Constant light (LL) and light-dark (LD) conditions were used to detect circadian oscillation because the circadian clock has some basic properties: one is self-sustaining oscillation under constant light and another is entrainment to environmental cycles such as light and temperature. In the results, 215 contigs were detected as common oscillating contigs under both LL and LD conditions. The 215 common oscillating contigs included clock gene-like contigs CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)-like, TOC1 (TIMING OF CAB EXPRESSION 1)-like and LHY (LATE ELONGATED HYPOCOTYL)-like, and their expression patterns were similar to those of Arabidopsis. Functional enrichment analysis by GO (gene ontology) Slim and GO Fat showed that the GO terms of response to light stimulus, response to stress, photosynthesis and circadian rhythms were enriched in the 215 common oscillating contigs and these terms were actually regulated by circadian clocks in plants. The 215 common oscillating contigs can be used to evaluate whether the gene expression pattern related to photosynthesis and optical response performs normally in lettuce.
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Affiliation(s)
- Takanobu Higashi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture UniversitySakai, Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture UniversitySakai, Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku UniversityOtsu, Japan
- Core Research for Evolutional Science and Technology – Japan Science and Technology AgencyKawaguchi, Japan
- Center for Ecological Research, Kyoto UniversityOtsu, Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto UniversityOtsu, Japan
| | - Hirokazu Fukuda
- Graduate School of Engineering, Osaka Prefecture UniversitySakai, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology AgencyKawaguchi, Japan
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18
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Preliminary genetic linkage map of Indian major carp, Labeo rohita (Hamilton 1822) based on microsatellite markers. J Genet 2016; 94:271-7. [PMID: 26174674 DOI: 10.1007/s12041-015-0528-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Linkage map with wide marker coverage is an essential resource for genetic improvement study for any species. Sex-averaged genetic linkage map of Labeo rohita, popularly known as 'rohu', widely cultured in the Indian subcontinent, was developed by placing 68 microsatellite markers generated by a simplified method. The parents and their F1 progeny (92 individuals) were used as segregating populations. The genetic linkage map spans a sex-averaged total length of 1462.2 cM, in 25 linkage groups. The genome length of rohu was estimated to be 3087.9 cM. This genetic linkage map may facilitate systematic searches of the genome to identify genes associated with commercially important characters and marker-assisted selection programmes of this species.
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19
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Kerbiriou PJ, Maliepaard CA, Stomph TJ, Koper M, Froissart D, Roobeek I, Lammerts Van Bueren ET, Struik PC. Genetic Control of Water and Nitrate Capture and Their Use Efficiency in Lettuce (Lactuca sativa L.). FRONTIERS IN PLANT SCIENCE 2016; 7:343. [PMID: 27064203 PMCID: PMC4812043 DOI: 10.3389/fpls.2016.00343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/06/2016] [Indexed: 05/13/2023]
Abstract
Robustness in lettuce, defined as the ability to produce stable yields across a wide range of environments, may be associated with below-ground traits such as water and nitrate capture. In lettuce, research on the role of root traits in resource acquisition has been rather limited. Exploring genetic variation for such traits and shoot performance in lettuce across environments can contribute to breeding for robustness. A population of 142 lettuce cultivars was evaluated during two seasons (spring and summer) in two different locations under organic cropping conditions, and water and nitrate capture below-ground and accumulation in the shoots were assessed at two sampling dates. Resource capture in each soil layer was measured using a volumetric method based on fresh and dry weight difference in the soil for soil moisture, and using an ion-specific electrode for nitrate. We used these results to carry out an association mapping study based on 1170 single nucleotide polymorphism markers. We demonstrated that our indirect, high-throughput phenotyping methodology was reliable and capable of quantifying genetic variation in resource capture. QTLs for below-ground traits were not detected at early sampling. Significant marker-trait associations were detected across trials for below-ground and shoot traits, in number and position varying with trial, highlighting the importance of the growing environment on the expression of the traits measured. The difficulty of identifying general patterns in the expression of the QTLs for below-ground traits across different environments calls for a more in-depth analysis of the physiological mechanisms at root level allowing sustained shoot growth.
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Affiliation(s)
- Pauline J. Kerbiriou
- Plant Sciences, Plant Breeding, Wageningen UniversityWageningen, Netherlands
- Plant Sciences, Centre for Crop Systems Analysis, Wageningen UniversityWageningen, Netherlands
| | - Chris A. Maliepaard
- Plant Sciences, Plant Breeding, Wageningen UniversityWageningen, Netherlands
| | - Tjeerd Jan Stomph
- Plant Sciences, Centre for Crop Systems Analysis, Wageningen UniversityWageningen, Netherlands
| | | | | | | | | | - Paul C. Struik
- Plant Sciences, Centre for Crop Systems Analysis, Wageningen UniversityWageningen, Netherlands
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20
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Damerum A, Selmes SL, Biggi GF, Clarkson GJJ, Rothwell SD, Truco MJ, Michelmore RW, Hancock RD, Shellcock C, Chapman MA, Taylor G. Elucidating the genetic basis of antioxidant status in lettuce (Lactuca sativa). HORTICULTURE RESEARCH 2015; 2:15055. [PMID: 26640696 PMCID: PMC4660231 DOI: 10.1038/hortres.2015.55] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 10/21/2015] [Accepted: 10/21/2015] [Indexed: 05/24/2023]
Abstract
A diet rich in phytonutrients from fruit and vegetables has been acknowledged to afford protection against a range of human diseases, but many of the most popular vegetables are low in phytonutrients. Wild relatives of crops may contain allelic variation for genes determining the concentrations of these beneficial phytonutrients, and therefore understanding the genetic basis of this variation is important for breeding efforts to enhance nutritional quality. In this study, lettuce recombinant inbred lines, generated from a cross between wild and cultivated lettuce (Lactuca serriola and Lactuca sativa, respectively), were analysed for antioxidant (AO) potential and important phytonutrients including carotenoids, chlorophyll and phenolic compounds. When grown in two environments, 96 quantitative trait loci (QTL) were identified for these nutritional traits: 4 for AO potential, 2 for carotenoid content, 3 for total chlorophyll content and 87 for individual phenolic compounds (two per compound on average). Most often, the L. serriola alleles conferred an increase in total AOs and metabolites. Candidate genes underlying these QTL were identified by BLASTn searches; in several cases, these had functions suggesting involvement in phytonutrient biosynthetic pathways. Analysis of a QTL on linkage group 3, which accounted for >30% of the variation in AO potential, revealed several candidate genes encoding multiple MYB transcription factors which regulate flavonoid biosynthesis and flavanone 3-hydroxylase, an enzyme involved in the biosynthesis of the flavonoids quercetin and kaempferol, which are known to have powerful AO activity. Follow-up quantitative RT-PCR of these candidates revealed that 5 out of 10 genes investigated were significantly differentially expressed between the wild and cultivated parents, providing further evidence of their potential involvement in determining the contrasting phenotypes. These results offer exciting opportunities to improve the nutritional content and health benefits of lettuce through marker-assisted breeding.
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Affiliation(s)
- Annabelle Damerum
- Centre for Biological Sciences, University of Southampton, Life Sciences, University Road, Southampton SO17 1BJ, UK
| | - Stacey L Selmes
- Centre for Biological Sciences, University of Southampton, Life Sciences, University Road, Southampton SO17 1BJ, UK
| | - Gaia F Biggi
- Centre for Biological Sciences, University of Southampton, Life Sciences, University Road, Southampton SO17 1BJ, UK
| | - Graham JJ Clarkson
- Centre for Biological Sciences, University of Southampton, Life Sciences, University Road, Southampton SO17 1BJ, UK
- Vitacress Limited, Lower Link Farm, St Mary Bourne, Andover, Hampshire SP11 6DB, UK
| | - Steve D Rothwell
- Vitacress Limited, Lower Link Farm, St Mary Bourne, Andover, Hampshire SP11 6DB, UK
| | - Maria José Truco
- The Genome Centre and the Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Richard W Michelmore
- The Genome Centre and the Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | | | | | - Mark A Chapman
- Centre for Biological Sciences, University of Southampton, Life Sciences, University Road, Southampton SO17 1BJ, UK
| | - Gail Taylor
- Centre for Biological Sciences, University of Southampton, Life Sciences, University Road, Southampton SO17 1BJ, UK
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21
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Hunter PJ, Pink DA, Bending GD. Cultivar-level genotype differences influence diversity and composition of lettuce ( Lactuca sp.) phyllosphere fungal communities. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2015.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Christopoulou M, McHale LK, Kozik A, Reyes-Chin Wo S, Wroblewski T, Michelmore RW. Dissection of Two Complex Clusters of Resistance Genes in Lettuce (Lactuca sativa). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:751-65. [PMID: 25650829 DOI: 10.1094/mpmi-06-14-0175-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Of the over 50 phenotypic resistance genes mapped in lettuce, 25 colocalize to three major resistance clusters (MRC) on chromosomes 1, 2, and 4. Similarly, the majority of candidate resistance genes encoding nucleotide binding-leucine rich repeat (NLR) proteins genetically colocalize with phenotypic resistance loci. MRC1 and MRC4 span over 66 and 63 Mb containing 84 and 21 NLR-encoding genes, respectively, as well as 765 and 627 genes that are not related to NLR genes. Forward and reverse genetic approaches were applied to dissect MRC1 and MRC4. Transgenic lines exhibiting silencing were selected using silencing of β-glucuronidase as a reporter. Silencing of two of five NLR-encoding gene families resulted in abrogation of nine of 14 tested resistance phenotypes mapping to these two regions. At MRC1, members of the coiled coil-NLR-encoding RGC1 gene family were implicated in host and nonhost resistance through requirement for Dm5/8- and Dm45-mediated resistance to downy mildew caused by Bremia lactucae as well as the hypersensitive response to effectors AvrB, AvrRpm1, and AvrRpt2 of the nonpathogen Pseudomonas syringae. At MRC4, RGC12 family members, which encode toll interleukin receptor-NLR proteins, were implicated in Dm4-, Dm7-, Dm11-, and Dm44-mediated resistance to B. lactucae. Lesions were identified in the sequence of a candidate gene within dm7 loss-of-resistance mutant lines, confirming that RGC12G confers Dm7.
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Affiliation(s)
- Marilena Christopoulou
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Leah K McHale
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Alex Kozik
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Sebastian Reyes-Chin Wo
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Tadeusz Wroblewski
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Richard W Michelmore
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
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23
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Bell JL, Burke IC, Neff MM. Genetic and biochemical evaluation of natural rubber from Eastern Washington prickly lettuce (Lactuca serriola L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:593-602. [PMID: 25513853 DOI: 10.1021/jf503934v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Alternative sources of natural rubber are of importance due to economic, biological, and political threats that could diminish supplies of this resource. Prickly lettuce (Lactuca serriola L.) synthesizes long-chain natural rubber and was studied to determine underlying genetic and phenotypic characteristics of rubber biosynthesis. Genotypic and phenotypic analysis of an F2 segregating population using EST-SSR markers led to the discovery of genetic regions linked to natural rubber production. Interval mapping (IM) and multiple QTL mapping (MQM) identified several QTL in the mapping population that had significance based on LOD score thresholds. The discovered QTL and the corresponding local markers are genetic resources for understanding rubber biosynthesis in prickly lettuce and could be used in marker-assisted selection (MAS) breeding. Prickly lettuce is an excellent candidate for elucidating the rubber synthesis mechanism and has potential as a crop plant for rubber production.
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Affiliation(s)
- Jared L Bell
- Discovery Research, Dow Agrosciences, Indianapolis, Indiana, United States
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24
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Ren Y, McGregor C, Zhang Y, Gong G, Zhang H, Guo S, Sun H, Cai W, Zhang J, Xu Y. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus). BMC PLANT BIOLOGY 2014; 14:33. [PMID: 24443961 PMCID: PMC3898567 DOI: 10.1186/1471-2229-14-33] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/15/2014] [Indexed: 05/17/2023]
Abstract
BACKGROUND Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. RESULTS Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. CONCLUSIONS The integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A large proportion of the markers in the integrated map are SSRs, InDels and SNPs, which are easily transferable across laboratories. Moreover, the populations used to construct the integrated map include all three watermelon subspecies, making this integrated map useful for the selection of breeding traits, identification of QTL, MAS, analysis of germplasm and commercial hybrid seed detection.
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Affiliation(s)
- Yi Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Cecilia McGregor
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| | - Yan Zhang
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Guoyi Gong
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Haiying Zhang
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Shaogui Guo
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Honghe Sun
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Wantao Cai
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Jie Zhang
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China
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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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Stassen JHM, den Boer E, Vergeer PWJ, Andel A, Ellendorff U, Pelgrom K, Pel M, Schut J, Zonneveld O, Jeuken MJW, Van den Ackerveken G. Specific in planta recognition of two GKLR proteins of the downy mildew Bremia lactucae revealed in a large effector screen in lettuce. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1259-70. [PMID: 23883357 DOI: 10.1094/mpmi-05-13-0142-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Breeding lettuce (Lactuca sativa) for resistance to the downy mildew pathogen Bremia lactucae is mainly achieved by introgression of dominant downy mildew resistance (Dm) genes. New Bremia races quickly render Dm genes ineffective, possibly by mutation of recognized host-translocated effectors or by suppression of effector-triggered immunity. We have previously identified 34 potential RXLR(-like) effector proteins of B. lactucae that were here tested for specific recognition within a collection of 129 B. lactucae-resistant Lactuca lines. Two effectors triggered a hypersensitive response: BLG01 in 52 lines, predominantly L. saligna, and BLG03 in two L. sativa lines containing Dm2 resistance. The N-terminal sequences of BLG01 and BLG03, containing the signal peptide and GKLR variant of the RXLR translocation motif, are not required for in planta recognition but function in effector delivery. The locus responsible for BLG01 recognition maps to the bottom of lettuce chromosome 9, whereas recognition of BLG03 maps in the RGC2 cluster on chromosome 2. Lactuca lines that recognize the BLG effectors are not resistant to Bremia isolate Bl:24 that expresses both BLG genes, suggesting that Bl:24 can suppress the triggered immune responses. In contrast, lettuce segregants displaying Dm2-mediated resistance to Bremia isolate Bl:5 are responsive to BLG03, suggesting that BLG03 is a candidate Avr2 protein.
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Atkinson LD, McHale LK, Truco MJ, Hilton HW, Lynn J, Schut JW, Michelmore RW, Hand P, Pink DAC. An intra-specific linkage map of lettuce (Lactuca sativa) and genetic analysis of postharvest discolouration traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2737-52. [PMID: 23959526 DOI: 10.1007/s00122-013-2168-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 07/12/2013] [Indexed: 06/02/2023]
Abstract
Minimally processed salad packs often suffer from discolouration on cut leaf edges within a few days after harvest. This limits shelf life of the product and results in high wastage. Recombinant inbred lines (RILs) derived from a cross between lettuce cvs. Saladin and Iceberg were shown to be suitable for genetic analysis of postharvest discolouration traits in lettuce. An intra-specific linkage map based on this population was generated to enable genetic analysis. A total of 424 markers were assigned to 18 linkage groups covering all nine chromosomes. The linkage map has a total length of 1,040 cM with an average marker distance of 2.4 cM within the linkage groups and was anchored to the ultra-dense, transcript-based consensus map. Significant genetic variation in the postharvest traits ‘pinking’, ‘browning’ and ‘overall discolouration’ was detected among the RILs. Seven significant quantitative trait loci (QTL) were identified for postharvest discolouration traits providing markers linked to the QTL that can be used for marker-assisted selection. Phenotypic stability was confirmed for extreme lines possessing the corresponding QTL parental alleles and which had shown transgressive segregation. This study indicates that a desired phenotype with reduced levels of postharvest discolouration can be achieved by breeding using natural variation.
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28
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Simko I, Atallah AJ, Ochoa OE, Antonise R, Galeano CH, Truco MJ, Michelmore RW. Identification of QTLs conferring resistance to downy mildew in legacy cultivars of lettuce. Sci Rep 2013; 3:2875. [PMID: 24096732 PMCID: PMC3791445 DOI: 10.1038/srep02875] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/18/2013] [Indexed: 12/03/2022] Open
Abstract
Many cultivars of lettuce (Lactuca sativa L.), the most popular leafy vegetable, are susceptible to downy mildew disease caused by Bremia lactucae. Cultivars Iceberg and Grand Rapids that were released in the 18th and 19th centuries, respectively, have high levels of quantitative resistance to downy mildew. We developed a population of recombinant inbred lines (RILs) originating from a cross between these two legacy cultivars, constructed a linkage map, and identified two QTLs for resistance on linkage groups 2 (qDM2.1) and 5 (qDM5.1) that determined resistance under field conditions in California and the Netherlands. The same QTLs determined delayed sporulation at the seedling stage in laboratory experiments. Alleles conferring elevated resistance at both QTLs originate from cultivar Iceberg. An additional QTL on linkage group 9 (qDM9.1) was detected through simultaneous analysis of all experiments with mixed-model approach. Alleles for elevated resistance at this locus originate from cultivar Grand Rapids.
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Affiliation(s)
- Ivan Simko
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA 93905, USA
| | - Amy J. Atallah
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA 93905, USA
| | - Oswaldo E. Ochoa
- The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Rudie Antonise
- KeyGene N.V., P.O. Box 216 6700 AE Wageningen, The Netherlands
| | - Carlos H. Galeano
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA 93905, USA
- The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Maria Jose Truco
- The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Richard W. Michelmore
- The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA
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29
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Jenni S, Truco MJ, Michelmore RW. Quantitative trait loci associated with tipburn, heat stress-induced physiological disorders, and maturity traits in crisphead lettuce. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:3065-3079. [PMID: 24078012 DOI: 10.1007/s00122-013-2193-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 09/06/2013] [Indexed: 05/08/2023]
Abstract
Crisphead lettuce (Lactuca sativa L.) crops exhibit several economically important, physiological disorders when grown in high temperature conditions. These include tipburn, rib discoloration, premature bolting, ribbiness, and internal rib cracking. We evaluated seven physiological disorders and three agronomic traits segregating in a recombinant inbred line (RIL) population consisting of 152 F7 RILs derived from an intra-specific cross between two crisphead cultivars, L. sativa cv. Emperor x L. sativa cv. El Dorado; evaluations were carried out at each of two parental maturities in one planting and at one intermediate maturity in a second planting in each of 2 years for a total of six evaluations. A genetic map was developed using 449 polymorphic SNP markers; it comprises 807 cM in 20 linkage groups that covered 51 % of the nine lettuce chromosomes. Composite interval mapping revealed a total of 36 significant QTLs for eight out of the ten traits evaluated. Significant QTLs were distributed in 11 linkage groups on seven of the chromosomes and accounted for up to 83 % of the phenotypic variation observed. The three largest QTLs for rib discoloration, which accounted individually for 7-21 % of the variation, were clustered with stem length, two with ribbiness and one with head firmness. Three major clusters of QTLs revealed pleiotropic effects or tight linkage between tipburn incidence and severity, head type, stem length, head firmness and ribbiness. One QTL, qTPB5.2, was detected in multiple trials and described 38-70 % of the variation in tipburn incidence. qTPB5.2 is, therefore, a useful candidate gene for breeding for tipburn resistance using marker-assisted selection.
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Affiliation(s)
- Sylvie Jenni
- Horticultural Research and Development Centre, Agriculture and Agri-Food Canada, 430 Boul. Gouin, St-Jean-sur-Richelieu, QC, J3B 3E6, Canada
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QTL mapping of growth-related traits in a full-sib family of rubber tree (Hevea brasiliensis) evaluated in a sub-tropical climate. PLoS One 2013; 8:e61238. [PMID: 23620732 PMCID: PMC3631230 DOI: 10.1371/journal.pone.0061238] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 03/06/2013] [Indexed: 11/23/2022] Open
Abstract
The rubber tree (Hevea spp.), cultivated in equatorial and tropical countries, is the primary plant used in natural rubber production. Due to genetic and physiological constraints, inbred lines of this species are not available. Therefore, alternative approaches are required for the characterization of this species, such as the genetic mapping of full-sib crosses derived from outbred parents. In the present study, an integrated genetic map was obtained for a full-sib cross family with simple sequence repeats (SSRs) and expressed sequence tag (EST-SSR) markers, which can display different segregation patterns. To study the genetic architecture of the traits related to growth in two different conditions (winter and summer), quantitative trait loci (QTL) mapping was also performed using the integrated map. Traits evaluated were height and girth growth, and the statistical model was based in an extension of composite interval mapping. The obtained molecular genetic map has 284 markers distributed among 23 linkage groups with a total length of 2688.8 cM. A total of 18 QTLs for growth traits during the summer and winter seasons were detected. A comparison between the different seasons was also conducted. For height, QTLs detected during the summer season were different from the ones detected during winter season. This type of difference was also observed for girth. Integrated maps are important for genetics studies in outbred species because they represent more accurately the polymorphisms observed in the genitors. QTL mapping revealed several interesting findings, such as a dominance effect and unique segregation patterns that each QTL could exhibit, which were independent of the flanking markers. The QTLs identified in this study, especially those related to phenotypic variation associated with winter could help studies of marker-assisted selection that are particularly important when the objective of a breeding program is to obtain phenotypes that are adapted to sub-optimal regions.
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Truco MJ, Ashrafi H, Kozik A, van Leeuwen H, Bowers J, Wo SRC, Stoffel K, Xu H, Hill T, Van Deynze A, Michelmore RW. An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce. G3 (BETHESDA, MD.) 2013; 3:617-631. [PMID: 23550116 PMCID: PMC3618349 DOI: 10.1534/g3.112.004929] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/07/2013] [Indexed: 02/07/2023]
Abstract
We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species.
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Affiliation(s)
- Maria José Truco
- The Genome Center, University of California, Davis, California 95616
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, Davis, California 95616
| | - Alexander Kozik
- The Genome Center, University of California, Davis, California 95616
| | - Hans van Leeuwen
- The Genome Center, University of California, Davis, California 95616
| | - John Bowers
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | | | - Kevin Stoffel
- Seed Biotechnology Center, University of California, Davis, California 95616
| | - Huaqin Xu
- The Genome Center, University of California, Davis, California 95616
| | - Theresa Hill
- Seed Biotechnology Center, University of California, Davis, California 95616
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, Davis, California 95616
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Richard W Michelmore
- The Genome Center, University of California, Davis, California 95616
- Department of Plant Sciences, University of California, Davis, California 95616
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Yang L, Li D, Li Y, Gu X, Huang S, Garcia-Mas J, Weng Y. A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci. BMC PLANT BIOLOGY 2013; 13:53. [PMID: 23531125 PMCID: PMC3626583 DOI: 10.1186/1471-2229-13-53] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 03/11/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cucumber is an important vegetable crop that is susceptible to many pathogens, but no disease resistance (R) genes have been cloned. The availability of whole genome sequences provides an excellent opportunity for systematic identification and characterization of the nucleotide binding and leucine-rich repeat (NB-LRR) type R gene homolog (RGH) sequences in the genome. Cucumber has a very narrow genetic base making it difficult to construct high-density genetic maps. Development of a consensus map by synthesizing information from multiple segregating populations is a method of choice to increase marker density. As such, the objectives of the present study were to identify and characterize NB-LRR type RGHs, and to develop a high-density, integrated cucumber genetic-physical map anchored with RGH loci. RESULTS From the Gy14 draft genome, 70 NB-containing RGHs were identified and characterized. Most RGHs were in clusters with uneven distribution across seven chromosomes. In silico analysis indicated that all 70 RGHs had EST support for gene expression. Phylogenetic analysis classified 58 RGHs into two clades: CNL and TNL. Comparative analysis revealed high-degree sequence homology and synteny in chromosomal locations of these RGH members between the cucumber and melon genomes. Fifty-four molecular markers were developed to delimit 67 of the 70 RGHs, which were integrated into a genetic map through linkage analysis. A 1,681-locus cucumber consensus map including 10 gene loci and spanning 730.0 cM in seven linkage groups was developed by integrating three component maps with a bin-mapping strategy. Physically, 308 scaffolds with 193.2 Mbp total DNA sequences were anchored onto this consensus map that covered 52.6% of the 367 Mbp cucumber genome. CONCLUSIONS Cucumber contains relatively few NB-LRR RGHs that are clustered and unevenly distributed in the genome. All RGHs seem to be transcribed and shared significant sequence homology and synteny with the melon genome suggesting conservation of these RGHs in the Cucumis lineage. The 1,681-locus consensus genetic-physical map developed and the RGHs identified and characterized herein are valuable genomics resources that may have many applications such as quantitative trait loci identification, map-based gene cloning, association mapping, marker-assisted selection, as well as assembly of a more complete cucumber genome.
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Affiliation(s)
- Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Dawei Li
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Yuhong Li
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100018, China
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100018, China
| | - Jordi Garcia-Mas
- IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, 08193, Spain
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
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Rauscher G, Simko I. Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes. BMC PLANT BIOLOGY 2013; 13:11. [PMID: 23339733 PMCID: PMC3557189 DOI: 10.1186/1471-2229-13-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/08/2013] [Indexed: 05/11/2023]
Abstract
BACKGROUND Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. RESULTS Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. CONCLUSIONS The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.
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Affiliation(s)
- Gilda Rauscher
- United States Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA, 93905, USA
- Present address: Agricultural Biotechnology, DuPont Pioneer, Wilmington, Wilmington, DE, 19880, USA
| | - Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA, 93905, USA
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Cloutier S, Ragupathy R, Miranda E, Radovanovic N, Reimer E, Walichnowski A, Ward K, Rowland G, Duguid S, Banik M. Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1783-95. [PMID: 22890805 PMCID: PMC3493668 DOI: 10.1007/s00122-012-1953-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/21/2012] [Indexed: 05/06/2023]
Abstract
Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence.
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Affiliation(s)
- Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada.
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Nakatsuka T, Yamada E, Saito M, Hikage T, Ushiku Y, Nishihara M. Construction of the first genetic linkage map of Japanese gentian (Gentianaceae). BMC Genomics 2012. [PMID: 23186361 PMCID: PMC3561071 DOI: 10.1186/1471-2164-13-672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Background Japanese gentians (Gentiana triflora and Gentiana scabra) are amongst the most popular floricultural plants in Japan. However, genomic resources for Japanese gentians have not yet been developed, mainly because of the heterozygous genome structure conserved by outcrossing, the long juvenile period, and limited knowledge about the inheritance of important traits. In this study, we developed a genetic linkage map to improve breeding programs of Japanese gentians. Results Enriched simple sequence repeat (SSR) libraries from a G. triflora double haploid line yielded almost 20,000 clones using 454 pyrosequencing technology, 6.7% of which could be used to design SSR markers. To increase the number of molecular markers, we identified three putative long terminal repeat (LTR) sequences using the recently developed inter-primer binding site (iPBS) method. We also developed retrotransposon microsatellite amplified polymorphism (REMAP) markers combining retrotransposon and inter-simple sequence repeat (ISSR) markers. In addition to SSR and REMAP markers, modified amplified fragment length polymorphism (AFLP) and random amplification polymorphic DNA (RAPD) markers were developed. Using 93 BC1 progeny from G. scabra backcrossed with a G. triflora double haploid line, 19 linkage groups were constructed with a total of 263 markers (97 SSR, 97 AFLP, 39 RAPD, and 30 REMAP markers). One phenotypic trait (stem color) and 10 functional markers related to genes controlling flower color, flowering time and cold tolerance were assigned to the linkage map, confirming its utility. Conclusions This is the first reported genetic linkage map for Japanese gentians and for any species belonging to the family Gentianaceae. As demonstrated by mapping of functional markers and the stem color trait, our results will help to explain the genetic basis of agronomic important traits, and will be useful for marker-assisted selection in gentian breeding programs. Our map will also be an important resource for further genetic analyses such as mapping of quantitative trait loci and map-based cloning of genes in this species.
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Affiliation(s)
- Takashi Nakatsuka
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate 024-0003, Japan
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Bohra A, Saxena RK, Gnanesh BN, Saxena K, Byregowda M, Rathore A, KaviKishor PB, Cook DR, Varshney RK. An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1325-38. [PMID: 22772726 PMCID: PMC3442162 DOI: 10.1007/s00122-012-1916-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 06/05/2012] [Indexed: 05/21/2023]
Abstract
Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750 kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59-140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6 cM have been constructed. Using these four genetic maps together with two recently published intra-specific genetic maps, a consensus map was constructed, comprising of 339 SSR loci spanning a distance of 1,059 cM. Furthermore, quantitative trait loci (QTL) analysis for fertility restoration (Rf) conducted in three mapping populations identified four major QTLs explaining phenotypic variances up to 24 %. To the best of our knowledge, this is the first report on construction of a consensus genetic map in pigeonpea and on the identification of QTLs for fertility restoration. The developed consensus genetic map should serve as a reference for developing new genetic maps as well as correlating with the physical map in pigeonpea to be developed in near future. The availability of more informative markers in the bins harbouring QTLs for sterility mosaic disease (SMD) and Rf will facilitate the selection of the most suitable markers for genetic analysis and molecular breeding applications in pigeonpea.
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Affiliation(s)
- Abhishek Bohra
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- Osmania University, Hyderabad, 500007 India
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- Osmania University, Hyderabad, 500007 India
| | - B. N. Gnanesh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- University of Agricultural Sciences, Bengaluru (UAS-B), 560065 India
| | - Kulbhushan Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
| | - M. Byregowda
- University of Agricultural Sciences, Bengaluru (UAS-B), 560065 India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
| | | | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, 06600 Mexico DF, Mexico
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Blenda A, Fang DD, Rami JF, Garsmeur O, Luo F, Lacape JM. A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. PLoS One 2012; 7:e45739. [PMID: 23029214 PMCID: PMC3454346 DOI: 10.1371/journal.pone.0045739] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 08/24/2012] [Indexed: 02/03/2023] Open
Abstract
A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous A(T) and D(T) chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per A(T)/D(T) chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton.
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Affiliation(s)
- Anna Blenda
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- Department of Biology, Erskine College, Due West, South Carolina, United States of America
| | - David D. Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, Louisiana, United States of America
| | | | | | - Feng Luo
- School of Computing, Clemson University, Clemson, South Carolina, United States of America
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Bodénès C, Chancerel E, Gailing O, Vendramin GG, Bagnoli F, Durand J, Goicoechea PG, Soliani C, Villani F, Mattioni C, Koelewijn HP, Murat F, Salse J, Roussel G, Boury C, Alberto F, Kremer A, Plomion C. Comparative mapping in the Fagaceae and beyond with EST-SSRs. BMC PLANT BIOLOGY 2012; 12:153. [PMID: 22931513 PMCID: PMC3493355 DOI: 10.1186/1471-2229-12-153] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 08/22/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. RESULTS We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. CONCLUSIONS This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.
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Affiliation(s)
- Catherine Bodénès
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Emilie Chancerel
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding Büsgen Institute Faculty of Forest Sciences and Forest Ecology Göttingen University, Büsgenweg 2, 37077, Göttingen, Germany
- New address: School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Giovanni G Vendramin
- Plant Genetics Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy
| | - Francesca Bagnoli
- Plant Protection Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy
| | - Jerome Durand
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Pablo G Goicoechea
- NEIKER-Tecnalia, Dpto Biotecnologia, PO Box 46, Vitoria-Gasteiz, 01080, Spain
| | - Carolina Soliani
- Unidad de Genética Ecológica y Mejoramiento Forestal, INTA EEA Bariloche, Bariloche, CC277 8400, Argentina
| | - Fiorella Villani
- CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy
| | - Claudia Mattioni
- CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy
| | | | - Florent Murat
- INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France
| | - Jerome Salse
- INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France
| | - Guy Roussel
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Christophe Boury
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Florian Alberto
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Antoine Kremer
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
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Uwimana B, D'Andrea L, Felber F, Hooftman DAP, Den Nijs HCM, Smulders MJM, Visser RGF, Van De Wiel CCM. A Bayesian analysis of gene flow from crops to their wild relatives: cultivated (Lactuca sativa L.) and prickly lettuce (L. serriola L.) and the recent expansion of L. serriola in Europe. Mol Ecol 2012; 21:2640-54. [PMID: 22512715 DOI: 10.1111/j.1365-294x.2012.05489.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interspecific gene flow can lead to the formation of hybrid populations that have a competitive advantage over the parental populations, even for hybrids from a cross between crops and wild relatives. Wild prickly lettuce (Lactuca serriola) has recently expanded in Europe and hybridization with the related crop species (cultivated lettuce, L. sativa) has been hypothesized as one of the mechanisms behind this expansion. In a basically selfing species, such as lettuce, assessing hybridization in natural populations may not be straightforward. Therefore, we analysed a uniquely large data set of plants genotyped with SSR (simple sequence repeat) markers with two programs for Bayesian population genetic analysis, STRUCTURE and NewHybrids. The data set comprised 7738 plants, including a complete genebank collection, which provided a wide coverage of cultivated germplasm and a fair coverage of wild accessions, and a set of wild populations recently sampled across Europe. STRUCTURE analysis inferred the occurrence of hybrids at a level of 7% across Europe. NewHybrids indicated these hybrids to be advanced selfed generations of a hybridization event or of one backcross after such an event, which is according to expectations for a basically selfing species. These advanced selfed generations could not be detected effectively with crop-specific alleles. In the northern part of Europe, where the expansion of L. serriola took place, the fewest putative hybrids were found. Therefore, we conclude that other mechanisms than crop/wild gene flow, such as an increase in disturbed habitats and/or climate warming, are more likely explanations for this expansion.
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Stoffel K, van Leeuwen H, Kozik A, Caldwell D, Ashrafi H, Cui X, Tan X, Hill T, Reyes-Chin-Wo S, Truco MJ, Michelmore RW, Van Deynze A. Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.). BMC Genomics 2012; 13:185. [PMID: 22583801 PMCID: PMC3490809 DOI: 10.1186/1471-2164-13-185] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 02/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). RESULTS We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. CONCLUSION By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.
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Affiliation(s)
- Kevin Stoffel
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
| | - Hans van Leeuwen
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
- Nunhems Netherlands B.V., P.O. Box 4005, 6080, AA, Haelen, The Netherlands
| | - Alexander Kozik
- Genome Center, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - David Caldwell
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
- Monsanto, Molecular Breeding Technology, 700 Chesterfield Pkwy W, BB34, Chesterfield, MO, 63017, England
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
| | - Xinping Cui
- Department of Statistics, University of California, Riverside, CA, 92521, USA
- Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Xiaoping Tan
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
| | - Theresa Hill
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
| | | | - Maria-Jose Truco
- Genome Center, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Richard W Michelmore
- Genome Center, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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Stoffel K, van Leeuwen H, Kozik A, Caldwell D, Ashrafi H, Cui X, Tan X, Hill T, Reyes-Chin-Wo S, Truco MJ, Michelmore RW, Van Deynze A. Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.). BMC Genomics 2012. [PMID: 22583801 DOI: 10.1186/1471‐2164‐13‐185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). RESULTS We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. CONCLUSION By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.
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Affiliation(s)
- Kevin Stoffel
- Seed Biotechnology Center, University of California-Davis, CA 95616, USA
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Uwimana B, Smulders MJM, Hooftman DAP, Hartman Y, van Tienderen PH, Jansen J, McHale LK, Michelmore RW, Visser RGF, van de Wiel CCM. Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations. BMC PLANT BIOLOGY 2012; 12:43. [PMID: 22448748 PMCID: PMC3384248 DOI: 10.1186/1471-2229-12-43] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Accepted: 03/26/2012] [Indexed: 05/09/2023]
Abstract
BACKGROUND After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F(1) hybrid was backcrossed to L. serriola to generate BC(1) and BC(2) populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC(1)S(1) and BC(2)S(1)). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). RESULTS Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC(1)S(1) and BC(2)S(1) hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC(1) and BC(2) hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. CONCLUSION As it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking.
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Affiliation(s)
- Brigitte Uwimana
- Wageningen UR Plant Breeding, Postbus 386, 6700AJ Wageningen, the Netherlands
| | - Marinus JM Smulders
- Wageningen UR Plant Breeding, Postbus 16, 6700AA Wageningen, the Netherlands
| | - Danny AP Hooftman
- Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Yorike Hartman
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Postbus 94248, 1090 GE Amsterdam, the Netherlands
| | - Peter H van Tienderen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Postbus 94248, 1090 GE Amsterdam, the Netherlands
| | - Johannes Jansen
- Wageningen UR Plant Biometris, Postbus 100, 6700AC Wageningen, the Netherlands
| | - Leah K McHale
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA
| | - Richard W Michelmore
- Genome Center and Department of Plant Sciences, University of California Davis, Davis, CA 95616-8816, USA
| | - Richard GF Visser
- Wageningen UR Plant Breeding, Postbus 386, 6700AJ Wageningen, the Netherlands
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Zhang WW, Pan JS, He HL, Zhang C, Li Z, Zhao JL, Yuan XJ, Zhu LH, Huang SW, Cai R. Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:249-59. [PMID: 21971891 DOI: 10.1007/s00122-011-1701-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 09/07/2011] [Indexed: 05/04/2023]
Abstract
The high-density consensus map was constructed based on the GY14 × PI 183967 map from an inter-subspecific cross and the extended S94 × S06 map from an intra-subspecific cross. The consensus map was composed of 1,369 loci, including 1,152 SSR loci, 192 SRAP loci, 21 SCAR loci and one STS locus as well as three gene loci of fruit external quality traits in seven chromosomes, and spanned 700.5 cM, of which 682.7 cM (97.5%) were covered by SSR markers. The average genetic distance and physical interval between loci were 0.51 cM and ~268 kbp, respectively. Additionally, the physical position of the sequence-associated markers aligned along the assembled cucumber genome sequence established a relationship between genetic maps and cucumber genome sequence and to a great extent validated the order of markers in individual maps and consensus map. This consensus map with a high marker density and well-ordered markers is a saturated and reliable linkage map for genetic analysis of cucumber or the Cucurbitaceae family of plants.
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Affiliation(s)
- Wei-Wei Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Diaz A, Fergany M, Formisano G, Ziarsolo P, Blanca J, Fei Z, Staub JE, Zalapa JE, Cuevas HE, Dace G, Oliver M, Boissot N, Dogimont C, Pitrat M, Hofstede R, van Koert P, Harel-Beja R, Tzuri G, Portnoy V, Cohen S, Schaffer A, Katzir N, Xu Y, Zhang H, Fukino N, Matsumoto S, Garcia-Mas J, Monforte AJ. A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.). BMC PLANT BIOLOGY 2011; 11:111. [PMID: 21797998 PMCID: PMC3163537 DOI: 10.1186/1471-2229-11-111] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 07/28/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). RESULTS Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm. CONCLUSIONS Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection).
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Affiliation(s)
- Aurora Diaz
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Ed. 8E. C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Mohamed Fergany
- IRTA, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB), Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
- Agronomy Department Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Gelsomina Formisano
- Department of Soil, Plant, Environmental and Animal Production Sciences, Federico II University of Naples, Via Università 100, 80055 Portici, Italy
| | - Peio Ziarsolo
- COMAV-UPV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - José Blanca
- COMAV-UPV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Zhanjun Fei
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Jack E Staub
- USDA-ARS, Vegetable Crops Research Unit, Department of Horticulture, 1575 Linden Dr, University of Wisconsin, Madison, WI 53706, USA
- Current address: USDA-ARS, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Juan E Zalapa
- USDA-ARS, Vegetable Crops Research Unit, Department of Horticulture, 1575 Linden Dr, University of Wisconsin, Madison, WI 53706, USA
| | - Hugo E Cuevas
- USDA-ARS, Vegetable Crops Research Unit, Department of Horticulture, 1575 Linden Dr, University of Wisconsin, Madison, WI 53706, USA
- Current address: USDA-ARS, Tropical Agricultural Research Station, 2200 Pedro Albizu Campus Ave, Mayaguez 00680-5470, Puerto Rico
| | - Gayle Dace
- Syngenta Biotechnology, Inc. Research Triangle Park, NC 27709, USA
| | - Marc Oliver
- Syngenta Seeds, 12 chemin de l'Hobit, F-31790 Saint-Sauveur, France
| | - Nathalie Boissot
- INRA, UR 1052, Unité de Génétique et d'Amélioration des Fruits et Légumes, Domaine St Maurice, BP 94, 84143 Montfavet Cedex, France
| | - Catherine Dogimont
- INRA, UR 1052, Unité de Génétique et d'Amélioration des Fruits et Légumes, Domaine St Maurice, BP 94, 84143 Montfavet Cedex, France
| | - Michel Pitrat
- INRA, UR 1052, Unité de Génétique et d'Amélioration des Fruits et Légumes, Domaine St Maurice, BP 94, 84143 Montfavet Cedex, France
| | - René Hofstede
- Keygene N.V. P.O. Box 216. 6700 AE Wageningen. The Netherlands
| | - Paul van Koert
- Keygene N.V. P.O. Box 216. 6700 AE Wageningen. The Netherlands
| | - Rotem Harel-Beja
- Institute of Plant Science, Agricultural Research Organization (ARO), Newe Ya'ar Research Center, Ramat Yishay 30095, Israel
| | - Galil Tzuri
- Institute of Plant Science, Agricultural Research Organization (ARO), Newe Ya'ar Research Center, Ramat Yishay 30095, Israel
| | - Vitaly Portnoy
- Institute of Plant Science, Agricultural Research Organization (ARO), Newe Ya'ar Research Center, Ramat Yishay 30095, Israel
| | - Shahar Cohen
- Institute of Plant Science, Agricultural Research Organization, Volcani Research Center, Bet Dagan 50250, Israel
| | - Arthur Schaffer
- Institute of Plant Science, Agricultural Research Organization, Volcani Research Center, Bet Dagan 50250, Israel
| | - Nurit Katzir
- Institute of Plant Science, Agricultural Research Organization (ARO), Newe Ya'ar Research Center, Ramat Yishay 30095, Israel
| | - Yong Xu
- National Engineering Research Center for Vegetables (NERCV), Beijing Academy Agricultural and Forestry Science, Beijing 100097, China
| | - Haiying Zhang
- National Engineering Research Center for Vegetables (NERCV), Beijing Academy Agricultural and Forestry Science, Beijing 100097, China
| | - Nobuko Fukino
- National Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Satoru Matsumoto
- National Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Jordi Garcia-Mas
- IRTA, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB), Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Ed. 8E. C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
- IRTA, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB), Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
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Hooftman DAP, Flavell AJ, Jansen H, den Nijs HCM, Syed NH, Sørensen AP, Orozco-Ter Wengel P, van de Wiel CCM. Locus-dependent selection in crop-wild hybrids of lettuce under field conditions and its implication for GM crop development. Evol Appl 2011; 4:648-59. [PMID: 25568012 PMCID: PMC3352534 DOI: 10.1111/j.1752-4571.2011.00188.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 03/28/2011] [Indexed: 12/01/2022] Open
Abstract
Gene escape from crops has gained much attention in the last two decades, as transgenes introgressing into wild populations could affect the latter's ecological characteristics. However, different genes have different likelihoods of introgression. The mixture of selective forces provided by natural conditions creates an adaptive mosaic of alleles from both parental species. We investigated segregation patterns after hybridization between lettuce (Lactuca sativa) and its wild relative, L. serriola. Three generations of hybrids (S1, BC1, and BC1S1) were grown in habitats mimicking the wild parent's habitat. As control, we harvested S1 seedlings grown under controlled conditions, providing very limited possibility for selection. We used 89 AFLP loci, as well as more recently developed dominant markers, 115 retrotransposon markers (SSAP), and 28 NBS loci linked to resistance genes. For many loci, allele frequencies were biased in plants exposed to natural field conditions, including over-representation of crop alleles for various loci. Furthermore, Linkage disequilibrium was locally changed, allegedly by selection caused by the natural field conditions, providing ample opportunity for genetic hitchhiking. Our study indicates that when developing genetically modified crops, a judicious selection of insertion sites, based on knowledge of selective (dis)advantages of the surrounding crop genome under field conditions, could diminish transgene persistence.
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Affiliation(s)
- Danny A P Hooftman
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, The Netherlands ; Centre for Ecology and Hydrology Wallingford, UK
| | | | - Hans Jansen
- Biometris Wageningen UR, Wageningen, The Netherlands
| | - Hans C M den Nijs
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, The Netherlands
| | | | | | - Pablo Orozco-Ter Wengel
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, The Netherlands ; Keygene N.V Wageningen, The Netherlands
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Argyris J, Truco MJ, Ochoa O, McHale L, Dahal P, Van Deynze A, Michelmore RW, Bradford KJ. A gene encoding an abscisic acid biosynthetic enzyme (LsNCED4) collocates with the high temperature germination locus Htg6.1 in lettuce (Lactuca sp.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:95-108. [PMID: 20703871 PMCID: PMC3015190 DOI: 10.1007/s00122-010-1425-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Accepted: 07/30/2010] [Indexed: 05/07/2023]
Abstract
Thermoinhibition, or failure of seeds to germinate when imbibed at warm temperatures, can be a significant problem in lettuce (Lactuca sativa L.) production. The reliability of stand establishment would be improved by increasing the ability of lettuce seeds to germinate at high temperatures. Genes encoding germination- or dormancy-related proteins were mapped in a recombinant inbred line population derived from a cross between L. sativa cv. Salinas and L. serriola accession UC96US23. This revealed several candidate genes that are located in the genomic regions containing quantitative trait loci (QTLs) associated with temperature and light requirements for germination. In particular, LsNCED4, a temperature-regulated gene in the biosynthetic pathway for abscisic acid (ABA), a germination inhibitor, mapped to the center of a previously detected QTL for high temperature germination (Htg6.1) from UC96US23. Three sets of sister BC(3)S(2) near-isogenic lines (NILs) that were homozygous for the UC96US23 allele of LsNCED4 at Htg6.1 were developed by backcrossing to cv. Salinas and marker-assisted selection followed by selfing. The maximum temperature for germination of NIL seed lots with the UC96US23 allele at LsNCED4 was increased by 2-3°C when compared with sister NIL seed lots lacking the introgression. In addition, the expression of LsNCED4 was two- to threefold lower in the former NIL lines as compared to expression in the latter. Together, these data strongly implicate LsNCED4 as the candidate gene responsible for the Htg6.1 phenotype and indicate that decreased ABA biosynthesis at high imbibition temperatures is a major factor responsible for the increased germination thermotolerance of UC96US23 seeds.
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Affiliation(s)
- Jason Argyris
- Department of Plant Sciences, One Shields Ave, University of California, Davis, CA 95616-8780 USA
- Present Address: Syngenta Seeds S.A, Centro De Investigación Y Ensayos Finca los Sauras, Ctra de IFEPA, 30700 Torre Pachec, Murcia Spain
| | - María José Truco
- Genome Center, One Shields Ave, University of California, Davis, CA 95616-8816 USA
| | - Oswaldo Ochoa
- Genome Center, One Shields Ave, University of California, Davis, CA 95616-8816 USA
| | - Leah McHale
- Genome Center, One Shields Ave, University of California, Davis, CA 95616-8816 USA
- Present Address: Department of Horticulture and Crop Science, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210 USA
| | - Peetambar Dahal
- Department of Plant Sciences, One Shields Ave, University of California, Davis, CA 95616-8780 USA
| | - Allen Van Deynze
- Seed Biotechnology Center, One Shields Ave, University of California, Davis, CA 95616-8780 USA
| | - Richard W. Michelmore
- Department of Plant Sciences, One Shields Ave, University of California, Davis, CA 95616-8780 USA
- Genome Center, One Shields Ave, University of California, Davis, CA 95616-8816 USA
| | - Kent J. Bradford
- Department of Plant Sciences, One Shields Ave, University of California, Davis, CA 95616-8780 USA
- Seed Biotechnology Center, One Shields Ave, University of California, Davis, CA 95616-8780 USA
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Riar DS, Rustgi S, Burke IC, Gill KS, Yenish JP. EST-SSR development from 5 Lactuca species and their use in studying genetic diversity among L. serriola biotypes. J Hered 2011; 102:17-28. [PMID: 21148616 DOI: 10.1093/jhered/esq103] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Prickly lettuce (Lactuca serriola L.) is a problematic weed of Pacific Northwest and recently developed resistance to the auxinic herbicide 2,4-D. There are no publically available simple sequence repeat (SSR) markers to tag 2,4-D resistance genes in L. serriola. Therefore, a study was conducted to develop SSR markers from expressed sequence tags (ESTs) of 5 Lactuca species. A total of 15,970 SSRs were identified among 57,126 EST assemblies belonging to 5 Lactuca species. SSR-containing ESTs (SSR-ESTs) ranged from 6.23% to 7.87%, and SSR densities ranged from 1.28 to 2.51 kb(-1) among the ESTs of 5 Lactuca species. Trinucleotide repeats were the most abundant SSRs detected during the study. As a representative sample, 45 ESTs carrying class I SSRs (≥ 20 nucleotides) were selected for designing primers and were also searched against the dbEST entries for L. sativa and Helianthus annuus (≤ 10(-50); score ≥ 100). In silico analysis of 45 SSR-ESTs showed 82% conservation across species and 68% conservation across genera. Primer pairs synthesized for the above 45 EST-SSRs were used to study genetic diversity among a collection of 22 L. serriola biotypes. Comparison of the resultant dendrogram to that developed using phenotypic evaluation of the same subset of lines showed limited correspondence. Taken together, this study reported a collection of useful SSR markers for L. serriola, confirmed transferability of these markers within and across genera, and demonstrated their usefulness in studying genetic diversity.
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Affiliation(s)
- Dilpreet S Riar
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
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Hunter PJ, Hand P, Pink D, Whipps JM, Bending GD. Both leaf properties and microbe-microbe interactions influence within-species variation in bacterial population diversity and structure in the lettuce (Lactuca Species) phyllosphere. Appl Environ Microbiol 2010; 76:8117-25. [PMID: 20952648 PMCID: PMC3008232 DOI: 10.1128/aem.01321-10] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 10/07/2010] [Indexed: 11/20/2022] Open
Abstract
Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.
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Affiliation(s)
- Paul J Hunter
- Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom.
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Schwember AR, Bradford KJ. Quantitative trait loci associated with longevity of lettuce seeds under conventional and controlled deterioration storage conditions. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:4423-36. [PMID: 20693410 PMCID: PMC2955753 DOI: 10.1093/jxb/erq248] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 06/16/2010] [Accepted: 07/19/2010] [Indexed: 05/20/2023]
Abstract
Lettuce (Lactuca sativa L.) seeds have poor shelf life and exhibit thermoinhibition (fail to germinate) above ∼25°C. Seed priming (controlled hydration followed by drying) alleviates thermoinhibition by increasing the maximum germination temperature, but reduces lettuce seed longevity. Controlled deterioration (CD) or accelerated ageing storage conditions (i.e. elevated temperature and relative humidity) are used to study seed longevity and to predict potential seed lifetimes under conventional storage conditions. Seeds produced in 2002 and 2006 of a recombinant inbred line (RIL) population derived from a cross between L. sativa cv. Salinas×L. serriola accession UC96US23 were utilized to identify quantitative trait loci (QTLs) associated with seed longevity under CD and conventional storage conditions. Multiple longevity-associated QTLs were identified under both conventional and CD storage conditions for control (non-primed) and primed seeds. However, seed longevity was poorly correlated between the two storage conditions, suggesting that deterioration processes under CD conditions are not predictive of ageing in conventional storage conditions. Additionally, the same QTLs were not identified when RIL populations were grown in different years, indicating that lettuce seed longevity is strongly affected by production environment. Nonetheless, a major QTL on chromosome 4 [Seed longevity 4.1 (Slg4.1)] was responsible for almost 23% of the phenotypic variation in viability of the conventionally stored control seeds of the 2006 RIL population, with improved longevity conferred by the Salinas allele. QTL analyses may enable identification of mechanisms responsible for the sensitivity of primed seeds to CD conditions and breeding for improved seed longevity.
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Affiliation(s)
| | - Kent J. Bradford
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616-8780 USA
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Schwember AR, Bradford KJ. A genetic locus and gene expression patterns associated with the priming effect on lettuce seed germination at elevated temperatures. PLANT MOLECULAR BIOLOGY 2010; 73:105-18. [PMID: 20047028 PMCID: PMC2850532 DOI: 10.1007/s11103-009-9591-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 12/16/2009] [Indexed: 05/18/2023]
Abstract
Seeds of most cultivated varieties of lettuce (Lactuca sativa L.) fail to germinate at warm temperatures (i.e., above 25-30 degrees C). Seed priming (controlled hydration followed by drying) alleviates this thermoinhibition by increasing the maximum germination temperature. We conducted a quantitative trait locus (QTL) analysis of seed germination responses to priming using a recombinant inbred line (RIL) population derived from a cross between L. sativa cv. Salinas and L. serriola accession UC96US23. Priming significantly increased the maximum germination temperature of the RIL population, and a single major QTL was responsible for 47% of the phenotypic variation due to priming. This QTL collocated with Htg6.1, a major QTL from UC96US23 associated with high temperature germination capacity. Seeds of three near-isogenic lines (NILs) carrying an Htg6.1 introgression from UC96US23 in a Salinas genetic background exhibited synergistic increases in maximum germination temperature in response to priming. LsNCED4, a gene encoding a key enzyme (9-cis-epoxycarotinoid dioxygenase) in the abscisic acid biosynthetic pathway, maps precisely with Htg6.1. Expression of LsNCED4 after imbibition for 24 h at high temperature was greater in non-primed seeds of Salinas, of a second cultivar (Titan) and of NILs containing Htg6.1 compared to primed seeds of the same genotypes. In contrast, expression of genes encoding regulated enzymes in the gibberellin and ethylene biosynthetic pathways (LsGA3ox1 and LsACS1, respectively) was enhanced by priming and suppressed by imbibition at elevated temperatures. Developmental and temperature regulation of hormonal biosynthetic pathways is associated with seed priming effects on germination temperature sensitivity.
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Affiliation(s)
- Andrés R. Schwember
- Department of Plant Sciences, One Shields Ave., University of California, Davis, CA 95616-8780 USA
| | - Kent J. Bradford
- Department of Plant Sciences, One Shields Ave., University of California, Davis, CA 95616-8780 USA
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