1
|
Bernád V, Al-Tamimi N, Langan P, Gillespie G, Dempsey T, Henchy J, Harty M, Ramsay L, Houston K, Macaulay M, Shaw PD, Raubach S, Mcdonnel KP, Russell J, Waugh R, Khodaeiaminjan M, Negrão S. Unlocking the genetic diversity and population structure of the newly introduced two-row spring European HerItage Barley collecTion (ExHIBiT). FRONTIERS IN PLANT SCIENCE 2024; 15:1268847. [PMID: 38571708 PMCID: PMC10987740 DOI: 10.3389/fpls.2024.1268847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
In the last century, breeding programs have traditionally favoured yield-related traits, grown under high-input conditions, resulting in a loss of genetic diversity and an increased susceptibility to stresses in crops. Thus, exploiting understudied genetic resources, that potentially harbour tolerance genes, is vital for sustainable agriculture. Northern European barley germplasm has been relatively understudied despite its key role within the malting industry. The European Heritage Barley collection (ExHIBiT) was assembled to explore the genetic diversity in European barley focusing on Northern European accessions and further address environmental pressures. ExHIBiT consists of 363 spring-barley accessions, focusing on two-row type. The collection consists of landraces (~14%), old cultivars (~18%), elite cultivars (~67%) and accessions with unknown breeding history (~1%), with 70% of the collection from Northern Europe. The population structure of the ExHIBiT collection was subdivided into three main clusters primarily based on the accession's year of release using 26,585 informative SNPs based on 50k iSelect single nucleotide polymorphism (SNP) array data. Power analysis established a representative core collection of 230 genotypically and phenotypically diverse accessions. The effectiveness of this core collection for conducting statistical and association analysis was explored by undertaking genome-wide association studies (GWAS) using 24,876 SNPs for nine phenotypic traits, four of which were associated with SNPs. Genomic regions overlapping with previously characterised flowering genes (HvZTLb) were identified, demonstrating the utility of the ExHIBiT core collection for locating genetic regions that determine important traits. Overall, the ExHIBiT core collection represents the high level of untapped diversity within Northern European barley, providing a powerful resource for researchers and breeders to address future climate scenarios.
Collapse
Affiliation(s)
- Villő Bernád
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Nadia Al-Tamimi
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Patrick Langan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Gary Gillespie
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Timothy Dempsey
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Joey Henchy
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Mary Harty
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Paul D. Shaw
- Department of Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Kevin P. Mcdonnel
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- School of Biosystems Engineering, University College Dublin, Dublin, Ireland
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Dundee, United Kingdom
| | | | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
2
|
Mleziva AD, Ngumbi EN. Comparative analysis of defensive secondary metabolites in wild teosinte and cultivated maize under flooding and herbivory stress. PHYSIOLOGIA PLANTARUM 2024; 176:e14216. [PMID: 38366721 DOI: 10.1111/ppl.14216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/18/2024]
Abstract
Climate change is driving an alarming increase in the frequency and intensity of abiotic and biotic stress factors, negatively impacting plant development and agricultural productivity. To survive, plants respond by inducing changes in below and aboveground metabolism with concomitant alterations in defensive secondary metabolites. While plant responses to the isolated stresses of flooding and insect herbivory have been extensively studied, much less is known about their response in combination. Wild relatives of cultivated plants with robust stress tolerance traits provide an excellent system for comparing how diverse plant species respond to combinatorial stress, and provide insight into potential germplasms for stress-tolerant hybrids. In this study, we compared the below and aboveground changes in the secondary metabolites of maize (Zea mays) and a flood-tolerant wild relative Nicaraguan teosinte (Zea nicaraguensis) in response to flooding, insect herbivory, and their combination. Root tissue was analyzed for changes in belowground metabolism. Leaf total phenolic content and headspace volatile organic compound emission were analyzed for changes in aboveground secondary metabolism. Results revealed significant differences in the root metabolome profiles of teosinte and maize. Notably, the accumulation of the flavonoids apigenin, naringenin, and luteolin during flooding and herbivory differentiated teosinte from maize. Aboveground, terpenes, including trans-α-bergamotene and (E)-4,8-dimethylnona-1,3,7-triene, shaped compositional differences in their volatile profiles between flooding, herbivory, and their combination. Taken together, these results suggest teosinte may be more tolerant than maize due to dynamic metabolic changes during flooding and herbivory that help relieve stress and influence plant-insect interactions.
Collapse
Affiliation(s)
- Aaron D Mleziva
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Esther N Ngumbi
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
3
|
Khodaverdi M, Mullinger MD, Shafer HR, Preston JC. Melica as an emerging model system for comparative studies in temperate Pooideae grasses. ANNALS OF BOTANY 2023; 132:1175-1190. [PMID: 37696761 PMCID: PMC10902897 DOI: 10.1093/aob/mcad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/10/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND AND AIMS Pooideae grasses contain some of the world's most important crop and forage species. Although much work has been conducted on understanding the genetic basis of trait diversification within a few annual Pooideae, comparative studies at the subfamily level are limited by a lack of perennial models outside 'core' Pooideae. We argue for development of the perennial non-core genus Melica as an additional model for Pooideae, and provide foundational data regarding the group's biogeography and history of character evolution. METHODS Supplementing available ITS and ndhF sequence data, we built a preliminary Bayesian-based Melica phylogeny, and used it to understand how the genus has diversified in relation to geography, climate and trait variation surveyed from various floras. We also determine biomass accumulation under controlled conditions for Melica species collected across different latitudes and compare inflorescence development across two taxa for which whole genome data are forthcoming. KEY RESULTS Our phylogenetic analyses reveal three strongly supported geographically structured Melica clades that are distinct from previously hypothesized subtribes. Despite less geographical affinity between clades, the two sister 'Ciliata' and 'Imperfecta' clades segregate from the more phylogenetically distant 'Nutans' clade in thermal climate variables and precipitation seasonality, with the 'Imperfecta' clade showing the highest levels of trait variation. Growth rates across Melica are positively correlated with latitude of origin. Variation in inflorescence morphology appears to be explained largely through differences in secondary branch distance, phyllotaxy and number of spikelets per secondary branch. CONCLUSIONS The data presented here and in previous studies suggest that Melica possesses many of the necessary features to be developed as an additional model for Pooideae grasses, including a relatively fast generation time, perenniality, and interesting variation in physiology and morphology. The next step will be to generate a genome-based phylogeny and transformation tools for functional analyses.
Collapse
Affiliation(s)
- Masoumeh Khodaverdi
- Department of Plant Biology, The University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Mark D Mullinger
- Department of Plant Biology, The University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Hannah R Shafer
- Department of Plant Biology, The University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Jill C Preston
- Department of Plant Biology, The University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
| |
Collapse
|
4
|
Zhou R, Jiang F, Yu X, Abdelhakim L, Li X, Rosenqvist E, Ottosen CO, Wu Z. Dominant and Priming Role of Waterlogging in Tomato at e[CO2] by Multivariate Analysis. Int J Mol Sci 2022; 23:ijms232012121. [PMID: 36292978 PMCID: PMC9602540 DOI: 10.3390/ijms232012121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/02/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022] Open
Abstract
The frequency of waterlogging episodes has increased due to unpredictable and intense rainfalls. However, less is known about waterlogging memory and its interaction with other climate change events, such as elevated CO2 concentration (e[CO2]). This study investigated the combined effects of e[CO2] and two rounds of waterlogging stress on the growth of cultivated tomato (Solanum lycopersicum) and wild tomato (S. pimpinellifolium). The aim is to elucidate the interaction between genotypes and environmental factors and thereby to improve crop resilience to climate change. We found that two rounds of treatments appeared to induce different acclimation strategies of the two tomato genotypes. S. pimpinellifolium responded more negatively to the first-time waterlogging than S. lycopersicum, as indicated by decreased photosynthesis and biomass loss. Nevertheless, the two genotypes respond similarly when waterlogging stress recurred, showing that they could maintain a higher leaf photosynthesis compared to single stress, especially for the wild genotype. This showed that waterlogging priming played a positive role in stress memory in both tomato genotypes. Multivariate analysis showed that waterlogging played a dominant role when combined with [CO2] for both the cultivated and wild tomato genotypes. This work will benefit agricultural production strategies by pinpointing the positive effects of e[CO2] and waterlogging memory.
Collapse
Affiliation(s)
- Rong Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Food Science, Aarhus University, DK-8200 Aarhus, Denmark
- Correspondence: (R.Z.); (Z.W.)
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaqing Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lamis Abdelhakim
- Department of Food Science, Aarhus University, DK-8200 Aarhus, Denmark
| | - Xiangnan Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Eva Rosenqvist
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-2630 Taastrup, Denmark
| | - Carl-Otto Ottosen
- Department of Food Science, Aarhus University, DK-8200 Aarhus, Denmark
| | - Zhen Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (R.Z.); (Z.W.)
| |
Collapse
|
5
|
Zhou R, Yu X, Song X, Rosenqvist E, Wan H, Ottosen CO. Salinity, waterlogging, and elevated [CO2] interact to induce complex responses in cultivated and wild tomato. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5252-5263. [PMID: 35218649 DOI: 10.1093/jxb/erac080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
The effects of individual climatic factors on crops are well documented, whereas the interaction of such factors in combination has received less attention. The frequency of salinity and waterlogging stress is increasing with climate change, accompanied by elevated CO2 concentration (e[CO2]). This study explored how these three variables interacted and affected two tomato genotypes. Cultivated and wild tomato (Solanum lycopersicum and Solanum pimpinellifolium) were grown at ambient [CO2] and e[CO2], and subjected to salinity, waterlogging, and combined stress. Leaf photosynthesis, chlorophyll fluorescence, quenching analysis, pigment, and plant growth were analyzed. The response of tomatoes depended on both genotype and stress type. In cultivated tomato, photosynthesis was inhibited by salinity and combined stress, whereas in wild tomato, both salinity and waterlogging stress, alone and in combination, decreased photosynthesis. e[CO2] increased photosynthesis and biomass of cultivated tomato under salinity and combined stress compared with ambient [CO2]. Differences between tomato genotypes in response to individual and combined stress were observed in key photosynthetic and growth parameters. Hierarchical clustering and principal component analysis revealed genetic variations of tomatoes responding to the three climatic factors. Understanding the interacting effects of salinity and waterlogging with e[CO2] in tomato will facilitate improvement of crop resilience to climate change.
Collapse
Affiliation(s)
- Rong Zhou
- Department of Food Science, Aarhus University, Aarhus, Denmark
- College of Horticulture, Nanjing Agricultural University, Jiangsu, Nanjing, China
| | - Xiaqing Yu
- College of Horticulture, Nanjing Agricultural University, Jiangsu, Nanjing, China
| | - Xiaoming Song
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Eva Rosenqvist
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Hongjian Wan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | | |
Collapse
|