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Murchie EH, Kefauver S, Araus JL, Muller O, Rascher U, Flood PJ, Lawson T. Measuring the dynamic photosynthome. ANNALS OF BOTANY 2018; 122:207-220. [PMID: 29873681 PMCID: PMC6070037 DOI: 10.1093/aob/mcy087] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/02/2018] [Indexed: 05/18/2023]
Abstract
Background Photosynthesis underpins plant productivity and yet is notoriously sensitive to small changes in environmental conditions, meaning that quantitation in nature across different time scales is not straightforward. The 'dynamic' changes in photosynthesis (i.e. the kinetics of the various reactions of photosynthesis in response to environmental shifts) are now known to be important in driving crop yield. Scope It is known that photosynthesis does not respond in a timely manner, and even a small temporal 'mismatch' between a change in the environment and the appropriate response of photosynthesis toward optimality can result in a fall in productivity. Yet the most commonly measured parameters are still made at steady state or a temporary steady state (including those for crop breeding purposes), meaning that new photosynthetic traits remain undiscovered. Conclusions There is a great need to understand photosynthesis dynamics from a mechanistic and biological viewpoint especially when applied to the field of 'phenomics' which typically uses large genetically diverse populations of plants. Despite huge advances in measurement technology in recent years, it is still unclear whether we possess the capability of capturing and describing the physiologically relevant dynamic features of field photosynthesis in sufficient detail. Such traits are highly complex, hence we dub this the 'photosynthome'. This review sets out the state of play and describes some approaches that could be made to address this challenge with reference to the relevant biological processes involved.
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Affiliation(s)
- Erik H Murchie
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Shawn Kefauver
- Section of Plant Physiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Jose Luis Araus
- Section of Plant Physiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Onno Muller
- Institute of Bio-and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Uwe Rascher
- Institute of Bio-and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Pádraic J Flood
- Max Planck Institute for Plant Breeding Research, Carl-Von-Linne-Weg, Köln, Germany
| | - Tracy Lawson
- School of Biological Sciences, University of Essex, Colchester, UK
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152
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Sannemann W, Lisker A, Maurer A, Léon J, Kazman E, Cöster H, Holzapfel J, Kempf H, Korzun V, Ebmeyer E, Pillen K. Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800. BMC Genomics 2018; 19:559. [PMID: 30064354 PMCID: PMC6069784 DOI: 10.1186/s12864-018-4915-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/02/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Multi-parent advanced generation intercross (MAGIC) populations are a newly established tool to dissect quantitative traits. We developed the high resolution MAGIC wheat population WM-800, consisting of 910 F4:6 lines derived from intercrossing eight recently released European winter wheat cultivars. RESULTS Genotyping WM-800 with 7849 SNPs revealed a low mean genetic similarity of 59.7% between MAGIC lines. WM-800 harbours distinct genomic regions exposed to segregation distortion. These are mainly located on chromosomes 2 to 6 of the wheat B genome where founder specific DNA segments were positively or negatively selected. This suggests adaptive selection of individual founder alleles during population development. The application of a genome-wide association study identified 14 quantitative trait loci (QTL) controlling plant height in WM-800, including the known semi-dwarf genes Rht-B1 and Rht-D1 and a potentially novel QTL on chromosome 5A. Additionally, epistatic effects controlled plant height. For example, two loci on chromosomes 2B and 7B gave rise to an additive epistatic effect of 13.7 cm. CONCLUSION The present study demonstrates that plant height in the MAGIC-WHEAT population WM-800 is mainly determined by large-effect QTL and di-genic epistatic interactions. As a proof of concept, our study confirms that WM-800 is a valuable tool to dissect the genetic architecture of important agronomic traits.
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Affiliation(s)
- Wiebke Sannemann
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
| | - Antonia Lisker
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
| | - Andreas Maurer
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, University of Bonn, Katzenburgweg 5, Bonn, Germany
| | - Ebrahim Kazman
- Syngenta Seeds GmbH, Kroppenstedter Straße 4, 39387 Oschersleben (Bode), Hadmersleben, Germany
| | - Hilmar Cöster
- RAGT 2n, Steinesche 5A, 38855 - Silstedt, Wernigerode, Germany
| | - Josef Holzapfel
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg an der Isar, Germany
| | - Hubert Kempf
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg an der Isar, Germany
| | - Viktor Korzun
- KWS SAAT SE, Grimsehlstraße 31, 37555 Einbeck, Germany
| | - Erhard Ebmeyer
- KWS LOCHOW GMBH, Ferdinand-Lochow-Straße 5, 29303 Bergen/Wohlde, Germany
| | - Klaus Pillen
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
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153
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Tardieu F, Cabrera-Bosquet L, Pridmore T, Bennett M. Plant Phenomics, From Sensors to Knowledge. Curr Biol 2018; 27:R770-R783. [PMID: 28787611 DOI: 10.1016/j.cub.2017.05.055] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Major improvements in crop yield are needed to keep pace with population growth and climate change. While plant breeding efforts have greatly benefited from advances in genomics, profiling the crop phenome (i.e., the structure and function of plants) associated with allelic variants and environments remains a major technical bottleneck. Here, we review the conceptual and technical challenges facing plant phenomics. We first discuss how, given plants' high levels of morphological plasticity, crop phenomics presents distinct challenges compared with studies in animals. Next, we present strategies for multi-scale phenomics, and describe how major improvements in imaging, sensor technologies and data analysis are now making high-throughput root, shoot, whole-plant and canopy phenomic studies possible. We then suggest that research in this area is entering a new stage of development, in which phenomic pipelines can help researchers transform large numbers of images and sensor data into knowledge, necessitating novel methods of data handling and modelling. Collectively, these innovations are helping accelerate the selection of the next generation of crops more sustainable and resilient to climate change, and whose benefits promise to scale from physiology to breeding and to deliver real world impact for ongoing global food security efforts.
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Affiliation(s)
- François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F34060, Montpellier, France.
| | - Llorenç Cabrera-Bosquet
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F34060, Montpellier, France
| | - Tony Pridmore
- School of Computer Science, University of Nottingham, NG8 1BB, UK
| | - Malcolm Bennett
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, LE12 3RD, UK.
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154
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Arjona JM, Royo C, Dreisigacker S, Ammar K, Villegas D. Effect of Ppd-A1 and Ppd-B1 Allelic Variants on Grain Number and Thousand Kernel Weight of Durum Wheat and Their Impact on Final Grain Yield. FRONTIERS IN PLANT SCIENCE 2018; 9:888. [PMID: 30008727 PMCID: PMC6033988 DOI: 10.3389/fpls.2018.00888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/07/2018] [Indexed: 05/16/2023]
Abstract
The main yield components in durum wheat are grain number per unit area (GN) and thousand kernel weight (TKW), both of which are affected by environmental conditions. The most critical developmental stage for their determination is flowering time, which partly depends on photoperiod sensitivity genes at Ppd-1 loci. Fifteen field experiments, involving 23 spring durum wheat genotypes containing all known allelic variants at the PHOTOPERIOD RESPONSE LOCUS (Ppd-A1 and Ppd-B1) were carried out at three sites at latitudes ranging from 41° to 27° N (Spain, Mexico-north, and Mexico-south, the latter in spring planting). Allele GS100 at Ppd-A1, which causes photoperiod insensitivity and results in early-flowering genotypes, tended to increase TKW and yield, albeit not substantially. Allele Ppd-B1a, also causing photoperiod insensitivity, did not affect flowering time or grain yield. Genotypes carrying the Ppd-B1b allele conferring photoperiod sensitivity had consistently higher GN, which did not translate into higher yield due to under-compensation in TKW. This increased GN was due to a greater number of grains spike-1 as a result of a higher number of spikelets spike-1. Daylength from double ridge to terminal spikelet stage was strongly and positively associated with the number of spikelets spike-1 in Spain. This association was not found in the Mexico sites, thereby indicating that Ppd-B1b had an intrinsic effect on spikelets spike-1 independently of environmental cues. Our results suggest that, in environments where yield is limited by the incapacity to produce a high GN, selecting for Ppd-B1b may be advisable.
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Affiliation(s)
- Jose M. Arjona
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Conxita Royo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | | | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Dolors Villegas
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
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155
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Tricker PJ, ElHabti A, Schmidt J, Fleury D. The physiological and genetic basis of combined drought and heat tolerance in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3195-3210. [PMID: 29562265 DOI: 10.1093/jxb/ery081] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/14/2018] [Indexed: 05/03/2023]
Abstract
Drought and heat stress cause losses in wheat productivity in major growing regions worldwide, and both the occurrence and the severity of these events are likely to increase with global climate change. Water deficits and high temperatures frequently occur simultaneously at sensitive growth stages, reducing wheat yields by reducing grain number or weight. Although genetic variation and underlying quantitative trait loci for either individual stress are known, the combination of the two stresses has rarely been studied. Complex and often antagonistic physiology means that genetic loci underlying tolerance to the combined stress are likely to differ from those for drought or heat stress tolerance alone. Here, we review what is known of the physiological traits and genetic control of drought and heat tolerance in wheat and discuss potential physiological traits to study for combined tolerance. We further place this knowledge in the context of breeding for new, more tolerant varieties and discuss opportunities and constraints. We conclude that a fine control of water relations across the growing cycle will be beneficial for combined tolerance and might be achieved through fine management of spatial and temporal gas exchange.
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Affiliation(s)
- Penny J Tricker
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Abdeljalil ElHabti
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Jessica Schmidt
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Delphine Fleury
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
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156
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Rapp M, Lein V, Lacoudre F, Lafferty J, Müller E, Vida G, Bozhanova V, Ibraliu A, Thorwarth P, Piepho HP, Leiser WL, Würschum T, Longin CFH. Simultaneous improvement of grain yield and protein content in durum wheat by different phenotypic indices and genomic selection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1315-1329. [PMID: 29511784 DOI: 10.1007/s00122-018-3080-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/24/2018] [Indexed: 05/19/2023]
Abstract
Simultaneous improvement of protein content and grain yield by index selection is possible but its efficiency largely depends on the weighting of the single traits. The genetic architecture of these indices is similar to that of the primary traits. Grain yield and protein content are of major importance in durum wheat breeding, but their negative correlation has hampered their simultaneous improvement. To account for this in wheat breeding, the grain protein deviation (GPD) and the protein yield were proposed as targets for selection. The aim of this work was to investigate the potential of different indices to simultaneously improve grain yield and protein content in durum wheat and to evaluate their genetic architecture towards genomics-assisted breeding. To this end, we investigated two different durum wheat panels comprising 159 and 189 genotypes, which were tested in multiple field locations across Europe and genotyped by a genotyping-by-sequencing approach. The phenotypic analyses revealed significant genetic variances for all traits and heritabilities of the phenotypic indices that were in a similar range as those of grain yield and protein content. The GPD showed a high and positive correlation with protein content, whereas protein yield was highly and positively correlated with grain yield. Thus, selecting for a high GPD would mainly increase the protein content whereas a selection based on protein yield would mainly improve grain yield, but a combination of both indices allows to balance this selection. The genome-wide association mapping revealed a complex genetic architecture for all traits with most QTL having small effects and being detected only in one germplasm set, thus limiting the potential of marker-assisted selection for trait improvement. By contrast, genome-wide prediction appeared promising but its performance strongly depends on the relatedness between training and prediction sets.
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Affiliation(s)
- M Rapp
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | | | - F Lacoudre
- Limagrain Europe, 11492, Castelnaudary Cedex, France
| | - J Lafferty
- Saatzucht Donau, 2301, Probstdorf, Austria
| | - E Müller
- Südwestdeutsche Saatzucht GmbH & Co. KG, Im Rheinfeld 1-13, 76437, Rastatt, Germany
| | - G Vida
- Centre for Agricultural Research, Hungarian Academy of Sciences, 2462, Martonvásár, Hungary
| | - V Bozhanova
- Field Crops Institute, 6200, Chirpan, Bulgaria
| | - A Ibraliu
- Department of Plant Science and Technology, Agricultural University of Tirana, 1029, Tirana, Albania
| | - P Thorwarth
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - H P Piepho
- Biostatistics Unit, University of Hohenheim, 70593, Stuttgart, Germany
| | - W L Leiser
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - T Würschum
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - C F H Longin
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany.
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157
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Chopin J, Kumar P, Miklavcic SJ. Land-based crop phenotyping by image analysis: consistent canopy characterization from inconsistent field illumination. PLANT METHODS 2018; 14:39. [PMID: 29849745 PMCID: PMC5970541 DOI: 10.1186/s13007-018-0308-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 05/18/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND One of the main challenges associated with image-based field phenotyping is the variability of illumination. During a single day's imaging session, or between different sessions on different days, the sun moves in and out of cloud cover and has varying intensity. How is one to know from consecutive images alone if a plant has become darker over time, or if the weather conditions have simply changed from clear to overcast? This is a significant problem to address as colour is an important phenotypic trait that can be measured automatically from images. RESULTS In this work we use an industry standard colour checker to balance the colour in images within and across every day of a field trial conducted over four months in 2016. By ensuring that the colour checker is present in every image we are afforded a 'ground truth' to correct for varying illumination conditions across images. We employ a least squares approach to fit a quadratic model for correcting RGB values of an image in such a way that the observed values of the colour checker tiles align with their true values after the transformation. CONCLUSIONS The proposed method is successful in reducing the error between observed and reference colour chart values in all images. Furthermore, the standard deviation of mean canopy colour across multiple days is reduced significantly after colour correction is applied. Finally, we use a number of examples to demonstrate the usefulness of accurate colour measurements in recording phenotypic traits and analysing variation among varieties and treatments.
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Affiliation(s)
- Joshua Chopin
- Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, 5095 Australia
| | - Pankaj Kumar
- Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, 5095 Australia
| | - Stanley J. Miklavcic
- Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, 5095 Australia
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158
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Slama A, Mallek-Maalej E, Ben Mohamed H, Rhim T, Radhouane L. A return to the genetic heritage of durum wheat to cope with drought heightened by climate change. PLoS One 2018; 13:e0196873. [PMID: 29795584 PMCID: PMC5967785 DOI: 10.1371/journal.pone.0196873] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/20/2018] [Indexed: 02/05/2023] Open
Abstract
The objective of this work was to perform a comparative analysis of the physiological, biochemical and agronomical parameters of recent and heritage durum wheat cultivars (Triticum durum Desf.) under water-deficit conditions. Five cultivars were grown under irrigated (control) and rainfall (stressed) conditions. Different agro-physiological and biochemical parameters were studied: electrolyte leakage, relative water content, chlorophyll fluorescence, proline, soluble sugars, specific peroxidase activity, yield and drought stress indices. It was revealed that a water deficit increased proline content, electrolyte leakage, soluble sugars and specific peroxidase activity and decreased relative water content, fluorescence and grain yield. According to these parameters and drought stress indices, our investigation indicated that old cultivars are the best-adapted to local conditions and showed characteristics of drought tolerance, while recent cultivars showed more drought susceptibility. Therefore, local cultivars of each country should be kept by farmers and plant breeders to preserve their genetic heritage.
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Affiliation(s)
- Amor Slama
- Science Faculty of Bizerte, Carthage University, Bizerte, Tunisia
- * E-mail:
| | | | - Hatem Ben Mohamed
- Arid and Oases Cropping Laboratory, Arid Regions Institute of Medenine, Medenine, Tunisia
| | - Thouraya Rhim
- Horticulture Laboratory, National Institute of Agronomic Research, Ariana, Tunisia
| | - Leila Radhouane
- Plant Physiology Laboratory, National Institute of Agronomic Research, Ariana, Tunisia
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159
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Slama A, Mallek-Maalej E, Ben Mohamed H, Rhim T, Radhouane L. A return to the genetic heritage of durum wheat to cope with drought heightened by climate change. PLoS One 2018. [DOI: https://doi.org/10.1371/journal.pone.0196873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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160
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Tardieu F, Simonneau T, Muller B. The Physiological Basis of Drought Tolerance in Crop Plants: A Scenario-Dependent Probabilistic Approach. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:733-759. [PMID: 29553801 DOI: 10.1146/annurev-arplant-042817-040218] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Drought tolerance involves mechanisms operating at different spatial and temporal scales, from rapid stomatal closure to maintenance of crop yield. We review how short-term mechanisms are controlled for stabilizing shoot water potential and how long-term processes have been constrained by evolution or breeding to fit into acclimation strategies for specific drought scenarios. These short- or long-term feedback processes participate in trade-offs between carbon accumulation and the risk of deleterious soil water depletion. Corresponding traits and alleles may therefore have positive or negative effects on crop yield depending on drought scenarios. We propose an approach that analyzes the genetic architecture of traits in phenotyping platforms and of yield in tens of field experiments. A combination of modeling and genomic prediction is then used to estimate the comparative interests of combinations of alleles depending on drought scenarios. Hence, drought tolerance is understood probabilistically by estimating the benefit and risk of each combination of alleles.
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Affiliation(s)
- François Tardieu
- INRA, Université Montpellier, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F-34060 Montpellier, France;
| | - Thierry Simonneau
- INRA, Université Montpellier, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F-34060 Montpellier, France;
| | - Bertrand Muller
- INRA, Université Montpellier, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F-34060 Montpellier, France;
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161
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Jimenez-Berni JA, Deery DM, Rozas-Larraondo P, Condon A(TG, Rebetzke GJ, James RA, Bovill WD, Furbank RT, Sirault XRR. High Throughput Determination of Plant Height, Ground Cover, and Above-Ground Biomass in Wheat with LiDAR. FRONTIERS IN PLANT SCIENCE 2018; 9:237. [PMID: 29535749 PMCID: PMC5835033 DOI: 10.3389/fpls.2018.00237] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/09/2018] [Indexed: 05/18/2023]
Abstract
Crop improvement efforts are targeting increased above-ground biomass and radiation-use efficiency as drivers for greater yield. Early ground cover and canopy height contribute to biomass production, but manual measurements of these traits, and in particular above-ground biomass, are slow and labor-intensive, more so when made at multiple developmental stages. These constraints limit the ability to capture these data in a temporal fashion, hampering insights that could be gained from multi-dimensional data. Here we demonstrate the capacity of Light Detection and Ranging (LiDAR), mounted on a lightweight, mobile, ground-based platform, for rapid multi-temporal and non-destructive estimation of canopy height, ground cover and above-ground biomass. Field validation of LiDAR measurements is presented. For canopy height, strong relationships with LiDAR (r2 of 0.99 and root mean square error of 0.017 m) were obtained. Ground cover was estimated from LiDAR using two methodologies: red reflectance image and canopy height. In contrast to NDVI, LiDAR was not affected by saturation at high ground cover, and the comparison of both LiDAR methodologies showed strong association (r2 = 0.92 and slope = 1.02) at ground cover above 0.8. For above-ground biomass, a dedicated field experiment was performed with destructive biomass sampled eight times across different developmental stages. Two methodologies are presented for the estimation of biomass from LiDAR: 3D voxel index (3DVI) and 3D profile index (3DPI). The parameters involved in the calculation of 3DVI and 3DPI were optimized for each sample event from tillering to maturity, as well as generalized for any developmental stage. Individual sample point predictions were strong while predictions across all eight sample events, provided the strongest association with biomass (r2 = 0.93 and r2 = 0.92) for 3DPI and 3DVI, respectively. Given these results, we believe that application of this system will provide new opportunities to deliver improved genotypes and agronomic interventions via more efficient and reliable phenotyping of these important traits in large experiments.
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Affiliation(s)
- Jose A. Jimenez-Berni
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organisation Agriculture and Food Agriculture and Food, Canberra, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, Australia
| | - David M. Deery
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
| | - Pablo Rozas-Larraondo
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organisation Agriculture and Food Agriculture and Food, Canberra, ACT, Australia
| | - Anthony (Tony) G. Condon
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, Australia
| | - Greg J. Rebetzke
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
| | - Richard A. James
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
| | - William D. Bovill
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
| | - Robert T. Furbank
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organisation Agriculture and Food Agriculture and Food, Canberra, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, Australia
| | - Xavier R. R. Sirault
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organisation Agriculture and Food Agriculture and Food, Canberra, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, Australia
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162
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Gracia-Romero A, Vergara-Díaz O, Thierfelder C, Cairns JE, Kefauver SC, Araus JL. Phenotyping Conservation Agriculture Management Effects on Ground and Aerial Remote Sensing Assessments of Maize Hybrids Performance in Zimbabwe. REMOTE SENSING 2018; 10:349. [PMID: 32704486 PMCID: PMC7340492 DOI: 10.3390/rs10020349] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 02/14/2018] [Indexed: 12/21/2022]
Abstract
In the coming decades, Sub-Saharan Africa (SSA) faces challenges to sustainably increase food production while keeping pace with continued population growth. Conservation agriculture (CA) has been proposed to enhance soil health and productivity to respond to this situation. Maize is the main staple food in SSA. To increase maize yields, the selection of suitable genotypes and management practices for CA conditions has been explored using remote sensing tools. They may play a fundamental role towards overcoming the traditional limitations of data collection and processing in large scale phenotyping studies. We present the result of a study in which Red-Green-Blue (RGB) and multispectral indexes were evaluated for assessing maize performance under conventional ploughing (CP) and CA practices. Eight hybrids under different planting densities and tillage practices were tested. The measurements were conducted on seedlings at ground level (0.8 m) and from an unmanned aerial vehicle (UAV) platform (30 m), causing a platform proximity effect on the images resolution that did not have any negative impact on the performance of the indexes. Most of the calculated indexes (Green Area (GA) and Normalized Difference Vegetation Index (NDVI)) were significantly affected by tillage conditions increasing their values from CP to CA. Indexes derived from the RGB-images related to canopy greenness performed better at assessing yield differences, potentially due to the greater resolution of the RGB compared with the multispectral data, although this performance was more precise for CP than CA. The correlations of the multispectral indexes with yield were improved by applying a soil-mask derived from a NDVI threshold with the aim of corresponding pixels with vegetation. The results of this study highlight the applicability of remote sensing approaches based on RGB images to the assessment of crop performance and hybrid choice.
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Affiliation(s)
- Adrian Gracia-Romero
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.G.-R.); (O.V.-D.); (J.L.A.)
| | - Omar Vergara-Díaz
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.G.-R.); (O.V.-D.); (J.L.A.)
| | - Christian Thierfelder
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, P.O. Box MP163, Harare, Zimbabwe; (C.T.); (J.E.C.)
| | - Jill E Cairns
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, P.O. Box MP163, Harare, Zimbabwe; (C.T.); (J.E.C.)
| | - Shawn C Kefauver
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.G.-R.); (O.V.-D.); (J.L.A.)
| | - José L Araus
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.G.-R.); (O.V.-D.); (J.L.A.)
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Sukumaran S, Reynolds MP, Sansaloni C. Genome-Wide Association Analyses Identify QTL Hotspots for Yield and Component Traits in Durum Wheat Grown under Yield Potential, Drought, and Heat Stress Environments. FRONTIERS IN PLANT SCIENCE 2018; 9:81. [PMID: 29467776 PMCID: PMC5808252 DOI: 10.3389/fpls.2018.00081] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/15/2018] [Indexed: 05/18/2023]
Abstract
Understanding the genetic bases of economically important traits is fundamentally important in enhancing genetic gains in durum wheat. In this study, a durum panel of 208 lines (comprised of elite materials and exotics from the International Maize and Wheat Improvement Center gene bank) were subjected to genome wide association study (GWAS) using 6,211 DArTseq single nucleotide polymorphisms (SNPs). The panel was phenotyped under yield potential (YP), drought stress (DT), and heat stress (HT) conditions for 2 years. Mean yield of the panel was reduced by 72% (to 1.64 t/ha) under HT and by 60% (to 2.33 t/ha) under DT, compared to YP (5.79 t/ha). Whereas, the mean yield of the panel under HT was 30% less than under DT. GWAS identified the largest number of significant marker-trait associations on chromosomes 2A and 2B with p-values 10-06 to 10-03 and the markers from the whole study explained 7-25% variation in the traits. Common markers were identified for stress tolerance indices: stress susceptibility index, stress tolerance, and stress tolerance index estimated for the traits under DT (82 cM on 2B) and HT (68 and 83 cM on 3B; 25 cM on 7A). GWAS of irrigated (YP and HT combined), stressed (DT and HT combined), combined analysis of three environments (YP + DT + HT), and its comparison with trait per se and stress indices identified QTL hotspots on chromosomes 2A (54-70 cM) and 2B (75-82 cM). This study enhances our knowledge about the molecular markers associated with grain yield and its components under different stress conditions. It identifies several marker-trait associations for further exploration and validation for marker-assisted breeding.
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Affiliation(s)
- Sivakumar Sukumaran
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Matthew P. Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Carolina Sansaloni
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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164
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Mangini G, Gadaleta A, Colasuonno P, Marcotuli I, Signorile AM, Simeone R, De Vita P, Mastrangelo AM, Laidò G, Pecchioni N, Blanco A. Genetic dissection of the relationships between grain yield components by genome-wide association mapping in a collection of tetraploid wheats. PLoS One 2018; 13:e0190162. [PMID: 29324803 PMCID: PMC5764242 DOI: 10.1371/journal.pone.0190162] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/09/2017] [Indexed: 11/29/2022] Open
Abstract
Increasing grain yield potential in wheat has been a major target of most breeding programs. Genetic advance has been frequently hindered by negative correlations among yield components that have been often observed in segregant populations and germplasm collections. A tetraploid wheat collection was evaluated in seven environments and genotyped with a 90K SNP assay to identify major and stable quantitative trait loci (QTL) for grain yield per spike (GYS), kernel number per spike (KNS) and thousand-kernel weight (TKW), and to analyse the genetic relationships between the yield components at QTL level. The genome-wide association analysis detected eight, eleven and ten QTL for KNS, TKW and GYS, respectively, significant in at least three environments or two environments and the mean across environments. Most of the QTL for TKW and KNS were found located in different marker intervals, indicating that they are genetically controlled independently by each other. Out of eight KNS QTL, three were associated to significant increases of GYS, while the increased grain number of five additional QTL was completely or partially compensated by decreases in grain weight, thus producing no or reduced effects on GYS. Similarly, four consistent and five suggestive TKW QTL resulted in visible increase of GYS, while seven additional QTL were associated to reduced effects in grain number and no effects on GYS. Our results showed that QTL analysis for detecting TKW or KNS alleles useful for improving grain yield potential should consider the pleiotropic effects of the QTL or the association to other QTLs.
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Affiliation(s)
- Giacomo Mangini
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
| | - Agata Gadaleta
- Department of Agricultural & Environmental Science, Research Unit of “Genetics and Plant Biotechnology”, University Aldo Moro, Bari, Italy
- * E-mail:
| | - Pasqualina Colasuonno
- Department of Agricultural & Environmental Science, Research Unit of “Genetics and Plant Biotechnology”, University Aldo Moro, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural & Environmental Science, Research Unit of “Genetics and Plant Biotechnology”, University Aldo Moro, Bari, Italy
| | - Antonio M. Signorile
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
| | - Rosanna Simeone
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
| | - Pasquale De Vita
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Anna M. Mastrangelo
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Giovanni Laidò
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Antonio Blanco
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
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165
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Lobos GA, Camargo AV, del Pozo A, Araus JL, Ortiz R, Doonan JH. Editorial: Plant Phenotyping and Phenomics for Plant Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:2181. [PMID: 29375593 PMCID: PMC5770690 DOI: 10.3389/fpls.2017.02181] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/12/2017] [Indexed: 05/25/2023]
Affiliation(s)
- Gustavo A. Lobos
- PIEI Adaptación de la Agricultura al Cambio Climático, Facultad de Ciencias Agrarias, Plant Breeding and Phenomic Center, Universidad de Talca, Talca, Chile
| | - Anyela V. Camargo
- The John Bingham Laboratory, Genetics and Breeding, National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Alejandro del Pozo
- PIEI Adaptación de la Agricultura al Cambio Climático, Facultad de Ciencias Agrarias, Plant Breeding and Phenomic Center, Universidad de Talca, Talca, Chile
| | - Jose L. Araus
- Plant Physiology Section, University of Barcelona, Barcelona, Spain
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - John H. Doonan
- National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
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166
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Gracia-Romero A, Kefauver SC, Vergara-Díaz O, Zaman-Allah MA, Prasanna BM, Cairns JE, Araus JL. Comparative Performance of Ground vs. Aerially Assessed RGB and Multispectral Indices for Early-Growth Evaluation of Maize Performance under Phosphorus Fertilization. FRONTIERS IN PLANT SCIENCE 2017; 8:2004. [PMID: 29230230 PMCID: PMC5711853 DOI: 10.3389/fpls.2017.02004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/10/2017] [Indexed: 05/25/2023]
Abstract
Low soil fertility is one of the factors most limiting agricultural production, with phosphorus deficiency being among the main factors, particularly in developing countries. To deal with such environmental constraints, remote sensing measurements can be used to rapidly assess crop performance and to phenotype a large number of plots in a rapid and cost-effective way. We evaluated the performance of a set of remote sensing indices derived from Red-Green-Blue (RGB) images and multispectral (visible and infrared) data as phenotypic traits and crop monitoring tools for early assessment of maize performance under phosphorus fertilization. Thus, a set of 26 maize hybrids grown under field conditions in Zimbabwe was assayed under contrasting phosphorus fertilization conditions. Remote sensing measurements were conducted in seedlings at two different levels: at the ground and from an aerial platform. Within a particular phosphorus level, some of the RGB indices strongly correlated with grain yield. In general, RGB indices assessed at both ground and aerial levels correlated in a comparable way with grain yield except for indices a* and u*, which correlated better when assessed at the aerial level than at ground level and Greener Area (GGA) which had the opposite correlation. The Normalized Difference Vegetation Index (NDVI) evaluated at ground level with an active sensor also correlated better with grain yield than the NDVI derived from the multispectral camera mounted in the aerial platform. Other multispectral indices like the Soil Adjusted Vegetation Index (SAVI) performed very similarly to NDVI assessed at the aerial level but overall, they correlated in a weaker manner with grain yield than the best RGB indices. This study clearly illustrates the advantage of RGB-derived indices over the more costly and time-consuming multispectral indices. Moreover, the indices best correlated with GY were in general those best correlated with leaf phosphorous content. However, these correlations were clearly weaker than against grain yield and only under low phosphorous conditions. This work reinforces the effectiveness of canopy remote sensing for plant phenotyping and crop management of maize under different phosphorus nutrient conditions and suggests that the RGB indices are the best option.
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Affiliation(s)
- Adrian Gracia-Romero
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Shawn C. Kefauver
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Omar Vergara-Díaz
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Mainassara A. Zaman-Allah
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, Harare, Zimbabwe
| | - Boddupalli M. Prasanna
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, Harare, Zimbabwe
| | - Jill E. Cairns
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, Harare, Zimbabwe
| | - José L. Araus
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain
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167
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Sadeghi-Tehran P, Virlet N, Sabermanesh K, Hawkesford MJ. Multi-feature machine learning model for automatic segmentation of green fractional vegetation cover for high-throughput field phenotyping. PLANT METHODS 2017; 13:103. [PMID: 29201134 PMCID: PMC5696775 DOI: 10.1186/s13007-017-0253-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 11/11/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Accurately segmenting vegetation from the background within digital images is both a fundamental and a challenging task in phenotyping. The performance of traditional methods is satisfactory in homogeneous environments, however, performance decreases when applied to images acquired in dynamic field environments. RESULTS In this paper, a multi-feature learning method is proposed to quantify vegetation growth in outdoor field conditions. The introduced technique is compared with the state-of the-art and other learning methods on digital images. All methods are compared and evaluated with different environmental conditions and the following criteria: (1) comparison with ground-truth images, (2) variation along a day with changes in ambient illumination, (3) comparison with manual measurements and (4) an estimation of performance along the full life cycle of a wheat canopy. CONCLUSION The method described is capable of coping with the environmental challenges faced in field conditions, with high levels of adaptiveness and without the need for adjusting a threshold for each digital image. The proposed method is also an ideal candidate to process a time series of phenotypic information throughout the crop growth acquired in the field. Moreover, the introduced method has an advantage that it is not limited to growth measurements only but can be applied on other applications such as identifying weeds, diseases, stress, etc.
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Affiliation(s)
| | - Nicolas Virlet
- Plant Science Department, Rothamsted Research, Harpenden, AL5 2JQ UK
| | - Kasra Sabermanesh
- Plant Science Department, Rothamsted Research, Harpenden, AL5 2JQ UK
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168
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Kefauver SC, Vicente R, Vergara-Díaz O, Fernandez-Gallego JA, Kerfal S, Lopez A, Melichar JPE, Serret Molins MD, Araus JL. Comparative UAV and Field Phenotyping to Assess Yield and Nitrogen Use Efficiency in Hybrid and Conventional Barley. FRONTIERS IN PLANT SCIENCE 2017; 8:1733. [PMID: 29067032 PMCID: PMC5641326 DOI: 10.3389/fpls.2017.01733] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/22/2017] [Indexed: 05/07/2023]
Abstract
With the commercialization and increasing availability of Unmanned Aerial Vehicles (UAVs) multiple rotor copters have expanded rapidly in plant phenotyping studies with their ability to provide clear, high resolution images. As such, the traditional bottleneck of plant phenotyping has shifted from data collection to data processing. Fortunately, the necessarily controlled and repetitive design of plant phenotyping allows for the development of semi-automatic computer processing tools that may sufficiently reduce the time spent in data extraction. Here we present a comparison of UAV and field based high throughput plant phenotyping (HTPP) using the free, open-source image analysis software FIJI (Fiji is just ImageJ) using RGB (conventional digital cameras), multispectral and thermal aerial imagery in combination with a matching suite of ground sensors in a study of two hybrids and one conventional barely variety with ten different nitrogen treatments, combining different fertilization levels and application schedules. A detailed correlation network for physiological traits and exploration of the data comparing between treatments and varieties provided insights into crop performance under different management scenarios. Multivariate regression models explained 77.8, 71.6, and 82.7% of the variance in yield from aerial, ground, and combined data sets, respectively.
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Affiliation(s)
- Shawn C. Kefauver
- Integrative Crop Ecophysiology Group, Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Rubén Vicente
- Integrative Crop Ecophysiology Group, Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Omar Vergara-Díaz
- Integrative Crop Ecophysiology Group, Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Jose A. Fernandez-Gallego
- Integrative Crop Ecophysiology Group, Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | | | | | | | - María D. Serret Molins
- Integrative Crop Ecophysiology Group, Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - José L. Araus
- Integrative Crop Ecophysiology Group, Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
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169
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Linkage mapping aided by de novo genome and transcriptome assembly in Portunus trituberculatus: applications in growth-related QTL and gene identification. Sci Rep 2017; 7:7874. [PMID: 28801606 PMCID: PMC5554138 DOI: 10.1038/s41598-017-08256-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/06/2017] [Indexed: 11/09/2022] Open
Abstract
A high-resolution genetic linkage map is an essential tool for decoding genetics and genomics in non-model organisms. In this study, a linkage map was constructed for the swimming crab (Portunus trituberculatus) with 10,963 markers; as far as we know, this number of markers has never been achieved in any other crustacean. The linkage map covered 98.85% of the whole genome with a mean marker interval of 0.51 cM. The de novo assembly based on genome and transcriptome sequencing data enabled 2,378 explicit annotated markers to be anchored to the map. Quantitative trait locus (QTL) mapping revealed 10 growth-related QTLs with a phenotypic variance explained (PVE) range of 12.0-35.9. Eight genes identified from the growth-related QTL regions, in particular, RE1-silencing transcription factor and RNA-directed DNA polymerase genes with nonsynonymous substitutions, were considered important growth-related candidate genes. We have demonstrated that linkage mapping aided by de novo assembly of genome and transcriptome sequencing could serve as an important platform for QTL mapping and the identification of trait-related genes.
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170
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Gahlaut V, Jaiswal V, Tyagi BS, Singh G, Sareen S, Balyan HS, Gupta PK. QTL mapping for nine drought-responsive agronomic traits in bread wheat under irrigated and rain-fed environments. PLoS One 2017; 12:e0182857. [PMID: 28793327 PMCID: PMC5550002 DOI: 10.1371/journal.pone.0182857] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/25/2017] [Indexed: 11/19/2022] Open
Abstract
In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits. Two-locus analysis allowed detection of 19 main effect QTL (M-QTL) for four traits (days to anthesis, days to maturity, grain filling duration and thousand grain weight) and 19 pairs of epistatic QTL (E-QTL) for two traits (days to anthesis and thousand grain weight). Eight QTL were common in single locus analysis and two locus analysis. These QTL (identified both in single- and two-locus analysis) were distributed on 20 different chromosomes (except 4D). Important genomic regions on chromosomes 5A and 7A were also identified (5A carried QTL for seven traits and 7A carried QTL for six traits). Marker-assisted recurrent selection (MARS) involving pyramiding of important QTL reported in the present study, together with important QTL reported earlier, may be used for improvement of drought tolerance in wheat. In future, more closely linked markers for the QTL reported here may be developed through fine mapping, and the candidate genes may be identified and used for developing a better understanding of the genetic basis of drought tolerance in wheat.
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Affiliation(s)
- Vijay Gahlaut
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Vandana Jaiswal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Bhudeva S. Tyagi
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sindhu Sareen
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Harindra S. Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
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171
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Iannucci A, Marone D, Russo MA, De Vita P, Miullo V, Ferragonio P, Blanco A, Gadaleta A, Mastrangelo AM. Mapping QTL for Root and Shoot Morphological Traits in a Durum Wheat × T. dicoccum Segregating Population at Seedling Stage. Int J Genomics 2017; 2017:6876393. [PMID: 28845431 PMCID: PMC5563412 DOI: 10.1155/2017/6876393] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/12/2017] [Accepted: 06/21/2017] [Indexed: 01/27/2023] Open
Abstract
A segregating population of 136 recombinant inbred lines derived from a cross between the durum wheat cv. "Simeto" and the T. dicoccum accession "Molise Colli" was grown in soil and evaluated for a number of shoot and root morphological traits. A total of 17 quantitative trait loci (QTL) were identified for shoot dry weight, number of culms, and plant height and for root dry weight, volume, length, surface area, and number of forks and tips, on chromosomes 1B, 2A, 3A, 4B, 5B, 6A, 6B, and 7B. LODs were 2.1 to 21.6, with percent of explained phenotypic variability between 0.07 and 52. Three QTL were mapped to chromosome 4B, one of which corresponds to the Rht-B1 locus and has a large impact on both shoot and root traits (LOD 21.6). Other QTL that have specific effects on root morphological traits were also identified. Moreover, meta-QTL analysis was performed to compare the QTL identified in the "Simeto" × "Molise Colli" segregating population with those described in previous studies in wheat, with three novel QTL defined. Due to the complexity of phenotyping for root traits, further studies will be helpful to validate these regions as targets for breeding programs for optimization of root function for field performance.
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Affiliation(s)
- Anna Iannucci
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Daniela Marone
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Maria Anna Russo
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Pasquale De Vita
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Vito Miullo
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Pina Ferragonio
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Agata Gadaleta
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Anna Maria Mastrangelo
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
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172
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Sun C, Zhang F, Yan X, Zhang X, Dong Z, Cui D, Chen F. Genome-wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:953-969. [PMID: 28055148 PMCID: PMC5506658 DOI: 10.1111/pbi.12690] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 05/18/2023]
Abstract
Bread wheat is a leading cereal crop worldwide. Limited amount of superior allele loci restricted the progress of molecular improvement in wheat breeding. Here, we revealed new allelic variation distribution for 13 yield-related traits in series of genome-wide association studies (GWAS) using the wheat 90K genotyping assay, characterized in 163 bread wheat cultivars. Agronomic traits were investigated in 14 environments at three locations over 3 years. After filtering SNP data sets, GWAS using 20 689 high-quality SNPs associated 1769 significant loci that explained, on average, ~20% of the phenotypic variation, both detected already reported loci and new promising genomic regions. Of these, repetitive and pleiotropic SNPs on chromosomes 6AS, 6AL, 6BS, 5BL and 7AS were significantly linked to thousand kernel weight, for example BS00021705_51 on 6BS and wsnp_Ex_c32624_41252144 on 6AS, with phenotypic variation explained (PVE) of ~24%, consistently identified in 12 and 13 of the 14 environments, respectively. Kernel length-related SNPs were mainly identified on chromosomes 7BS, 6AS, 5AL and 5BL. Plant height-related SNPs on chromosomes 4DS, 6DL, 2DS and 1BL were, respectively, identified in more than 11 environments, with averaged PVE of ~55%. Four SNPs were confirmed to be important genetic loci in two RIL populations. Based on repetivity and PVE, a total of 41 SNP loci possibly played the key role in modulating yield-related traits of the cultivars surveyed. Distribution of superior alleles at the 41 SNP loci indicated that superior alleles were getting popular with time and modern cultivars had integrated many superior alleles, especially for peduncle length- and plant height-related superior alleles. However, there were still 19 SNP loci showing less than percentages of 50% in modern cultivars, suggesting they should be paid more attention to improve yield-related traits of cultivars in the Yellow and Huai wheat region. This study could provide useful information for dissection of yield-related traits and valuable genetic loci for marker-assisted selection in Chinese wheat breeding programme.
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Affiliation(s)
- Congwei Sun
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Fuyan Zhang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Nuclear Agricultural Sciences/Isotope Institute Co., LtdHenan Academy of SciencesZhengzhouChina
| | - Xuefang Yan
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Xiangfen Zhang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Zhongdong Dong
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Dangqun Cui
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Feng Chen
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
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Luo Z, Wang M, Long Y, Huang Y, Shi L, Zhang C, Liu X, Fitt BDL, Xiang J, Mason AS, Snowdon RJ, Liu P, Meng J, Zou J. Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1569-1585. [PMID: 28455767 PMCID: PMC5719798 DOI: 10.1007/s00122-017-2911-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 04/19/2017] [Indexed: 05/10/2023]
Abstract
A comprehensive linkage atlas for seed yield in rapeseed. Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.
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Affiliation(s)
- Ziliang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Meng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yongju Huang
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB UK
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bruce D. L. Fitt
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB UK
| | - Jinxia Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Annaliese S. Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Peifa Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
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174
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Wang X, Luo G, Yang W, Li Y, Sun J, Zhan K, Liu D, Zhang A. Genetic diversity, population structure and marker-trait associations for agronomic and grain traits in wild diploid wheat Triticum urartu. BMC PLANT BIOLOGY 2017; 17:112. [PMID: 28668082 PMCID: PMC5494140 DOI: 10.1186/s12870-017-1058-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/14/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND Wild diploid wheat, Triticum urartu (T. urartu) is the progenitor of bread wheat, and understanding its genetic diversity and genome function will provide considerable reference for dissecting genomic information of common wheat. RESULTS In this study, we investigated the morphological and genetic diversity and population structure of 238 T. urartu accessions collected from different geographic regions. This collection had 19.37 alleles per SSR locus and its polymorphic information content (PIC) value was 0.76, and the PIC and Nei's gene diversity (GD) of high-molecular-weight glutenin subunits (HMW-GSs) were 0.86 and 0.88, respectively. UPGMA clustering analysis indicated that the 238 T. urartu accessions could be classified into two subpopulations, of which Cluster I contained accessions from Eastern Mediterranean coast and those from Mesopotamia and Transcaucasia belonged to Cluster II. The wide range of genetic diversity along with the manageable number of accessions makes it one of the best collections for mining valuable genes based on marker-trait association. Significant associations were observed between simple sequence repeats (SSR) or HMW-GSs and six morphological traits: heading date (HD), plant height (PH), spike length (SPL), spikelet number per spike (SPLN), tiller angle (TA) and grain length (GL). CONCLUSIONS Our data demonstrated that SSRs and HMW-GSs were useful markers for identification of beneficial genes controlling important traits in T. urartu, and subsequently for their conservation and future utilization, which may be useful for genetic improvement of the cultivated hexaploid wheat.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Kehui Zhan
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, 450002 China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, 450002 China
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175
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Tardieu F, Parent B. Predictable 'meta-mechanisms' emerge from feedbacks between transpiration and plant growth and cannot be simply deduced from short-term mechanisms. PLANT, CELL & ENVIRONMENT 2017; 40:846-857. [PMID: 27569520 DOI: 10.1111/pce.12822] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 05/19/2023]
Abstract
Growth under water deficit is controlled by short-term mechanisms but, because of numerous feedbacks, the combination of these mechanisms over time often results in outputs that cannot be deduced from the simple inspection of individual mechanisms. It can be analysed with dynamic models in which causal relationships between variables are considered at each time-step, allowing calculation of outputs that are routed back to inputs for the next time-step and that can change the system itself. We first review physiological mechanisms involved in seven feedbacks of transpiration on plant growth, involving changes in tissue hydraulic conductance, stomatal conductance, plant architecture and underlying factors such as hormones or aquaporins. The combination of these mechanisms over time can result in non-straightforward conclusions as shown by examples of simulation outputs: 'over production of abscisic acid (ABA) can cause a lower concentration of ABA in the xylem sap ', 'decreasing root hydraulic conductance when evaporative demand is maximum can improve plant performance' and 'rapid root growth can decrease yield'. Systems of equations simulating feedbacks over numerous time-steps result in logical and reproducible emergent properties that can be viewed as 'meta-mechanisms' at plant level, which have similar roles as mechanisms at cell level.
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Affiliation(s)
- François Tardieu
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Montpellier, F-34060, France
| | - Boris Parent
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Montpellier, F-34060, France
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176
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Soriano JM, Malosetti M, Roselló M, Sorrells ME, Royo C. Dissecting the old Mediterranean durum wheat genetic architecture for phenology, biomass and yield formation by association mapping and QTL meta-analysis. PLoS One 2017; 12:e0178290. [PMID: 28542488 PMCID: PMC5444813 DOI: 10.1371/journal.pone.0178290] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/10/2017] [Indexed: 12/01/2022] Open
Abstract
Association mapping was used to identify genome regions affecting yield formation, crop phenology and crop biomass in a collection of 172 durum wheat landraces representative of the genetic diversity of ancient local durum varieties from the Mediterranean Basin. The collection was genotyped with 1,149 DArT markers and phenotyped in Spanish northern and southern locations during three years. A total of 245 significant marker trait associations (MTAs) (P<0.01) were detected. Some of these associations confirmed previously identified quantitative trait loci (QTL) and/or candidate genes, and others are reported for the first time here. Eighty-six MTAs corresponded with yield and yield component traits, 70 to phenology and 89 to biomass production. Twelve genomic regions harbouring stable MTAs (significant in three or more environments) were identified, while five and two regions showed specific MTAs for northern and southern environments, respectively. Sixty per cent of MTAs were located on the B genome and 29% on the A genome. The marker wPt-9859 was detected in 12 MTAs, associated with six traits in four environments and the mean across years. To refine QTL positions, a meta-analysis was performed. A total of 477 unique QTLs were projected onto a durum wheat consensus map and were condensed to 71 meta-QTLs and left 13 QTLs as singletons. Sixty-one percent of QTLs explained less than 10% of the phenotypic variance confirming the high genetic complexity of the traits analysed.
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Affiliation(s)
- Jose Miguel Soriano
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
| | - Marcos Malosetti
- Biometrics, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Martina Roselló
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
| | - Mark Earl Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Conxita Royo
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
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177
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Salmanowicz BP, Langner M, Mrugalska B, Ratajczak D, Górny AG. Grain quality characteristics and dough rheological properties in Langdon durum-wild emmer wheat chromosome substitution lines under nitrogen and water deficits. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:2030-2041. [PMID: 27558295 DOI: 10.1002/jsfa.8006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Wild emmer wheat could serve as a source of novel variation in grain quality and stress resistance for wheat breeding. A set of Triticum durum-T. dicoccoides chromosome substitution lines [LDN(DIC)] and the parental recipient cv. Langdon grown under contrasting water and nitrogen availability in the soil was examined in this study to identify differences in grain quality traits and dough rheological properties. RESULTS Significant genotypic variation was found among the materials for studied traits. This variation was also considerably affected by soil treatments and G × E interactions. The substitutions LDN(DIC-1A) and LDN(DIC-1B) showed separate differentiation in the composition of glutenin sub-units. The results indicated that primarily chromosome DIC-6B is stable source of an enhanced grain protein content and advantageous dough rheological properties. Similar features seem to be shown by the substitutions with the DIC-1A, DIC-2A and DIC-6A, but not under nitrogen shortage, when generally a considerable decrease was noticed in the range of genotypic variation in grain quality. CONCLUSIONS The substitution lines, particularly those with DIC-6B and DIC-6A and to a lesser extent DIC-1A and DIC-2A, were distinguished by advantageous grain quality traits, mixing properties and dough functionality and appear to be the most promising sources of innovative genes for wheat breeding. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Bolesław P Salmanowicz
- Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszynska Str., PL, 60-479, Poznan, Poland
| | - Monika Langner
- Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszynska Str., PL, 60-479, Poznan, Poland
| | - Beata Mrugalska
- Faculty of Engineering Management, Poznañ University of Technology, 11 Strzelecka Str., PL, 60-965, Poznan, Poland
| | - Dominika Ratajczak
- Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszynska Str., PL, 60-479, Poznan, Poland
| | - Andrzej G Górny
- Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszynska Str., PL, 60-479, Poznan, Poland
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178
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Mazzeo MF, Di Stasio L, D'Ambrosio C, Arena S, Scaloni A, Corneti S, Ceriotti A, Tuberosa R, Siciliano RA, Picariello G, Mamone G. Identification of Early Represented Gluten Proteins during Durum Wheat Grain Development. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:3242-3250. [PMID: 28347138 DOI: 10.1021/acs.jafc.7b00571] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The time course of biosynthesis and accumulation of storage proteins in developing grains of durum wheat (Triticum turgidum ssp. durum (Desf.) Husn.) pasta-quality reference cv. Svevo was investigated at the protein level for the first time. Seeds were harvested at key kernel developmental stages, namely, 3 (seed increase 3-fold in size), 5 (kernel development, water-ripe stage), 11 (kernel development, water-ripe stage), 16 (kernel full development, water-ripe stage), 21 (milk-ripe stage), and 30 (dough stage) days postanthesis (dpa). Gliadins and glutenins were fractionated according to their different solubility and individually analyzed after fractionation by reversed-phase high performance liquid chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Proteins were identified by liquid chromatography-tandem mass spectrometry of proteolytic peptides. The α- and γ-gliadin were already detected at 3 dpa. The biosynthesis of high molecular mass glutenin Bx7 was slightly delayed (11 dpa). Most of the gluten proteins accumulated rapidly between 11 and 21 dpa, with a minor further increase up to 30 dpa. The expression pattern of gluten proteins in Triticum durum at the early stages of synthesis provides reference data sets for future applications in crop breeding and growth monitoring.
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Affiliation(s)
| | - Luigia Di Stasio
- Institute of Food Sciences, National Research Council (CNR) , 83100 Avellino, Italy
- Department of Agriculture, University of Naples "Federico II" , 80100 Portici, Italy
| | - Chiara D'Ambrosio
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council (CNR) , 80147 Naples, Italy
| | - Simona Arena
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council (CNR) , 80147 Naples, Italy
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council (CNR) , 80147 Naples, Italy
| | - Simona Corneti
- Department of Agricultural Sciences, University of Bologna , 40127 Bologna, Italy
| | - Aldo Ceriotti
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR) , 20133 Milan, Italy
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna , 40127 Bologna, Italy
| | - Rosa Anna Siciliano
- Institute of Food Sciences, National Research Council (CNR) , 83100 Avellino, Italy
| | - Gianluca Picariello
- Institute of Food Sciences, National Research Council (CNR) , 83100 Avellino, Italy
| | - Gianfranco Mamone
- Institute of Food Sciences, National Research Council (CNR) , 83100 Avellino, Italy
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179
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Guo W, Zheng B, Duan T, Fukatsu T, Chapman S, Ninomiya S. EasyPCC: Benchmark Datasets and Tools for High-Throughput Measurement of the Plant Canopy Coverage Ratio under Field Conditions. SENSORS 2017; 17:s17040798. [PMID: 28387746 PMCID: PMC5422159 DOI: 10.3390/s17040798] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/25/2017] [Accepted: 04/04/2017] [Indexed: 11/29/2022]
Abstract
Understanding interactions of genotype, environment, and management under field conditions is vital for selecting new cultivars and farming systems. Image analysis is considered a robust technique in high-throughput phenotyping with non-destructive sampling. However, analysis of digital field-derived images remains challenging because of the variety of light intensities, growth environments, and developmental stages. The plant canopy coverage (PCC) ratio is an important index of crop growth and development. Here, we present a tool, EasyPCC, for effective and accurate evaluation of the ground coverage ratio from a large number of images under variable field conditions. The core algorithm of EasyPCC is based on a pixel-based segmentation method using a decision-tree-based segmentation model (DTSM). EasyPCC was developed under the MATLAB® and R languages; thus, it could be implemented in high-performance computing to handle large numbers of images following just a single model training process. This study used an experimental set of images from a paddy field to demonstrate EasyPCC, and to show the accuracy improvement possible by adjusting key points (e.g., outlier deletion and model retraining). The accuracy (R2 = 0.99) of the calculated coverage ratio was validated against a corresponding benchmark dataset. The EasyPCC source code is released under GPL license with benchmark datasets of several different crop types for algorithm development and for evaluating ground coverage ratios.
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Affiliation(s)
- Wei Guo
- International Field Phenomics Laboratory, Institute for Sustainable Agro-ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Midori-cho, Nishitokyo, Tokyo 188-0002, Japan.
| | - Bangyou Zheng
- CSIRO Agriculture & Food, Queensland Biosciences Precinct, 306 Carmody Rd., St. Lucia, QLD 4067, Australia.
| | - Tao Duan
- CSIRO Agriculture & Food, Queensland Biosciences Precinct, 306 Carmody Rd., St. Lucia, QLD 4067, Australia.
- Institute College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Tokihiro Fukatsu
- Institute of Agricultural Machinery, National Agriculture and Food Research Organization, Kannondai 1-31-1, Tsukuba-shi, Ibaraki 305-0856, Japan.
| | - Scott Chapman
- CSIRO Agriculture & Food, Queensland Biosciences Precinct, 306 Carmody Rd., St. Lucia, QLD 4067, Australia.
- School of Agriculture and Food Sciences, Building 8117A NRSM, The University of Queensland, Gatton, QLD 4343, Australia.
| | - Seishi Ninomiya
- International Field Phenomics Laboratory, Institute for Sustainable Agro-ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Midori-cho, Nishitokyo, Tokyo 188-0002, Japan.
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180
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He S, Reif JC, Korzun V, Bothe R, Ebmeyer E, Jiang Y. Genome-wide mapping and prediction suggests presence of local epistasis in a vast elite winter wheat populations adapted to Central Europe. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:635-647. [PMID: 27995275 DOI: 10.1007/s00122-016-2840-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/01/2016] [Indexed: 05/05/2023]
Abstract
Genome-wide association mapping as well as marker- and haplotype-based genome-wide selection unraveled a complex genetic architecture of grain yield with absence of large effect QTL and presence of local epistatic effects. The genetic architecture of grain yield determines to a large extent the optimum design of genomic-assisted wheat breeding programs. The main goal of our study was to examine the potential and limitations to dissect the genetic architecture of grain yield in wheat using a large experimental data set. Our study was based on phenotypic information and genomic data of 13,901 SNPs of a diverse set of 3816 elite wheat lines adapted to Central Europe. We applied genome-wide association mapping based on experimental and simulated data sets and performed marker- and haplotype-based genomic prediction. Computer simulations revealed for our mapping population a high power to detect QTL, even if they individually explained only 2.5% of the genetic variation. Despite this, we found no stable marker-trait associations when validating in independent subsets. A two-dimensional scan for marker-marker interactions indicated presence of local epistasis which was further supported by improved prediction abilities when shifting from marker- to haplotype-based genome-wide prediction approaches. We observed that marker effects estimated using genome-wide prediction approaches strongly varied across years albeit resulting in high prediction abilities. Thus, our results suggested that the prediction accuracy of genomic selection in wheat is mainly driven by relatedness rather than by exploiting knowledge of the genetic architecture.
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Affiliation(s)
- Sang He
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany.
| | | | | | | | - Yong Jiang
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
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181
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QTL Analysis for Drought Tolerance in Wheat: Present Status and Future Possibilities. AGRONOMY-BASEL 2017. [DOI: 10.3390/agronomy7010005] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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182
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Wang J, Dun X, Shi J, Wang X, Liu G, Wang H. Genetic Dissection of Root Morphological Traits Related to Nitrogen Use Efficiency in Brassica napus L. under Two Contrasting Nitrogen Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:1709. [PMID: 29033971 PMCID: PMC5626847 DOI: 10.3389/fpls.2017.01709] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/19/2017] [Indexed: 05/21/2023]
Abstract
As the major determinant for nutrient uptake, root system architecture (RSA) has a massive impact on nitrogen use efficiency (NUE). However, little is known the molecular control of RSA as related to NUE in rapeseed. Here, a rapeseed recombinant inbred line population (BnaZNRIL) was used to investigate root morphology (RM, an important component for RSA) and NUE-related traits under high-nitrogen (HN) and low-nitrogen (LN) conditions by hydroponics. Data analysis suggested that RM-related traits, particularly root size had significantly phenotypic correlations with plant dry biomass and N uptake irrespective of N levels, but no or little correlation with N utilization efficiency (NUtE), providing the potential to identify QTLs with pleiotropy or specificity for RM- and NUE-related traits. A total of 129 QTLs (including 23 stable QTLs, which were repeatedly detected at least two environments or different N levels) were identified and 83 of them were integrated into 22 pleiotropic QTL clusters. Five RM-NUE, ten RM-specific and three NUE-specific QTL clusters with same directions of additive-effect implied two NUE-improving approaches (RM-based and N utilization-based directly) and provided valuable genomic regions for NUE improvement in rapeseed. Importantly, all of four major QTLs and most of stable QTLs (20 out of 23) detected here were related to RM traits under HN and/or LN levels, suggested that regulating RM to improve NUE would be more feasible than regulating N efficiency directly. These results provided the promising genomic regions for marker-assisted selection on RM-based NUE improvement in rapeseed.
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183
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Simko I, Jimenez-Berni JA, Sirault XRR. Phenomic Approaches and Tools for Phytopathologists. PHYTOPATHOLOGY 2017; 107:6-17. [PMID: 27618193 DOI: 10.1094/phyto-02-16-0082-rvw] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Plant phenomics approaches aim to measure traits such as growth, performance, and composition of plants using a suite of noninvasive technologies. The goal is to link phenotypic traits to the genetic information for particular genotypes, thus creating the bridge between the phenome and genome. Application of sensing technologies for detecting specific phenotypic reactions occurring during plant-pathogen interaction offers new opportunities for elucidating the physiological mechanisms that link pathogen infection and disease symptoms in the host, and also provides a faster approach in the selection of genetic material that is resistant to specific pathogens or strains. Appropriate phenomics methods and tools may also allow presymptomatic detection of disease-related changes in plants or to identify changes that are not visually apparent. This review focuses on the use of sensor-based phenomics tools in plant pathology such as those related to digital imaging, chlorophyll fluorescence imaging, spectral imaging, and thermal imaging. A brief introduction is provided for less used approaches like magnetic resonance, soft x-ray imaging, ultrasound, and detection of volatile compounds. We hope that this concise review will stimulate further development and use of tools for automatic, nondestructive, and high-throughput phenotyping of plant-pathogen interaction.
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Affiliation(s)
- Ivan Simko
- First author: U.S. Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St., Salinas, CA 93905; and second and third authors: CSIRO Agriculture and Food, High Resolution Plant Phenomics Centre, Australian Plant Phenomics Facility, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Jose A Jimenez-Berni
- First author: U.S. Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St., Salinas, CA 93905; and second and third authors: CSIRO Agriculture and Food, High Resolution Plant Phenomics Centre, Australian Plant Phenomics Facility, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Xavier R R Sirault
- First author: U.S. Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St., Salinas, CA 93905; and second and third authors: CSIRO Agriculture and Food, High Resolution Plant Phenomics Centre, Australian Plant Phenomics Facility, GPO Box 1600, Canberra, ACT 2601, Australia
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184
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Genetic Diversity and Association Mapping for Agromorphological and Grain Quality Traits of a Structured Collection of Durum Wheat Landraces Including subsp. durum, turgidum and diccocon. PLoS One 2016; 11:e0166577. [PMID: 27846306 PMCID: PMC5113043 DOI: 10.1371/journal.pone.0166577] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/31/2016] [Indexed: 12/25/2022] Open
Abstract
Association mapping was performed for 18 agromorphological and grain quality traits in a set of 183 Spanish landraces, including subspecies durum, turgidum and dicoccon, genotyped with 749 DArT (Diversity Array Technology) markers. Large genetic and phenotypic variability was detected, being the level of diversity among the chromosomes and genomes heterogeneous, and sometimes complementary, among subspecies. Overall, 356 were monomorphic in at least one subspecies, mainly in dicoccon, and some of them coincidental between subspecies, especially between turgidum and dicoccon. Several of those fixed markers were associated to plant responses to environmental stresses or linked to genes subjected to selection during tetraploid wheat domestication process. A total of 85 stable MTAs (marker–trait associations) have been identified for the agromorphological and quality parameters, some of them common among subspecies and others subspecies-specific. For all the traits, we have found MTAs explaining more than 10% of the phenotypic variation in any of the three subspecies. The number of MTAs on the B genome exceeded that on the A genome in subsp. durum, equalled in turgidum and was below in dicoccon. The validation of several adaptive and quality trait MTAs by combining the association mapping with an analysis of the signature of selection, identifying the putative gene function of the marker, or by coincidences with previous reports, showed that our approach was successful for the detection of MTAs and the high potential of the collection to identify marker–trait associations. Novel MTAs not previously reported, some of them subspecies specific, have been described and provide new information about the genetic control of complex traits.
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Feng Y, Lu Q, Zhai R, Zhang M, Xu Q, Yang Y, Wang S, Yuan X, Yu H, Wang Y, Wei X. Genome wide association mapping for grain shape traits in indica rice. PLANTA 2016; 244:819-30. [PMID: 27198135 PMCID: PMC5018019 DOI: 10.1007/s00425-016-2548-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/06/2016] [Indexed: 05/20/2023]
Abstract
Using genome-wide association mapping, 47 SNPs within 27 significant loci were identified for four grain shape traits, and 424 candidate genes were predicted from public database. Grain shape is a key determinant of grain yield and quality in rice (Oryza sativa L.). However, our knowledge of genes controlling rice grain shape remains limited. Genome-wide association mapping based on linkage disequilibrium (LD) has recently emerged as an effective approach for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, association mapping based on 5291 single nucleotide polymorphisms (SNPs) was conducted to identify significant loci associated with grain shape traits in a global collection of 469 diverse rice accessions. A total of 47 SNPs were located in 27 significant loci for four grain traits, and explained ~44.93-65.90 % of the phenotypic variation for each trait. In total, 424 candidate genes within a 200 kb extension region (±100 kb of each locus) of these loci were predicted. Of them, the cloned genes GS3 and qSW5 showed very strong effects on grain length and grain width in our study. Comparing with previously reported QTLs for grain shape traits, we found 11 novel loci, including 3, 3, 2 and 3 loci for grain length, grain width, grain length-width ratio and thousand grain weight, respectively. Validation of these new loci would be performed in the future studies. These results revealed that besides GS3 and qSW5, multiple novel loci and mechanisms were involved in determining rice grain shape. These findings provided valuable information for understanding of the genetic control of grain shape and molecular marker assistant selection (MAS) breeding in rice.
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Affiliation(s)
- Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Qing Lu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Rongrong Zhai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Mengchen Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Qun Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Shan Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Xiaoping Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Hanyong Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yiping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
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186
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Millet EJ, Welcker C, Kruijer W, Negro S, Coupel-Ledru A, Nicolas SD, Laborde J, Bauland C, Praud S, Ranc N, Presterl T, Tuberosa R, Bedo Z, Draye X, Usadel B, Charcosset A, Van Eeuwijk F, Tardieu F. Genome-Wide Analysis of Yield in Europe: Allelic Effects Vary with Drought and Heat Scenarios. PLANT PHYSIOLOGY 2016; 172:749-764. [PMID: 27436830 PMCID: PMC5047082 DOI: 10.1104/pp.16.00621] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/12/2016] [Indexed: 05/18/2023]
Abstract
Assessing the genetic variability of plant performance under heat and drought scenarios can contribute to reduce the negative effects of climate change. We propose here an approach that consisted of (1) clustering time courses of environmental variables simulated by a crop model in current (35 years × 55 sites) and future conditions into six scenarios of temperature and water deficit as experienced by maize (Zea mays L.) plants; (2) performing 29 field experiments in contrasting conditions across Europe with 244 maize hybrids; (3) assigning individual experiments to scenarios based on environmental conditions as measured in each field experiment; frequencies of temperature scenarios in our experiments corresponded to future heat scenarios (+5°C); (4) analyzing the genetic variation of plant performance for each environmental scenario. Forty-eight quantitative trait loci (QTLs) of yield were identified by association genetics using a multi-environment multi-locus model. Eight and twelve QTLs were associated to tolerances to heat and drought stresses because they were specific to hot and dry scenarios, respectively, with low or even negative allelic effects in favorable scenarios. Twenty-four QTLs improved yield in favorable conditions but showed nonsignificant effects under stress; they were therefore associated with higher sensitivity. Our approach showed a pattern of QTL effects expressed as functions of environmental variables and scenarios, allowing us to suggest hypotheses for mechanisms and candidate genes underlying each QTL. It can be used for assessing the performance of genotypes and the contribution of genomic regions under current and future stress situations and to accelerate breeding for drought-prone environments.
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Affiliation(s)
- Emilie J Millet
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Claude Welcker
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Willem Kruijer
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Sandra Negro
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Aude Coupel-Ledru
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Stéphane D Nicolas
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Jacques Laborde
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Cyril Bauland
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Sebastien Praud
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Nicolas Ranc
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Thomas Presterl
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Roberto Tuberosa
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Zoltan Bedo
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Xavier Draye
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Björn Usadel
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Alain Charcosset
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - Fred Van Eeuwijk
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
| | - François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France (E.J.M., C.W., A.C.-L., F.T.);Biometris - Applied Statistics, Department of Plant Science, Wageningen University, 6700AA Wageningen, Netherlands (W.K., F.V.E.);INRA, UMR 0320 / UMR 8120 Génétique Quantitative et Evolution, 91190 Gif-sur-Yvette, France (S.N, S.D.N., C.B., A.C.); INRA, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, 40390 Saint-Martin-De-Hinx, France (J.L.); Centre de Recherche de Chappes, Biogemma, 63720 Chappes, France (S.P.); Syngenta France SAS, 12, Chemin de l'Hobit, BP 27, 31790, Saint-Sauveur, France (N.R.); KWS Saat SE, 37555 Einbeck, Germany (T.P.); Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy (R.T.);MTA ATK/ AI CAR HAS, Martonvasar 2462, Hungary (Z.B.);UCL ELIA, 1348 Louvain-la-Neuve, Belgium (X.D.); andInstitute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany (B.U.)
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Mengistu DK, Kidane YG, Catellani M, Frascaroli E, Fadda C, Pè ME, Dell'Acqua M. High-density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1800-12. [PMID: 26853077 PMCID: PMC5067613 DOI: 10.1111/pbi.12538] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/11/2015] [Accepted: 01/06/2016] [Indexed: 05/18/2023]
Abstract
Durum wheat (Triticum turgidum subsp. durum) is a key crop worldwide, and yet, its improvement and adaptation to emerging environmental threats is made difficult by the limited amount of allelic variation included in its elite pool. New allelic diversity may provide novel loci to international crop breeding through quantitative trait loci (QTL) mapping in unexplored material. Here, we report the extensive molecular and phenotypic characterization of hundreds of Ethiopian durum wheat landraces and several Ethiopian improved lines. We test 81 587 markers scoring 30 155 single nucleotide polymorphisms and use them to survey the diversity, structure, and genome-specific variation in the panel. We show the uniqueness of Ethiopian germplasm using a siding collection of Mediterranean durum wheat accessions. We phenotype the Ethiopian panel for ten agronomic traits in two highly diversified Ethiopian environments for two consecutive years and use this information to conduct a genome-wide association study. We identify several loci underpinning agronomic traits of interest, both confirming loci already reported and describing new promising genomic regions. These loci may be efficiently targeted with molecular markers already available to conduct marker-assisted selection in Ethiopian and international wheat. We show that Ethiopian durum wheat represents an important and mostly unexplored source of durum wheat diversity. The panel analysed in this study allows the accumulation of QTL mapping experiments, providing the initial step for a quantitative, methodical exploitation of untapped diversity in producing a better wheat.
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Affiliation(s)
- Dejene Kassahun Mengistu
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- Department of Dryland Crop and Horticultural Sciences, Mekelle University, Mekelle, Ethiopia
| | - Yosef Gebrehawaryat Kidane
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- Sirinka Agricultural Research Center, Sirinka, Woldia, Ethiopia
| | | | | | - Carlo Fadda
- Bioversity International, C/O International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
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188
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Duan T, Chapman SC, Holland E, Rebetzke GJ, Guo Y, Zheng B. Dynamic quantification of canopy structure to characterize early plant vigour in wheat genotypes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4523-34. [PMID: 27312669 PMCID: PMC4973728 DOI: 10.1093/jxb/erw227] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Early vigour is an important physiological trait to improve establishment, water-use efficiency, and grain yield for wheat. Phenotyping large numbers of lines is challenging due to the fast growth and development of wheat seedlings. Here we developed a new photo-based workflow to monitor dynamically the growth and development of the wheat canopy of two wheat lines with a contrasting early vigour trait. Multiview images were taken using a 'vegetation stress' camera at 2 d intervals from emergence to the sixth leaf stage. Point clouds were extracted using the Multi-View Stereo and Structure From Motion (MVS-SFM) algorithm, and segmented into individual organs using the Octree method, with leaf midribs fitted using local polynomial function. Finally, phenotypic parameters were calculated from the reconstructed point cloud including: tiller and leaf number, plant height, Haun index, phyllochron, leaf length, angle, and leaf elongation rate. There was good agreement between the observed and estimated leaf length (RMSE=8.6mm, R (2)=0.98, n=322) across both lines. Significant contrasts of phenotyping parameters were observed between the two lines and were consistent with manual observations. The early vigour line had fewer tillers (2.4±0.6) and larger leaves (308.0±38.4mm and 17.1±2.7mm for leaf length and width, respectively). While the phyllochron of both lines was quite similar, the non-vigorous line had a greater Haun index (more leaves on the main stem) on any date, as the vigorous line had slower development of its first two leaves. The workflow presented in this study provides an efficient method to phenotype individual plants using a low-cost camera (an RGB camera is also suitable) and could be applied in phenotyping for applications in both simulation modelling and breeding. The rapidity and accuracy of this novel method can characterize the results of specific selection criteria (e.g. width of leaf three, number of tillers, rate of leaf appearance) that have been or can now be utilized to breed for early leaf growth and tillering in wheat.
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Affiliation(s)
- T Duan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China CSIRO Agriculture, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - S C Chapman
- CSIRO Agriculture, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - E Holland
- CSIRO Agriculture, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - G J Rebetzke
- CSIRO Agriculture, PO Box 1600, Canberra, ACT 2601, Australia
| | - Y Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - B Zheng
- CSIRO Agriculture, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
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189
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Vergara-Díaz O, Zaman-Allah MA, Masuka B, Hornero A, Zarco-Tejada P, Prasanna BM, Cairns JE, Araus JL. A Novel Remote Sensing Approach for Prediction of Maize Yield Under Different Conditions of Nitrogen Fertilization. FRONTIERS IN PLANT SCIENCE 2016; 7:666. [PMID: 27242867 PMCID: PMC4870241 DOI: 10.3389/fpls.2016.00666] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 05/01/2016] [Indexed: 05/19/2023]
Abstract
Maize crop production is constrained worldwide by nitrogen (N) availability and particularly in poor tropical and subtropical soils. The development of affordable high-throughput crop monitoring and phenotyping techniques is key to improving maize cultivation under low-N fertilization. In this study several vegetation indices (VIs) derived from Red-Green-Blue (RGB) digital images at the leaf and canopy levels are proposed as low-cost tools for plant breeding and fertilization management. They were compared with the performance of the normalized difference vegetation index (NDVI) measured at ground level and from an aerial platform, as well as with leaf chlorophyll content (LCC) and other leaf composition and structural parameters at flowering stage. A set of 10 hybrids grown under five different nitrogen regimes and adequate water conditions were tested at the CIMMYT station of Harare (Zimbabwe). Grain yield and leaf N concentration across N fertilization levels were strongly predicted by most of these RGB indices (with R (2)~ 0.7), outperforming the prediction power of the NDVI and LCC. RGB indices also outperformed the NDVI when assessing genotypic differences in grain yield and leaf N concentration within a given level of N fertilization. The best predictor of leaf N concentration across the five N regimes was LCC but its performance within N treatments was inefficient. The leaf traits evaluated also seemed inefficient as phenotyping parameters. It is concluded that the adoption of RGB-based phenotyping techniques may significantly contribute to the progress of plant breeding and the appropriate management of fertilization.
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Affiliation(s)
- Omar Vergara-Díaz
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of BarcelonaBarcelona, Spain
| | - Mainassara A. Zaman-Allah
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional OfficeHarare, Zimbabwe
| | - Benhildah Masuka
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional OfficeHarare, Zimbabwe
| | - Alberto Hornero
- Laboratory for Research Methods in Quantitative Remote Sensing, QuantaLab, Institute for Sustainable Agriculture, National Research CouncilCordoba, Spain
| | - Pablo Zarco-Tejada
- Laboratory for Research Methods in Quantitative Remote Sensing, QuantaLab, Institute for Sustainable Agriculture, National Research CouncilCordoba, Spain
| | - Boddupalli M. Prasanna
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional OfficeHarare, Zimbabwe
| | - Jill E. Cairns
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional OfficeHarare, Zimbabwe
| | - José L. Araus
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of BarcelonaBarcelona, Spain
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190
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Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat. PLoS One 2016; 11:e0154609. [PMID: 27171472 PMCID: PMC4865223 DOI: 10.1371/journal.pone.0154609] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/15/2016] [Indexed: 11/19/2022] Open
Abstract
Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays.
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191
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Shirdelmoghanloo H, Taylor JD, Lohraseb I, Rabie H, Brien C, Timmins A, Martin P, Mather DE, Emebiri L, Collins NC. A QTL on the short arm of wheat (Triticum aestivum L.) chromosome 3B affects the stability of grain weight in plants exposed to a brief heat shock early in grain filling. BMC PLANT BIOLOGY 2016; 16:100. [PMID: 27101979 PMCID: PMC4841048 DOI: 10.1186/s12870-016-0784-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/14/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Molecular markers and knowledge of traits associated with heat tolerance are likely to provide breeders with a more efficient means of selecting wheat varieties able to maintain grain size after heat waves during early grain filling. RESULTS A population of 144 doubled haploids derived from a cross between the Australian wheat varieties Drysdale and Waagan was mapped using the wheat Illumina iSelect 9,000 feature single nucleotide polymorphism marker array and used to detect quantitative trait loci for heat tolerance of final single grain weight and related traits. Plants were subjected to a 3 d heat treatment (37 °C/27 °C day/night) in a growth chamber at 10 d after anthesis and trait responses calculated by comparison to untreated control plants. A locus for single grain weight stability was detected on the short arm of chromosome 3B in both winter- and autumn-sown experiments, determining up to 2.5 mg difference in heat-induced single grain weight loss. In one of the experiments, a locus with a weaker effect on grain weight stability was detected on chromosome 6B. Among the traits measured, the rate of flag leaf chlorophyll loss over the course of the heat treatment and reduction in shoot weight due to heat were indicators of loci with significant grain weight tolerance effects, with alleles for grain weight stability also conferring stability of chlorophyll ('stay-green') and shoot weight. Chlorophyll loss during the treatment, requiring only two non-destructive readings to be taken, directly before and after a heat event, may prove convenient for identifying heat tolerant germplasm. These results were consistent with grain filling being limited by assimilate supply from the heat-damaged photosynthetic apparatus, or alternatively, accelerated maturation in the grains that was correlated with leaf senescence responses merely due to common genetic control of senescence responses in the two organs. There was no evidence for a role of mobilized stem reserves (water soluble carbohydrates) in determining grain weight responses. CONCLUSIONS Molecular markers for the 3B or 6B loci, or the facile measurement of chlorophyll loss over the heat treatment, could be used to assist identification of heat tolerant genotypes for breeding.
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Affiliation(s)
- Hamid Shirdelmoghanloo
- />The Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064 Australia
| | - Julian D. Taylor
- />School of Agriculture Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064 Australia
| | - Iman Lohraseb
- />The Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064 Australia
| | - Huwaida Rabie
- />Phenomics and Bioinformatics Research Centre, University of South Australia, GPO Box 2471, Adelaide, SA 5001 Australia
- />Present address: Mathematics Department, Bethlehem University, PO Box 11407, Rue des Freres, Bethlehem, 92248 Jerusalem Palestine
| | - Chris Brien
- />Phenomics and Bioinformatics Research Centre, University of South Australia, GPO Box 2471, Adelaide, SA 5001 Australia
- />The Plant Accelerator, The University of Adelaide, PMB 1, Glen Osmond, SA 5064 Australia
| | - Andy Timmins
- />The Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064 Australia
| | - Peter Martin
- />EH Graham Centre for Agricultural Innovation, Pine Gully Road, Wagga Wagga, NSW 2650 Australia
| | - Diane E. Mather
- />School of Agriculture Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064 Australia
| | - Livinus Emebiri
- />EH Graham Centre for Agricultural Innovation, Pine Gully Road, Wagga Wagga, NSW 2650 Australia
| | - Nicholas C. Collins
- />The Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064 Australia
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192
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Merchuk-Ovnat L, Barak V, Fahima T, Ordon F, Lidzbarsky GA, Krugman T, Saranga Y. Ancestral QTL Alleles from Wild Emmer Wheat Improve Drought Resistance and Productivity in Modern Wheat Cultivars. FRONTIERS IN PLANT SCIENCE 2016; 7:452. [PMID: 27148287 PMCID: PMC4832586 DOI: 10.3389/fpls.2016.00452] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/22/2016] [Indexed: 05/21/2023]
Abstract
Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs) from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum) and bread (T. aestivum) wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4) were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690-710 mm) and water-limited (290-320 mm) conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS), and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS). In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass-specifically under drought (7AS QTL in cv. Bar Nir background), under both treatments (2BS QTL), and a greater stability across treatments (1BL QTL). The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance.
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Affiliation(s)
- Lianne Merchuk-Ovnat
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Vered Barak
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Tzion Fahima
- Institute of Evolution and Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Institute for Resistance Research and Stress ToleranceQuedlinburg, Germany
| | - Gabriel A. Lidzbarsky
- Institute of Evolution and Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Tamar Krugman
- Institute of Evolution and Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Yehoshua Saranga
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
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193
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Cao L, Hayashi K, Tokui M, Mori M, Miura H, Onishi K. Detection of QTLs for traits associated with pre-harvest sprouting resistance in bread wheat (Triticum aestivum L.). BREEDING SCIENCE 2016; 66:260-70. [PMID: 27162497 PMCID: PMC4785003 DOI: 10.1270/jsbbs.66.260] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/26/2015] [Indexed: 05/20/2023]
Abstract
Pre-harvest sprouting (PHS) is one of the serious problems for wheat production, especially in rainy regions. Although seed dormancy is the most critical trait for PHS resistance, the control of heading time should also be considered to prevent seed maturation during unfavorable conditions. In addition, awning is known to enhance water absorption by the spike, causing PHS. In this study, we conducted QTL analysis for three PHS resistant related traits, seed dormancy, heading time and awn length, by using recombinant inbred lines from 'Zenkouji-komugi' (high PHS resistance) × 'Chinese Spring' (weak PHS resistance). QTLs for seed dormancy were detected on chromosomes 1B (QDor-1B) and 4A (QDor-4A), in addition to a QTL on chromosome 3A, which was recently cloned as TaMFT-3A. In addition, the accumulation of the QTLs and their epistatic interactions contributed significantly to a higher level of dormancy. QDor-4A is co-located with the Hooded locus for awn development. Furthermore, an effective QTL, which confers early heading by the Zenkouji-komugi allele, was detected on the short arm of chromosome 7B, where the Vrn-B3 locus is located. Understanding the genetic architecture of traits associated with PHS resistance will facilitate the marker assisted selection to breed new varieties with higher PHS resistance.
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194
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Zhou W, Wu S, Ding M, Li J, Shi Z, Wei W, Guo J, Zhang H, Jiang Y, Rong J. Mapping of Ppd-B1, a Major Candidate Gene for Late Heading on Wild Emmer Chromosome Arm 2BS and Assessment of Its Interactions with Early Heading QTLs on 3AL. PLoS One 2016; 11:e0147377. [PMID: 26848576 PMCID: PMC4743932 DOI: 10.1371/journal.pone.0147377] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 01/04/2016] [Indexed: 11/18/2022] Open
Abstract
Wheat heading date is an important agronomic trait determining maturation time and yield. A set of common wheat (Triticum aestivum var. Chinese Spring; CS)-wild emmer (T. turgidum L. subsp. dicoccoides (TDIC)) chromosome arm substitution lines (CASLs) was used to identify and allocate QTLs conferring late or early spike emergence by examining heading date. Genetic loci accelerating heading were found on TDIC chromosome arms 3AL and 7BS, while loci delaying heading were located on 4AL and 2BS. To map QTLs conferring late heading on 2BS, F2 populations derived from two cross combinations of CASL2BS × CS and CASL3AL × CASL2BS were developed and each planted at two times, constituting four F2 mapping populations. Heading date varied continuously among individuals of these four populations, suggesting quantitative characteristics. A genetic map of 2BS, consisting of 23 SSR and one single-stranded conformation polymorphism (SSCP) marker(s), was constructed using these F2 populations. This map spanned a genetic length of 53.2 cM with average marker density of 2.3 cM. The photoperiod-sensitivity gene Ppd-B1 was mapped to chromosome arm 2BS as a SSCP molecular marker, and was validated as tightly linked to a major QTL governing late heading of CASL2BS in all mapping populations. A significant dominance by additive effect of Ppd-B1 with the LUX gene located on 3AL was also detected. CS had more copies of Ppd-B1 than CASL2BS, implying that increased copy number could elevate the expression of Ppd-1 in CS, also increasing expression of LUX and FT genes and causing CS to have an earlier heading date than CASL2BS in long days.
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Affiliation(s)
- Wei Zhou
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China
| | - Shasha Wu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China
| | - Jingjuan Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China
| | - Zhaobin Shi
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China
| | - Wei Wei
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China
| | - Jialian Guo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China
| | - Hua Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China
- * E-mail:
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195
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Thapa R, Brown-Guedira G, Ohm HW, Mateos-Hernandez M, Wise KA, Goodwin SB. Determining the order of resistance genes against Stagonospora nodorum blotch, Fusarium head blight and stem rust on wheat chromosome arm 3BS. BMC Res Notes 2016; 9:58. [PMID: 26833226 PMCID: PMC4736272 DOI: 10.1186/s13104-016-1859-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/14/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Stagonospora nodorum blotch (SNB), Fusarium head blight (FHB) and stem rust (SR), caused by the fungi Parastagonospora (synonym Stagonospora) nodorum, Fusarium graminearum and Puccinia graminis, respectively, significantly reduce yield and quality of wheat. Three resistance factors, QSng.sfr-3BS, Fhb1 and Sr2, conferring resistance, respectively, to SNB, FHB and SR, each from a unique donor line, were mapped previously to the short arm of wheat chromosome 3B. Based on published reports, our hypothesis was that Sr2 is the most distal, Fhb1 the most proximal and QSng.sfr-3BS is in between Sr2 and Fhb1 on wheat chromosome arm 3BS. RESULTS To test this hypothesis, 1600 F2 plants from crosses between parental lines Arina, Alsen and Ocoroni86, conferring resistance genes QSng.sfr-3BS, Fhb1 and Sr2, respectively, were genotyped and phenotyped for SNB along with the parental lines. Five closely linked single-nucleotide polymorphism (SNP) markers were used to make the genetic map and determine the gene order. CONCLUSIONS The results indicate that QSng.sfr-3BS is located between the other two resistance genes on chromosome 3BS. Knowing the positional order of these resistance genes will aid in developing a wheat line with all three genes in coupling, which has the potential to provide broad-spectrum resistance preventing grain yield and quality losses.
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Affiliation(s)
- Rima Thapa
- Department of Agronomy, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA.
| | - Gina Brown-Guedira
- USDA-ARS Plant Science Research, North Carolina State University, Raleigh, NC, 27695-7620, USA.
| | - Herbert W Ohm
- Department of Agronomy, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA.
| | | | - Kiersten A Wise
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA.
| | - Stephen B Goodwin
- USDA-ARS, Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907-2054, USA.
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196
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Virlet N, Sabermanesh K, Sadeghi-Tehran P, Hawkesford MJ. Field Scanalyzer: An automated robotic field phenotyping platform for detailed crop monitoring. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 44:143-153. [PMID: 32480553 DOI: 10.1071/fp16163] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/02/2016] [Indexed: 05/20/2023]
Abstract
Current approaches to field phenotyping are laborious or permit the use of only a few sensors at a time. In an effort to overcome this, a fully automated robotic field phenotyping platform with a dedicated sensor array that may be accurately positioned in three dimensions and mounted on fixed rails has been established, to facilitate continual and high-throughput monitoring of crop performance. Employed sensors comprise of high-resolution visible, chlorophyll fluorescence and thermal infrared cameras, two hyperspectral imagers and dual 3D laser scanners. The sensor array facilitates specific growth measurements and identification of key growth stages with dense temporal and spectral resolution. Together, this platform produces a detailed description of canopy development across the crops entire lifecycle, with a high-degree of accuracy and reproducibility.
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Affiliation(s)
- Nicolas Virlet
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Kasra Sabermanesh
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Pouria Sadeghi-Tehran
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Malcolm J Hawkesford
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
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197
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Milner SG, Maccaferri M, Huang BE, Mantovani P, Massi A, Frascaroli E, Tuberosa R, Salvi S. A multiparental cross population for mapping QTL for agronomic traits in durum wheat (Triticum turgidum ssp. durum). PLANT BIOTECHNOLOGY JOURNAL 2016; 14:735-48. [PMID: 26132599 DOI: 10.1111/pbi.12424] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 04/08/2015] [Accepted: 04/29/2015] [Indexed: 05/02/2023]
Abstract
Multiparental cross designs for mapping quantitative trait loci (QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line (RIL) population in durum wheat (Triticum turgidum ssp. durum) obtained by crossing four elite cultivars. A linkage map spanning 2664 cM and including 7594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs. QTL analysis was carried out by both interval mapping on founder haplotype probabilities and SNP bi-allelic tests for heading date and maturity date, plant height and grain yield from four field experiments. Sixteen QTL were identified across environments and detection methods, including two yield QTL on chromosomes 2BL and 7AS, with the former mapped independently from the photoperiod response gene Ppd-B1, while the latter overlapped with the vernalization locus VRN-A3. Additionally, 21 QTL with environment-specific effects were found. Our results indicated a prevalence of environment-specific QTL with relatively small effect on the control of grain yield. For all traits, functionally different QTL alleles in terms of direction and size of genetic effect were distributed among parents. We showed that QTL results based on founder haplotypes closely matched functional alleles at known heading date loci. Despite the four founders, only 2.1 different functional haplotypes were estimated per QTL, on average. This durum wheat population provides a mapping resource for detailed genetic dissection of agronomic traits in an elite background typical of breeding programmes.
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Affiliation(s)
- Sara Giulia Milner
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Bevan Emma Huang
- Digital Productivity Flagship and Agriculture Flagship, CSIRO, St Lucia, Qld, Australia
| | - Paola Mantovani
- Società Produttori Sementi Bologna, Argelato, Bologna, Italy
| | - Andrea Massi
- Società Produttori Sementi Bologna, Argelato, Bologna, Italy
| | | | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
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198
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Duan T, Zheng B, Guo W, Ninomiya S, Guo Y, Chapman SC. Comparison of ground cover estimates from experiment plots in cotton, sorghum and sugarcane based on images and ortho-mosaics captured by UAV. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 44:169-183. [PMID: 32480555 DOI: 10.1071/fp16123] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 10/06/2016] [Indexed: 05/21/2023]
Abstract
Ground cover is an important physiological trait affecting crop radiation capture, water-use efficiency and grain yield. It is challenging to efficiently measure ground cover with reasonable precision for large numbers of plots, especially in tall crop species. Here we combined two image-based methods to estimate plot-level ground cover for three species, from either an ortho-mosaic or undistorted (i.e. corrected for lens and camera effects) images captured by cameras using a low-altitude unmanned aerial vehicle (UAV). Reconstructed point clouds and ortho-mosaics for the whole field were created and a customised image processing workflow was developed to (1) segment the 'whole-field' datasets into individual plots, and (2) 'reverse-calculate' each plot from each undistorted image. Ground cover for individual plots was calculated by an efficient vegetation segmentation algorithm. For 79% of plots, estimated ground cover was greater from the ortho-mosaic than from images, particularly when plants were small, or when older/taller in large plots. While there was a good agreement between the ground cover estimates from ortho-mosaic and images when the target plot was positioned at a near-nadir view near the centre of image (cotton: R2=0.97, sorghum: R2=0.98, sugarcane: R2=0.84), ortho-mosaic estimates were 5% greater than estimates from these near-nadir images. Because each plot appeared in multiple images, there were multiple estimates of the ground cover, some of which should be excluded, e.g. when the plot is near edge within an image. Considering only the images with near-nadir view, the reverse calculation provides a more precise estimate of ground cover compared with the ortho-mosaic. The methodology is suitable for high throughput phenotyping for applications in agronomy, physiology and breeding for different crop species and can be extended to provide pixel-level data from other types of cameras including thermal and multi-spectral models.
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Affiliation(s)
- Tao Duan
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, Qld 4067, Australia
| | - Bangyou Zheng
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, Qld 4067, Australia
| | - Wei Guo
- Institute for Sustainable Agro-ecosystem Services, The University of Tokyo, Tokyo 188-0002, Japan
| | - Seishi Ninomiya
- Institute for Sustainable Agro-ecosystem Services, The University of Tokyo, Tokyo 188-0002, Japan
| | - Yan Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Scott C Chapman
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, Qld 4067, Australia
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199
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Zhao W, Wang X, Wang H, Tian J, Li B, Chen L, Chao H, Long Y, Xiang J, Gan J, Liang W, Li M. Genome-Wide Identification of QTL for Seed Yield and Yield-Related Traits and Construction of a High-Density Consensus Map for QTL Comparison in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:17. [PMID: 26858737 PMCID: PMC4729939 DOI: 10.3389/fpls.2016.00017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/08/2016] [Indexed: 05/18/2023]
Abstract
Seed yield (SY) is the most important trait in rapeseed, is determined by multiple seed yield-related traits (SYRTs) and is also easily subject to environmental influence. Many quantitative trait loci (QTLs) for SY and SYRTs have been reported in Brassica napus; however, no studies have focused on seven agronomic traits simultaneously affecting SY. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs using a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that were expressed stably in winter cultivation area for 3 years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq.A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5, and uq.C6-6 could also affect more than two SYRTs. According to the constructed high-density consensus map and QTL comparison from literatures, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologous genes were observed, including five each gene for SY and thousand seed weight, and one gene each for biomass yield, branch height, and plant height. The genomic information of these QTLs will be valuable in hybrid cultivar breeding and in analyzing QTL expression in different environments.
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Affiliation(s)
- Weiguo Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Xiaodong Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- *Correspondence: Hao Wang
| | - Jianhua Tian
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Baojun Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Li Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Jianping Gan
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Wusheng Liang
- Department of Applied Biological Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- Maoteng Li
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200
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Prince SJ, Beena R, Gomez SM, Senthivel S, Babu RC. Mapping Consistent Rice (Oryza sativa L.) Yield QTLs under Drought Stress in Target Rainfed Environments. RICE (NEW YORK, N.Y.) 2015; 8:53. [PMID: 26206756 PMCID: PMC4513014 DOI: 10.1186/s12284-015-0053-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 05/22/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND Drought stress is a major limitation to rainfed rice production and yield stability. Identifying yield-associated quantitative trait loci (QTLs) that are consistent under drought stress predominant in target production environments, as well as across different genetic backgrounds, will help to develop high-yielding rice cultivars suitable for water-limited environments through marker-assisted breeding (MAB). Considerable progress has been made in mapping QTLs for drought resistance traits in rice; however, few have been successfully used in MAB. RESULTS Recombinant inbred lines of IR20 × Nootripathu, two indica cultivars adapted to rainfed target populations of environments (TPEs), were evaluated in one and two seasons under managed stress and in a rainfed target drought stress environment, respectively. In the managed stress environment, the severity of the stress meant that measurements could be made only on secondary traits and biomass. In the target environment, the lines experienced varying timings, durations, and intensities of drought stress. The rice recombinant inbred lines exhibited significant genotypic variation for physio-morphological, phenological, and plant production traits under drought. Nine and 24 QTLs for physio-morphological and plant production traits were identified in managed and natural drought stress conditions in the TPEs, respectively. Yield QTLs that were consistent in the target environment over seasons were identified on chromosomes 1, 4, and 6, which could stabilize the productivity in high-yielding rice lines in a water-limited rainfed ecosystem. These yield QTLs also govern highly heritable key secondary traits, such as leaf drying, canopy temperature, panicle harvest index and harvest index. CONCLUSION Three QTL regions on chromosome 1 (RM8085), chromosome 4 (I12S), and chromosome 6 (RM6836) harbor significant additive QTLs for various physiological and yield traits under drought stress. The similar chromosomal region on 4 and 6 were found to harbor QTLs for canopy temperature and leaf drying under drought stress conditions. Thus, the identified large effect yield QTLs could be introgressed to develop rice lines with stable yields under varying natural drought stress predominant in TPEs.
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Affiliation(s)
- Silvas J Prince
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641 003 India
| | - R Beena
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641 003 India
| | - S Michael Gomez
- International Center for Tropical Agriculture (CIAT), Colombia, 6713 Colombia
| | - S Senthivel
- Agricultural Research Station, Tamil Nadu Agricultural University (TNAU), Paramakudi, 623707 India
| | - R Chandra Babu
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641 003 India
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