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Knoch D, Abbadi A, Grandke F, Meyer RC, Samans B, Werner CR, Snowdon RJ, Altmann T. Strong temporal dynamics of QTL action on plant growth progression revealed through high-throughput phenotyping in canola. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:68-82. [PMID: 31125482 PMCID: PMC6920335 DOI: 10.1111/pbi.13171] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 05/08/2023]
Abstract
A major challenge of plant biology is to unravel the genetic basis of complex traits. We took advantage of recent technical advances in high-throughput phenotyping in conjunction with genome-wide association studies to elucidate genotype-phenotype relationships at high temporal resolution. A diverse Brassica napus population from a commercial breeding programme was analysed by automated non-invasive phenotyping. Time-resolved data for early growth-related traits, including estimated biovolume, projected leaf area, early plant height and colour uniformity, were established and complemented by fresh and dry weight biomass. Genome-wide SNP array data provided the framework for genome-wide association analyses. Using time point data and relative growth rates, multiple robust main effect marker-trait associations for biomass and related traits were detected. Candidate genes involved in meristem development, cell wall modification and transcriptional regulation were detected. Our results demonstrate that early plant growth is a highly complex trait governed by several medium and many small effect loci, most of which act only during short phases. These observations highlight the importance of taking the temporal patterns of QTL/allele actions into account and emphasize the need for detailed time-resolved analyses to effectively unravel the complex and stage-specific contributions of genes affecting growth processes that operate at different developmental phases.
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Affiliation(s)
- Dominic Knoch
- Molecular Genetics/HeterosisLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Amine Abbadi
- Norddeutsche Pflanzenzucht Innovation GmbH (NPZi)HoltseeGermany
| | - Fabian Grandke
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
| | - Rhonda C. Meyer
- Molecular Genetics/HeterosisLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Birgit Samans
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
- Present address:
Technische Hochschule Mittelhessen (THM), University of Applied SciencesFachbereich Gesundheit35390GiessenGermany
| | - Christian R. Werner
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
- Present address:
The Roslin InstituteUniversity of EdinburghEaster Bush CampusMidlothianEH25 9RGUK
| | - Rod J. Snowdon
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
| | - Thomas Altmann
- Molecular Genetics/HeterosisLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
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Braun EM, Tsvetkova N, Rotter B, Siekmann D, Schwefel K, Krezdorn N, Plieske J, Winter P, Melz G, Voylokov AV, Hackauf B. Gene Expression Profiling and Fine Mapping Identifies a Gibberellin 2-Oxidase Gene Co-segregating With the Dominant Dwarfing Gene Ddw1 in Rye ( Secale cereale L.). FRONTIERS IN PLANT SCIENCE 2019; 10:857. [PMID: 31333700 PMCID: PMC6616298 DOI: 10.3389/fpls.2019.00857] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/14/2019] [Indexed: 06/03/2023]
Abstract
The gibberellin (GA)-sensitive dwarfing gene Ddw1 provides an opportunity to genetically reduce plant height in rye. Genetic analysis in a population of recombinant inbred lines confirmed a monogenetic dominant inheritance of Ddw1. Significant phenotypic differences in PH between homo- and heterozygotic genotypes indicate an incomplete dominance of Ddw1. De novo transcriptome sequencing of Ddw1 mutant as well as tall genotypes resulted in 113,547 contigs with an average length of 318 bp covering 36.18 Mbp rye DNA. A hierarchical cluster analysis based on individual groups of rye homologs of functionally characterized rice genes controlling morphological or physiological traits including plant height, flowering time, and source activity identified the gene expression profile of stems at the begin of heading to most comprehensively mirror effects of Ddw1. Genome-wide expression profiling identified 186 transcripts differentially expressed between semi-dwarf and tall genotypes in stems. In total, 29 novel markers have been established and mapped to a 27.2 cM segment in the distal part of the long arm of chromosome 5R. Ddw1 could be mapped within a 0.4 cM interval co-segregating with a marker representing the C20-GA2-oxidase gene ScGA2ox12, that is up-regulated in stems of Ddw1 genotypes. The increased expression of ScGA2ox12 observed in semi-dwarf rye as well as structural alterations in transcript sequences associated with the ScGA2ox12 gene implicate, that Ddw1 is a dominant gain-of-function mutant. Integration of the target interval in the wheat reference genome sequence indicated perfect micro-colinearity between the Ddw1 locus and a 831 kb segment on chromosome 5A, which resides inside of a 11.21 Mb interval carrying the GA-sensitive dwarfing gene Rht12 in wheat. The potential of Ddw1 as a breeder's option to improve lodging tolerance in rye is discussed.
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Affiliation(s)
- Eva-Maria Braun
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Quedlinburg, Germany
| | - Natalia Tsvetkova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Dörthe Siekmann
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Quedlinburg, Germany
- HYBRO Saatzucht GmbH & Co. KG, Schenkenberg, Germany
| | - Konrad Schwefel
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Quedlinburg, Germany
| | | | | | | | | | - Anatoly V. Voylokov
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Bernd Hackauf
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Quedlinburg, Germany
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3
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Ayalew H, Kumssa TT, Butler TJ, Ma XF. Triticale Improvement for Forage and Cover Crop Uses in the Southern Great Plains of the United States. FRONTIERS IN PLANT SCIENCE 2018; 9:1130. [PMID: 30127797 PMCID: PMC6087761 DOI: 10.3389/fpls.2018.01130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/13/2018] [Indexed: 05/28/2023]
Abstract
Triticale (×Triticosecale Wittmack) is a man-made species developed by crossing wheat (Triticum spp.) and rye (Secale cereale L.). It incorporates favorable alleles from both progenitor species (wheat and rye), enabling adaptation to environments that are less favorable for wheat yet providing better biomass yield and forage quality. Triticale has huge potential for both grain and forage production, though research to improve the crop for better adaptation and grain quality is lagging behind that of other small grains. It is also gaining popularity as a cover crop to improve soil health and reduce nutrient leaching. Because of its genetic and flower structure, triticale is suitable for both line and hybrid breeding methods. Advances in the areas of molecular biology and the wealth of genomic resources from both wheat and rye can be exploited for triticale improvement. Gene mapping and genomic selection will facilitate triticale breeding by increasing selection precision and reducing time and cost. The objectives of this review are to summarize current triticale production status, breeding, and genetics research achievements and to highlight gaps for future research.
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Tyrka M, Oleszczuk S, Rabiza-Swider J, Wos H, Wedzony M, Zimny J, Ponitka A, Ślusarkiewicz-Jarzina A, Metzger RJ, Baenziger PS, Lukaszewski AJ. Populations of doubled haploids for genetic mapping in hexaploid winter triticale. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:46. [PMID: 29623004 PMCID: PMC5878199 DOI: 10.1007/s11032-018-0804-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
To create a framework for genetic dissection of hexaploid triticale, six populations of doubled haploid (DH) lines were developed from pairwise hybrids of high-yielding winter triticale cultivars. The six populations comprise between 97 and 231 genotyped DH lines each, totaling 957 DH lines. A consensus genetic map spans 4593.9 cM is composed of 1576 unique DArT markers. The maps reveal several structural rearrangements in triticale genomes. In preliminary tests of the populations and maps, markers specific to wheat segments of the engineered rye chromosome 1R (RM1B) were identified. Example QTL mapping of days to heading in cv. Krakowiak revealed loci on chromosomes 2BL and 2R responsible for extended vernalization requirement, and candidate genes were identified. The material is available to all parties interested in triticale genetics.
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Affiliation(s)
- M. Tyrka
- Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Rzeszow, Poland
| | - S. Oleszczuk
- Institute of Plant Breeding and Acclimatization, National Research Institute, Radzikow, Poland
| | - J. Rabiza-Swider
- Department of Ornamental Plants, Warsaw University of Life Sciences, Warsaw, Poland
| | - H. Wos
- Plant Breeding Strzelce Ltd., Co. - IHAR-PIB Group, Strzelce, Poland
| | - M. Wedzony
- Department of Cell Biology and Genetics, Pedagogical University of Cracow, Kraków, Poland
| | - J. Zimny
- Institute of Plant Breeding and Acclimatization, National Research Institute, Radzikow, Poland
| | - A. Ponitka
- Institute of Plant Genetics, Poznan, Poland
| | | | - R. J. Metzger
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-3002 USA
| | - P. S. Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE USA
| | - A. J. Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
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5
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Background controlled QTL mapping in pure-line genetic populations derived from four-way crosses. Heredity (Edinb) 2017; 119:256-264. [PMID: 28722705 PMCID: PMC5597784 DOI: 10.1038/hdy.2017.42] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 11/24/2022] Open
Abstract
Pure lines derived from multiple parents are becoming more important because of the increased genetic diversity, the possibility to conduct replicated phenotyping trials in multiple environments and potentially high mapping resolution of quantitative trait loci (QTL). In this study, we proposed a new mapping method for QTL detection in pure-line populations derived from four-way crosses, which is able to control the background genetic variation through a two-stage mapping strategy. First, orthogonal variables were created for each marker and used in an inclusive linear model, so as to completely absorb the genetic variation in the mapping population. Second, inclusive composite interval mapping approach was implemented for one-dimensional scanning, during which the inclusive linear model was employed to control the background variation. Simulation studies using different genetic models demonstrated that the new method is efficient when considering high detection power, low false discovery rate and high accuracy in estimating quantitative trait loci locations and effects. For illustration, the proposed method was applied in a reported wheat four-way recombinant inbred line population.
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6
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Würschum T, Maurer HP, Weissmann S, Hahn V, Leiser WL. Accuracy of within- and among-family genomic prediction in triticale. PLANT BREEDING 2017. [PMID: 0 DOI: 10.1111/pbr.12465] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- Tobias Würschum
- State Plant Breeding Institute; University of Hohenheim; 70599 Stuttgart Germany
| | - Hans Peter Maurer
- State Plant Breeding Institute; University of Hohenheim; 70599 Stuttgart Germany
| | | | - Volker Hahn
- State Plant Breeding Institute; University of Hohenheim; 70599 Stuttgart Germany
| | - Willmar L. Leiser
- State Plant Breeding Institute; University of Hohenheim; 70599 Stuttgart Germany
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7
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Muraya MM, Chu J, Zhao Y, Junker A, Klukas C, Reif JC, Altmann T. Genetic variation of growth dynamics in maize (Zea mays L.) revealed through automated non-invasive phenotyping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:366-380. [PMID: 27714888 DOI: 10.1111/tpj.13390] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 05/02/2023]
Abstract
Hitherto, most quantitative trait loci of maize growth and biomass yield have been identified for a single time point, usually the final harvest stage. Through this approach cumulative effects are detected, without considering genetic factors causing phase-specific differences in growth rates. To assess the genetics of growth dynamics, we employed automated non-invasive phenotyping to monitor the plant sizes of 252 diverse maize inbred lines at 11 different developmental time points; 50 k SNP array genotype data were used for genome-wide association mapping and genomic selection. The heritability of biomass was estimated to be over 71%, and the average prediction accuracy amounted to 0.39. Using the individual time point data, 12 main effect marker-trait associations (MTAs) and six pairs of epistatic interactions were detected that displayed different patterns of expression at various developmental time points. A subset of them also showed significant effects on relative growth rates in different intervals. The detected MTAs jointly explained up to 12% of the total phenotypic variation, decreasing with developmental progression. Using non-parametric functional mapping and multivariate mapping approaches, four additional marker loci affecting growth dynamics were detected. Our results demonstrate that plant biomass accumulation is a complex trait governed by many small effect loci, most of which act at certain restricted developmental phases. This highlights the need for investigation of stage-specific growth affecting genes to elucidate important processes operating at different developmental phases.
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Affiliation(s)
- Moses M Muraya
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
- Department of Plant Sciences, Chuka University, P.O. Box 109 - 60400, Chuka, Kenya
| | - Jianting Chu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Christian Klukas
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
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8
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Wang SB, Wen YJ, Ren WL, Ni YL, Zhang J, Feng JY, Zhang YM. Mapping small-effect and linked quantitative trait loci for complex traits in backcross or DH populations via a multi-locus GWAS methodology. Sci Rep 2016; 6:29951. [PMID: 27435756 PMCID: PMC4951730 DOI: 10.1038/srep29951] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/24/2016] [Indexed: 11/09/2022] Open
Abstract
Composite interval mapping (CIM) is the most widely-used method in linkage analysis. Its main feature is the ability to control genomic background effects via inclusion of co-factors in its genetic model. However, the result often depends on how the co-factors are selected, especially for small-effect and linked quantitative trait loci (QTL). To address this issue, here we proposed a new method under the framework of genome-wide association studies (GWAS). First, a single-locus random-SNP-effect mixed linear model method for GWAS was used to scan each putative QTL on the genome in backcross or doubled haploid populations. Here, controlling background via selecting markers in the CIM was replaced by estimating polygenic variance. Then, all the peaks in the negative logarithm P-value curve were selected as the positions of multiple putative QTL to be included in a multi-locus genetic model, and true QTL were automatically identified by empirical Bayes. This called genome-wide CIM (GCIM). A series of simulated and real datasets was used to validate the new method. As a result, the new method had higher power in QTL detection, greater accuracy in QTL effect estimation, and stronger robustness under various backgrounds as compared with the CIM and empirical Bayes methods.
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Affiliation(s)
- Shi-Bo Wang
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang-Jun Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen-Long Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan-Li Ni
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian-Ying Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan-Ming Zhang
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Pauli D, Andrade-Sanchez P, Carmo-Silva AE, Gazave E, French AN, Heun J, Hunsaker DJ, Lipka AE, Setter TL, Strand RJ, Thorp KR, Wang S, White JW, Gore MA. Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton. G3 (BETHESDA, MD.) 2016; 6:865-79. [PMID: 26818078 PMCID: PMC4825657 DOI: 10.1534/g3.115.023515] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 01/24/2016] [Indexed: 01/01/2023]
Abstract
The application of high-throughput plant phenotyping (HTPP) to continuously study plant populations under relevant growing conditions creates the possibility to more efficiently dissect the genetic basis of dynamic adaptive traits. Toward this end, we employed a field-based HTPP system that deployed sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L.) recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across 2010-2012. Canopy temperature, normalized difference vegetation index (NDVI), height, and leaf area index (LAI) displayed moderate-to-high broad-sense heritabilities, as well as varied interactions among genotypes with water regime and time of day. Distinct temporal patterns of quantitative trait loci (QTL) expression were mostly observed for canopy temperature and NDVI, and varied across plant developmental stages. In addition, the strength of correlation between HTPP canopy traits and agronomic traits, such as lint yield, displayed a time-dependent relationship. We also found that the genomic position of some QTL controlling HTPP canopy traits were shared with those of QTL identified for agronomic and physiological traits. This work demonstrates the novel use of a field-based HTPP system to study the genetic basis of stress-adaptive traits in cotton, and these results have the potential to facilitate the development of stress-resilient cotton cultivars.
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Affiliation(s)
- Duke Pauli
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - Pedro Andrade-Sanchez
- Department of Agricultural and Biosystems Engineering, University of Arizona, Maricopa Agricultural Center, Arizona 85138
| | - A Elizabete Carmo-Silva
- Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Maricopa, Arizona 85138
| | - Elodie Gazave
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - Andrew N French
- Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Maricopa, Arizona 85138
| | - John Heun
- Department of Agricultural and Biosystems Engineering, University of Arizona, Maricopa Agricultural Center, Arizona 85138
| | - Douglas J Hunsaker
- Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Maricopa, Arizona 85138
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - Tim L Setter
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - Robert J Strand
- Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Maricopa, Arizona 85138
| | - Kelly R Thorp
- Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Maricopa, Arizona 85138
| | - Sam Wang
- School of Plant Sciences, University of Arizona, Maricopa Agricultural Center, Arizona 85138
| | - Jeffrey W White
- Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Maricopa, Arizona 85138
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
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10
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Salvi S, Tuberosa R. The crop QTLome comes of age. Curr Opin Biotechnol 2015; 32:179-185. [PMID: 25614069 DOI: 10.1016/j.copbio.2015.01.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 12/31/2014] [Accepted: 01/02/2015] [Indexed: 12/15/2022]
Abstract
Recent progress in genomics and phenomics allows for a more accurate and comprehensive characterization of the Quantitative Trait Loci (QTLs)—hereafter defined 'QTLome' as a whole—that govern the variation targeted in breeding programs. High-density genotyping now provides unambiguous identification of QTL alleles, and for several traits beneficial alleles at major QTLs have already been deployed in marker-assisted breeding. However, the amount of QTLome information is enormous and approaches to distill and translate this information to breeders remain to be refined. Improved QTL meta-analyses, better estimation of QTL effects, improved crop modelling and full sharing of raw QTL data will enable a more effective exploitation of the QTLome.
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Affiliation(s)
- Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
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