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Lai D, Zhang K, He Y, Fan Y, Li W, Shi Y, Gao Y, Huang X, He J, Zhao H, Lu X, Xiao Y, Cheng J, Ruan J, Georgiev MI, Fernie AR, Zhou M. Multi-omics identification of a key glycosyl hydrolase gene FtGH1 involved in rutin hydrolysis in Tartary buckwheat (Fagopyrum tataricum). PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1206-1223. [PMID: 38062934 PMCID: PMC11022807 DOI: 10.1111/pbi.14259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 04/18/2024]
Abstract
Rutin, a flavonoid rich in buckwheat, is important for human health and plant resistance to external stresses. The hydrolysis of rutin to quercetin underlies the bitter taste of Tartary buckwheat. In order to identify rutin hydrolysis genes, a 200 genotypes mini-core Tartary buckwheat germplasm resource was re-sequenced with 30-fold coverage depth. By combining the content of the intermediate metabolites of rutin metabolism with genome resequencing data, metabolite genome-wide association analyses (GWAS) eventually identified a glycosyl hydrolase gene FtGH1, which could hydrolyse rutin to quercetin. This function was validated both in Tartary buckwheat overexpression hairy roots and in vitro enzyme activity assays. Mutation of the two key active sites, which were determined by molecular docking and experimentally verified via overexpression in hairy roots and transient expression in tobacco leaves, exhibited abnormal subcellular localization, suggesting functional changes. Sequence analysis revealed that mutation of the FtGH1 promoter in accessions of two haplotypes might be necessary for enzymatic activity. Co-expression analysis and GWAS revealed that FtbHLH165 not only repressed FtGH1 expression, but also increased seed length. This work reveals a potential mechanism behind rutin metabolism, which should provide both theoretical support in the study of flavonoid metabolism and in the molecular breeding of Tartary buckwheat.
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Affiliation(s)
- Dili Lai
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- College of AgricultureGuizhou UniversityGuiyangChina
| | - Kaixuan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yuqi He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yu Fan
- School of Food and Biological EngineeringChengdu UniversityChengduChina
| | - Wei Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yaliang Shi
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yuanfen Gao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xu Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jiayue He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hui Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xiang Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yawen Xiao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | | | - Jingjun Ruan
- College of AgricultureGuizhou UniversityGuiyangChina
| | - Milen I. Georgiev
- Laboratory of Metabolomics, Institute of MicrobiologyBulgarian Academy of SciencesPlovdivBulgaria
- Center of Plant Systems Biology and BiotechnologyPlovdivBulgaria
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and BiotechnologyPlovdivBulgaria
- Department of Molecular PhysiologyMax‐Planck‐Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Meiliang Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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2
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Cosenza F, Shrestha A, Van Inghelandt D, Casale FA, Wu PY, Weisweiler M, Li J, Wespel F, Stich B. Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2385-2402. [PMID: 38330219 PMCID: PMC11016846 DOI: 10.1093/jxb/erae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
Flowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Despite their role in plant physiological regulation, a complete overview of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Using a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as to identify new genetic variants by single and multi-population QTL analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected new QTLs for flowering time and plant height. Finally, we identified a new functional allelic variant of the main regulatory gene Ppd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect, or low-frequency genetic variants underlie the control of these two traits.
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Affiliation(s)
- Francesco Cosenza
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Delphine Van Inghelandt
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Federico A Casale
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Po-Ya Wu
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Marius Weisweiler
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jinquan Li
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Franziska Wespel
- Saatzucht Josef Breun GmbH Co. KG, Amselweg 1, 91074 Herzogenaurach, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
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3
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Afsharyan NP, Sannemann W, Ballvora A, Léon J. Identifying developmental QTL alleles with favorable effect on grain yield components under late-terminal drought in spring barley MAGIC population. PLANT DIRECT 2023; 7:e516. [PMID: 37538189 PMCID: PMC10394678 DOI: 10.1002/pld3.516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 05/27/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Barley is the fourth most cultivated cereal worldwide, and drought is a major cause of its yield loss by negatively affecting its development. Hence, better understanding developmental mechanisms that control complex polygenic yield-related traits under drought is essential to uncover favorable yield regulators. This study evaluated seven above-ground yield-related traits under well-watered (WW) and late-terminal drought (TD) treatment using 534 spring barley multiparent advanced generation intercross double haploid (DH) lines. The analysis of quantitative trait loci (QTL) for WW, TD, marker by treatment interaction, and drought stress tolerance identified 69, 64, 25, and 25 loci, respectively, for seven traits from which 15 loci were common for at least three traits and 17 were shared by TD and drought stress tolerance. Evaluation of allelic effects for a QTL revealed varying effect of parental alleles. Results showed prominent QTL located on major flowering time gene Ppd-H1 with favorable effects for grain weight under TD when flowering time was not significantly affected, suggesting that this gene might be linked with increasing grain weight by ways other than timing of flowering under late-terminal drought stress. Furthermore, a desirable novel QTL allele was identified on chromosome 5H for grain number under TD nearby sucrose transporter gene HvSUT2. The findings indicated that spring barley multiparent advanced generation intercross population can provide insights to improve yield under complex condition of drought.
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Affiliation(s)
- Nazanin P. Afsharyan
- Institute for Crop Science and Resource Conservation, Chair of Plant BreedingUniversity of BonnBonnGermany
- Department of Plant BreedingJustus Liebig University GiessenGiessenGermany
| | - Wiebke Sannemann
- Institute for Crop Science and Resource Conservation, Chair of Plant BreedingUniversity of BonnBonnGermany
- KWS Saat SE & Co. KGaAEinbeckGermany
| | - Agim Ballvora
- Institute for Crop Science and Resource Conservation, Chair of Plant BreedingUniversity of BonnBonnGermany
| | - Jens Léon
- Institute for Crop Science and Resource Conservation, Chair of Plant BreedingUniversity of BonnBonnGermany
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4
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Koua AP, Oyiga BC, Dadshani S, Benaouda S, Sadeqi MB, Rascher U, Léon J, Ballvora A. Chromosome 3A harbors several pleiotropic and stable drought-responsive alleles for photosynthetic efficiency selected through wheat breeding. PLANT DIRECT 2022; 6:e438. [PMID: 36091876 PMCID: PMC9440346 DOI: 10.1002/pld3.438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 06/29/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Water deficit is the most severe stress factor in crop production threatening global food security. In this study, we evaluated the genetic variation in photosynthetic traits among 200 wheat cultivars evaluated under drought and rainfed conditions. Significant genotypic, treatments, and their interaction effects were detected for chlorophyll content and chlorophyll fluorescence parameters. Drought stress reduced the effective quantum yield of photosystem II (YII) from the anthesis growth stage on. Leaf chlorophyll content measured at anthesis growth stages was significantly correlated with YII and non-photochemical quenching under drought conditions, suggesting that high throughput chlorophyll content screening can serve as a good indicator of plant drought tolerance status in wheat. Breeding significantly increased the photosynthetic efficiency as newer released genotypes had higher YII and chlorophyll content than the older ones. GWAS identified a stable drought-responsive QTL on chromosome 3A for YII, while under rainfed conditions, it detected another QTL on chromosome 7A for chlorophyll content across both growing seasons. Molecular analysis revealed that the associated alleles of AX-158576783 (515.889 Mbp) on 3A co-segregates with the NADH-ubiquinone oxidoreductase (TraesCS3A02G287600) gene involved in ATP synthesis coupled electron transport and is proximal to WKRY transcription factor locus. This allele on 3A has been positively selected through breeding and has contributed to increasing the grain yield.
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Affiliation(s)
| | | | - Said Dadshani
- INRES PflanzenzüchtungRheinische Friedrich Wilhelms UniversityBonnGermany
| | - Salma Benaouda
- INRES PflanzenzüchtungRheinische Friedrich Wilhelms UniversityBonnGermany
| | | | | | - Jens Léon
- INRES PflanzenzüchtungRheinische Friedrich Wilhelms UniversityBonnGermany
- Field Lab Campus Klein‐AltendorfUniversity of BonnRheinbachGermany
| | - Agim Ballvora
- INRES PflanzenzüchtungRheinische Friedrich Wilhelms UniversityBonnGermany
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5
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Zhang M, Lu N, Jiang L, Liu B, Fei Y, Ma W, Shi C, Wang J. Multiple dynamic models reveal the genetic architecture for growth in height of Catalpa bungei in the field. TREE PHYSIOLOGY 2022; 42:1239-1255. [PMID: 34940852 DOI: 10.1093/treephys/tpab171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
Growth in height (GH) is a critical determinant for tree survival and development in forests and can be depicted using logistic growth curves. Our understanding of the genetic mechanism underlying dynamic GH, however, is limited, particularly under field conditions. We applied two mapping models (Funmap and FVTmap) to find quantitative trait loci responsible for dynamic GH and two epistatic models (2HiGWAS and 1HiGWAS) to detect epistasis in Catalpa bungei grown in the field. We identified 13 co-located quantitative trait loci influencing the growth curve by Funmap and three heterochronic parameters (the timing of the inflection point, maximum acceleration and maximum deceleration) by FVTmap. The combined use of FVTmap and Funmap reduced the number of candidate genes by >70%. We detected 76 significant epistatic interactions, amongst which a key gene, COMT14, co-located by three models (but not 1HiGWAS) interacted with three other genes, implying that a novel network of protein interaction centered on COMT14 may control the dynamic GH of C. bungei. These findings provide new insights into the genetic mechanisms underlying the dynamic growth in tree height in natural environments and emphasize the necessity of incorporating multiple dynamic models for screening more reliable candidate genes.
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Affiliation(s)
- Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Libo Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Bingyang Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yue Fei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Chaozhong Shi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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6
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Fernández-Calleja M, Casas AM, Igartua E. Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1867-1897. [PMID: 33969431 PMCID: PMC8263424 DOI: 10.1007/s00122-021-03824-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/24/2021] [Indexed: 05/10/2023]
Abstract
This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their effects, and genetic and environmental interactions will facilitate plant breeders manipulating flowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major flowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL effects, interactions between genes and with the environment are presented. Pleiotropic effects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large effects on phenology that became relevant in modern barley breeding. The parallelisms between flowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic effects that provide enormous plasticity in barley flowering behavior, which opens new avenues to breeders for fine-tuning phenology of the barley crop.
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Affiliation(s)
- Miriam Fernández-Calleja
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain
| | - Ana M Casas
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain
| | - Ernesto Igartua
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain.
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7
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Puglisi D, Delbono S, Visioni A, Ozkan H, Kara İ, Casas AM, Igartua E, Valè G, Piero ARL, Cattivelli L, Tondelli A, Fricano A. Genomic Prediction of Grain Yield in a Barley MAGIC Population Modeling Genotype per Environment Interaction. FRONTIERS IN PLANT SCIENCE 2021; 12:664148. [PMID: 34108982 PMCID: PMC8183822 DOI: 10.3389/fpls.2021.664148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Multi-parent Advanced Generation Inter-crosses (MAGIC) lines have mosaic genomes that are generated shuffling the genetic material of the founder parents following pre-defined crossing schemes. In cereal crops, these experimental populations have been extensively used to investigate the genetic bases of several traits and dissect the genetic bases of epistasis. In plants, genomic prediction models are usually fitted using either diverse panels of mostly unrelated accessions or individuals of biparental families and several empirical analyses have been conducted to evaluate the predictive ability of models fitted to these populations using different traits. In this paper, we constructed, genotyped and evaluated a barley MAGIC population of 352 individuals developed with a diverse set of eight founder parents showing contrasting phenotypes for grain yield. We combined phenotypic and genotypic information of this MAGIC population to fit several genomic prediction models which were cross-validated to conduct empirical analyses aimed at examining the predictive ability of these models varying the sizes of training populations. Moreover, several methods to optimize the composition of the training population were also applied to this MAGIC population and cross-validated to estimate the resulting predictive ability. Finally, extensive phenotypic data generated in field trials organized across an ample range of water regimes and climatic conditions in the Mediterranean were used to fit and cross-validate multi-environment genomic prediction models including G×E interaction, using both genomic best linear unbiased prediction and reproducing kernel Hilbert space along with a non-linear Gaussian Kernel. Overall, our empirical analyses showed that genomic prediction models trained with a limited number of MAGIC lines can be used to predict grain yield with values of predictive ability that vary from 0.25 to 0.60 and that beyond QTL mapping and analysis of epistatic effects, MAGIC population might be used to successfully fit genomic prediction models. We concluded that for grain yield, the single-environment genomic prediction models examined in this study are equivalent in terms of predictive ability while, in general, multi-environment models that explicitly split marker effects in main and environmental-specific effects outperform simpler multi-environment models.
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Affiliation(s)
- Damiano Puglisi
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Catania, Italy
| | - Stefano Delbono
- Council for Agricultural Research and Economics–Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Andrea Visioni
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas, Avenue Hafiane Cherkaoui, Rabat, Morocco
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, University of Cukurova, Adana, Turkey
| | - İbrahim Kara
- Bahri Dagdas International Agricultural Research Institute, Konya, Turkey
| | - Ana M. Casas
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Ernesto Igartua
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Giampiero Valè
- DiSIT, Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Angela Roberta Lo Piero
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Catania, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics–Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics–Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics–Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
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8
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Scott MF, Ladejobi O, Amer S, Bentley AR, Biernaskie J, Boden SA, Clark M, Dell'Acqua M, Dixon LE, Filippi CV, Fradgley N, Gardner KA, Mackay IJ, O'Sullivan D, Percival-Alwyn L, Roorkiwal M, Singh RK, Thudi M, Varshney RK, Venturini L, Whan A, Cockram J, Mott R. Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding. Heredity (Edinb) 2020; 125:396-416. [PMID: 32616877 PMCID: PMC7784848 DOI: 10.1038/s41437-020-0336-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.
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Affiliation(s)
| | | | - Samer Amer
- University of Reading, Reading, RG6 6AH, UK
- Faculty of Agriculture, Alexandria University, Alexandria, 23714, Egypt
| | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Jay Biernaskie
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Scott A Boden
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | | | | | - Laura E Dixon
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Carla V Filippi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Nicolas Repetto y Los Reseros s/n, 1686, Hurlingham, Buenos Aires, Argentina
| | - Nick Fradgley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Keith A Gardner
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Ian J Mackay
- SRUC, West Mains Road, Kings Buildings, Edinburgh, EH9 3JG, UK
| | | | | | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rakesh Kumar Singh
- International Center for Biosaline Agriculture, Academic City, Dubai, United Arab Emirates
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Alex Whan
- CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - James Cockram
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Richard Mott
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, UK
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9
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Szala K, Ogonowska H, Lugowska B, Zmijewska B, Wyszynska R, Dmochowska-Boguta M, Orczyk W, Nadolska-Orczyk A. Different sets of TaCKX genes affect yield-related traits in wheat plants grown in a controlled environment and in field conditions. BMC PLANT BIOLOGY 2020; 20:496. [PMID: 33121443 PMCID: PMC7597040 DOI: 10.1186/s12870-020-02713-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/20/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND TaCKX wheat gene family members (GFMs) encode the enzyme cytokinin oxidase/dehydrogenase (CKX), which irreversibly degrades cytokinins. The genes are important regulators of cytokinin content and take part in growth and development, with a major impact on yield-related traits. The goal of this research was to test whether these genes might be differentially expressed in the field compared to laboratory conditions and consequently differently affect plant development and yield. RESULTS We compared expression and crosstalk of the TaCKX GFMs and TaNAC2-5A gene in modern varieties grown in a growth chamber (GC) and in the field and looked for differences in their impact on yield-related traits. The TaNAC2-5A gene was included in the research since it was expected to play an important role in co-regulation of these genes. The range of relative expression levels of TaCKX GFMs and TaNAC2-5A gene among tested cultivars was from 5 for TaCKX8 to more than 100 for TaCKX9 in the GC and from 6 for TaCKX8 to 275 for TaCKX10 in the field. The range was similar for four of them in the GC, but was much higher for seven others and TaNAC2-5A in the field. The TaCKX GFMs and TaNAC2-5A form co-expression groups, which differ depending on growth conditions. Consequently, the genes also differently regulate yield-related traits in the GC and in the field. TaNAC2-5A took part in negative regulation of tiller number and CKX activity in seedling roots only in controlled GC conditions. Grain number and grain yield were negatively regulated by TaCKX10 in the GC but positively by TaCKX8 and others in the field. Some of the genes, which were expressed in seedling roots, negatively influenced tiller number and positively regulated seedling root weight, CKX activity in the spikes, thousand grain weight (TGW) as well as formation of semi-empty spikes. CONCLUSIONS We have documented that: 1) natural variation in expression levels of tested genes in both environments is very high, indicating the possibility of selection of beneficial genotypes for breeding purposes, 2) to create a model of an ideotype for breeding, we need to take into consideration the natural environment.
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Affiliation(s)
- Karolina Szala
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Hanna Ogonowska
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | | | - Barbara Zmijewska
- Plant Breeding Strzelce Ltd., Co. - IHAR Group, Konczewice 1, 87-140, Chelmza, Poland
| | - Renata Wyszynska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Marta Dmochowska-Boguta
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Waclaw Orczyk
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Anna Nadolska-Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland.
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Christov NK. The role of epistasis and its interaction with environment in fine-tuning heading time in barley. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:743-746. [PMID: 31971242 PMCID: PMC6977021 DOI: 10.1093/jxb/erz503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
This article comments on: Afsharyan NP, Sannemann W, Léon J, Ballvora A. 2020. Effect of epistasis and environment on flowering time of barley reveals novel flowering-delaying QTL allele. Journal of Experimental Botany 71, 893–906.
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Affiliation(s)
- Nikolai K Christov
- Functional Genetics Department, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
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