101
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Sánchez-Bermejo E, Méndez-Vigo B, Picó FX, Martínez-Zapater JM, Alonso-Blanco C. Novel natural alleles at FLC and LVR loci account for enhanced vernalization responses in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2012; 35:1672-84. [PMID: 22494398 DOI: 10.1111/j.1365-3040.2012.02518.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Vernalization, the induction of flowering by low winter temperatures, is likely to be involved in plant climatic adaptation. However, the genetic, molecular and ecological bases underlying the quantitative variation that tunes vernalization sensitivity to natural environments are largely unknown. To address these questions, we have studied the enhanced vernalization response shown by the Ll-0 accession of Arabidopsis thaliana. Quantitative trait locus (QTL) mapping for several flowering initiation traits in relation to vernalization, in a new Ler × Ll-0 recombinant inbred line (RIL) population, identified large effect alleles at FRI, FLC and HUA2, together with two small effect loci named as Llagostera vernalization response (LVR) 1 and 2. Phenotypic analyses of near isogenic lines validated LVR1 effect on flowering vernalization responses. To further characterize the FLC allele from Ll-0, we carried out genetic association analyses using a regional collection of wild genotypes. FLC-Ll-0 appeared as a low-frequency allele that is distinguished by polymorphism Del(-57), a 50-bp-deletion in the 5'-UTR. Del(-57) was significantly associated with enhanced vernalization responses and FLC RNA expression, as well as with altitude and minimum temperatures. These results are consistent with Del(-57) acting as a novel cis-regulatory FLC polymorphism that may confer climatic adaptation by increasing vernalization sensitivity.
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Affiliation(s)
- Eduardo Sánchez-Bermejo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
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102
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Khan N, Kazmi RH, Willems LAJ, van Heusden AW, Ligterink W, Hilhorst HWM. Exploring the natural variation for seedling traits and their link with seed dimensions in tomato. PLoS One 2012; 7:e43991. [PMID: 22952841 PMCID: PMC3431394 DOI: 10.1371/journal.pone.0043991] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 07/27/2012] [Indexed: 11/18/2022] Open
Abstract
The success of germination, growth and final yield of every crop depends to a large extent on the quality of the seeds used to grow the crop. Seed quality is defined as the viability and vigor attribute of a seed that enables the emergence and establishment of normal seedlings under a wide range of environments. We attempt to dissect the mechanisms involved in the acquisition of seed quality, through a combined approach of physiology and genetics. To achieve this goal we explored the genetic variation found in a RIL population of Solanum lycopersicum (cv. Moneymaker) x Solanum pimpinellifolium through extensive phenotyping of seed and seedling traits under both normal and nutrient stress conditions and root system architecture (RSA) traits under optimal conditions. We have identified 62 major QTLs on 21 different positions for seed, seedling and RSA traits in this population. We identified QTLs that were common across both conditions, as well as specific to stress conditions. Most of the QTLs identified for seedling traits co-located with seed size and seed weight QTLs and the positive alleles were mostly contributed by the S. lycopersicum parent. Co-location of QTLs for different traits might suggest that the same locus has pleiotropic effects on multiple traits due to a common mechanistic basis. We show that seed weight has a strong effect on seedling vigor and these results are of great importance for the isolation of the corresponding genes and elucidation of the underlying mechanisms.
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Affiliation(s)
- Noorullah Khan
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Rashid H. Kazmi
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Leo A. J. Willems
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | | | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Henk W. M. Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
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103
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Vasseur F, Violle C, Enquist BJ, Granier C, Vile D. A common genetic basis to the origin of the leaf economics spectrum and metabolic scaling allometry. Ecol Lett 2012; 15:1149-57. [DOI: 10.1111/j.1461-0248.2012.01839.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 04/20/2012] [Accepted: 06/29/2012] [Indexed: 11/28/2022]
Affiliation(s)
- François Vasseur
- UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE); INRA, Montpellier SupAgro; F-34060 Montpellier France
| | - Cyrille Violle
- Department of Ecology and Evolutionary Biology; University of Arizona; 1041 E Lowell St Tucson Arizona 85721 USA
- Centre d'Ecologie Fonctionnelle et Evolutive; CNRS, UMR5175; F-34000 Montpellier France
| | - Brian J. Enquist
- Department of Ecology and Evolutionary Biology; University of Arizona; 1041 E Lowell St Tucson Arizona 85721 USA
- The Santa Fe Institute; 1399 Hyde Park Road Santa Fe New Mexico 87501 USA
| | - Christine Granier
- UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE); INRA, Montpellier SupAgro; F-34060 Montpellier France
| | - Denis Vile
- UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE); INRA, Montpellier SupAgro; F-34060 Montpellier France
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104
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Kazmi RH, Khan N, Willems LAJ, VAN Heusden AW, Ligterink W, Hilhorst HWM. Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium. PLANT, CELL & ENVIRONMENT 2012; 35:929-51. [PMID: 22074055 DOI: 10.1111/j.1365-3040.2011.02463.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small- to large-effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and genetically complex. Using a recombinant inbred line population of Solanum lycopersicum × Solanum pimpinellifolium, we identified quantitative trait loci (QTLs) influencing seed quality phenotypes under non-stress, as well as salt, osmotic, cold, high-temperature and oxidative stress conditions. In total, 42 seed quality traits were analysed and 120 QTLs were identified for germination traits under different conditions. Significant phenotypic correlations were observed between germination traits under optimal conditions, as well as under different stress conditions. In conclusion, one or more QTLs were identified for each trait with some of these QTLs co-locating. Co-location of QTLs for different traits can be an indication that a locus has pleiotropic effects on multiple traits due to a common mechanistic basis. However, several QTLs also dissected seed quality in its separate components, suggesting different physiological mechanisms and signalling pathways for different seed quality attributes.
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Affiliation(s)
- Rashid H Kazmi
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, the Netherlands
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105
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Toubiana D, Semel Y, Tohge T, Beleggia R, Cattivelli L, Rosental L, Nikoloski Z, Zamir D, Fernie AR, Fait A. Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit, and plant relations. PLoS Genet 2012; 8:e1002612. [PMID: 22479206 PMCID: PMC3315483 DOI: 10.1371/journal.pgen.1002612] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 02/07/2012] [Indexed: 01/20/2023] Open
Abstract
To investigate the regulation of seed metabolism and to estimate the degree of metabolic natural variability, metabolite profiling and network analysis were applied to a collection of 76 different homozygous tomato introgression lines (ILs) grown in the field in two consecutive harvest seasons. Factorial ANOVA confirmed the presence of 30 metabolite quantitative trait loci (mQTL). Amino acid contents displayed a high degree of variability across the population, with similar patterns across the two seasons, while sugars exhibited significant seasonal fluctuations. Upon integration of data for tomato pericarp metabolite profiling, factorial ANOVA identified the main factor for metabolic polymorphism to be the genotypic background rather than the environment or the tissue. Analysis of the coefficient of variance indicated greater phenotypic plasticity in the ILs than in the M82 tomato cultivar. Broad-sense estimate of heritability suggested that the mode of inheritance of metabolite traits in the seed differed from that in the fruit. Correlation-based metabolic network analysis comparing metabolite data for the seed with that for the pericarp showed that the seed network displayed tighter interdependence of metabolic processes than the fruit. Amino acids in the seed metabolic network were shown to play a central hub-like role in the topology of the network, maintaining high interactions with other metabolite categories, i.e., sugars and organic acids. Network analysis identified six exceptionally highly co-regulated amino acids, Gly, Ser, Thr, Ile, Val, and Pro. The strong interdependence of this group was confirmed by the mQTL mapping. Taken together these results (i) reflect the extensive redundancy of the regulation underlying seed metabolism, (ii) demonstrate the tight co-ordination of seed metabolism with respect to fruit metabolism, and (iii) emphasize the centrality of the amino acid module in the seed metabolic network. Finally, the study highlights the added value of integrating metabolic network analysis with mQTL mapping. Seeds represent 70% of the food source for man and livestock. However, as a result of millennia of domestication, crop plants have undergone major genetic deterioration, leading to a loss of important quality traits. Thus, the reintroduction of these quality traits is the key to the improvement of crops in modern agriculture. Seed quality traits include nutritional components, such as proteins and amino acids, and seed germination and storability, which are, in turn, inherently related to metabolism. To understand the genetic basis of seed metabolism—a strategic need in the improvement of seed crops—we studied a collection of offspring plants stemming from the cross between a domesticated tomato cultivar Solanum lycopersicum cv M82 and its distant wild relative S. pennellii. We monitored the changes in metabolism and studied the mode of regulation of the concentration of metabolites in the seeds as a result of genetic introgression, by taking advantage of state-of-the-art technologies and methods of data elaboration such as network-based analysis. We identified a number of candidate genes that may be useful in manipulations to enhance nutritional values in seeds. Finally, in an effort to study the relation among the seed, the fruit, and the mother plant, we determined potential yield-associated metabolic markers.
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Affiliation(s)
- David Toubiana
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer, Israel
| | - Yaniv Semel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Faculty of Agriculture, Rehovot, Israel
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Leah Rosental
- French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer, Israel
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Dani Zamir
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Faculty of Agriculture, Rehovot, Israel
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- * E-mail: (AF); (ARF)
| | - Aaron Fait
- French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer, Israel
- * E-mail: (AF); (ARF)
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106
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Weigel D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. PLANT PHYSIOLOGY 2012; 158:2-22. [PMID: 22147517 PMCID: PMC3252104 DOI: 10.1104/pp.111.189845] [Citation(s) in RCA: 242] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 12/05/2011] [Indexed: 05/18/2023]
Affiliation(s)
- Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany.
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107
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Abstract
The development of near isogenic lines (NILs) through repeated backcrossing of genetically distinct parental lines is rather straightforward. Nonetheless, depending on the available resources and the purpose of the lines to be generated, several choices can be made to guide the design of such inbred populations. Here we outline the implications of these choices and provide recommendations for the efficient and proper development of NILs for a number of common scenarios.
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108
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Kim KH, Kang YJ, Kim DH, Yoon MY, Moon JK, Kim MY, Van K, Lee SH. RNA-Seq analysis of a soybean near-isogenic line carrying bacterial leaf pustule-resistant and -susceptible alleles. DNA Res 2011; 18:483-97. [PMID: 21987089 PMCID: PMC3223079 DOI: 10.1093/dnares/dsr033] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 08/30/2011] [Indexed: 01/19/2023] Open
Abstract
Bacterial leaf pustule (BLP) disease is caused by Xanthomonas axonopodis pv. glycines (Xag). To investigate the plant basal defence mechanisms induced in response to Xag, differential gene expression in near-isogenic lines (NILs) of BLP-susceptible and BLP-resistant soybean was analysed by RNA-Seq. Of a total of 46 367 genes that were mapped to soybean genome reference sequences, 1978 and 783 genes were found to be up- and down-regulated, respectively, in the BLP-resistant NIL relative to the BLP-susceptible NIL at 0, 6, and 12h after inoculation (hai). Clustering analysis revealed that these genes could be grouped into 10 clusters with different expression patterns. Functional annotation based on gene ontology (GO) categories was carried out. Among the putative soybean defence response genes identified (GO:0006952), 134 exhibited significant differences in expression between the BLP-resistant and -susceptible NILs. In particular, pathogen-associated molecular pattern (PAMP) and damage-associated molecular pattern (DAMP) receptors and the genes induced by these receptors were highly expressed at 0 hai in the BLP-resistant NIL. Additionally, pathogenesis-related (PR)-1 and -14 were highly expressed at 0 hai, and PR-3, -6, and -12 were highly expressed at 12 hai. There were also significant differences in the expression of the core JA-signalling components MYC2 and JASMONATE ZIM-motif. These results indicate that powerful basal defence mechanisms involved in the recognition of PAMPs or DAMPs and a high level of accumulation of defence-related gene products may contribute to BLP resistance in soybean.
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Affiliation(s)
- Kil Hyun Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, Republic of Korea
| | - Yang Jae Kang
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, Republic of Korea
| | - Dong Hyun Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, Republic of Korea
| | - Min Young Yoon
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, Republic of Korea
| | - Jung-Kyung Moon
- Rural Development Administration, Gyeonggi 441-770, Republic of Korea
| | - Moon Young Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, Republic of Korea
| | - Kyujung Van
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, Republic of Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, Republic of Korea
- Plant Genomic and Breeding Research Institute, Seoul National University, Seoul 151-921, Republic of Korea
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109
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Rockman MV. The QTN program and the alleles that matter for evolution: all that's gold does not glitter. Evolution 2011; 66:1-17. [PMID: 22220860 DOI: 10.1111/j.1558-5646.2011.01486.x] [Citation(s) in RCA: 462] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The search for the alleles that matter, the quantitative trait nucleotides (QTNs) that underlie heritable variation within populations and divergence among them, is a popular pursuit. But what is the question to which QTNs are the answer? Although their pursuit is often invoked as a means of addressing the molecular basis of phenotypic evolution or of estimating the roles of evolutionary forces, the QTNs that are accessible to experimentalists, QTNs of relatively large effect, may be uninformative about these issues if large-effect variants are unrepresentative of the alleles that matter. Although 20th century evolutionary biology generally viewed large-effect variants as atypical, the field has recently undergone a quiet realignment toward a view of readily discoverable large-effect alleles as the primary molecular substrates for evolution. I argue that neither theory nor data justify this realignment. Models and experimental findings covering broad swaths of evolutionary phenomena suggest that evolution often acts via large numbers of small-effect polygenes, individually undetectable. Moreover, these small-effect variants are different in kind, at the molecular level, from the large-effect alleles accessible to experimentalists. Although discoverable QTNs address some fundamental evolutionary questions, they are essentially misleading about many others.
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Affiliation(s)
- Matthew V Rockman
- Department of Biology and Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
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110
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Kovi MR, Zhang Y, Yu S, Yang G, Yan W, Xing Y. Candidacy of a chitin-inducible gibberellin-responsive gene for a major locus affecting plant height in rice that is closely linked to Green Revolution gene sd1. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:705-14. [PMID: 21637999 DOI: 10.1007/s00122-011-1620-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 05/14/2011] [Indexed: 05/03/2023]
Abstract
Appropriate plant height is crucial for lodging resistance to improve the rice crop yield. The application of semi-dwarf 1 led to the green revolution in the 1960s, by predominantly increasing the rice yield. However, the frequent use of single sd1 gene sources may cause genetic vulnerability to pests and diseases. Identifying useful novel semi-dwarf genes is important for the genetic manipulation of plant architecture in practical rice breeding. In this study, introgression lines derived from two parents contrasting in plant height, Zhenshan 97 and Pokkali were employed to locate a gene with a large effect on plant height by the bulk segregant analysis method. A major gene, ph1, was mapped to a region closely linked to sd1 on chromosome 1; the additive effects of ph1 were more than 50 cm on the plant height and 2 days on the heading date in a BC(4)F(2) population and its progeny. ph1 was then fine mapped to BAC AP003227. Gene annotation indicated that LOC_OS01g65990 encoding a chitin-inducible gibberellin-responsive protein (CIGR), which belongs to the GRAS family, might be the right candidate gene of ph1. Co-segregation analysis of the candidate gene-derived marker finally confirmed its identity as the candidate gene. A higher expression level of the CIGR was detected in all the tested tissues in tall plants compared to those of short plants, especially in the young leaf sheath containing elongating tissues, which indicated its importance role in regulating plant height. ph1 showed a tremendous genetic effect on plant height, which is distinct from sd1 and could be a new resource for breeding semi-dwarf varieties.
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Affiliation(s)
- Mallikarjuna Rao Kovi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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111
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Environmental memory from a circadian oscillator: the Arabidopsis thaliana clock differentially integrates perception of photic vs. thermal entrainment. Genetics 2011; 189:655-64. [PMID: 21840862 DOI: 10.1534/genetics.111.131417] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The constraint of a rotating earth has led to the evolution of a circadian clock that drives anticipation of future environmental changes. During this daily rotation, the circadian clock of Arabidopsis thaliana (Arabidopsis) intersects with the diurnal environment to orchestrate virtually all transcriptional processes of the plant cell, presumably by detecting, interpreting, and anticipating the environmental alternations of light and temperature. To comparatively assess differential inputs toward phenotypic and physiological responses on a circadian parameter, we surveyed clock periodicity in a recombinant inbred population modified to allow for robust periodicity measurements after entrainment to respective photic vs. thermal cues, termed zeitgebers. Lines previously thermally entrained generally displayed reduced period length compared to those previously photically entrained. This differential zeitgeber response was also detected in a set of diverse Arabidopsis accessions. Thus, the zeitgebers of the preceding environment direct future behavior of the circadian oscillator. Allelic variation at quantitative trait loci generated significant differences in zeitgeber responses in the segregating population. These were important for periodicity variation dependent on the nature of the subsequent entrainment source. Collectively, our results provide a genetic paradigm for the basis of environmental memory of a preceding environment, which leads to the integrated coordination of circadian periodicity.
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112
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High-Resolution Genotyping of Wild Barley Introgression Lines and Fine-Mapping of the Threshability Locus thresh-1 Using the Illumina GoldenGate Assay. G3-GENES GENOMES GENETICS 2011; 1:187-96. [PMID: 22384330 PMCID: PMC3276139 DOI: 10.1534/g3.111.000182] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 05/25/2011] [Indexed: 11/24/2022]
Abstract
Genetically well-characterized mapping populations are a key tool for rapid and precise localization of quantitative trait loci (QTL) and subsequent identification of the underlying genes. In this study, a set of 73 introgression lines (S42ILs) originating from a cross between the spring barley cultivar Scarlett (Hordeum vulgare ssp. vulgare) and the wild barley accession ISR42-8 (H. v. ssp. spontaneum) was subjected to high-resolution genotyping with an Illumina 1536-SNP array. The array enabled a precise localization of the wild barley introgressions in the elite barley background. Based on 636 informative SNPs, the S42IL set represents 87.3% of the wild barley genome, where each line contains on average 3.3% of the donor genome. Furthermore, segregating high-resolution mapping populations (S42IL-HRs) were developed for 70 S42ILs in order to facilitate QTL fine-mapping and cloning. As a case study, we used the developed genetic resources to rapidly identify and fine-map the novel locus thresh-1 on chromosome 1H that controls grain threshability. Here, the recessive wild barley allele confers a difficult to thresh phenotype, suggesting that thresh-1 played an important role during barley domestication. Using a S42IL-HR population, thresh-1 was fine-mapped within a 4.3cM interval that was predicted to contain candidate genes involved in regulation of plant cell wall composition. The set of wild barley introgression lines and derived high-resolution populations are ideal tools to speed up the process of mapping and further dissecting QTL, which ultimately clears the way for isolating the genes behind QTL effects.
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113
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Eichten SR, Foerster JM, de Leon N, Kai Y, Yeh CT, Liu S, Jeddeloh JA, Schnable PS, Kaeppler SM, Springer NM. B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize. PLANT PHYSIOLOGY 2011; 156:1679-90. [PMID: 21705654 PMCID: PMC3149956 DOI: 10.1104/pp.111.174748] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation.
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114
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Identification of the Arabidopsis REDUCED DORMANCY 2 gene uncovers a role for the polymerase associated factor 1 complex in seed dormancy. PLoS One 2011; 6:e22241. [PMID: 21799800 PMCID: PMC3143138 DOI: 10.1371/journal.pone.0022241] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 06/17/2011] [Indexed: 12/20/2022] Open
Abstract
The life of a plant is characterized by major phase transitions. This includes the agriculturally important transitions from seed to seedling (germination) and from vegetative to generative growth (flowering induction). In many plant species, including Arabidopsis thaliana, freshly harvested seeds are dormant and incapable of germinating. Germination can occur after the release of dormancy and the occurrence of favourable environmental conditions. Although the hormonal control of seed dormancy is well studied, the molecular mechanisms underlying the induction and release of dormancy are not yet understood. In this study, we report the cloning and characterization of the mutant reduced dormancy 2-1 (rdo2-1). We found that RDO2 is allelic to the recently identified dormancy gene TFIIS, which is a transcription elongation factor. HUB1, which was previously called RDO4, was identified in the same mutagenesis screen for reduced dormancy as rdo2-1 and was also shown to be involved in transcription elongation. The human homologues of RDO2 and HUB1 interact with the RNA Polymerase II Associated Factor 1 Complex (PAF1C). Therefore, we investigated the effect of other Arabidopsis PAF1C related factors; VIP4, VIP5, ELF7, ELF8 and ATXR7 on seed dormancy. Mutations in these genes resulted in reduced dormancy, similar to hub1-2 and rdo2-1. Consistent with a role at the end of seed maturation, we found that HUB1, RDO2 and VIP5 are upregulated during this developmental phase. Since mutants in PAF1C related factors are also described to be early flowering, we conclude that these components are involved in the regulation of both major developmental transitions in the plant.
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115
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A QTL Study for Regions Contributing to Arabidopsis thaliana Root Skewing on Tilted Surfaces. G3-GENES GENOMES GENETICS 2011; 1:105-15. [PMID: 22384323 PMCID: PMC3276130 DOI: 10.1534/g3.111.000331] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 05/06/2011] [Indexed: 11/29/2022]
Abstract
Plant root systems must grow in a manner that is dictated by endogenous genetic pathways, yet sensitive to environmental input. This allows them to provide the plant with water and nutrients while navigating a heterogeneous soil environment filled with obstacles, toxins, and pests. Gravity and touch, which constitute important cues for roots growing in soil, have been shown to modulate root architecture by altering growth patterns. This is illustrated by Arabidopsis thaliana roots growing on tilted hard agar surfaces. Under these conditions, the roots are exposed to both gravity and touch stimulation. Consequently, they tend to skew their growth away from the vertical and wave along the surface. This complex growth behavior is believed to help roots avoid obstacles in nature. Interestingly, A. thaliana accessions display distinct growth patterns under these conditions, suggesting the possibility of using this variation as a tool to identify the molecular mechanisms that modulate root behavior in response to their mechanical environment. We have used the Cvi/Ler recombinant inbred line population to identify quantitative trait loci that contribute to root skewing on tilted hard agar surfaces. A combination of fine mapping for one of these QTL and microarray analysis of expression differences between Cvi and Ler root tips identifies a region on chromosome 2 as contributing to root skewing on tilted surfaces, potentially by modulating cell wall composition.
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Chung CL, Poland J, Kump K, Benson J, Longfellow J, Walsh E, Balint-Kurti P, Nelson R. Targeted discovery of quantitative trait loci for resistance to northern leaf blight and other diseases of maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:307-26. [PMID: 21526397 DOI: 10.1007/s00122-011-1585-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Accepted: 03/24/2011] [Indexed: 05/02/2023]
Abstract
To capture diverse alleles at a set of loci associated with disease resistance in maize, heterogeneous inbred family (HIF) analysis was applied for targeted QTL mapping and near-isogenic line (NIL) development. Tropical maize lines CML52 and DK888 were chosen as donors of alleles based on their known resistance to multiple diseases. Chromosomal regions ("bins"; n = 39) associated with multiple disease resistance (MDR) were targeted based on a consensus map of disease QTLs in maize. We generated HIFs segregating for the targeted loci but isogenic at ~97% of the genome. To test the hypothesis that CML52 and DK888 alleles at MDR hotspots condition broad-spectrum resistance, HIFs and derived NILs were tested for resistance to northern leaf blight (NLB), southern leaf blight (SLB), gray leaf spot (GLS), anthracnose leaf blight (ALB), anthracnose stalk rot (ASR), common rust, common smut, and Stewart's wilt. Four NLB QTLs, two ASR QTLs, and one Stewart's wilt QTL were identified. In parallel, a population of 196 recombinant inbred lines (RILs) derived from B73 × CML52 was evaluated for resistance to NLB, GLS, SLB, and ASR. The QTLs mapped (four for NLB, five for SLB, two for GLS, and two for ASR) mostly corresponded to those found using the NILs. Combining HIF- and RIL-based analyses, we discovered two disease QTLs at which CML52 alleles were favorable for more than one disease. A QTL in bin 1.06-1.07 conferred resistance to NLB and Stewart's wilt, and a QTL in 6.05 conferred resistance to NLB and ASR.
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Affiliation(s)
- Chia-Lin Chung
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY14853, USA
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Christians JK, Cheema MS, Vergara IA, Watt CA, Pinto LJ, Chen N, Moore MM. Quantitative trait locus (QTL) mapping reveals a role for unstudied genes in Aspergillus virulence. PLoS One 2011; 6:e19325. [PMID: 21559404 PMCID: PMC3084825 DOI: 10.1371/journal.pone.0019325] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 03/25/2011] [Indexed: 12/17/2022] Open
Abstract
Infections caused by the fungus Aspergillus are a major cause of morbidity and mortality in immunocompromised populations. To identify genes required for virulence that could be used as targets for novel treatments, we mapped quantitative trait loci (QTL) affecting virulence in the progeny of a cross between two strains of A. nidulans (FGSC strains A4 and A91). We genotyped 61 progeny at 739 single nucleotide polymorphisms (SNP) spread throughout the genome, and constructed a linkage map that was largely consistent with the genomic sequence, with the exception of one potential inversion of ∼527 kb on Chromosome V. The estimated genome size was 3705 cM and the average intermarker spacing was 5.0 cM. The average ratio of physical distance to genetic distance was 8.1 kb/cM, which is similar to previous estimates, and variation in recombination rate was significantly positively correlated with GC content, a pattern seen in other taxa. To map QTL affecting virulence, we measured the ability of each progeny strain to kill model hosts, larvae of the wax moth Galleria mellonella. We detected three QTL affecting in vivo virulence that were distinct from QTL affecting in vitro growth, and mapped the virulence QTL to regions containing 7-24 genes, excluding genes with no sequence variation between the parental strains and genes with only synonymous SNPs. None of the genes in our QTL target regions have been previously associated with virulence in Aspergillus, and almost half of these genes are currently annotated as "hypothetical". This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation.
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Affiliation(s)
- Julian K Christians
- Department of Biological Sciences and Simon Fraser University, Burnaby, British Columbia, Canada.
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Sharma S, Xu S, Ehdaie B, Hoops A, Close TJ, Lukaszewski AJ, Waines JG. Dissection of QTL effects for root traits using a chromosome arm-specific mapping population in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:759-69. [PMID: 21153397 PMCID: PMC3037480 DOI: 10.1007/s00122-010-1484-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 10/22/2010] [Indexed: 05/18/2023]
Abstract
A high-resolution chromosome arm-specific mapping population was used in an attempt to locate/detect gene(s)/QTL for different root traits on the short arm of rye chromosome 1 (1RS) in bread wheat. This population consisted of induced homoeologous recombinants of 1RS with 1BS, each originating from a different crossover event and distinct from all other recombinants in the proportions of rye and wheat chromatin present. It provides a simple and powerful approach to detect even small QTL effects using fewer progeny. A promising empirical Bayes method was applied to estimate additive and epistatic effects for all possible marker pairs simultaneously in a single model. This method has an advantage for QTL analysis in minimizing the error variance and detecting interaction effects between loci with no main effect. A total of 15 QTL effects, 6 additive and 9 epistatic, were detected for different traits of root length and root weight in 1RS wheat. Epistatic interactions were further partitioned into inter-genomic (wheat and rye alleles) and intra-genomic (rye-rye or wheat-wheat alleles) interactions affecting various root traits. Four common regions were identified involving all the QTL for root traits. Two regions carried QTL for almost all the root traits and were responsible for all the epistatic interactions. Evidence for inter-genomic interactions is provided. Comparison of mean values supported the QTL detection.
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Affiliation(s)
- Sundrish Sharma
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124 USA
- Present Address: Syngenta Seeds, Inc., Naples, FL 34114 USA
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124 USA
| | - Bahman Ehdaie
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124 USA
| | - Aaron Hoops
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124 USA
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124 USA
| | - Adam J. Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124 USA
| | - J. Giles Waines
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124 USA
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Fructose sensitivity is suppressed in Arabidopsis by the transcription factor ANAC089 lacking the membrane-bound domain. Proc Natl Acad Sci U S A 2011; 108:3436-41. [PMID: 21300879 DOI: 10.1073/pnas.1018665108] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In living organisms sugars not only provide energy and carbon skeletons but also act as evolutionarily conserved signaling molecules. The three major soluble sugars in plants are sucrose, glucose, and fructose. Information on plant glucose and sucrose signaling is available, but to date no fructose-specific signaling pathway has been reported. In this study, sugar repression of seedling development was used to study fructose sensitivity in the Landsberg erecta (Ler)/Cape Verde Islands (Cvi) recombinant inbred line population, and eight fructose-sensing quantitative trait loci (QTLs) (FSQ1-8) were mapped. Among them, FSQ6 was confirmed to be a fructose-specific QTL by analyzing near-isogenic lines in which Cvi genomic fragments were introgressed in the Ler background. These results indicate the existence of a fructose-specific signaling pathway in Arabidopsis. Further analysis demonstrated that the FSQ6-associated fructose-signaling pathway functions independently of the hexokinase1 (HXK1) glucose sensor. Remarkably, fructose-specific FSQ6 downstream signaling interacts with abscisic acid (ABA)- and ethylene-signaling pathways, similar to HXK1-dependent glucose signaling. The Cvi allele of FSQ6 acts as a suppressor of fructose signaling. The FSQ6 gene was identified using map-based cloning approach, and FSQ6 was shown to encode the transcription factor gene Arabidopsis NAC (petunia No apical meristem and Arabidopsis transcription activation factor 1, 2 and Cup-shaped cotyledon 2) domain containing protein 89 (ANAC089). The Cvi allele of FSQ6/ANAC089 is a gain-of-function allele caused by a premature stop in the third exon of the gene. The truncated Cvi FSQ6/ANAC089 protein lacks a membrane association domain that is present in ANAC089 proteins from other Arabidopsis accessions. As a result, Cvi FSQ6/ANAC089 is constitutively active as a transcription factor in the nucleus.
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Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, Stein N, Waugh R. Genetic dissection of barley morphology and development. PLANT PHYSIOLOGY 2011; 155:617-27. [PMID: 21088227 PMCID: PMC3032454 DOI: 10.1104/pp.110.166249] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Accepted: 11/14/2010] [Indexed: 05/18/2023]
Abstract
Since the early 20th century, barley (Hordeum vulgare) has been a model for investigating the effects of physical and chemical mutagens and for exploring the potential of mutation breeding in crop improvement. As a consequence, extensive and well-characterized collections of morphological and developmental mutants have been assembled that represent a valuable resource for exploring a wide range of complex and fundamental biological processes. We constructed a collection of 881 backcrossed lines containing mutant alleles that induce a majority of the morphological and developmental variation described in this species. After genotyping these lines with up to 3,072 single nucleotide polymorphisms, comparison to their recurrent parent defined the genetic location of 426 mutant alleles to chromosomal segments, each representing on average <3% of the barley genetic map. We show how the gene content in these segments can be predicted through conservation of synteny with model cereal genomes, providing a route to rapid gene identification.
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Affiliation(s)
- Arnis Druka
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom.
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121
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Salvi S, Corneti S, Bellotti M, Carraro N, Sanguineti MC, Castelletti S, Tuberosa R. Genetic dissection of maize phenology using an intraspecific introgression library. BMC PLANT BIOLOGY 2011; 11:4. [PMID: 21211047 PMCID: PMC3025946 DOI: 10.1186/1471-2229-11-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 01/06/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND Collections of nearly isogenic lines where each line carries a delimited portion of a donor source genome into a common recipient genetic background are known as introgression libraries and have already shown to be instrumental for the dissection of quantitative traits. By means of marker-assisted backcrossing, we have produced an introgression library using the extremely early-flowering maize (Zea mays L.) variety Gaspé Flint and the elite line B73 as donor and recipient genotypes, respectively, and utilized this collection to investigate the genetic basis of flowering time and related traits of adaptive and agronomic importance in maize. RESULTS The collection includes 75 lines with an average Gaspé Flint introgression length of 43.1 cM. The collection was evaluated for flowering time, internode length, number of ears, number of nodes (phytomeres), number of nodes above the ear, number and proportion of nodes below the ear and plant height. Five QTLs for flowering time were mapped, all corresponding to major QTLs for number of nodes. Three additional QTLs for number of nodes were mapped. Besides flowering time, the QTLs for number of nodes drove phenotypic variation for plant height and number of nodes below and above the top ear, but not for internode length. A number of apparently Mendelian-inherited phenotypes were also observed. CONCLUSIONS While the inheritance of flowering time was dominated by the well-known QTL Vgt1, a number of other important flowering time QTLs were identified and, thanks to the type of plant material here utilized, immediately isogenized and made available for fine mapping. At each flowering time QTL, early flowering correlated with fewer vegetative phytomeres, indicating the latter as a key developmental strategy to adapt the maize crop from the original tropical environment to the northern border of the temperate zone (southern Canada), where Gaspé Flint was originally cultivated. Because of the trait differences between the two parental genotypes, this collection will serve as a permanent source of nearly isogenic materials for multiple studies of QTL analysis and cloning.
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Affiliation(s)
- Silvio Salvi
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Simona Corneti
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Massimo Bellotti
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Nicola Carraro
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
- Department of Horticulture and Landscape Architecture, 625 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, USA
| | - Maria C Sanguineti
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Sara Castelletti
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Roberto Tuberosa
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
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Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, Filichkina T, Johnson EA, Hayes PM. Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics 2011; 12:4. [PMID: 21205322 PMCID: PMC3023751 DOI: 10.1186/1471-2164-12-4] [Citation(s) in RCA: 231] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 01/04/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Linkage maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage map construction, employing barley as a model system. Using the published high density EST-based SNP map in the Oregon Wolfe Barley (OWB) mapping population as a reference, we created a RAD map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both maps for detection of quantitative trait loci (QTL). RESULTS Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines--the "dominant" and "recessive" marker stocks--and scored in a 93 member doubled haploid (DH) mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic map was constructed. The assembled RAD-only map consists of 445 markers with an average interval length of 5 cM, while an integrated map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the Hordeum genome. Total map lengths are comparable and the order of common markers is identical in both maps. The same large-effect QTL for reproductive fitness traits were detected with both maps and the majority of these QTL were coincident with a dwarfing gene (ZEO) and the VRS1 gene, which determines the two-row and six-row germplasm groups of barley. CONCLUSIONS We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in de novo genome assembly, development of ultra-high density genetic maps and association mapping.
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Affiliation(s)
- Yada Chutimanitsakun
- Crop and Soil Science Department, Oregon State University, Corvallis, Oregon, USA
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Fernie AR, Klee HJ. The use of natural genetic diversity in the understanding of metabolic organization and regulation. FRONTIERS IN PLANT SCIENCE 2011; 2:59. [PMID: 22645543 PMCID: PMC3355787 DOI: 10.3389/fpls.2011.00059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 09/12/2011] [Indexed: 05/02/2023]
Abstract
The study of metabolic regulation has traditionally focused on analysis of specific enzymes, emphasizing kinetic properties, and the influence of protein interactions and post-translational modifications. More recently, reverse genetic approaches permit researchers to directly determine the effects of a deficiency or a surplus of a given enzyme on the biochemistry and physiology of a plant. Furthermore, in many model species, gene expression atlases that give important spatial information concerning the quantitative expression level of metabolism-associated genes are being produced. In parallel, "top-down" approaches to understand metabolic regulation have recently been instigated whereby broad genetic diversity is screened for metabolic traits and the genetic basis of this diversity is defined thereafter. In this article we will review recent examples of this latter approach both in the model species Arabidopsis thaliana and the crop species tomato (Solanum lycopersicum). In addition to highlighting examples in which this genetic diversity approach has proven promising, we will discuss the challenges associated with this approach and provide a perspective for its future utility.
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Affiliation(s)
- Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
- *Correspondence: Alisdair R. Fernie, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany. e-mail:
| | - Harry J. Klee
- Horticultural Sciences Department and the Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
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Bentsink L, Koornneef M. Identification and characterization of quantitative trait loci that control seed dormancy in Arabidopsis. Methods Mol Biol 2011; 773:165-184. [PMID: 21898256 DOI: 10.1007/978-1-61779-231-1_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Seed dormancy is a trait that is under multigenic control and affected strongly by environmental factors. Thus, seed dormancy is a typical quantitative trait. Natural accessions of Arabidopsis thaliana exhibit a great deal of genetic variation for seed dormancy. This natural variation can be used to identify genes controlling this trait by means of quantitative trait loci (QTL) mapping. In this chapter, we describe how QTL mapping for seed dormancy in Arabidopsis thaliana can be performed and how QTL analyses can be used to eventually identify the causal gene. Methods and recourses available specifically for Arabidopsis are described or referred to.
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Affiliation(s)
- Leónie Bentsink
- Department of Molecular Plant Physiology, Utrecht University, CH, Utrecht, 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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Frérot H. A challenge for hyperaccumulating plant models: 'cycling' as fast as Arabidopsis thaliana. THE NEW PHYTOLOGIST 2011; 189:357-359. [PMID: 21175629 DOI: 10.1111/j.1469-8137.2010.03591.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- Hélène Frérot
- Université Lille 1, GEPV, Bâtiment SN2, Villeneuve d'Ascq 59655, France.
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127
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Bergelson J, Roux F. Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nat Rev Genet 2010; 11:867-79. [PMID: 21085205 DOI: 10.1038/nrg2896] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A major challenge in evolutionary biology and plant breeding is to identify the genetic basis of complex quantitative traits, including those that contribute to adaptive variation. Here we review the development of new methods and resources to fine-map intraspecific genetic variation that underlies natural phenotypic variation in plants. In particular, the analysis of 107 quantitative traits reported in the first genome-wide association mapping study in Arabidopsis thaliana sets the stage for an exciting time in our understanding of plant adaptation. We also argue for the need to place phenotype-genotype association studies in an ecological context if one is to predict the evolutionary trajectories of plant species.
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Affiliation(s)
- Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA.
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128
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Yin T, Zhang X, Gunter L, Priya R, Sykes R, Davis M, Wullschleger SD, Tuskan GA. Differential detection of genetic Loci underlying stem and root lignin content in Populus. PLoS One 2010; 5:e14021. [PMID: 21151641 PMCID: PMC2999904 DOI: 10.1371/journal.pone.0014021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2010] [Accepted: 08/20/2010] [Indexed: 01/16/2023] Open
Abstract
In this study, we established a comprehensive genetic map with a large number of progeny from a three-generation hybrid Populus intercross, and phenotyped the lignin content, S/G ratio and 28 cell wall subcomponents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content and syringyl-to-guaiacyl (S/G) ratio using pyrolysis molecular beam mass spectroscopy (pyMBMS) varied among mapping individuals. Phenotypic analysis revealed that stem lignin content is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations observed among components within organs. Altogether, 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci, 27 of which appear to be pleiotropic. Many of the detected genetic loci were detected differentially in stem and root. This is the first report of separate genetic loci controlling cell wall phenotypes above and below ground. These results suggest that it may be possible to modify lignin content and composition via breed and/or engineer as a means of simultaneously improving Populus for cellulosic ethanol production and carbon sequestration.
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Affiliation(s)
- Tongming Yin
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
- The Key Lab of Forest Genetics and Gene Engineering, Nanjing Forestry University, Nanjing, China
| | - Xinye Zhang
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
| | - Lee Gunter
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
| | - Ranjan Priya
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
| | - Robert Sykes
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, Colorado, United States of America
| | - Mark Davis
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, Colorado, United States of America
| | - Stan D. Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Gerald A. Tuskan
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
- * E-mail:
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129
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Power and false-positive rate in QTL detection with near-isogenic line libraries. Heredity (Edinb) 2010; 106:576-84. [PMID: 20683482 DOI: 10.1038/hdy.2010.87] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Libraries of near-isogenic lines (NILs) were used for quantitative trait locus (QTL) detection in model species and economically important crops. The experimental design and genetic architecture of the considered traits determine the statistical properties of QTL detection. The objectives of our simulation study were to (i) investigate the population sizes required to develop NIL libraries in barley and maize, (ii) compare NIL libraries with nonoverlapping and overlapping donor segments and (iii) study the number of QTLs and the size of their effects with respect to the power and the false-positive rate of QTL detection. In barley, the development of NIL libraries with target segment lengths of 10 c and marker distances of 5 cM was possible using a BC(3)S(2) backcrossing scheme and population sizes of 140. In maize, population sizes larger than 200 were required. Selection for the recipient parent genome at markers flanking the target segments with distances between 5 and 10 cM was required for an efficient control of the false-positive rate. NIL libraries with nonoverlapping donor chromosome segments had a greater power of QTL detection and a smaller false-positive rate than libraries with overlapping segments. Major genes explaining 30% of the genotypic difference between the donor and recipient were successfully detected even with low heritabilities of 0.5, whereas for minor genes explaining 5 !or 10%, high heritabilities of 0.8 or 0.9 were required. The presented results can assist geneticists and breeders in the efficient development of NIL libraries for QTL detection.
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130
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Chung CL, Longfellow JM, Walsh EK, Kerdieh Z, Van Esbroeck G, Balint-Kurti P, Nelson RJ. Resistance loci affecting distinct stages of fungal pathogenesis: use of introgression lines for QTL mapping and characterization in the maize--Setosphaeria turcica pathosystem. BMC PLANT BIOLOGY 2010; 10:103. [PMID: 20529319 PMCID: PMC3017769 DOI: 10.1186/1471-2229-10-103] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Accepted: 06/08/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Studies on host-pathogen interactions in a range of pathosystems have revealed an array of mechanisms by which plants reduce the efficiency of pathogenesis. While R-gene mediated resistance confers highly effective defense responses against pathogen invasion, quantitative resistance is associated with intermediate levels of resistance that reduces disease progress. To test the hypothesis that specific loci affect distinct stages of fungal pathogenesis, a set of maize introgression lines was used for mapping and characterization of quantitative trait loci (QTL) conditioning resistance to Setosphaeria turcica, the causal agent of northern leaf blight (NLB). To better understand the nature of quantitative resistance, the identified QTL were further tested for three secondary hypotheses: (1) that disease QTL differ by host developmental stage; (2) that their performance changes across environments; and (3) that they condition broad-spectrum resistance. RESULTS Among a set of 82 introgression lines, seven lines were confirmed as more resistant or susceptible than B73. Two NLB QTL were validated in BC4F2 segregating populations and advanced introgression lines. These loci, designated qNLB1.02 and qNLB1.06, were investigated in detail by comparing the introgression lines with B73 for a series of macroscopic and microscopic disease components targeting different stages of NLB development. Repeated greenhouse and field trials revealed that qNLB1.06(Tx303) (the Tx303 allele at bin 1.06) reduces the efficiency of fungal penetration, while qNLB1.02(B73) (the B73 allele at bin 1.02) enhances the accumulation of callose and phenolics surrounding infection sites, reduces hyphal growth into the vascular bundle and impairs the subsequent necrotrophic colonization in the leaves. The QTL were equally effective in both juvenile and adult plants; qNLB1.06(Tx303) showed greater effectiveness in the field than in the greenhouse. In addition to NLB resistance, qNLB1.02(B73) was associated with resistance to Stewart's wilt and common rust, while qNLB1.06(Tx303) conferred resistance to Stewart's wilt. The non-specific resistance may be attributed to pleiotropy or linkage. CONCLUSIONS Our research has led to successful identification of two reliably-expressed QTL that can potentially be utilized to protect maize from S. turcica in different environments. This approach to identifying and dissecting quantitative resistance in plants will facilitate the application of quantitative resistance in crop protection.
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Affiliation(s)
- Chia-Lin Chung
- Dept. of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Joy M Longfellow
- Dept. of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ellie K Walsh
- Dept. of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zura Kerdieh
- Dept. of Biology, West Virginia State University, Institute, WV 25112, USA
| | - George Van Esbroeck
- Dept. of Crop Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Peter Balint-Kurti
- USDA-ARS, Plant Science Research Unit; Dept. of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Rebecca J Nelson
- Dept. of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
- Dept. of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA
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131
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Vlad D, Rappaport F, Simon M, Loudet O. Gene transposition causing natural variation for growth in Arabidopsis thaliana. PLoS Genet 2010; 6:e1000945. [PMID: 20485571 PMCID: PMC2869320 DOI: 10.1371/journal.pgen.1000945] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 04/09/2010] [Indexed: 11/19/2022] Open
Abstract
A major challenge in biology is to identify molecular polymorphisms responsible for variation in complex traits of evolutionary and agricultural interest. Using the advantages of Arabidopsis thaliana as a model species, we sought to identify new genes and genetic mechanisms underlying natural variation for shoot growth using quantitative genetic strategies. More quantitative trait loci (QTL) still need be resolved to draw a general picture as to how and where in the pathways adaptation is shaping natural variation and the type of molecular variation involved. Phenotypic variation for shoot growth in the Bur-0 × Col-0 recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation controlled by opposite linked loci and masked by the segregation bias due to the defective phenotype of SG3 (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping strategy, we have identified the underlying gene causing phenotypic variation at SG3: At4g30720 codes for a new chloroplast-located protein essential to ensure a correct electron flow through the photosynthetic chain and, hence, photosynthesis efficiency and normal growth. The SG3/SG3i interaction is the result of a structural polymorphism originating from the duplication of the gene followed by divergent paralogue's loss between parental accessions. Species-wide, our results illustrate the very dynamic rate of duplication/transposition, even over short periods of time, resulting in several divergent—but still functional—combinations of alleles fixed in different backgrounds. In predominantly selfing species like Arabidopsis, this variation remains hidden in wild populations but is potentially revealed when divergent individuals outcross. This work highlights the need for improved tools and algorithms to resolve structural variation polymorphisms using high-throughput sequencing, because it remains challenging to distinguish allelic from paralogous variation at this scale. Plant growth is a very complex character impacted by almost any aspect of plant biology and showing continuous variation among natural populations of a single species like Arabidopsis thaliana. Although difficult, it is important to reveal the precise genetic architecture of such a trait's variation to improve our understanding of the mechanisms and evolutionary significance of phenotypic variation. By using recombinant inbred lines derived from a cross between the reference strain ‘Col-0’ and the Irish strain ‘Bur-0’, we have localized several regions of the genome impacting plant growth. When attempting to confirm one of this region's effect, we revealed an even more complex genetic architecture where a first locus (which had remained undetected initially) has a major effect on growth only when a specific genotype was present at a second locus. We have shown here that the reason for this epistatic interaction between the two loci is that the functional allele for a gene important for photosynthesis efficiency and, consequently, growth, had been transposed from one locus to the other in Bur-0 compared to Col-0. This type of structural polymorphism seems to be frequent among strains and, although more difficult to detect, is likely to be of significant evolutionary importance.
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Affiliation(s)
- Daniela Vlad
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Fabrice Rappaport
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, Paris, France
| | - Matthieu Simon
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
- * E-mail:
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132
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Zhao H, Liu J, Shi L, Xu F, Wang Y. Development of boron-efficient near isogenic lines of Brassica napus and their response to low boron stress at seedling stage. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410010096] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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133
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van Zanten M, Basten Snoek L, van Eck-Stouten E, Proveniers MCG, Torii KU, Voesenek LACJ, Peeters AJM, Millenaar FF. Ethylene-induced hyponastic growth in Arabidopsis thaliana is controlled by ERECTA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:83-95. [PMID: 19796369 DOI: 10.1111/j.1365-313x.2009.04035.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants can respond quickly and profoundly to detrimental changes in their environment. For example, Arabidopsis thaliana can induce an upward leaf movement response through differential petiole growth (hyponastic growth) to outgrow complete submergence. This response is induced by accumulation of the phytohormone ethylene in the plant. Currently, only limited information is available on how this response is molecularly controlled. In this study, we utilized quantitative trait loci (QTL) analysis of natural genetic variation among Arabidopsis accessions to isolate novel factors controlling constitutive petiole angles and ethylene-induced hyponastic growth. Analysis of mutants in various backgrounds and complementation analysis of naturally occurring mutant accessions provided evidence that the leucin-rich repeat receptor-like Ser/Thr kinase gene, ERECTA, controls ethylene-induced hyponastic growth. Moreover, ERECTA controls leaf positioning in the absence of ethylene treatment. Our data demonstrate that this is not due to altered ethylene production or sensitivity.
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Affiliation(s)
- Martijn van Zanten
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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134
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Meyer RC, Kusterer B, Lisec J, Steinfath M, Becher M, Scharr H, Melchinger AE, Selbig J, Schurr U, Willmitzer L, Altmann T. QTL analysis of early stage heterosis for biomass in Arabidopsis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:227-37. [PMID: 19504257 PMCID: PMC2793381 DOI: 10.1007/s00122-009-1074-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 05/18/2009] [Indexed: 05/19/2023]
Abstract
The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F (1) hybrid exhibited 44% heterosis for biomass. Mid-parent heterosis in the RILs ranged from -31 to 99% for dry weight and from -58 to 143% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.
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Affiliation(s)
- Rhonda Christiane Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany.
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135
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Dalziel AC, Rogers SM, Schulte PM. Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology. Mol Ecol 2009; 18:4997-5017. [PMID: 19912534 DOI: 10.1111/j.1365-294x.2009.04427.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The accessibility of new genomic resources, high-throughput molecular technologies and analytical approaches such as genome scans have made finding genes contributing to fitness variation in natural populations an increasingly feasible task. Once candidate genes are identified, we argue that it is necessary to take a mechanistic approach and work up through the levels of biological organization to fully understand the impacts of genetic variation at these candidate genes. We demonstrate how this approach provides testable hypotheses about the causal links among levels of biological organization, and assists in designing relevant experiments to test the effects of genetic variation on phenotype, whole-organism performance capabilities and fitness. We review some of the research programs that have incorporated mechanistic approaches when examining naturally occurring genetic and phenotypic variation and use these examples to highlight the value of developing a comprehensive understanding of the relationship between genotype and fitness. We give suggestions to guide future research aimed at uncovering and understanding the genetic basis of adaptation and argue that further integration of mechanistic approaches will help molecular ecologists better understand the evolution of natural populations.
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Affiliation(s)
- Anne C Dalziel
- Department of Zoology, University of British Columbia, Vancouver, Canada.
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136
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Tessadori F, van Zanten M, Pavlova P, Clifton R, Pontvianne F, Snoek LB, Millenaar FF, Schulkes RK, van Driel R, Voesenek LACJ, Spillane C, Pikaard CS, Fransz P, Peeters AJM. Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genet 2009; 5:e1000638. [PMID: 19730687 PMCID: PMC2728481 DOI: 10.1371/journal.pgen.1000638] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 08/08/2009] [Indexed: 11/18/2022] Open
Abstract
Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. Studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. It has been previously shown that chromatin compaction changes during development and biotic stress. To gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phenotype of 21 selected Arabidopsis accessions from different geographic origins and habitats. We show natural variation in chromatin compaction and demonstrate a positive correlation with latitude of geographic origin. The level of compaction appeared to be dependent on light intensity. A novel approach, combining Quantitative Trait Locus (QTL) mapping and microscopic examination, pointed at PHYTOCHROME-B (PHYB) and HISTONE DEACETYLASE-6 (HDA6) as positive regulators of light-controlled chromatin compaction. Indeed, mutant analyses demonstrate that both factors affect global chromatin organization. HDA6, in addition, strongly promotes the light-mediated compaction of the Nucleolar Organizing Regions (NORs). The accession Cape Verde Islands-0 (Cvi-0), which shows sequence polymorphism in the PHYB gene and in the HDA6 promotor, resembles the hda6 mutant in having reduced chromatin compaction and decreased methylation levels of DNA and histone H3K9 at the NORs. We provide evidence that chromatin organization is controlled by light intensity. We propose that chromatin plasticity is associated with acclimation of Arabidopsis to its environment. The polymorphic alleles such as PHYB and HDA6 control this process. The habitat of the plant model species Arabidopsis thaliana can be found throughout the Northern hemisphere. As a consequence, individual populations have acclimated to a great diversity of environmental conditions. This is reflected by a wealth of natural genetic variation in many phenotypic traits. We utilized this natural variation via a novel approach, combining microscopic examination, quantitative genetics, and analysis of environmental parameters, to understand the regulation of nuclear chromatin compaction in leaf mesophyll cells. We show that the level of chromatin compaction among natural Arabidopsis thaliana accessions correlates with latitude of origin and depends on local light intensity. Our study provides evidence that the photoreceptor PHYTOCHROME-B (PHYB) and the histone modifier HISTONE DEACETYLASE 6 (HDA6) are positive regulators of global chromatin organization in a light-dependent manner. In addition, HDA6 specifically controls light-mediated chromatin compaction of the Nucleolar Organizing Regions (NORs). We propose that the observed light-controlled plasticity of chromatin plays a role in acclimation and survival of plants in their natural environment.
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Affiliation(s)
- Federico Tessadori
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijn van Zanten
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Penka Pavlova
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory of Genetics, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Rachel Clifton
- Genetics & Biotechnology Laboratory, Department of Biochemistry & Biosciences Institute, University College Cork, Cork, Republic of Ireland
| | - Frédéric Pontvianne
- Biology Department, Washington University, St. Louis, Missouri, United States of America
| | - L. Basten Snoek
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Frank F. Millenaar
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Roeland Kees Schulkes
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Roel van Driel
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Charles Spillane
- Genetics & Biotechnology Laboratory, Department of Biochemistry & Biosciences Institute, University College Cork, Cork, Republic of Ireland
| | - Craig S. Pikaard
- Biology Department, Washington University, St. Louis, Missouri, United States of America
| | - Paul Fransz
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail: (PF); (AJMP)
| | - Anton J. M. Peeters
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
- * E-mail: (PF); (AJMP)
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137
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Lisec J, Steinfath M, Meyer RC, Selbig J, Melchinger AE, Willmitzer L, Altmann T. Identification of heterotic metabolite QTL in Arabidopsis thaliana RIL and IL populations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:777-88. [PMID: 19453458 DOI: 10.1111/j.1365-313x.2009.03910.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Two mapping populations of a cross between the Arabidopsis thaliana accessions Col-0 and C24 were cultivated and analyzed with respect to the levels of 181 metabolites to elucidate the biological phenomenon of heterosis at the metabolic level. The relative mid-parent heterosis in the F(1) hybrids was <20% for most metabolic traits. The first mapping population consisting of 369 recombinant inbred lines (RILs) and their test cross progeny with both parents allowed us to determine the position and effect of 147 quantitative trait loci (QTL) for metabolite absolute mid-parent heterosis (aMPH). Furthermore, we identified 153 and 83 QTL for augmented additive (Z(1)) and dominance effects (Z(2)), respectively. We identified putative candidate genes for these QTL using the aracyc database (http://www.arabidopsis.org/biocyc), and calculated the average degree of dominance, which was within the dominance and over-dominance range for most metabolites. Analyzing a second population of 41 introgression lines (ILs) and their test crosses with the recurrent parent, we identified 634 significant differences in metabolite levels. Nine per cent of these effects were classified as over-dominant, according to the mode of inheritance. A comparison of both approaches suggested epistasis as a major contributor to metabolite heterosis in Arabidopsis. A linear combination of metabolite levels was shown to significantly correlate with biomass heterosis (r = 0.62).
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Affiliation(s)
- Jan Lisec
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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138
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Major flowering time gene, flowering locus C, regulates seed germination in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2009; 106:11661-6. [PMID: 19564609 DOI: 10.1073/pnas.0901367106] [Citation(s) in RCA: 197] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Flowering locus C (FLC) is a major regulator of flowering responses to seasonal environmental factors. Here, we document that FLC also regulates another major life-history transition-seed germination, and that natural variation at the FLC locus and in FLC expression is associated with natural variation in temperature-dependent germination. FLC-mediated germination acts through additional genes in the flowering pathway (FT, SOC1, and AP1) before involving the abscisic acid catabolic pathway (via CYP707A2) and gibberellins biosynthetic pathway (via GA20ox1) in seeds. Also, FLC regulation of germination is largely maternally controlled, with FLC peaking and FT, SOC1, and AP1 levels declining at late stages of seed maturation. High FLC expression during seed maturation is associated with altered expression of hormonal genes (CYP707A2 and GA20ox1) in germinating seeds, indicating that gene expression before the physiological independence of seeds can influence gene expression well after any physical connection between maternal plants and seeds exists. The major role of FLC in temperature-dependent germination documented here reveals a much broader adaptive significance of natural variation in FLC. Therefore, pleiotropy between these major life stages likely influences patterns of natural selection on this important gene, making FLC a promising case for examining how pleiotropy influences adaptive evolution.
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139
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Doroszuk A, Snoek LB, Fradin E, Riksen J, Kammenga J. A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans. Nucleic Acids Res 2009; 37:e110. [PMID: 19542186 PMCID: PMC2760803 DOI: 10.1093/nar/gkp528] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recombinant inbred lines (RILs) derived from Caenorhabditis elegans wild-type N2 and CB4856 are increasingly being used for mapping genes underlying complex traits. To speed up mapping and gene discovery, introgression lines (ILs) offer a powerful tool for more efficient QTL identification. We constructed a library of 90 ILs, each carrying a single homozygous CB4856 genomic segment introgressed into the genetic background of N2. The ILs were genotyped by 123 single-nucleotide polymorphism (SNP) markers. The proportion of the CB4856 segments in most lines does not exceed 3%, and together the introgressions cover 96% of the CB4856 genome. The value of the IL library was demonstrated by identifying novel loci underlying natural variation in two ageing-related traits, i.e. lifespan and pharyngeal pumping rate. Bin mapping of lifespan resulted in six QTLs, which all have a lifespan-shortening effect on the CB4856 allele. We found five QTLs for the decrease in pumping rate, of which four colocated with QTLs found for average lifespan. This suggests pleiotropic or closely linked QTL associated with lifespan and pumping rate. Overall, the presented IL library provides a versatile resource toward easier and efficient fine mapping and functional analyses of loci and genes underlying complex traits in C. elegans.
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Affiliation(s)
- Agnieszka Doroszuk
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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140
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Takai T, Ohsumi A, San-oh Y, Laza MRC, Kondo M, Yamamoto T, Yano M. Detection of a quantitative trait locus controlling carbon isotope discrimination and its contribution to stomatal conductance in japonica rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:1401-10. [PMID: 19242671 DOI: 10.1007/s00122-009-0990-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 02/03/2009] [Indexed: 05/19/2023]
Abstract
Increasing leaf photosynthesis offers a possible way to improve yield potential in rice (Oryza sativa L.). Carbon isotope discrimination (Delta(13)C) has potential as an indirect selection criterion. In this study, we searched for quantitative trait loci (QTLs) controlling Delta(13)C, and assessed their association with leaf photosynthesis. Substitution mapping by using chromosome segment substitution lines (CSSLs), that carry segments from the indica cultivar Kasalath in the genetic background of the japonica cultivar Koshihikari, identified genomic regions affecting Delta(13)C on chromosomes (Chr.) 2, 3, 6, 7, and 12. One of the CSSLs, SL208, in which most regions on Chr. 3 were substituted with Kasalath segments, showed higher leaf stomatal conductance for CO(2) (g (s)) and Delta(13)C than Koshihikari during the vegetative stage although leaf photosynthetic rate did not differ between them. These results suggest an association between Delta(13)C and g (s). To test this association, we performed a QTL analysis for Delta(13)C at vegetative and heading stages in an F(2) population derived from a cross between SL208 and Koshihikari. The results confirmed a QTL controlling Delta(13)C on the long arm of Chr. 3. By using a near-isogenic line specific to Hd6, we ruled out the possibility that variation in Delta(13)C was generated through the pleiotropic effect of heading date.
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Affiliation(s)
- Toshiyuki Takai
- National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki, Japan
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141
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Bikard D, Patel D, Le Metté C, Giorgi V, Camilleri C, Bennett MJ, Loudet O. Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana. Science 2009; 323:623-6. [PMID: 19179528 DOI: 10.1126/science.1165917] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Genetic incompatibilities resulting from interactions between two loci represent a potential source of postzygotic barriers and may be an important factor in evolution when they impair the outcome of interspecific crosses. We show that, in crosses between strains of the plant Arabidopsis thaliana, loci interact epistatically, controlling a recessive embryo lethality. This interaction is explained by divergent evolution occurring among paralogs of an essential duplicate gene, for which the functional copy is not located at the same locus in different accessions. These paralogs demonstrate genetic heterogeneity in their respective evolutionary trajectories, which results in widespread incompatibility among strains. Our data suggest that these passive mechanisms, gene duplication and extinction, could represent an important source of genetic incompatibilities across all taxa.
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Affiliation(s)
- David Bikard
- Genetics and Plant Breeding, INRA, SGAP UR254, F-78026 Versailles, France
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142
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Genetic Background and Environmental Effects on Expression of QTL for Sheath Blight Resistance in Reciprocal Introgression Lines of Rice. ACTA AGRONOMICA SINICA 2009. [DOI: 10.3724/sp.j.1006.2008.01885] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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143
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Balasubramanian S, Schwartz C, Singh A, Warthmann N, Kim MC, Maloof JN, Loudet O, Trainer GT, Dabi T, Borevitz JO, Chory J, Weigel D. QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines. PLoS One 2009; 4:e4318. [PMID: 19183806 PMCID: PMC2629843 DOI: 10.1371/journal.pone.0004318] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2008] [Accepted: 12/22/2008] [Indexed: 12/30/2022] Open
Abstract
Background Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL) mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs). Methodology/Principal Findings We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F2 population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions. Conclusions/Significance The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col) to Estland (Est-1) and Kendallville (Kend-L) provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping.
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Affiliation(s)
- Sureshkumar Balasubramanian
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Christopher Schwartz
- Plant Biology Laboratory, The Salk Institute for Biological Sciences, La Jolla, California, United States of America
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Anandita Singh
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Norman Warthmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Plant Biology Laboratory, The Salk Institute for Biological Sciences, La Jolla, California, United States of America
| | - Min Chul Kim
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Julin N. Maloof
- Plant Biology Laboratory, The Salk Institute for Biological Sciences, La Jolla, California, United States of America
- Section of Plant Biology, University of California Davis, Davis, California, United States of America
| | - Olivier Loudet
- Plant Biology Laboratory, The Salk Institute for Biological Sciences, La Jolla, California, United States of America
- INRA, Genetics and plant breeding - SGAP, Versailles, France
| | - Gabriel T. Trainer
- Plant Biology Laboratory, The Salk Institute for Biological Sciences, La Jolla, California, United States of America
| | - Tsegaye Dabi
- Plant Biology Laboratory, The Salk Institute for Biological Sciences, La Jolla, California, United States of America
| | - Justin O. Borevitz
- Plant Biology Laboratory, The Salk Institute for Biological Sciences, La Jolla, California, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Joanne Chory
- Plant Biology Laboratory, The Salk Institute for Biological Sciences, La Jolla, California, United States of America
- Howard Hughes Medical Institute, The Salk Institute for Biological Sciences, La Jolla, California, United States of America
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Plant Biology Laboratory, The Salk Institute for Biological Sciences, La Jolla, California, United States of America
- * E-mail:
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144
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Schmalenbach I, Léon J, Pillen K. Identification and verification of QTLs for agronomic traits using wild barley introgression lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:483-97. [PMID: 18979081 DOI: 10.1007/s00122-008-0915-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 10/09/2008] [Indexed: 05/18/2023]
Abstract
A set of 39 wild barley introgression lines (hereafter abbreviated with S42ILs) was subjected to a QTL study to verify genetic effects for agronomic traits, previously detected in the BC2DH population S42 (von Korff et al. 2006 in Theor Appl Genet 112:1221-1231) and, in addition, to identify new QTLs and favorable wild barley alleles. Each line within the S42IL set contains a single marker-defined chromosomal introgression from wild barley (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is exclusively derived from elite spring barley (H. vulgare ssp. vulgare). Agronomic field data of the S42ILs were collected for seven traits from three different environments during the 2007 growing season. For detection of putative QTLs, a two-factorial mixed model ANOVA and, subsequently, a Dunnett test with the recurrent parent as a control were conducted. The presence of a QTL effect on a wild barley introgression was accepted, if the trait value of a particular S42IL was significantly (P<0.05) different from the control, either across all environments and/or in a particular environment. A total of 47 QTLs were localized in the S42IL set, among which 39 QTLs were significant across all tested environments. For 19 QTLs (40.4%), the wild barley introgression was associated with a favorable effect on trait performance. Von Korff et al. (2006 in Theor Appl Genet 112:1221-1231) mapped altogether 44 QTLs for six agronomic traits to genomic regions, which are represented by wild barley introgressions of the S42IL set. Here, 18 QTLs (40.9%) revealed a favorable wild barley effect on the trait performance. By means of the S42ILs, 20 out of the 44 QTLs (45.5%) and ten out of the 18 favorable effects (55.6%) were verified. Most QTL effects were confirmed for the traits days until heading and plant height. For the six corresponding traits, a total of 17 new QTLs were identified, where at six QTLs (35.3%) the exotic introgression caused an improved trait performance. In addition, eight QTLs for the newly studied trait grains per ear were detected. Here, no QTL from wild barley exhibited a favorable effect. The introgression line S42IL-107, which carries an introgression on chromosome 2H, 17-42 cM is an example for S42ILs carrying several QTL effects simultaneously. This line exhibited improved performance across all tested environments for the traits days until heading, plant height and thousand grain weight. The line can be directly used to transfer valuable Hsp alleles into modern elite cultivars, and, thus, for breeding of improved varieties.
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Affiliation(s)
- Inga Schmalenbach
- Max-Planck-Institute for Plant Breeding Research, Barley Genetics Research Group, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
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145
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Jones N, Ougham H, Thomas H, Pašakinskienė I. Markers and mapping revisited: finding your gene. THE NEW PHYTOLOGIST 2009; 183:935-966. [PMID: 19594696 DOI: 10.1111/j.1469-8137.2009.02933.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of this highly dynamic arena of plant science.
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Affiliation(s)
- Neil Jones
- IBERS, Aberystwyth University, Edward Llwyd Building, Penglais Campus, Aberystwyth, Ceredigion SY23 3DA, UK
| | - Helen Ougham
- IBERS, Aberystwyth University, Gogerddan Campus, Aberystwyth, Ceredigion SY23 3EB, UK
| | - Howard Thomas
- IBERS, Aberystwyth University, Edward Llwyd Building, Penglais Campus, Aberystwyth, Ceredigion SY23 3DA, UK
| | - Izolda Pašakinskienė
- Botanical Garden of Vilnius University, Kairenu 43, LT-10239 Vilnius, Lithuania
- Faculty of Natural Sciences, Department of Botany and Genetics, MK Čiurlionio g. 21, LT-03101 Vilnius, Lithuania
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146
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Abstract
Libraries of near-isogenic lines (NILs) are a powerful plant genetic resource to map quantitative trait loci (QTL). Nevertheless, QTL mapping with NILs is mostly restricted to genetic main effects. Here we propose a two-step procedure to map additive-by-additive digenic epistasis with NILs. In the first step, a generation means analysis of parents, their F(1) hybrid, and one-segment NILs and their triple testcross (TTC) progenies is used to identify in a one-dimensional scan loci exhibiting QTL-by-background interactions. In a second step, one-segment NILs with significant additive-by-additive background interactions are used to produce particular two-segment NILs to test for digenic epistatic interactions between these segments. We evaluated our approach by analyzing a random subset of a genomewide Arabidopsis thaliana NIL library for growth-related traits. The results of our experimental study illustrated the potential of the presented two-step procedure to map additive-by-additive digenic epistasis with NILs. Furthermore, our findings suggested that additive main effects as well as additive-by-additive digenic epistasis strongly influence the genetic architecture underlying growth-related traits of A. thaliana.
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147
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Genetic Background and Environmental Effects on QTLs for Sheath Blight Resistance Revealed by Reciprocal Introgression Lines in Rice. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1875-2780(09)60013-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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148
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Schmalenbach I, Körber N, Pillen K. Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:1093-1106. [PMID: 18663425 DOI: 10.1007/c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 07/05/2008] [Indexed: 05/29/2023]
Abstract
A set of 59 spring barley introgression lines (ILs) was developed from the advanced backcross population S42. The ILs were generated by three rounds of backcrossing, two to four subsequent selfings, and, in parallel, marker-assisted selection. Each line includes a single marker-defined chromosomal segment of the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is derived from the elite barley cultivar Scarlett (H. vulgare ssp. vulgare). Based on a map containing 98 SSR markers, the IL set covers so far 86.6% (1041.5 cM) of the donor genome. Each single line contains an average exotic introgression of 39.2 cM, representing 3.2% of the exotic genome. The utility of the developed IL set is illustrated by verification of QTLs controlling resistance to powdery mildew (Blumeria graminis f. sp. hordei L.) and leaf rust (Puccinia hordei L.) which were previously identified in the advanced backcross population S42. Altogether 57.1 and 75.0% of QTLs conferring resistance to powdery mildew and leaf rust, respectively, were verified by ILs. The strongest favorable effects were mapped to regions 1H, 0-85 cM and 4H, 125-170 cM, where susceptibility to powdery mildew and leaf rust was decreased by 66.1 and 34.7%, respectively, compared to the recurrent parent. In addition, three and one new QTLs were localized, respectively. A co-localization of two favorable QTLs was identified for line S42IL-138, which holds an introgressed segment in region 7H, 166-181. Here, a reduction effect was revealed for powdery mildew as well as for leaf rust severity. This line might be a valuable resource for transferring new resistance alleles into elite cultivars. In future, we aim to cover the complete exotic genome by selecting additional ILs. We intend to conduct further phenotype studies with the IL set in regard to the trait complexes agronomic performance, malting quality, biotic stress, and abiotic stress.
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Affiliation(s)
- Inga Schmalenbach
- Max-Planck-Institute for Plant Breeding Research, Barley Genetics Research Group, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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149
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Schmalenbach I, Körber N, Pillen K. Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:1093-1106. [PMID: 18663425 DOI: 10.1007/s00122-008-0847-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 07/05/2008] [Indexed: 05/26/2023]
Abstract
A set of 59 spring barley introgression lines (ILs) was developed from the advanced backcross population S42. The ILs were generated by three rounds of backcrossing, two to four subsequent selfings, and, in parallel, marker-assisted selection. Each line includes a single marker-defined chromosomal segment of the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is derived from the elite barley cultivar Scarlett (H. vulgare ssp. vulgare). Based on a map containing 98 SSR markers, the IL set covers so far 86.6% (1041.5 cM) of the donor genome. Each single line contains an average exotic introgression of 39.2 cM, representing 3.2% of the exotic genome. The utility of the developed IL set is illustrated by verification of QTLs controlling resistance to powdery mildew (Blumeria graminis f. sp. hordei L.) and leaf rust (Puccinia hordei L.) which were previously identified in the advanced backcross population S42. Altogether 57.1 and 75.0% of QTLs conferring resistance to powdery mildew and leaf rust, respectively, were verified by ILs. The strongest favorable effects were mapped to regions 1H, 0-85 cM and 4H, 125-170 cM, where susceptibility to powdery mildew and leaf rust was decreased by 66.1 and 34.7%, respectively, compared to the recurrent parent. In addition, three and one new QTLs were localized, respectively. A co-localization of two favorable QTLs was identified for line S42IL-138, which holds an introgressed segment in region 7H, 166-181. Here, a reduction effect was revealed for powdery mildew as well as for leaf rust severity. This line might be a valuable resource for transferring new resistance alleles into elite cultivars. In future, we aim to cover the complete exotic genome by selecting additional ILs. We intend to conduct further phenotype studies with the IL set in regard to the trait complexes agronomic performance, malting quality, biotic stress, and abiotic stress.
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Affiliation(s)
- Inga Schmalenbach
- Max-Planck-Institute for Plant Breeding Research, Barley Genetics Research Group, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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150
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Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast. Genetics 2008; 180:1661-70. [PMID: 18780730 DOI: 10.1534/genetics.108.092932] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Several quantitative trait loci (QTL) mapping strategies can successfully identify major-effect loci, but often have poor success detecting loci with minor effects, potentially due to the confounding effects of major loci, epistasis, and limited sample sizes. To overcome such difficulties, we used a targeted backcross mapping strategy that genetically eliminated the effect of a previously identified major QTL underlying high-temperature growth (Htg) in yeast. This strategy facilitated the mapping of three novel QTL contributing to Htg of a clinically derived yeast strain. One QTL, which is linked to the previously identified major-effect QTL, was dissected, and NCS2 was identified as the causative gene. The interaction of the NCS2 QTL with the first major-effect QTL was background dependent, revealing a complex QTL architecture spanning these two linked loci. Such complex architecture suggests that more genes than can be predicted are likely to contribute to quantitative traits. The targeted backcrossing approach overcomes the difficulties posed by sample size, genetic linkage, and epistatic effects and facilitates identification of additional alleles with smaller contributions to complex traits.
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