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Farooqi MQU, Moody D, Bai G, Bernardo A, St. Amand P, Diggle AJ, Rengel Z. Genetic characterization of root architectural traits in barley ( Hordeum vulgare L.) using SNP markers. FRONTIERS IN PLANT SCIENCE 2023; 14:1265925. [PMID: 37860255 PMCID: PMC10582755 DOI: 10.3389/fpls.2023.1265925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/05/2023] [Indexed: 10/21/2023]
Abstract
Increasing attention is paid to providing new tools to breeders for targeted breeding for specific root traits that are beneficial in low-fertility, drying soils; however, such information is not available for barley (Hordeum vulgare L.). A panel of 191 barley accessions (originating from Australia, Europe, and Africa) was phenotyped for 26 root and shoot traits using the semi-hydroponic system and genotyped using 21 062 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). The population structure analysis of the barley panel identified six distinct groups. We detected 1199 significant (P<0.001) marker-trait associations (MTAs) with r2 values up to 0.41. The strongest MTAs were found for root diameter in the top 20 cm and the longest root length. Based on the physical locations of these MTAs in the barley reference genome, we identified 37 putative QTLs for the root traits, and three QTLs for shoot traits, with nine QTLs located in the same physical regions. The genomic region 640-653 Mb on chromosome 7H was significant for five root length-related traits, where 440 annotated genes were located. The putative QTLs for various root traits identified in this study may be useful for genetic improvement regarding the adaptation of new barley cultivars to suboptimal environments and abiotic stresses.
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Affiliation(s)
- M. Q. U. Farooqi
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | | | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, United States
| | - Amy Bernardo
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, United States
| | - Paul St. Amand
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, United States
| | - Art J. Diggle
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Zed Rengel
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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Thingnam SS, Lourembam DS, Tongbram PS, Lokya V, Tiwari S, Khan MK, Pandey A, Hamurcu M, Thangjam R. A Perspective Review on Understanding Drought Stress Tolerance in Wild Banana Genetic Resources of Northeast India. Genes (Basel) 2023; 14:genes14020370. [PMID: 36833297 PMCID: PMC9957078 DOI: 10.3390/genes14020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
The enormous perennial monocotyledonous herb banana (Musa spp.), which includes dessert and cooking varieties, is found in more than 120 countries and is a member of the order Zingiberales and family Musaceae. The production of bananas requires a certain amount of precipitation throughout the year, and its scarcity reduces productivity in rain-fed banana-growing areas due to drought stress. To increase the tolerance of banana crops to drought stress, it is necessary to explore crop wild relatives (CWRs) of banana. Although molecular genetic pathways involved in drought stress tolerance of cultivated banana have been uncovered and understood with the introduction of high-throughput DNA sequencing technology, next-generation sequencing (NGS) techniques, and numerous "omics" tools, unfortunately, such approaches have not been thoroughly implemented to utilize the huge potential of wild genetic resources of banana. In India, the northeastern region has been reported to have the highest diversity and distribution of Musaceae, with more than 30 taxa, 19 of which are unique to the area, accounting for around 81% of all wild species. As a result, the area is regarded as one of the main locations of origin for the Musaceae family. The understanding of the response of the banana genotypes of northeastern India belonging to different genome groups to water deficit stress at the molecular level will be useful for developing and improving drought tolerance in commercial banana cultivars not only in India but also worldwide. Hence, in the present review, we discuss the studies conducted to observe the effect of drought stress on different banana species. Moreover, the article highlights the tools and techniques that have been used or that can be used for exploring and understanding the molecular basis of differentially regulated genes and their networks in different drought stress-tolerant banana genotypes of northeast India, especially wild types, for unraveling their potential novel traits and genes.
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Affiliation(s)
| | | | - Punshi Singh Tongbram
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
| | - Vadthya Lokya
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Robert Thangjam
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
- Department of Life Sciences, School of Life Sciences, Manipur University, Imphal 795003, India
- Correspondence:
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Kashyap A, Garg P, Tanwar K, Sharma J, Gupta NC, Ha PTT, Bhattacharya RC, Mason AS, Rao M. Strategies for utilization of crop wild relatives in plant breeding programs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4151-4167. [PMID: 36136128 DOI: 10.1007/s00122-022-04220-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Crop wild relatives (CWRs) are weedy and wild relatives of the domesticated and cultivated crops, which usually occur and are maintained in natural forms in their centres of origin. These include the ancestors or progenitors of all cultivated species and comprise rich sources of diversity for many important traits useful in plant breeding. CWRs can play an important role in broadening genetic bases and introgression of economical traits into crops, but their direct use by breeders for varietal improvement program is usually not advantageous due to the presence of crossing or chromosome introgression barriers with cultivated species as well as their high frequencies of agronomically undesirable alleles. Linkage drag may subsequently result in unfavourable traits in the subsequent progeny when segments of the genome linked with quantitative trait loci (QTL), or a phenotype, are introgressed from wild germplasm. Here, we first present an overview in regards to the contribution that wild species have made to improve biotic, abiotic stress tolerances and yield-related traits in crop varieties, and secondly summarise the various challenges which are experienced in interspecific hybridization along with their probable solutions. We subsequently suggest techniques for readily harnessing these wild relatives for fast and effective introgression of exotic alleles in pre-breeding research programs.
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Affiliation(s)
- Anamika Kashyap
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Pooja Garg
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Kunal Tanwar
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Jyoti Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Navin C Gupta
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Pham Thi Thu Ha
- Genomic Research Institute & Seed, Ton Duc Thang University, Ho Chi Minh, Vietnam
| | - R C Bhattacharya
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | | | - Mahesh Rao
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India.
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Natural selection under conventional and organic cropping systems affect root architecture in spring barley. Sci Rep 2022; 12:20095. [PMID: 36418861 PMCID: PMC9684413 DOI: 10.1038/s41598-022-23298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/29/2022] [Indexed: 11/24/2022] Open
Abstract
A beneficial root system is crucial for efficient nutrient uptake and stress tolerance. Therefore, evaluating the root system variation for breeding crop plants towards stress adaptation is critically important. Here, we phenotyped root architectural traits of naturally adapted populations from organic and conventional cropping systems under hydroponic and field trails. Long-term natural selection under these two cropping systems resulted in a microevolution of root morphological and anatomical traits. Barley lines developed under an organic system possessed longer roots with narrow root angle, larger surface area, increased root mass density, and a thinner root diameter with an increased number of metaxylem vessels. In contrast, lines adapted to the conventional system tend to have a shorter and wider root system with a larger root volume with a thicker diameter but fewer metaxylem vessels. Allometry analysis established a relationship between root traits and plant size among barley genotypes, which specifies that root angle could be a good candidate among studied root traits to determine root-borne shoot architecture. Further, multivariate analyses showed a strong tendency towards increased variability of the organically adapted population's root morphological and anatomical traits. The genotyping of ancestor populations validated the observations made in these experiments. Collectively, this results indicate significant differences in root phenotypes between conventional and organic populations, which could be useful in comparative genomics and breeding.
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Genome-Wide Association Studies of Root-Related Traits in Brassica napus L. under Low-Potassium Conditions. PLANTS 2022; 11:plants11141826. [PMID: 35890461 PMCID: PMC9318150 DOI: 10.3390/plants11141826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/20/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Roots are essential organs for a plant’s ability to absorb water and obtain mineral nutrients, hence they are critical to its development. Plants use root architectural alterations to improve their chances of absorbing nutrients when their supply is low. Nine root traits of a Brassica napus association panel were explored in hydroponic-system studies under low potassium (K) stress to unravel the genetic basis of root growth in rapeseed. The quantitative trait loci (QTL) and candidate genes for root development were discovered using a multilocus genome-wide association study (ML-GWAS). For the nine traits, a total of 453 significant associated single-nucleotide polymorphism (SNP) loci were discovered, which were then integrated into 206 QTL clusters. There were 45 pleiotropic clusters, and qRTA04-4 and qRTC04-7 were linked to TRL, TSA, and TRV at the same time, contributing 5.25–11.48% of the phenotypic variance explained (PVE) to the root traits. Additionally, 1360 annotated genes were discovered by examining genomic regions within 100 kb upstream and downstream of lead SNPs within the 45 loci. Thirty-five genes were identified as possibly regulating root-system development. As per protein–protein interaction analyses, homologs of three genes (BnaC08g29120D, BnaA07g10150D, and BnaC04g45700D) have been shown to influence root growth in earlier investigations. The QTL clusters and candidate genes identified in this work will help us better understand the genetics of root growth traits and could be employed in marker-assisted breeding for rapeseed adaptable to various conditions with low K levels.
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Eyland D, Luchaire N, Cabrera‐Bosquet L, Parent B, Janssens SB, Swennen R, Welcker C, Tardieu F, Carpentier SC. High-throughput phenotyping reveals differential transpiration behaviour within the banana wild relatives highlighting diversity in drought tolerance. PLANT, CELL & ENVIRONMENT 2022; 45:1647-1663. [PMID: 35297073 PMCID: PMC9310827 DOI: 10.1111/pce.14310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Crop wild relatives, the closely related species of crops, may harbour potentially important sources of new allelic diversity for (a)biotic tolerance or resistance. However, to date, wild diversity is only poorly characterized and evaluated. Banana has a large wild diversity but only a narrow proportion is currently used in breeding programmes. The main objective of this study was to evaluate genotype-dependent transpiration responses in relation to the environment. By applying continuous high-throughput phenotyping, we were able to construct genotype-specific transpiration response models in relation to light, VPD and soil water potential. We characterized and evaluated six (sub)species and discerned four phenotypic clusters. Significant differences were observed in leaf area, cumulative transpiration and transpiration efficiency. We confirmed a general stomatal-driven 'isohydric' drought avoidance behaviour, but discovered genotypic differences in the onset and intensity of stomatal closure. We pinpointed crucial genotype-specific soil water potentials when drought avoidance mechanisms were initiated and when stress kicked in. Differences between (sub)species were dependent on environmental conditions, illustrating the need for high-throughput dynamic phenotyping, modelling and validation. We conclude that the banana wild relatives contain useful drought tolerance traits, emphasising the importance of their conservation and potential for use in breeding programmes.
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Affiliation(s)
- David Eyland
- Laboratory of Tropical Crop Improvement, Division of Crop BiotechnicsKU LeuvenLeuvenBelgium
| | - Nathalie Luchaire
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Llorenç Cabrera‐Bosquet
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Boris Parent
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Steven B. Janssens
- Department ResearchMeise Botanic GardenMeiseBelgium
- Department of BiologyKU LeuvenLeuvenBelgium
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop BiotechnicsKU LeuvenLeuvenBelgium
- Banana and Plantain Crop ImprovementInternational Institute of Tropical AgricultureKampalaUganda
| | - Claude Welcker
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - François Tardieu
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Sebastien C. Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop BiotechnicsKU LeuvenLeuvenBelgium
- Biodiversity for Food and AgricultureBioversity InternationalLeuvenBelgium
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Hudzenko VM, Polishchuk TP, Lysenko AA, Fedorenko IV, Fedorenko MV, Khudolii LV, Ishchenko VA, Kozelets HM, Babenko AI, Tanchyk SP, Mandrovska SM. Elucidation of gene action and combining ability for productive tillering in spring barley. REGULATORY MECHANISMS IN BIOSYSTEMS 2022. [DOI: 10.15421/022225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The purpose of the present study is to identify breeding and genetic peculiarities for productive tillering in spring barley genotypes of different origin, purposes of usage and botanical affiliation, as well as to identify effective genetic sources to further improving of the trait. There were created two complete (6 × 6) diallel crossing schemes. Into the Scheme I elite Ukrainian (MIP Tytul and Avhur) and Western European (Datcha, Quench, Gladys, and Beatrix) malting spring barley varieties were involved. Scheme II included awnless covered barley varieties Kozyr and Vitrazh bred at the Plant Production Institute named after V. Y. Yuriev of NAAS of Ukraine, naked barley varieties Condor and CDC Rattan from Canada, as well as awned feed barley variety MIP Myroslav created at MIW and malting barley variety Sebastian from Denmark. For more reliable and informative characterization of barley varieties and their progeny for productive tillering in terms of inheritance, parameters of genetic variation and general combining ability (GCA) statistical analyses of experimental data from different (2019 and 2020) growing seasons were conducted. Accordingly to the indicator of phenotypic dominance all possible modes of inheritance were detected, except for negative dominance in the Scheme I in 2020. The degree of phenotypic dominance significantly varied depending on both varieties involved in crossing schemes and conditions of the years of trials. There was overdominance in loci in both schemes in both years. The other parameters of genetic variation showed significant differences in gene action for productive tillering between crossing Schemes. In Scheme I in both years the dominance was mainly unidirectional and due to dominant effects. In the Scheme II in both years there was multidirectional dominance. In Scheme I compliance with the additive-dominant system was revealed in 2019, but in 2020 there was a strong epistasis. In Scheme II in both years non-allelic interaction was identified. In general, the mode of gene action showed a very complex gene action for productive tillering in barley and a significant role of non-genetic factors in phenotypic manifestation of the trait. Despite this, the level of heritability in the narrow sense in both Schemes pointed to the possibility of the successful selection of individuals with genetically determined increased productive tillering in the splitting generations. In Scheme I the final selection for productive tillering will be more effective in later generations, when dominant alleles become homozygous. In Scheme II it is theoretically possible to select plants with high productive tillering on both recessive and dominant basis. In both schemes the non-allelic interaction should be taken into consideration. Spring barley varieties Beatrix, Datcha, MIP Myroslav and Kozyr can be used as effective genetic sources for involvement in crossings aimed at improving the productive tillering. The results of present study contribute to further development of studies devoted to evaluation of gene action for yield-related traits in spring barley, as well as identification of new genetic sources for plant improvement.
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Manik SMN, Quamruzzaman M, Zhao C, Johnson P, Hunt I, Shabala S, Zhou M. Genome-Wide Association Study Reveals Marker Trait Associations (MTA) for Waterlogging-Triggered Adventitious Roots and Aerenchyma Formation in Barley. Int J Mol Sci 2022; 23:ijms23063341. [PMID: 35328762 PMCID: PMC8954902 DOI: 10.3390/ijms23063341] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 12/31/2022] Open
Abstract
Waterlogging is an environmental stress, which severely affects barley growth and development. Limited availability of oxygen in the root zone negatively affects the metabolism of the whole plant. Adventitious roots (AR) and root cortical aerenchyma (RCA) formation are the most important adaptive traits that contribute to a plant's ability to survive in waterlogged soil conditions. This study used a genome-wide association (GWAS) approach using 18,132 single nucleotide polymorphisms (SNPs) in a panel of 697 barley genotypes to reveal marker trait associations (MTA) conferring the above adaptive traits. Experiments were conducted over two consecutive years in tanks filled with soil and then validated in field experiments. GWAS analysis was conducted using general linear models (GLM), mixed linear models (MLM), and fixed and random model circulating probability unification models (FarmCPU model), with the FarmCPU showing to be the best suited model. Six and five significant (approximately -log10 (p) ≥ 5.5) MTA were identified for AR and RCA formation under waterlogged conditions, respectively. The highest -log10 (p) MTA for adventitious root and aerenchyma formation were approximately 9 and 8 on chromosome 2H and 4H, respectively. The combination of different MTA showed to be more effective in forming RCA and producing more AR under waterlogging stress. Genes from major facilitator superfamily (MFS) transporter and leucine-rich repeat (LRR) families for AR formation, and ethylene responsive factor (ERF) family genes and potassium transporter family genes for RCA formation were the potential candidate genes involved under waterlogging conditions. Several genotypes, which performed consistently well under different conditions, can be used in breeding programs to develop waterlogging-tolerant varieties.
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Affiliation(s)
- S. M. Nuruzzaman Manik
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
| | - Md Quamruzzaman
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
| | - Peter Johnson
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
| | - Ian Hunt
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
- Correspondence:
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Toulotte JM, Pantazopoulou CK, Sanclemente MA, Voesenek LACJ, Sasidharan R. Water stress resilient cereal crops: Lessons from wild relatives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:412-430. [PMID: 35029029 PMCID: PMC9255596 DOI: 10.1111/jipb.13222] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/10/2022] [Indexed: 05/20/2023]
Abstract
Cereal crops are significant contributors to global diets. As climate change disrupts weather patterns and wreaks havoc on crops, the need for generating stress-resilient, high-yielding varieties is more urgent than ever. One extremely promising avenue in this regard is to exploit the tremendous genetic diversity expressed by the wild ancestors of current day crop species. These crop wild relatives thrive in a range of environments and accordingly often harbor an array of traits that allow them to do so. The identification and introgression of these traits into our staple cereal crops can lessen yield losses in stressful environments. In the last decades, a surge in extreme drought and flooding events have severely impacted cereal crop production. Climate models predict a persistence of this trend, thus reinforcing the need for research on water stress resilience. Here we review: (i) how water stress (drought and flooding) impacts crop performance; and (ii) how identification of tolerance traits and mechanisms from wild relatives of the main cereal crops, that is, rice, maize, wheat, and barley, can lead to improved survival and sustained yields in these crops under water stress conditions.
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Affiliation(s)
- Justine M. Toulotte
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Chrysoula K. Pantazopoulou
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Maria Angelica Sanclemente
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Laurentius A. C. J. Voesenek
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Rashmi Sasidharan
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
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Tay Fernandez C. Making a Pangenome Using the Iterative Mapping Approach. Methods Mol Biol 2022; 2443:259-271. [PMID: 35037211 DOI: 10.1007/978-1-0716-2067-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pangenomes have replaced single reference genomes as genetic references, as they contain a better scope of the diversity found in a single species. This protocol outlines the iterative mapping approach in constructing a pangenome, including how to check the raw data, align the data to a reference, how to assemble the data, and how to remove potential contaminants from the final assembly.
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Sayed MA, Tarawneh R, Youssef HM, Pillen K, Börner A. Detection and Verification of QTL for Salinity Tolerance at Germination and Seedling Stages Using Wild Barley Introgression Lines. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112246. [PMID: 34834608 PMCID: PMC8624391 DOI: 10.3390/plants10112246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Salinity is one of the major environmental factors that negatively affect crop development, particularly at the early growth stage of a plant and consequently the final yield. Therefore, a set of 50 wild barley (Hordeum vulgare ssp. spontaneum, Hsp) introgression lines (ILs) was used to detect QTL alleles improving germination and seedling growth under control, 75 mM, and 150 mM NaCl conditions. Large variation was observed for germination and seedling growth related traits that were highly heritable under salinity stress. In addition, highly significant differences were obtained for five salinity tolerance indices and between treatments as well. A total of 90 and 35 significant QTL were identified for ten investigated traits and for tolerance indices, respectively. The Hsp introgression alleles are involved in improving salinity tolerance at forty (43.9%) out of 90 QTL including introgression lines S42IL-109 (2H), S42IL-116 (4H), S42IL-132 (6H), S42IL-133 (7H), S42IL-148 (6H), and S42IL-176 (5H). Interestingly, seven exotic QTL alleles were successfully validated in the wild barley ILs including S42IL-127 (5H), 139 (7H), 125 (5H), 117 (4H), 118 (4H), 121 (4H), and 137 (7H). We conclude that the barley introgression lines contain numerous germination and seedling growth-improving novel QTL alleles, which are effective under salinity conditions.
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Affiliation(s)
- Mohammed Abdelaziz Sayed
- Agronomy Department, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
- Resources Genetics and Reproduction, Gene Bank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, D-06466 Seeland, Germany;
| | - Rasha Tarawneh
- Resources Genetics and Reproduction, Gene Bank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, D-06466 Seeland, Germany;
| | - Helmy Mohamed Youssef
- Faculty of Agriculture, Cairo University, Giza 12613, Egypt;
- Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany;
| | - Klaus Pillen
- Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany;
| | - Andreas Börner
- Resources Genetics and Reproduction, Gene Bank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, D-06466 Seeland, Germany;
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Proline-Mediated Drought Tolerance in the Barley ( Hordeum vulgare L.) Isogenic Line Is Associated with Lateral Root Growth at the Early Seedling Stage. PLANTS 2021; 10:plants10102177. [PMID: 34685984 PMCID: PMC8538694 DOI: 10.3390/plants10102177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 12/02/2022]
Abstract
A vigorous root system in barley promotes water uptake from the soil under water-limited conditions. We investigated three spring barley genotypes with varying water stress responses using rhizoboxes at the seedling stage. The genotypes comprised two elite German cultivars, Barke and Scarlett, and a near-isogenic line, NIL 143. The isogenic line harbors the wild allele pyrroline-5-carboxylate synthase1-P5cs1. Root growth in rhizoboxes under reduced water availability conditions caused a significant reduction in total root length, rooting depth, root maximum width, and root length density. On average, root growth was reduced by more than 20% due to water stress. Differences in organ proline concentrations were observed for all genotypes, with shoots grown under water stress exhibiting at least a 30% higher concentration than the roots. Drought induced higher leaf and root proline concentrations in NIL 143 compared with any of the other genotypes. Under reduced water availability conditions, NIL 143 showed less severe symptoms of drought, higher lateral root length, rooting depth, maximum root width, root length density, and convex hull area compared with Barke and Scarlett. Within the same comparison, under water stress, NIL 143 had a higher proportion of lateral roots (+30%), which were also placed at deeper substrate horizons. NIL 143 had a less negative plant water potential and higher relative leaf water content and stomatal conductance compared with the other genotypes under water stress. Under these conditions, this genotype also maintained an enhanced net photosynthetic rate and exhibited considerable fine root growth (diameter class 0.05–0.35 mm). These results show that water stress induces increased shoot and root proline accumulation in the NIL 143 barley genotype at the seedling stage and that this effect is associated with increased lateral root growth.
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Reynolds M, Atkin OK, Bennett M, Cooper M, Dodd IC, Foulkes MJ, Frohberg C, Hammer G, Henderson IR, Huang B, Korzun V, McCouch SR, Messina CD, Pogson BJ, Slafer GA, Taylor NL, Wittich PE. Addressing Research Bottlenecks to Crop Productivity. TRENDS IN PLANT SCIENCE 2021; 26:607-630. [PMID: 33893046 DOI: 10.1016/j.tplants.2021.03.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 05/22/2023]
Abstract
Asymmetry of investment in crop research leads to knowledge gaps and lost opportunities to accelerate genetic gain through identifying new sources and combinations of traits and alleles. On the basis of consultation with scientists from most major seed companies, we identified several research areas with three common features: (i) relatively underrepresented in the literature; (ii) high probability of boosting productivity in a wide range of crops and environments; and (iii) could be researched in 'precompetitive' space, leveraging previous knowledge, and thereby improving models that guide crop breeding and management decisions. Areas identified included research into hormones, recombination, respiration, roots, and source-sink, which, along with new opportunities in phenomics, genomics, and bioinformatics, make it more feasible to explore crop genetic resources and improve breeding strategies.
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Affiliation(s)
- Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico, El Batan, Texcoco, Mexico.
| | - Owen K Atkin
- Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT 2601, Australia.
| | - Malcolm Bennett
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire, LE12 5RD, UK.
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ian C Dodd
- The Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - M John Foulkes
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire, LE12 5RD, UK
| | - Claus Frohberg
- BASF BBC-Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - Graeme Hammer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901, USA.
| | | | - Susan R McCouch
- Plant Breeding & Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850, USA.
| | - Carlos D Messina
- Corteva Agriscience, 7250 NW 62nd Avenue, Johnston, IA 50310, USA.
| | - Barry J Pogson
- Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT 2601, Australia
| | - Gustavo A Slafer
- Department of Crop and Forest Sciences, University of Lleida, AGROTECNIO, CERCA Center, Av. R. Roure 191, 25198 Lleida, Spain; ICREA, Catalonian Institution for Research and Advanced Studies, Barcelona, Spain.
| | - Nicolas L Taylor
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Peter E Wittich
- Syngenta Seeds B.V., Westeinde 62, 1601 BK, Enkhuizen, The Netherlands.
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Kofsky J, Zhang H, Song BH. Novel resistance strategies to soybean cyst nematode (SCN) in wild soybean. Sci Rep 2021; 11:7967. [PMID: 33846373 PMCID: PMC8041904 DOI: 10.1038/s41598-021-86793-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Soybean cyst nematode (SCN, Heterodera glycine Ichinohe) is the most damaging soybean pest worldwide and management of SCN remains challenging. The current SCN resistant soybean cultivars, mainly developed from the cultivated soybean gene pool, are losing resistance due to SCN race shifts. The domestication process and modern breeding practices of soybean cultivars often involve strong selection for desired agronomic traits, and thus, decreased genetic variation in modern cultivars, which consequently resulted in limited sources of SCN resistance. Wild soybean (Glycine soja) is the wild ancestor of cultivated soybean (Glycine max) and it's gene pool is indisputably more diverse than G. max. Our aim is to identify novel resistant genetic resources from wild soybean for the development of new SCN resistant cultivars. In this study, resistance response to HG type 2.5.7 (race 5) of SCN was investigated in a newly identified SCN resistant ecotype, NRS100. To understand the resistance mechanism in this ecotype, we compared RNA seq-based transcriptomes of NRS100 with two SCN-susceptible accessions of G. soja and G. max, as well as an extensively studied SCN resistant cultivar, Peking, under both control and nematode J2-treated conditions. The proposed mechanisms of resistance in NRS100 includes the suppression of the jasmonic acid (JA) signaling pathway in order to allow for salicylic acid (SA) signaling-activated resistance response and polyamine synthesis to promote structural integrity of root cell walls. Our study identifies a set of novel candidate genes and associated pathways involved in SCN resistance and the finding provides insight into the mechanism of SCN resistance in wild soybean, advancing the understanding of resistance and the use of wild soybean-sourced resistance for soybean improvement.
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Affiliation(s)
- Janice Kofsky
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Hengyou Zhang
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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Siddiqui MN, Léon J, Naz AA, Ballvora A. Genetics and genomics of root system variation in adaptation to drought stress in cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1007-1019. [PMID: 33096558 PMCID: PMC7904151 DOI: 10.1093/jxb/eraa487] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/19/2020] [Indexed: 05/03/2023]
Abstract
Cereals are important crops worldwide that help meet food demands and nutritional needs. In recent years, cereal production has been challenged globally by frequent droughts and hot spells. A plant's root is the most relevant organ for the plant adaptation to stress conditions, playing pivotal roles in anchorage and the acquisition of soil-based resources. Thus, dissecting root system variations and trait selection for enhancing yield and sustainability under drought stress conditions should aid in future global food security. This review highlights the variations in root system attributes and their interplay with shoot architecture features to face water scarcity and maintain thus yield of major cereal crops. Further, we compile the root-related drought responsive quantitative trait loci/genes in cereal crops including their interspecies relationships using microsynteny to facilitate comparative genomic analyses. We then discuss the potential of an integrated strategy combining genomics and phenomics at genetic and epigenetic levels to explore natural genetic diversity as a basis for knowledge-based genome editing. Finally, we present an outline to establish innovative breeding leads for the rapid and optimized selection of root traits necessary to develop resilient crop varieties.
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Affiliation(s)
- Md Nurealam Siddiqui
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Ali A Naz
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
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16
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Frimpong F, Windt CW, van Dusschoten D, Naz AA, Frei M, Fiorani F. A Wild Allele of Pyrroline-5-Carboxylate Synthase1 Leads to Proline Accumulation in Spikes and Leaves of Barley Contributing to Improved Performance Under Reduced Water Availability. FRONTIERS IN PLANT SCIENCE 2021; 12:633448. [PMID: 33719307 PMCID: PMC7947243 DOI: 10.3389/fpls.2021.633448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/25/2021] [Indexed: 05/05/2023]
Abstract
Water stress (WS) during spike development strongly affects final grain yield and grain quality in cereals. Proline, an osmoprotectant amino-acid, may contribute to alleviating the effects of cell and tissue dehydration. We studied five spring barley genotypes contrasting in their drought response, including two introgression lines, S42IL-143 and S42IL-141, harboring a Pyrroline-5-carboxylate synthase1- P5cs1 allele originating from the wild barley accession ISR42-8. We tested the hypothesis that barley genotypes harboring a wild allele at P5cs1 locus are comparatively more drought-tolerant at the reproductive stage by inducing proline accumulation in their immature spikes. At the booting stage, we subjected plants to well-watered and WS treatments until physiological maturity. Several morpho-physiological traits had significant genotype by treatment interaction and reduction under WS. Varying levels of genotypic proline accumulation and differences in WS tolerance were observed. Spike proline accumulation was higher than leaf proline accumulation for all genotypes under WS. Also, introgression lines carrying a wild allele at P5cs1 locus had a markedly higher spike and leaf proline content compared with the other genotypes. These introgression lines showed milder drought symptoms compared with elite genotypes, remained photosynthetically active under WS, and maintained their intrinsic water use efficiency. These combined responses contributed to the achievement of higher final seed productivity. Magnetic resonance imaging (MRI) of whole spikes at the soft dough stage showed an increase in seed abortion among the elite genotypes compared with the introgression lines 15 days after WS treatment. Our results suggest that proline accumulation at the reproductive stage contributes to the maintenance of grain formation under water shortage.
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Affiliation(s)
- Felix Frimpong
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- CSIR-Crops Research Institute, Kumasi, Ghana
| | - Carel W. Windt
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dagmar van Dusschoten
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ali A. Naz
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Michael Frei
- Institute of Agronomy and Plant Breeding, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Fabio Fiorani
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- *Correspondence: Fabio Fiorani,
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17
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Harnessing High-throughput Phenotyping and Genotyping for Enhanced Drought Tolerance in Crop Plants. J Biotechnol 2020; 324:248-260. [PMID: 33186658 DOI: 10.1016/j.jbiotec.2020.11.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/28/2020] [Accepted: 11/08/2020] [Indexed: 12/17/2022]
Abstract
Development of drought-tolerant cultivars is one of the challenging tasks for the plant breeders due to its complex inheritance and polygenic regulation. Evaluating genetic material for drought tolerance is a complex process due to its spatiotemporal interactions with environmental factors. The conventional breeding approaches are costly, lengthy, and inefficient to achieve the expected gain in drought tolerance. In this regard, genomics-assisted breeding (GAB) offers promise to develop cultivars with improved drought tolerance in a more efficient, quicker, and cost-effective manner. The success of GAB depends upon the precision in marker-trait association and estimation of genomic estimated breeding values (GEBVs), which mostly depends on coverage and precision of genotyping and phenotyping. A wide gap between the discovery and practical use of quantitative trait loci (QTL) for crop improvement has been observed for many important agronomical traits. Such a limitation could be due to the low accuracy in QTL detection, mainly resulting from low marker density and manually collected phenotypes of complex agronomic traits. Increasing marker density using the high-throughput genotyping (HTG), and accurate and precise phenotyping using high-throughput digital phenotyping (HTP) platforms can improve the precision and power of QTL detection. Therefore, both HTG and HTP can enhance the practical utility of GAB along with a faster characterization of germplasm and breeding material. In the present review, we discussed how the recent innovations in HTG and HTP would assist in the breeding of improved drought-tolerant varieties. We have also discussed strategies, tools, and analytical advances made on the HTG and HTP along with their pros and cons.
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18
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Moursi YS, Thabet SG, Amro A, Dawood MFA, Baenziger PS, Sallam A. Detailed Genetic Analysis for Identifying QTLs Associated with Drought Tolerance at Seed Germination and Seedling Stages in Barley. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9111425. [PMID: 33114292 PMCID: PMC7690857 DOI: 10.3390/plants9111425] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/14/2020] [Accepted: 10/16/2020] [Indexed: 05/08/2023]
Abstract
Drought induces several challenges for plant development, growth, and production. These challenges become more severe, in particular, in arid and semiarid countries like Egypt. In terms of production, barley ranks fourth after wheat, maize, and rice. Seed germination and seedling stages are critical stages for plant establishment and growth. In the current study, 60 diverse barley genotypes were tested for drought tolerance using two different treatments: control (0-PEG) and drought (20%-PEG). Twenty-two traits were estimated for seed germination and seedling parameters. All traits were reduced under drought stress, and a significant variation was found among genotypes under control and stress conditions. The broad-sense heritability estimates were very high under both control and drought for all traits. It ranged from 0.63 to 0.97 under the control condition and from 0.89 to 0.97 under drought, respectively. These high heritabilities suggested that genetic improvement of drought tolerance in barley at both stages is feasible. The principal component analysis revealed that root-related parameters account for the largest portion of phenotypic variation in this collection. The single-marker analysis (SMA) resulted in 71 quantitative trait loci (QTLs) distributed across the seven chromosomes of barley. Thirty-three QTLs were detected for root-length-related traits. Many hotspots of QTLs were detected for various traits. Interestingly, some markers controlled many traits in a pleiotropic manner; thus, they can be used to control multiple traits at a time. Some QTLs were constitutive, i.e., they are mapped under control and drought, and targeting these QTLs makes the selection for drought tolerance a single-step process. The results of gene annotation analysis revealed very potential candidate genes that can be targeted to select for drought tolerance.
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Affiliation(s)
- Yasser S. Moursi
- Department of Botany, Faculty of Science, University of Fayoum, Fayoum 63514, Egypt; (Y.S.M.); (S.G.T.)
| | - Samar G. Thabet
- Department of Botany, Faculty of Science, University of Fayoum, Fayoum 63514, Egypt; (Y.S.M.); (S.G.T.)
| | - Ahmed Amro
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Asyut 71516, Egypt; (A.A.); (M.F.A.D.)
| | - Mona F. A. Dawood
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Asyut 71516, Egypt; (A.A.); (M.F.A.D.)
| | - P. Stephen Baenziger
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Asyut 71526, Egypt
- Correspondence:
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19
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Natural Genetic Variation Underlying Tiller Development in Barley ( Hordeum vulgare L). G3-GENES GENOMES GENETICS 2020; 10:1197-1212. [PMID: 31996357 PMCID: PMC7144072 DOI: 10.1534/g3.119.400612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In barley (Hordeum vulgare L.), lateral branches called tillers contribute to grain yield and define shoot architecture, but genetic control of tiller number and developmental rate are not well characterized. The primary objectives of this work were to examine relationships between tiller number and other agronomic and morphological traits and identify natural genetic variation associated with tiller number and rate, and related traits. We grew 768 lines from the USDA National Small Grain Collection in the field and collected data over two years for tiller number and rate, and agronomic and morphological traits. Our results confirmed that spike row-type and days to heading are correlated with tiller number, and as much as 28% of tiller number variance was associated with these traits. In addition, negative correlations between tiller number and leaf width and stem diameter were observed, indicating trade-offs between tiller development and other vegetative growth. Thirty-three quantitative trait loci (QTL) were associated with tiller number or rate. Of these, 40% overlapped QTL associated with days to heading and 22% overlapped QTL associated with spike row-type, further supporting that tiller development is associated with these traits. Some QTL associated with tiller number or rate, including the major QTL on chromosome 3H, were not associated with other traits, suggesting that some QTL may be directly related to rate of tiller development or axillary bud number. These results enhance our knowledge of the genetic control of tiller development in barley, which is important for optimizing tiller number and rate for yield improvement.
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20
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Kreszies T, Eggels S, Kreszies V, Osthoff A, Shellakkutti N, Baldauf JA, Zeisler-Diehl VV, Hochholdinger F, Ranathunge K, Schreiber L. Seminal roots of wild and cultivated barley differentially respond to osmotic stress in gene expression, suberization, and hydraulic conductivity. PLANT, CELL & ENVIRONMENT 2020; 43:344-357. [PMID: 31762057 DOI: 10.1111/pce.13675] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/23/2019] [Accepted: 11/03/2019] [Indexed: 05/13/2023]
Abstract
Wild barley, Hordeum vulgare spp. spontaneum, has a wider genetic diversity than its cultivated progeny, Hordeum vulgare spp. vulgare. Osmotic stress leads to a series of different responses in wild barley seminal roots, ranging from no changes in suberization to enhanced endodermal suberization of certain zones and the formation of a suberized exodermis, which was not observed in the modern cultivars studied so far. Further, as a response to osmotic stress, the hydraulic conductivity of roots was not affected in wild barley, but it was 2.5-fold reduced in cultivated barley. In both subspecies, osmotic adjustment by increasing proline concentration and decreasing osmotic potential in roots was observed. RNA-sequencing indicated that the regulation of suberin biosynthesis and water transport via aquaporins were different between wild and cultivated barley. These results indicate that wild barley uses different strategies to cope with osmotic stress compared with cultivated barley. Thus, it seems that wild barley is better adapted to cope with osmotic stress by maintaining a significantly higher hydraulic conductivity of roots during water deficit.
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Affiliation(s)
- Tino Kreszies
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, 53115, Germany
| | - Stella Eggels
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, 53115, Germany
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, 85354, Germany
| | - Victoria Kreszies
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, 53115, Germany
| | - Alina Osthoff
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Nandhini Shellakkutti
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, 53115, Germany
| | - Jutta A Baldauf
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Viktoria V Zeisler-Diehl
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, 53115, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Kosala Ranathunge
- School of Biological Sciences, Faculty of Science, University of Western Australia, Perth, 6009, Australia
| | - Lukas Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, 53115, Germany
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21
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Sun P, Jia H, Zhang Y, Li J, Lu M, Hu J. Deciphering Genetic Architecture of Adventitious Root and Related Shoot Traits in Populus Using QTL Mapping and RNA-Seq Data. Int J Mol Sci 2019; 20:ijms20246114. [PMID: 31817197 PMCID: PMC6941115 DOI: 10.3390/ijms20246114] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 11/16/2022] Open
Abstract
Understanding the genetic architecture of adventitious root and related shoot traits will facilitate the cultivation of superior genotypes. In this study, we measured 12 adventitious root and related shoot traits of 434 F1 genotypes originating from Populus deltoides ‘Danhong’ × Populus simonii ‘Tongliao1’ and conducted an integrative analysis of quantitative trait locus (QTL) mapping and RNA-Seq data to dissect their genetic architecture and regulatory genes. Extensive segregation, high repeatability, and significant correlation relationship were detected for the investigated traits. A total of 150 QTLs were associated with adventitious root traits, explaining 3.1–6.1% of phenotypic variation (PVE); while 83 QTLs were associated with shoot traits, explaining 3.1–19.8% of PVE. Twenty-five QTL clusters and 40 QTL hotspots were identified for the investigated traits. Ten QTL clusters were overlapped in both adventitious root traits and related shoot traits. Transcriptome analysis identified 10,172 differentially expressed genes (DEGs) among two parents, three fine rooting and three poor-rooting genotypes, 143 of which were physically located within the QTL intervals. K-means cluster and weighted gene co-expression network analysis showed that PtAAAP19 (Potri.004G111400) encoding amino acid transport protein was tightly associated with adventitious roots and highly expressed in fine-rooting genotypes. Compare with ‘Danhong’, 153 bp deletion in the coding sequence of PtAAAP19 in ‘Tongliao1’ gave rise to lack one transmembrane domain, which might cause the variation of adventitious roots. Taken together, this study deciphered the genetic basis of adventitious root and related shoot traits and provided potential function genes for genetic improvement of poplar breeding.
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Affiliation(s)
- Pei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (P.S.); (H.J.); (M.L.)
| | - Huixia Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (P.S.); (H.J.); (M.L.)
| | - Yahong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (P.S.); (H.J.); (M.L.)
| | - Jianbo Li
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing 102300, China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (P.S.); (H.J.); (M.L.)
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (P.S.); (H.J.); (M.L.)
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel: +86-10-62888862
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22
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Liu Z, Marella CBN, Hartmann A, Hajirezaei MR, von Wirén N. An Age-Dependent Sequence of Physiological Processes Defines Developmental Root Senescence. PLANT PHYSIOLOGY 2019; 181:993-1007. [PMID: 31515448 PMCID: PMC6836830 DOI: 10.1104/pp.19.00809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/02/2019] [Indexed: 05/22/2023]
Abstract
Aging-related processes in plant tissues are associated with changes in developmental and physiological processes relevant for stress tolerance and plant performance. While senescence-regulated processes have been extensively characterized in leaves, they remain poorly described in roots. Here, we investigated the physiological processes and molecular determinants underlying the senescence of seminal roots in hydroponically grown barley (Hordeum vulgare). Transcriptome profiling in apical and basal root tissues revealed that several NAC-, WRKY-, and APETALA2 (AP2)-type transcription factors were upregulated just before the arrest of root elongation, when root cortical cell lysis and nitrate uptake, as well as cytokinin concentrations ceased. At this time point, root abscisic acid levels peaked, suggesting that abscisic acid is involved in root aging-related processes characterized by expression changes of genes involved in oxidative stress responses. This temporal sequence of aging-related processes in roots is highly reminiscent of typical organ senescence, with the exception of evidence for the retranslocation of nutrients from roots. Supported by the identification of senescence-related transcription factors, some of which are not expressed in leaves, our study indicates that roots undergo an intrinsic genetically determined senescence program, predominantly influenced by plant age.
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Affiliation(s)
- Zhaojun Liu
- Molecular Plant Nutrition, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Chakravarthy B N Marella
- Molecular Plant Nutrition, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Anja Hartmann
- Molecular Plant Nutrition, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Mohammad R Hajirezaei
- Molecular Plant Nutrition, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany vonwiren@ipk-gatersleben
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23
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Sallam A, Alqudah AM, Dawood MFA, Baenziger PS, Börner A. Drought Stress Tolerance in Wheat and Barley: Advances in Physiology, Breeding and Genetics Research. Int J Mol Sci 2019; 20:ijms20133137. [PMID: 31252573 DOI: 10.3390/ijms.20133137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 05/26/2023] Open
Abstract
Climate change is a major threat to most of the agricultural crops grown in tropical and sub-tropical areas globally. Drought stress is one of the consequences of climate change that has a negative impact on crop growth and yield. In the past, many simulation models were proposed to predict climate change and drought occurrences, and it is extremely important to improve essential crops to meet the challenges of drought stress which limits crop productivity and production. Wheat and barley are among the most common and widely used crops due to their economic and social values. Many parts of the world depend on these two crops for food and feed, and both crops are vulnerable to drought stress. Improving drought stress tolerance is a very challenging task for wheat and barley researchers and more research is needed to better understand this stress. The progress made in understanding drought tolerance is due to advances in three main research areas: physiology, breeding, and genetic research. The physiology research focused on the physiological and biochemical metabolic pathways that plants use when exposed to drought stress. New wheat and barley genotypes having a high degree of drought tolerance are produced through breeding by making crosses from promising drought-tolerant genotypes and selecting among their progeny. Also, identifying genes contributing to drought tolerance is very important. Previous studies showed that drought tolerance is a polygenic trait and genetic constitution will help to dissect the gene network(s) controlling drought tolerance. This review explores the recent advances in these three research areas to improve drought tolerance in wheat and barley.
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Affiliation(s)
- Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt.
| | - Ahmad M Alqudah
- Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany.
| | - Mona F A Dawood
- Department of Botany & Microbiology, Faculty of Science, Assiut University, 71516 Assiut, Egypt
| | - P Stephen Baenziger
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Andreas Börner
- Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
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24
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Sallam A, Alqudah AM, Dawood MFA, Baenziger PS, Börner A. Drought Stress Tolerance in Wheat and Barley: Advances in Physiology, Breeding and Genetics Research. Int J Mol Sci 2019; 20:E3137. [PMID: 31252573 PMCID: PMC6651786 DOI: 10.3390/ijms20133137] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Climate change is a major threat to most of the agricultural crops grown in tropical and sub-tropical areas globally. Drought stress is one of the consequences of climate change that has a negative impact on crop growth and yield. In the past, many simulation models were proposed to predict climate change and drought occurrences, and it is extremely important to improve essential crops to meet the challenges of drought stress which limits crop productivity and production. Wheat and barley are among the most common and widely used crops due to their economic and social values. Many parts of the world depend on these two crops for food and feed, and both crops are vulnerable to drought stress. Improving drought stress tolerance is a very challenging task for wheat and barley researchers and more research is needed to better understand this stress. The progress made in understanding drought tolerance is due to advances in three main research areas: physiology, breeding, and genetic research. The physiology research focused on the physiological and biochemical metabolic pathways that plants use when exposed to drought stress. New wheat and barley genotypes having a high degree of drought tolerance are produced through breeding by making crosses from promising drought-tolerant genotypes and selecting among their progeny. Also, identifying genes contributing to drought tolerance is very important. Previous studies showed that drought tolerance is a polygenic trait and genetic constitution will help to dissect the gene network(s) controlling drought tolerance. This review explores the recent advances in these three research areas to improve drought tolerance in wheat and barley.
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Affiliation(s)
- Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt.
| | - Ahmad M Alqudah
- Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany.
| | - Mona F A Dawood
- Department of Botany & Microbiology, Faculty of Science, Assiut University, 71516 Assiut, Egypt
| | - P Stephen Baenziger
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Andreas Börner
- Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
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25
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Abdel-Ghani AH, Sharma R, Wabila C, Dhanagond S, Owais SJ, Duwayri MA, Al-Dalain SA, Klukas C, Chen D, Lübberstedt T, von Wirén N, Graner A, Kilian B, Neumann K. Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage. BMC PLANT BIOLOGY 2019; 19:216. [PMID: 31122195 PMCID: PMC6533710 DOI: 10.1186/s12870-019-1828-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/13/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits. RESULTS A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stress-specific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1, HvCry2, HvCO4 and HvPRR73. Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate. CONCLUSIONS This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley. Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation.
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Affiliation(s)
- Adel H. Abdel-Ghani
- Department of Plant Production, Faculty of Agriculture, Mutah University, Mutah, Karak, 61710 Jordan
| | - Rajiv Sharma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
- Division of Plant Science, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA UK
| | - Celestine Wabila
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
| | - Sidram Dhanagond
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
| | - Saed J. Owais
- Department of Plant Production, Faculty of Agriculture, Mutah University, Mutah, Karak, 61710 Jordan
| | - Mahmud A. Duwayri
- Department of Horticulture and Agronomy, Faculty of Agriculture, University of Jordan, Amman, Jordan
| | - Saddam A. Al-Dalain
- Al-Shoubak University College, Al-Balqa’ Applied University, Al-, Salt, 19117 Jordan
| | - Christian Klukas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
- Digitalization in Research & Development (ROM), BASF SE, 67056 Ludwigshafen, Germany
| | - Dijun Chen
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt University Berlin, 10115 Berlin, Germany
| | - Thomas Lübberstedt
- Department of Agronomy, Agronomy Hall, Iowa State University, Ames, IA 50011 USA
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
- Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle/Saale, Germany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
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Pham AT, Maurer A, Pillen K, Brien C, Dowling K, Berger B, Eglinton JK, March TJ. Genome-wide association of barley plant growth under drought stress using a nested association mapping population. BMC PLANT BIOLOGY 2019; 19:134. [PMID: 30971212 PMCID: PMC6458831 DOI: 10.1186/s12870-019-1723-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/17/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Barley (Hordeum vulgare L.) is the fourth most important cereal crop worldwide. Barley production is compromised by many abiotic stresses including drought. Wild barley is a valuable source of alleles that can improve adaptation of cultivated barley to drought stress. RESULTS In the present study, a nested association mapping population named HEB-25, consisting of 1420 BC1S3 lines that were developed by crossing 25 different wild barley accessions to the elite barley cultivar 'Barke', was evaluated under both control and drought-stressed conditions in the Australian Plant Phenomics Facility, University of Adelaide. Overall, 14 traits reflecting the performance of individual plants in each treatment were calculated from non-destructive imaging over time and destructive end-of-experiment measurements. For each trait, best linear unbiased estimators (BLUEs) were calculated and used for genome-wide association study (GWAS) analysis. Among the quantitative trait loci (QTL) identified for the 14 traits, many co-localise with known inflorescence and developmental genes. We identified a QTL on chromosome 4H where, under drought and control conditions, wild barley alleles increased biomass by 10 and 17% respectively compared to the Barke allele. CONCLUSIONS Across all traits, QTL which increased phenotypic values were identified, providing a wider range of genetic diversity for the improvement of drought tolerance in barley.
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Affiliation(s)
- Anh-Tung Pham
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Chris Brien
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
- Phenomics and Bioinformatics Research Centre, University of South Australia, North Terrace, Adelaide, SA 5000 Australia
- Australian Plant Phenomics Facility, The Plant Accelerator, University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
| | - Kate Dowling
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
- Phenomics and Bioinformatics Research Centre, University of South Australia, North Terrace, Adelaide, SA 5000 Australia
- Australian Plant Phenomics Facility, The Plant Accelerator, University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
| | - Bettina Berger
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
- Australian Plant Phenomics Facility, The Plant Accelerator, University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
| | - Jason K. Eglinton
- Sugar Research Australia, 71378 Bruce Highway, Gordonvale, QLD 4865 Australia
| | - Timothy J. March
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
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Jia Z, Liu Y, Gruber BD, Neumann K, Kilian B, Graner A, von Wirén N. Genetic Dissection of Root System Architectural Traits in Spring Barley. FRONTIERS IN PLANT SCIENCE 2019; 10:400. [PMID: 31001309 PMCID: PMC6454135 DOI: 10.3389/fpls.2019.00400] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/18/2019] [Indexed: 05/19/2023]
Abstract
Breeding new crop cultivars with efficient root systems carries great potential to enhance resource use efficiency and plant adaptation to unstable climates. Here, we evaluated the natural variation of root system architectural traits in a diverse spring barley association panel and conducted genome-wide association mapping to identify genomic regions associated with root traits. For six studied traits, root system depth, root spreading angle, seminal root number, total seminal root length, and average seminal root length 1.9- to 4.2-fold variations were recorded. Using a mixed linear model, 55 QTLs were identified cumulatively explaining between 12.1% of the phenotypic variance for seminal root number to 48.1% of the variance for root system depth. Three major QTLs controlling root system depth, root spreading angle and total seminal root length were found on Chr 2H (56.52 cM), Chr 3H (67.92 cM), and Chr 2H (76.20 cM) and explained 12.4%, 18.4%, and 22.2% of the phenotypic variation, respectively. Meta-analysis and allele combination analysis indicated that root system depth and root spreading angle are valuable candidate traits for improving grain yield by pyramiding of favorable alleles.
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Affiliation(s)
- Zhongtao Jia
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Ying Liu
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Benjamin D. Gruber
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Kerstin Neumann
- Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Benjamin Kilian
- Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Andreas Graner
- Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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He Y, Hu D, You J, Wu D, Cui Y, Dong H, Li J, Qian W. Genome-wide association study and protein network analysis for understanding candidate genes involved in root development at the rapeseed seedling stage. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 137:42-52. [PMID: 30738216 DOI: 10.1016/j.plaphy.2019.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/20/2019] [Accepted: 01/26/2019] [Indexed: 05/23/2023]
Abstract
Root system is essential for plants to absorb water and nutrients. The root related traits are complex quantitative traits and regulated by genetic control. Here, we used two association mapping panels to perform a genome-wide association study (GWAS) on seven root related traits in Brassica napus at the seedling stage and obtained 27 SNP loci significantly associated with the phenotypes. We further conducted a genome-wide LD block analysis of the candidate peak regions and obtained 295 candidate genes with high association peaks across seven phenotypes in LD region. In addition, a protein interaction network using the candidate genes identified here was constructed, and 113 genes were associated. Seven genes, BnaA03g47330D, BnaC09g16810D, BnaA06g22840D, BnaA03g28390D, BnaA08g19920D, BnaA03g28930D and BnaA03g11440D were in a large cluster, and may play important roles in interacting with other related genes. Our data may provide resources for molecular breeding and functional analysis of root growth and development in rapeseed.
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Affiliation(s)
- Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Dingxue Hu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jingcan You
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Daoming Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
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29
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Gill MB, Zeng F, Shabala L, Zhang G, Yu M, Demidchik V, Shabala S, Zhou M. Identification of QTL Related to ROS Formation under Hypoxia and Their Association with Waterlogging and Salt Tolerance in Barley. Int J Mol Sci 2019; 20:E699. [PMID: 30736310 PMCID: PMC6387252 DOI: 10.3390/ijms20030699] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 01/19/2023] Open
Abstract
Waterlogging is a serious environmental problem that limits agricultural production in low-lying rainfed areas around the world. The major constraint that plants face in a waterlogging situation is the reduced oxygen availability. Accordingly, all previous efforts of plant breeders focused on traits providing adequate supply of oxygen to roots under waterlogging conditions, such as enhanced aerenchyma formation or reduced radial oxygen loss. However, reduced oxygen concentration in waterlogged soils also leads to oxygen deficiency in plant tissues, resulting in an excessive accumulation of reactive oxygen species (ROS) in plants. To the best of our knowledge, this trait has never been targeted in breeding programs and thus represents an untapped resource for improving plant performance in waterlogged soils. To identify the quantitative trait loci (QTL) for ROS tolerance in barley, 187 double haploid (DH) lines from a cross between TX9425 and Naso Nijo were screened for superoxide anion (O₂•-) and hydrogen peroxide (H₂O₂)-two major ROS species accumulated under hypoxia stress. We show that quantifying ROS content after 48 h hypoxia could be a fast and reliable approach for the selection of waterlogging tolerant barley genotypes. The same QTL on chromosome 2H was identified for both O₂•- (QSO.TxNn.2H) and H₂O₂ (QHP.TxNn.2H) contents. This QTL was located at the same position as the QTL for the overall waterlogging and salt tolerance reported in previous studies, explaining 23% and 24% of the phenotypic variation for O₂•- and H₂O2 contents, respectively. The analysis showed a causal association between ROS production and both waterlogging and salt stress tolerance. Waterlogging and salinity are two major abiotic factors affecting crop production around the globe and frequently occur together. The markers associated with this QTL could potentially be used in future breeding programs to improve waterlogging and salinity tolerance.
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Affiliation(s)
- Muhammad Bilal Gill
- International Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China.
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas 7005, Australia.
| | - Fanrong Zeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Lana Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas 7005, Australia.
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Min Yu
- International Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China.
| | - Vadim Demidchik
- International Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China.
- Department of Plant Cell Biology and Bioengineering, Biological Faculty, Belarusian State University, 222030 Minsk, Belarus.
| | - Sergey Shabala
- International Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China.
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas 7005, Australia.
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas 7005, Australia.
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30
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De la Fuente Cantó C, Russell J, Hackett CA, Booth A, Dancey S, George TS, Waugh R. Genetic dissection of quantitative and qualitative traits using a minimum set of barley Recombinant Chromosome Substitution Lines. BMC PLANT BIOLOGY 2018; 18:340. [PMID: 30526499 PMCID: PMC6286510 DOI: 10.1186/s12870-018-1527-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Exploring the natural occurring genetic variation of the wild barley genepool has become a major target of barley crop breeding programmes aiming to increase crop productivity and sustainability in global climate change scenarios. However this diversity remains unexploited and effective approaches are required to investigate the benefits that unadapted genomes could bring to crop improved resilience. In the present study, a set of Recombinant Chromosome Substitution Lines (RCSLs) derived from an elite barley cultivar 'Harrington' as the recurrent parent, and a wild barley accession from the Fertile Crescent 'Caesarea 26-24', as the donor parent (Matus et al. Genome 46:1010-23, 2003) have been utilised in field and controlled conditions to examine the contribution of wild barley genome as a source of novel allelic variation for the cultivated barley genepool. METHODS Twenty-eight RCSLs which were selected to represent the entire genome of the wild barley accession, were genotyped using the 9 K iSelect SNP markers (Comadran et al. Nat Genet 44:1388-92, 2012) and phenotyped for a range of morphological, developmental and agronomic traits in 2 years using a rain-out shelter with four replicates and three water treatments. Data were analysed for marker traits associations using a mixed model approach. RESULTS We identified lines that differ significantly from the elite parent for both qualitative and quantitative traits across growing seasons and water regimes. The detailed genotypic characterisation of the lines for over 1800 polymorphic SNP markers and the design of a mixed model analysis identified chromosomal regions associated with yield related traits where the wild barley allele had a positive response increasing grain weight and size. In addition, variation for qualitative characters, such as the presence of cuticle waxes on the developing spikes, was associated with the wild barley introgressions. Despite the coarse location of the QTLs, interesting candidate genes for the major marker-trait associations were identified using the recently released barley genome assembly. CONCLUSION This study has highlighted the role of exotic germplasm to contribute novel allelic variation by using an optimised experimental approach focused on an exotic genetic library. The results obtained constitute a step forward to the development of more tolerant and resilient varieties.
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Affiliation(s)
| | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | | | - Allan Booth
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - Siobhan Dancey
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | | | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
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31
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Turner SD, Ellison SL, Senalik DA, Simon PW, Spalding EP, Miller ND. An Automated Image Analysis Pipeline Enables Genetic Studies of Shoot and Root Morphology in Carrot ( Daucus carota L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1703. [PMID: 30542356 PMCID: PMC6277879 DOI: 10.3389/fpls.2018.01703] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 11/01/2018] [Indexed: 05/04/2023]
Abstract
Carrot is a globally important crop, yet efficient and accurate methods for quantifying its most important agronomic traits are lacking. To address this problem, we developed an automated image analysis platform that extracts components of size and shape for carrot shoots and roots, which are necessary to advance carrot breeding and genetics. This method reliably measured variation in shoot size and shape, petiole number, petiole length, and petiole width as evidenced by high correlations with hundreds of manual measurements. Similarly, root length and biomass were accurately measured from the images. This platform also quantified shoot and root shapes in terms of principal components, which do not have traditional, manually measurable equivalents. We applied the pipeline in a study of a six-parent diallel population and an F2 mapping population consisting of 316 individuals. We found high levels of repeatability within a growing environment, with low to moderate repeatability across environments. We also observed co-localization of quantitative trait loci for shoot and root characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably quantified, the development of a rapid, automated image analysis pipeline to measure carrot shoot and root morphology will expand the scope and scale of breeding and genetic studies.
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Affiliation(s)
- Sarah D. Turner
- Department of Horticulture, University of Wisconsin–Madison, Madison, WI, United States
| | - Shelby L. Ellison
- Vegetable Crops Research Unit, United States Department of Agriculture–Agricultural Research Service, Madison, WI, United States
| | - Douglas A. Senalik
- Vegetable Crops Research Unit, United States Department of Agriculture–Agricultural Research Service, Madison, WI, United States
| | - Philipp W. Simon
- Department of Horticulture, University of Wisconsin–Madison, Madison, WI, United States
- Vegetable Crops Research Unit, United States Department of Agriculture–Agricultural Research Service, Madison, WI, United States
| | - Edgar P. Spalding
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Nathan D. Miller
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
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Muzammil S, Shrestha A, Dadshani S, Pillen K, Siddique S, Léon J, Naz AA. An Ancestral Allele of Pyrroline-5-carboxylate synthase1 Promotes Proline Accumulation and Drought Adaptation in Cultivated Barley. PLANT PHYSIOLOGY 2018; 178:771-782. [PMID: 30131422 PMCID: PMC6181029 DOI: 10.1104/pp.18.00169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/08/2018] [Indexed: 05/20/2023]
Abstract
Water scarcity is a critical threat to global crop production. Here, we used the natural diversity of barley (Hordeum vulgare) to dissect the genetic control of proline (Pro) mediated drought stress adaptation. Genetic mapping and positional cloning of a major drought-inducible quantitative trait locus (QPro.S42-1H) revealed unique allelic variation in pyrroline-5-carboxylate synthase (P5cs1) between the cultivated cultivar Scarlett (ssp. vulgare) and the wild barley accession ISR42-8 (ssp. spontaneum). The putative causative mutations were located in the promoter of P5cs1 across the DNA binding motifs for abscisic acid-responsive element binding transcription factors. Introgression line (IL) S42IL-143 carrying the wild allele of P5cs1 showed significant up-regulation of P5cs1 expression compared to Scarlett, which was consistent with variation in Pro accumulation under drought. Next, we transiently expressed promoter::reporter constructs of ISR42-8 and Scarlett alleles in Arabidopsis (Arabidopsis thaliana) mesophyll protoplasts. GUS expression analysis showed a significantly higher activation of the ISR42-8 promoter compared to Scarlett upon abscisic acid treatment. Notably, the ISR42-8 promoter activity was impaired in protoplasts isolated from the loss-of-function abf1abf2abf3abf4 quadruple mutant. A series of phenotypic evaluations demonstrated that S42IL-143 maintained leaf water content and photosynthetic activity longer than Scarlett under drought. These findings suggest that the ancestral variant of P5cs1 has the potential for drought tolerance and understanding drought physiology of barley and related crops.
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Affiliation(s)
- Shumaila Muzammil
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Asis Shrestha
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Said Dadshani
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Klaus Pillen
- Department of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Shahid Siddique
- Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Jens Léon
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Ali Ahmad Naz
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
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Guo J, Chen G, Zhang X, Li T, Yu H, Liu C. Quantitative trait locus analysis of adventitious and lateral root morphology of barley grown at low and high P. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:957-967. [PMID: 32291059 DOI: 10.1071/fp17271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/15/2018] [Indexed: 05/21/2023]
Abstract
Barley (Hordeum vulgare L) may alter its root morphology to improve P acquisition efficiency under low-P (LP) stress. This research studied the variations in adventitious and lateral root morphological traits of barley and mapped their quantitative trait loci (QTLs) under LP and high P (HP). The recombinant inbred lines were derived from the F1 population of a cross between CN4027 and Baudin. Two experiments aimed to identify QTLs related to adventitious and lateral root morphological traits under LP and HP. The length, surface area and volume of adventitious and lateral roots were measured. Under HP, Baudin had larger root morphology, especially lateral root morphology, than CN4027. LP stress induced lateral root growth but inhibited adventitious root growth. Nineteen QTLs for root morphological traits were detected. These QTLs clustered within four regions (Cl-2H, Cl-3H, Cl-4H and Cl-7H) on chromosomes 2H, 3H, 4H and 7H, with corresponding contributions of 12.0-42.9%. Some QTLs are linked with the QTLs for P efficiency detected previously, demonstrating the role of root morphological traits in P efficiency. The Cl-2H region was identified in the interval bPb3927665-bPb3265744 on chromosome 2H and had major effects on lateral root growth, especially under LP. Lateral root length and surface area increased when alleles from Baudin were present at the QTLs in Cl-2H. This study demonstrated the patterns of growth among root types and the role of lateral roots in barley's adaption to LP stress. The QTL clusters, especially Cl-2H, may offer clues for fine mapping and map-based cloning.
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Affiliation(s)
- Jingyi Guo
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xizhou Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Tingxuan Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Haiying Yu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunji Liu
- CSIRO Agriculture, 306 Carmody Road, St Lucia, Qld 4067, Australia
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Ivanizs L, Farkas A, Linc G, Molnár-Láng M, Molnár I. Molecular cytogenetic and morphological characterization of two wheat-barley translocation lines. PLoS One 2018; 13:e0198758. [PMID: 29889875 PMCID: PMC5995406 DOI: 10.1371/journal.pone.0198758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/24/2018] [Indexed: 11/18/2022] Open
Abstract
Barley chromosome 5H, carrying important QTLs for plant adaptation and tolerance to abiotic stresses, is extremely instable in the wheat genetic background and is eliminated in the early generations of wheat-barley crosses. A spontaneous wheat-barley 5HS-7DS.7DL translocation was previously obtained among the progenies of the Mv9kr1 x Igri hybrid. The present work reports on the transfer of the 5HS-7DS.7DL translocation into a modern wheat cultivar, Mv Bodri, in order to use it in the wheat breeding program. The comparison of the hybridization bands of DNA repeats HvT01, pTa71, (GAA)n and the barley centromere-specific (AGGGAG)n in Igri barley and the 5HS-7DS.7DL translocation, together with the visualization of the barley chromatin made it possible to determine the size of the introgressed barley segment, which was approximately 74% of the whole 5HS. Of the 29 newly developed PCR markers, whose source ESTs were selected from the Genome Zipper of barley chromosome 5H, 23 were mapped in the introgressed 1-0.26 FL 5HS bin, three were located in the missing C-0.26 FL region, while three markers were specific for 5HL. The translocation breakpoint was flanked by markers Hv7502 and Hv3949. A comparison of the parental wheat cultivars and the wheat-barley introgression lines indicated that the presence of the translocation improved tillering ability in the Mv9kr1 and Mv Bodri genetic background. The similar or better yield components under high- or low-input cultivation environments, respectively, indicated that the 5HS-7DS.7DL translocation had little or no negative effect on yield components, making it a promising genotype to improve wheat genetic diversity. These results promise to accelerate functional genomic studies on barley chromosome 5H and to support pre-breeding and breeding research on wheat.
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Affiliation(s)
- László Ivanizs
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Brunszvik u. 2, Hungary
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Brunszvik u. 2, Hungary
| | - Gabriella Linc
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Brunszvik u. 2, Hungary
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Brunszvik u. 2, Hungary
| | - István Molnár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Brunszvik u. 2, Hungary
- Institute of Experimental Botany of the Czech Academy of Sciences (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc-Holice, Czech Republic
- * E-mail:
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He R, Ni Y, Li J, Jiao Z, Zhu X, Jiang Y, Li Q, Niu J. Quantitative Changes in the Transcription of Phytohormone-Related Genes: Some Transcription Factors Are Major Causes of the Wheat Mutant dmc Not Tillering. Int J Mol Sci 2018; 19:ijms19051324. [PMID: 29710831 PMCID: PMC5983577 DOI: 10.3390/ijms19051324] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/17/2023] Open
Abstract
Tiller number is an important agronomic trait for grain yield of wheat (Triticum aestivum L.). A dwarf-monoculm wheat mutant (dmc) was obtained from cultivar Guomai 301 (wild type, WT). Here, we explored the molecular basis for the restrained tiller development of the mutant dmc. Two bulked samples of the mutant dmc (T1, T2 and T3) and WT (T4, T5 and T6) with three biological replicates were comparatively analyzed at the transcriptional level by bulked RNA sequencing (RNA-Seq). In total, 68.8 Gb data and 463 million reads were generated, 80% of which were mapped to the wheat reference genome of Chinese Spring. A total of 4904 differentially expressed genes (DEGs) were identified between the mutant dmc and WT. DEGs and their related major biological functions were characterized based on GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) categories. These results were confirmed by quantitatively analyzing the expression profiles of twelve selected DEGs via real-time qRT-PCR. The down-regulated gene expressions related to phytohormone syntheses of auxin, zeatin, cytokinin and some transcription factor (TF) families of TALE, and WOX might be the major causes of the mutant dmc, not tillering. Our work provides a foundation for subsequent tiller development research in the future.
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Affiliation(s)
- Ruishi He
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Yongjing Ni
- Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu 476000, Henan, China.
| | - Junchang Li
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Zhixin Jiao
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Xinxin Zhu
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Yumei Jiang
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Qiaoyun Li
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Jishan Niu
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
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Wang Q, Sun G, Ren X, Wang J, Du B, Li C, Sun D. Detection of QTLs for seedling characteristics in barley (Hordeum vulgare L.) grown under hydroponic culture condition. BMC Genet 2017; 18:94. [PMID: 29115942 PMCID: PMC5678765 DOI: 10.1186/s12863-017-0562-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/30/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Seedling characteristics play significant roles in the growth and development of barley (Hordeum vulgare L.), including stable stand establishment, water and nutrients uptake, biotic resistance and abiotic stresses, and can influence yield and quality. However, the genetic mechanisms underlying seedling characteristics in barley are largely unknown and little research has been done. In the present work, 21 seedling-related characteristics are assessed in a barley double haploid (DH) population, grown under hydroponic conditions. Of them, leaf age (LAG), shoot height (SH), maximum root length (MRL), main root number (MRN) and seedling fresh weight (SFW) were investigated at the 13th, 20th, 27th, and 34th day after germination. The objectives were to identify quantitative trait loci (QTLs) underlying these seedling characteristics using a high-density linkage map and to reveal the QTL expression pattern by comparing the QTLs among four different seedling growth stages. RESULTS A total of 70 QTLs were distributed over all chromosomes except 4H, and, individually, accounted for 5.01%-77.78% of phenotypic variation. Out of the 70 detected QTLs, 23 showed a major effect on 14 seedling-related characteristics. Ten co-localized chromosomal regions on 2H (five regions), 3H (two regions) and 7H (three regions) involved 39 QTLs (55.71%), each simultaneously influenced more than one trait. Meanwhile, 9 co-localized genomic regions involving 22 QTLs for five seedling characteristics (LAG, SH, MRL, MRN and SFW) at the 13th, 20th, 27th and 34th day-old seedling were common for two or more growth stages of seedling. QTL in the vicinity of Vrs1 locus on chromosome 2H with the favorable alleles from Huadamai 6 was found to have the largest main effects on multiple seedling-related traits. CONCLUSIONS Six QTL cluster regions associated with 16 seedling-related characteristics were observed on chromosome 2H, 3H and 7H. The majority of the 29 regions identified for five seedling characteristics were selectively expressed at different developmental stages. The genetic effects of 9 consecutive expression regions displayed different developmental influences at different developmental stages. These findings enhanced our understanding of a genetic basis underlying seedling characteristics in barley. Some QTLs detected here could be used for marker-assisted selection (MAS) in barley breeding.
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Affiliation(s)
- Qifei Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Genlou Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Biology Department, Saint Mary’s University, 923 Robie Street, Halifax, NS B3H 3C3 Canada
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jibin Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Binbin Du
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chengdao Li
- Department of Agriculture & Food/Agricultural Research Western Australia, 3 Baron-Hay Court, South Perth, WA 6155 Australia
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, Hubei 434025 China
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Honsdorf N, March TJ, Pillen K. QTL controlling grain filling under terminal drought stress in a set of wild barley introgression lines. PLoS One 2017; 12:e0185983. [PMID: 29053716 PMCID: PMC5650137 DOI: 10.1371/journal.pone.0185983] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/24/2017] [Indexed: 11/18/2022] Open
Abstract
Drought is a major abiotic stress impeding the yield of cereal crops globally. Particularly in Mediterranean environments, water becomes a limiting factor during the reproductive developmental stage, causing yield losses. The wild progenitor of cultivated barley Hordeum vulgare ssp spontaneum (Hsp) is a potentially useful source of drought tolerance alleles. Wild barley introgression lines like the S42IL library may facilitate the introduction of favorable exotic alleles into breeding material. The complete set of 83 S42ILs was genotyped with the barley 9k iSelect platform in order to complete genetic information obtained in previous studies. The new map comprises 2,487 SNPs, spanning 989.8 cM and covering 94.5% of the Hsp genome. Extent and positions of introgressions were confirmed and new information for ten additional S42ILs was collected. A subset of 49 S42ILs was evaluated for drought response in four greenhouse experiments. Plants were grown under well-watered conditions until ten days post anthesis. Subsequently drought treatment was applied by reducing the available water. Several morphological and harvest parameters were evaluated. Under drought treatment, trait performance was reduced. However, there was no interaction effect between genotype and treatment, indicating that genotypes, which performed best under control treatment, also performed best under drought treatment. In total, 40 QTL for seven traits were detected in this study. For instance, favorable Hsp effects were found for thousand grain weight (TGW) and number of grains per ear under drought stress. In particular, line S42IL-121 is a promising candidate for breeding improved malting cultivars, displaying a TGW, which was increased by 17% under terminal drought stress due to the presence of an unknown wild barley QTL allele on chromosome 4H. The introgression line showed a similar advantage in previous field experiments and in greenhouse experiments under early drought stress. We, thus, recommend using S42IL-121 in barley breeding programs to enhance terminal drought tolerance.
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Affiliation(s)
- Nora Honsdorf
- Plant Breeding, Institute of Agricultural and Nutritional Sciences, University of Halle-Wittenberg, Halle/Saale, Germany
| | - Timothy J. March
- Plant Breeding, Institute of Agricultural and Nutritional Sciences, University of Halle-Wittenberg, Halle/Saale, Germany
| | - Klaus Pillen
- Plant Breeding, Institute of Agricultural and Nutritional Sciences, University of Halle-Wittenberg, Halle/Saale, Germany
- * E-mail:
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Gong X, McDonald G. QTL mapping of root traits in phosphorus-deficient soils reveals important genomic regions for improving NDVI and grain yield in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1885-1902. [PMID: 28593327 DOI: 10.1007/s00122-017-2931-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 05/30/2017] [Indexed: 05/05/2023]
Abstract
Major QTLs for root rhizosheath size are not correlated with grain yield or yield response to phosphorus. Important QTLs were found to improve phosphorus efficiency. Root traits are important for phosphorus (P) acquisition, but they are often difficult to characterize and their breeding values are seldom assessed under field conditions. This has shed doubts on using seedling-based criteria of root traits to select and breed for P efficiency. Eight root traits were assessed under controlled conditions in a barley doubled-haploid population in soils differing in P levels. The population was also phenotyped for grain yield, normalized difference vegetation index (NDVI), grain P uptake and P utilization efficiency at maturity (PutEGY) under field conditions. Several quantitative traits loci (QTLs) from the root screening and the field trials were co-incident. QTLs for root rhizosheath size and root diameter explained the highest phenotypic variation in comparison to QTLs for other root traits. Shared QTLs were found between root diameter and grain yield, and total root length and PutEGY. A common major QTL for rhizosheath size and NDVI was mapped to the HvMATE gene marker on chromosome 4H. Collocations between major QTLs for NDVI and grain yield were detected on chromosomes 6H and 7H. When results from BIP and MET were combined, QTLs detected for grain yield were also those QTLs found for NDVI. QTLs qGY5H, qGY6H and qGY7Hb on 7H were robust QTLs in improving P efficiency. A selection of multiple loci may be needed to optimize the breeding outcomes due to the QTL x Environment interaction. We suggest that rhizosheath size alone is not a reliable trait to predict P efficiency or grain yield.
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Affiliation(s)
- Xue Gong
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, 5064, Adelaide, SA, Australia.
| | - Glenn McDonald
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, 5064, Adelaide, SA, Australia
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Zhang M, Bo W, Xu F, Li H, Ye M, Jiang L, Shi C, Fu Y, Zhao G, Huang Y, Gosik K, Liang D, Wu R. The genetic architecture of shoot-root covariation during seedling emergence of a desert tree, Populus euphratica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:918-928. [PMID: 28244225 DOI: 10.1111/tpj.13518] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 05/12/2023]
Abstract
The coordination of shoots and roots is critical for plants to adapt to changing environments by fine-tuning energy production in leaves and the availability of water and nutrients from roots. To understand the genetic architecture of how these two organs covary during developmental ontogeny, we conducted a mapping experiment using Euphrates poplar (Populus euphratica), a so-called hero tree able to grow in the desert. We geminated intraspecific F1 seeds of Euphrates Poplar individually in a tube to obtain a total of 370 seedlings, whose shoot and taproot lengths were measured repeatedly during the early stage of growth. By fitting a growth equation, we estimated asymptotic growth, relative growth rate, the timing of inflection point and duration of linear growth for both shoot and taproot growth. Treating these heterochronic parameters as phenotypes, a univariate mapping model detected 19 heterochronic quantitative trait loci (hQTLs), of which 15 mediate the forms of shoot growth and four mediate taproot growth. A bivariate mapping model identified 11 pleiotropic hQTLs that determine the covariation of shoot and taproot growth. Most QTLs detected reside within the region of candidate genes with various functions, thus confirming their roles in the biochemical processes underlying plant growth.
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Affiliation(s)
- Miaomiao Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wenhao Bo
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Fang Xu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Huan Li
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chaozhong Shi
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yaru Fu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Guomiao Zhao
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yuejiao Huang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Kirk Gosik
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA
| | - Dan Liang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA
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Zhang H, Mittal N, Leamy LJ, Barazani O, Song B. Back into the wild-Apply untapped genetic diversity of wild relatives for crop improvement. Evol Appl 2017; 10:5-24. [PMID: 28035232 PMCID: PMC5192947 DOI: 10.1111/eva.12434] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/07/2016] [Indexed: 12/18/2022] Open
Abstract
Deleterious effects of climate change and human activities, as well as diverse environmental stresses, present critical challenges to food production and the maintenance of natural diversity. These challenges may be met by the development of novel crop varieties with increased biotic or abiotic resistance that enables them to thrive in marginal lands. However, considering the diverse interactions between crops and environmental factors, it is surprising that evolutionary principles have been underexploited in addressing these food and environmental challenges. Compared with domesticated cultivars, crop wild relatives (CWRs) have been challenged in natural environments for thousands of years and maintain a much higher level of genetic diversity. In this review, we highlight the significance of CWRs for crop improvement by providing examples of CWRs that have been used to increase biotic and abiotic stress resistance/tolerance and overall yield in various crop species. We also discuss the surge of advanced biotechnologies, such as next-generation sequencing technologies and omics, with particular emphasis on how they have facilitated gene discovery in CWRs. We end the review by discussing the available resources and conservation of CWRs, including the urgent need for CWR prioritization and collection to ensure continuous crop improvement for food sustainability.
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Affiliation(s)
- Hengyou Zhang
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Neha Mittal
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Larry J. Leamy
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Oz Barazani
- The Institute for Plant SciencesIsrael Plant Gene BankAgricultural Research OrganizationBet DaganIsrael
| | - Bao‐Hua Song
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
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Hein JA, Sherrard ME, Manfredi KP, Abebe T. The fifth leaf and spike organs of barley (Hordeum vulgare L.) display different physiological and metabolic responses to drought stress. BMC PLANT BIOLOGY 2016; 16:248. [PMID: 27829376 PMCID: PMC5103489 DOI: 10.1186/s12870-016-0922-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/21/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Photosynthetic organs of the cereal spike (ear) provide assimilate for grain filling, but their response to drought is poorly understood. In this study, we characterized the drought response of individual organs of the barley spike (awn, lemma, and palea) and compared them with a vegetative organ (fifth leaf). Understanding differences in physiological and metabolic responses between the leaf and spike organs during drought can help us develop high yielding cultivars for environments where terminal drought is prevalent. RESULTS We exposed barley plants to drought by withholding water for 4 days at the grain filling stage and compared changes in: (1) relative water content (RWC), (2) osmotic potential (Ψs), (3) osmotic adjustment (OA), (4) gas exchange, and (5) metabolite content between organs. Drought reduced RWC and Ψs in all four organs, but the decrease in RWC was greater and there was a smaller change in Ψs in the fifth leaf than the spike organs. We detected evidence of OA in the awn, lemma, and palea, but not in the fifth leaf. Rates of gas exchange declined more rapidly in the fifth leaf than awn during drought. We identified 18 metabolites but, only ten metabolites accumulated significantly during drought in one or more organs. Among these, proline accumulated in all organs during drought while accumulation of the other metabolites varied between organs. This may suggest that each organ in the same plant uses a different set of osmolytes for drought resistance. CONCLUSIONS Our results suggest that photosynthetic organs of the barley spike maintain higher water content, greater osmotic adjustment, and higher rates of gas exchange than the leaf during drought.
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Affiliation(s)
- Jordan A. Hein
- Department of Biology, University of Northern Iowa, Cedar Falls, IA 50614 USA
| | - Mark E. Sherrard
- Department of Biology, University of Northern Iowa, Cedar Falls, IA 50614 USA
| | - Kirk P. Manfredi
- Department of Chemistry and Biochemistry, University of Northern Iowa, Cedar Falls, IA 50614 USA
| | - Tilahun Abebe
- Department of Biology, University of Northern Iowa, Cedar Falls, IA 50614 USA
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Mahoney AK, Babiker EM, Paulitz TC, See D, Okubara PA, Hulbert SH. Characterizing and Mapping Resistance in Synthetic-Derived Wheat to Rhizoctonia Root Rot in a Green Bridge Environment. PHYTOPATHOLOGY 2016; 106:1170-1176. [PMID: 27349737 DOI: 10.1094/phyto-02-16-0055-fi] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Root rot caused by Rhizoctonia spp. is an economically important soilborne disease of spring-planted wheat in growing regions of the Pacific Northwest (PNW). The main method of controlling the disease currently is through tillage, which deters farmers from adopting the benefits of minimal tillage. Genetic resistance to this disease would provide an economic and environmentally sustainable resource for farmers. In this study, a collection of synthetic-derived genotypes was screened in high-inoculum and low-inoculum field environments. Six genotypes were found to have varying levels of resistance and tolerance to Rhizoctonia root rot. One of the lines, SPBC-3104 ('Vorobey'), exhibited good tolerance in the field and was crossed to susceptible PNW-adapted 'Louise' to examine the inheritance of the trait. A population of 190 BC1-derived recombinant inbred lines was assessed in two field green bridge environments and in soils artificially infested with Rhizoctonia solani AG8. Genotyping by sequencing and composite interval mapping identified three quantitative trait loci (QTL) controlling tolerance. Beneficial alleles of all three QTL were contributed by the synthetic-derived genotype SPCB-3104.
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Affiliation(s)
- A K Mahoney
- All authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and fifth authors: United States Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430
| | - E M Babiker
- All authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and fifth authors: United States Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430
| | - T C Paulitz
- All authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and fifth authors: United States Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430
| | - D See
- All authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and fifth authors: United States Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430
| | - P A Okubara
- All authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and fifth authors: United States Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430
| | - S H Hulbert
- All authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and fifth authors: United States Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430
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Arifuzzaman M, Günal S, Bungartz A, Muzammil S, P. Afsharyan N, Léon J, Naz AA. Genetic Mapping Reveals Broader Role of Vrn-H3 Gene in Root and Shoot Development beyond Heading in Barley. PLoS One 2016; 11:e0158718. [PMID: 27442506 PMCID: PMC4956229 DOI: 10.1371/journal.pone.0158718] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/21/2016] [Indexed: 11/18/2022] Open
Abstract
The aim of the present study was to dissect the genetic inheritance and interplay of root, shoot and heading attributes for a better understanding of these traits in crop production. For this, we utilized quantitative trait loci (QTL) and candidate gene analysis approach using a second filial (F2) population originated from a cross between spring cultivar Cheri and wild barley accession ICB181160. The F2 population comprising 182 plants was phenotyped for root dry weight (RDW), root volume (RV), root length (RL) and shoot dry weight (SDW), tiller number per plant (TIL) and days to heading (HEA). In parallel, this population was genotyped using polymerase chain reaction (PCR) based cleaved amplified polymorphic sequence (CAPS) markers distributed across the whole genome. Marker by trait analysis revealed 16 QTL for root and shoot traits localized on chromosomes 1H, 3H, 4H, 5H and 7H. The strongest and a common QTL effect for root, shoot and heading traits was identified on chromosome 7H at the putative region of Vrn-H3 gene. Later, we have established PCR based gene specific marker HvVrnH3 revealing polymorphism for early heading Vrn-H3 allele in Cheri and late heading allele vrn-H3 in ICB181160. Genotyping of these alleles revealed a clear co-segregation of early heading Vrn-H3 allele with lower root and shoot attributes, while late heading vrn-H3 allele with more TIL and higher root biomass suggesting a primary insight on the function of Vrn-H3 gene beyond flowering. Genetic interactions of vernalization genes Vrn-H3 with Vrn-H2 and Vrn-H1 also suggested the major role of Vrn-H3 alleles in determining root and shoot trait variations in barley. We believe, these data provide an opportunity for further research to test a precise significance of early heading on yield components and root associated sustainability in crops like barley and wheat.
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Affiliation(s)
- Md. Arifuzzaman
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115, Bonn, Germany
| | - Süleyman Günal
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115, Bonn, Germany
| | - Annemarie Bungartz
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115, Bonn, Germany
| | - Shumaila Muzammil
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115, Bonn, Germany
| | - Nazanin P. Afsharyan
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115, Bonn, Germany
| | - Jens Léon
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115, Bonn, Germany
| | - Ali Ahmad Naz
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115, Bonn, Germany
- * E-mail:
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Abou-Elwafa SF. Association mapping for yield and yield-contributing traits in barley under drought conditions with genome-based SSR markers. C R Biol 2016; 339:153-162. [PMID: 27129392 DOI: 10.1016/j.crvi.2016.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/13/2016] [Accepted: 03/14/2016] [Indexed: 11/16/2022]
Abstract
Drought negatively affects plant development, growth, yield, and ultimately production of crop species. Association analysis of yield and yield-contributing traits was conducted for a barley germplasm collection consisting 107 wild (Hordeum spontaneum L.) genotypes, originating from 12 countries using 76 SSR markers. Phenotypic evaluations were performed for days to heading, plant height, number of tillers/plant, spike length, thousand kernel weight, single plant yield under well-watered and drought-stress conditions. Highly significant differences between well-watered and drought-stress conditions were observed in all measured traits. Association analysis revealed a total of 83 significant marker-trait associations for all six measured traits. The results revealed that several chromosomal regions significantly influence more than one trait, suggesting a possible existence of pleiotropic or indirect effects. The phenotypic variation explained by individual marker-trait associations ranged from 5.08 to 27.84%. The results demonstrated that wild barley is a valuable source for improving yield and yield-contributing traits for drought tolerance. Our data provide a tool kit for the potential application of marker-assisted selection for drought tolerance in barley.
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Brozynska M, Furtado A, Henry RJ. Genomics of crop wild relatives: expanding the gene pool for crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1070-85. [PMID: 26311018 DOI: 10.1111/pbi.12454] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/26/2015] [Accepted: 07/16/2015] [Indexed: 05/20/2023]
Abstract
Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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Pérez-Jaramillo JE, Mendes R, Raaijmakers JM. Impact of plant domestication on rhizosphere microbiome assembly and functions. PLANT MOLECULAR BIOLOGY 2016; 90:635-44. [PMID: 26085172 PMCID: PMC4819786 DOI: 10.1007/s11103-015-0337-7] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/04/2015] [Indexed: 05/18/2023]
Abstract
The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.
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Affiliation(s)
- Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000, Brazil
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands.
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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Robinson H, Hickey L, Richard C, Mace E, Kelly A, Borrell A, Franckowiak J, Fox G. Genomic Regions Influencing Seminal Root Traits in Barley. THE PLANT GENOME 2016; 9. [PMID: 27898766 DOI: 10.3835/plantgenome2015.03.0012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Water availability is a major limiting factor for crop production, making drought adaptation and its many component traits a desirable attribute of plant cultivars. Previous studies in cereal crops indicate that root traits expressed at early plant developmental stages, such as seminal root angle and root number, are associated with water extraction at different depths. Here, we conducted the first study to map seminal root traits in barley ( L.). Using a recently developed high-throughput phenotyping method, a panel of 30 barley genotypes and a doubled-haploid (DH) population (ND24260 × 'Flagship') comprising 330 lines genotyped with diversity array technology (DArT) markers were evaluated for seminal root angle (deviation from vertical) and root number under controlled environmental conditions. A high degree of phenotypic variation was observed in the panel of 30 genotypes: 13.5 to 82.2 and 3.6 to 6.9° for root angle and root number, respectively. A similar range was observed in the DH population: 16.4 to 70.5 and 3.6 to 6.5° for root angle and number, respectively. Seven quantitative trait loci (QTL) for seminal root traits (root angle, two QTL; root number, five QTL) were detected in the DH population. A major QTL influencing both root angle and root number (/) was positioned on chromosome 5HL. Across-species analysis identified 10 common genes underlying root trait QTL in barley, wheat ( L.), and sorghum [ (L.) Moench]. Here, we provide insight into seminal root phenotypes and provide a first look at the genetics controlling these traits in barley.
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Association mapping for drought tolerance in barley at the reproductive stage. C R Biol 2016; 339:51-9. [DOI: 10.1016/j.crvi.2015.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 12/18/2015] [Accepted: 12/19/2015] [Indexed: 11/19/2022]
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Bungartz A, Klaus M, Mathew B, Léon J, Naz AA. Development of new SNP derived cleaved amplified polymorphic sequence marker set and its successful utilization in the genetic analysis of seed color variation in barley. Genomics 2016; 107:100-107. [PMID: 26738469 DOI: 10.1016/j.ygeno.2015.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 12/11/2015] [Accepted: 12/23/2015] [Indexed: 11/18/2022]
Abstract
The aim of the present study was to develop a new cost effective PCR based CAPS marker set using advantages of high-throughput SNP genotyping. Initially, SNP survey was made using 20 diverse barley genotypes via 9k iSelect array genotyping that resulted in 6334 polymorphic SNP markers. Principle component analysis using this marker data showed fine differentiation of barley diverse gene pool. Till this end, we developed 200 SNP derived CAPS markers distributed across the genome covering around 991cM with an average marker density of 5.09cM. Further, we genotyped 68 CAPS markers in an F2 population (Cheri×ICB181160) segregating for seed color variation in barley. Genetic mapping of seed color revealed putative linkage of single nuclear gene on chromosome 1H. These findings showed the proof of concept for the development and utility of a newer cost effective genomic tool kit to analyze broader genetic resources of barley worldwide.
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Affiliation(s)
- Annemarie Bungartz
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115 Bonn, Germany
| | - Marius Klaus
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115 Bonn, Germany
| | - Boby Mathew
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115 Bonn, Germany
| | - Jens Léon
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115 Bonn, Germany
| | - Ali Ahmad Naz
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115 Bonn, Germany.
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Reinert S, Kortz A, Léon J, Naz AA. Genome-Wide Association Mapping in the Global Diversity Set Reveals New QTL Controlling Root System and Related Shoot Variation in Barley. FRONTIERS IN PLANT SCIENCE 2016; 7:1061. [PMID: 27486472 PMCID: PMC4949209 DOI: 10.3389/fpls.2016.01061] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/06/2016] [Indexed: 05/19/2023]
Abstract
The fibrous root system is a visible sign of ecological adaptation among barley natural populations. In the present study, we utilized rich barley diversity to dissect the genetic basis of root system variation and its link with shoot attributes under well-water and drought conditions. Genome-wide association mapping of phenotype data using a dense genetic map (5892 SNP markers) revealed 17 putative QTL for root and shoot traits. Among these, at 14 loci the preeminence of exotic QTL alleles resulted in trait improvements. The most promising QTL were quantified using haplotype analysis at local and global genome levels. The strongest QTL was found on chromosome 1H which accounted for root dry weight and tiller number simultaneously. Candidate gene analysis across the targeted region detected a crucial amino acid substitution mutation in the conserved domain of a WRKY29 transcription factor among genotypes bearing major and minor QTL alleles. Similarly, the drought inducible QTL QRdw.5H (5H, 95.0 cM) seems to underlie 37 amino acid deletion and substitution mutations in the conserved domain of two related genes CBF10B and CBF10A, respectively. The identification and further characterization of these candidate genes will be essential to decipher genetics behind developmental and natural adaptation mechanisms of barley.
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