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
|
Schreiber M, Wonneberger R, Haaning AM, Coulter M, Russell J, Himmelbach A, Fiebig A, Muehlbauer GJ, Stein N, Waugh R. Genomic resources for a historical collection of cultivated two-row European spring barley genotypes. Sci Data 2024; 11:66. [PMID: 38216606 PMCID: PMC10786862 DOI: 10.1038/s41597-023-02850-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 12/12/2023] [Indexed: 01/14/2024] Open
Abstract
Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one of the latest developments. Two-row spring barley cultivars are intensely studied as they are the source of high-quality grain for malting and distilling. Here we provide data from a European two-row spring barley population containing 209 different genotypes registered for the UK market between 1830 to 2014. The dataset encompasses RNA-sequencing data from six different tissues across a range of barley developmental stages, phenotypic datasets from two consecutive years of field-grown trials in the United Kingdom, Germany and the USA; and whole genome shotgun sequencing from all cultivars, which was used to complement the RNA-sequencing data for variant calling. The outcomes are a filtered SNP marker file, a phenotypic database and a large gene expression dataset providing a comprehensive resource which allows for downstream analyses like genome wide association studies or expression associations.
Collapse
Affiliation(s)
- Miriam Schreiber
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK
| | - Ronja Wonneberger
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Allison M Haaning
- Department of Agronomy and Plant Genetics, The University of Minnesota, St. Paul, MN, 55108, USA
| | - Max Coulter
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, The University of Minnesota, St. Paul, MN, 55108, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK.
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK.
| |
Collapse
|
3
|
Du B, Wu J, Wang M, Wu J, Sun C, Zhang X, Ren X, Wang Q. Detection of consensus genomic regions and candidate genes for quality traits in barley using QTL meta-analysis. FRONTIERS IN PLANT SCIENCE 2024; 14:1319889. [PMID: 38283973 PMCID: PMC10811794 DOI: 10.3389/fpls.2023.1319889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
Improving barley grain quality is a major goal in barley breeding. In this study, a total of 35 papers focusing on quantitative trait loci (QTLs) mapping for barley quality traits published since 2000 were collected. Among the 454 QTLs identified in these studies, 349 of them were mapped onto high-density consensus maps, which were used for QTL meta-analysis. Through QTL meta-analysis, the initial QTLs were integrated into 41 meta-QTLs (MQTLs) with an average confidence interval (CI) of 1. 66 cM, which is 88.9% narrower than that of the initial QTLs. Among the 41 identified MQTLs, 25 were subsequently validated in publications using genome-wide association study (GWAS). From these 25 validated MQTLs, ten breeder's MQTLs were selected. Synteny analysis comparing barley and wheat MQTLs revealed orthologous relationships between eight breeder's MQTLs and 45 wheat MQTLs. Additionally, 17 barley homologs associated with rice quality traits were identified within the regions of the breeder's MQTLs through comparative analysis. The findings of this study provide valuable insights for molecular marker-assisted breeding and the identification of candidate genes related to quality traits in barley.
Collapse
Affiliation(s)
- Binbin Du
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Jindong Wu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Meng Wang
- Xingtai Agriculture and Rural Bureau, Xingtai, Hebei, China
| | - Jia Wu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Chaoyue Sun
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Xingen Zhang
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Xifeng Ren
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qifei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| |
Collapse
|
4
|
Taketa S, Kim JS, Takahashi H, Yajima S, Koshiishi Y, Sotome T, Kato T, Mochida K. Genomic traces of Japanese malting barley breeding in two modern high-quality cultivars, 'Sukai Golden' and 'Sachiho Golden'. BREEDING SCIENCE 2023; 73:435-444. [PMID: 38737917 PMCID: PMC11082453 DOI: 10.1270/jsbbs.23031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/08/2023] [Indexed: 05/14/2024]
Abstract
Two modern high-quality Japanese malting barley cultivars, 'Sukai Golden' and 'Sachiho Golden', were subjected to RNA-sequencing of transcripts extracted from 20-day-old immature seeds. Despite their close relation, 2,419 Sukai Golden-specific and 3,058 Sachiho Golden-specific SNPs were detected in comparison to the genome sequences of two reference cultivars: 'Morex' and 'Haruna Nijo'. Two single nucleotide polymorphism (SNP) clusters respectively showing the incorporation of (1) the barley yellow mosaic virus (BaYMV) resistance gene rym5 from six-row non-malting Chinese landrace Mokusekko 3 on the long arm of 3H, and (2) the anthocyanin-less ant2 gene from a two-row Dutch cultivar on the long arm of 2H were detected specifically in 'Sukai Golden'. Using 221 recombinant inbred lines of a cross between 'Ishukushirazu' and 'Nishinochikara', another BaYMV resistance rym3 gene derived from six-row non-malting Japanese cultivar 'Haganemugi' was mapped to a 0.4-cM interval on the proximal region of 5H. Haplotype analysis of progenitor accessions of the two modern malting cultivars revealed that rym3 of 'Haganemugi' was independently introduced into 'Sukai Golden' and 'Sachiho Golden'. Residual chromosome 5H segments of 'Haganemugi' surrounding rym3 were larger in 'Sukai Golden'. Available results suggest possibilities for malting quality improvement by minimizing residual segments surrounding rym3.
Collapse
Affiliation(s)
- Shin Taketa
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - June-Sik Kim
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hidekazu Takahashi
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima 960-1296, Japan
| | - Shunsuke Yajima
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yuichi Koshiishi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Toshinori Sotome
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, Tochigi 320-0002, Japan
| | - Tsuneo Kato
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, Tochigi 320-0002, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| |
Collapse
|
5
|
Li M, Cai K, Zheng N, Zhang G, Ye L. Identification of the Key Transcription Factors Regulating the Expression of the Genes Associated with Barley Malt Quality during Malting. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:8241-8251. [PMID: 37192323 DOI: 10.1021/acs.jafc.3c00988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Barley malt is produced through a malting process; it begins with steeping followed by germination and kilning, in which dramatic changes happen for a large number of physiological and biochemical traits in barley seeds. The objectives of this study were to comprehensively investigate the phenotypic changes during malting, and identify the key regulators that modulate the expression of genes associated with malt quality traits. The results showed that there was a significant positive correlation between gibberellic acid (GA) content and the activities of some hydrolytic enzymes, including α-amylases, β-amylases, and limit dextrinase (LD), and a significant negative correlation between GA and β-glucan content. Starch content had little change, but starch granules were pitted severely during malting. Weighted gene coexpression analysis (WGCNA) identified the genes associated with the greatest changes of the examined malt traits during malting. The correlation analysis and protein-protein interaction (PPI) analysis detected several key transcriptional factor (TF) regulating genes associated with malt quality. These genes and TFs regulating malting traits are potentially useful in barley breeding for malt quality improvement.
Collapse
Affiliation(s)
- Mengdi Li
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
| | - Kangfeng Cai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310058, PR China
| | - Nannan Zheng
- Zhongyuan Institute, Zhejiang University, Zhengzhou 450000, PR China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
- Zhongyuan Institute, Zhejiang University, Zhengzhou 450000, PR China
| | - Lingzhen Ye
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
- Zhongyuan Institute, Zhejiang University, Zhengzhou 450000, PR China
| |
Collapse
|
6
|
Houston K, Learmonth A, Hassan AS, Lahnstein J, Looseley M, Little A, Waugh R, Burton RA, Halpin C. Natural variation in HvAT10 underlies grain cell wall-esterified phenolic acid content in cultivated barley. FRONTIERS IN PLANT SCIENCE 2023; 14:1095862. [PMID: 37235033 PMCID: PMC10206312 DOI: 10.3389/fpls.2023.1095862] [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: 11/11/2022] [Accepted: 04/06/2023] [Indexed: 05/28/2023]
Abstract
The phenolic acids, ferulic acid and p-coumaric acid, are components of plant cell walls in grasses, including many of our major food crops. They have important health-promoting properties in grain, and influence the digestibility of biomass for industrial processing and livestock feed. Both phenolic acids are assumed to be critical to cell wall integrity and ferulic acid, at least, is important for cross-linking cell wall components, but the role of p-coumaric acid is unclear. Here we identify alleles of a BAHD p-coumaroyl arabinoxylan transferase, HvAT10, as responsible for the natural variation in cell wall-esterified phenolic acids in whole grain within a cultivated two-row spring barley panel. We show that HvAT10 is rendered non-functional by a premature stop codon mutation in half of the genotypes in our mapping panel. This results in a dramatic reduction in grain cell wall-esterifed p-coumaric acid, a moderate rise in ferulic acid, and a clear increase in the ferulic acid to p-coumaric acid ratio. The mutation is virtually absent in wild and landrace germplasm suggesting an important function for grain arabinoxylan p-coumaroylation pre-domestication that is dispensable in modern agriculture. Intriguingly, we detected detrimental impacts of the mutated locus on grain quality traits where it was associated with smaller grain and poorer malting properties. HvAT10 could be a focus for improving grain quality for malting or phenolic acid content in wholegrain foods.
Collapse
Affiliation(s)
- Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Scotland, United Kingdom
| | - Amy Learmonth
- Division of Plant Sciences, School of Life Sciences, University of Dundee at The James Hutton Institute, Scotland, United Kingdom
| | - Ali Saleh Hassan
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Jelle Lahnstein
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Mark Looseley
- Cell and Molecular Sciences, The James Hutton Institute, Scotland, United Kingdom
| | - Alan Little
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Scotland, United Kingdom
- Division of Plant Sciences, School of Life Sciences, University of Dundee at The James Hutton Institute, Scotland, United Kingdom
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Rachel A. Burton
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee at The James Hutton Institute, Scotland, United Kingdom
| |
Collapse
|
7
|
Rooney TE, Sweeney DW, Kunze KH, Sorrells ME, Walling JG. Malting quality and preharvest sprouting traits are genetically correlated in spring malting barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:59. [PMID: 36912946 PMCID: PMC10011292 DOI: 10.1007/s00122-023-04257-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Malt for craft "all-malt" brewing can have high quality, PHS resistance, and malted in normal timeframes. Canadian style adjunct malt is associated with PHS susceptibility. Expansion of malting barley production into non-traditional growing regions and erratic weather has increased the demand for preharvest sprouting (PHS) resistant, high quality malting barley cultivars. This is hindered by the relatively unknown relationships between PHS resistance and malting quality. Here we present a three-year study of malting quality and germination at different after-ripening durations post physiological maturity. Malting quality traits alpha amylase (AA) and free amino nitrogen (FAN) and germination rate at six days post PM shared a common association with a SNP in HvMKK3 on chromosome 5H in the Seed Dormancy 2 (SD2) region responsible for PHS susceptibility. Soluble protein (SP) and soluble over total protein (S/T) both shared a common association with a marker in the SD2 region. Significant genetic correlations between PHS resistance and the malting quality traits AA, FAN, SP, S/T were detected across and within HvMKK3 allele groups. High adjunct malt quality was related to PHS susceptibility. Selection for PHS resistance led to a correlated response in malting quality traits. Results strongly suggest pleiotropy of HvMKK3 on malting quality traits and that the classic "Canadian-style" malt is caused by a PHS susceptible allele of HvMKK3. PHS susceptibility appears to benefit the production of malt intended for adjunct brewing, while PHS resistance is compatible with all-malt brewing specifications. Here we present our analysis on the effect of combining complexly inherited and correlated traits with contrasting goals to inform breeding practice in malting barley, the general principles of which can be extended to other breeding programs.
Collapse
Affiliation(s)
- Travis E Rooney
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel W Sweeney
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Karl H Kunze
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Jason G Walling
- USDA-ARS - Cereal Crops Research Unit, 502 Walnut St, Madison, WI, 53726, USA.
| |
Collapse
|
8
|
Bouhlal O, Visioni A, Verma RPS, Kandil M, Gyawali S, Capettini F, Sanchez-Garcia M. CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world. FRONTIERS IN PLANT SCIENCE 2022; 13:1034322. [PMID: 36452106 PMCID: PMC9702823 DOI: 10.3389/fpls.2022.1034322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Breeding programs in developing countries still cannot afford the new genotyping technologies, hindering their research. We aimed to assemble an Association Mapping panel to serve as CGIAR Barley Breeding Toolbox (CBBT), especially for the Developing World. The germplasm had to be representative of the one grown in the Developing World; with high genetic variability and be of public domain. For it, we genotyped with the Infinium iSelect 50K chip, a Global Barley Panel (GBP) of 530 genotypes representing a wide range of row-types, end-uses, growth habits, geographical origins and environments. 40,342 markers were polymorphic with an average polymorphism information content of 0.35 and 66% of them exceeding 0.25. The analysis of the population structure identified 8 subpopulations mostly linked to geographical origin, four of them with significant ICARDA origin. The 16 allele combinations at 4 major flowering genes (HvVRN-H3, HvPPD-H1, HvVRN-H1 and HvCEN) explained 11.07% genetic variation and were linked to the geographic origins of the lines. ICARDA material showed the widest diversity as revealed by the highest number of polymorphic loci (99.76% of all polymorphic SNPs in GBP), number of private alleles and the fact that ICARDA lines were present in all 8 subpopulations and carried all 16 allelic combinations. Due to their genetic diversity and their representativity of the germplasm adapted to the Developing World, ICARDA-derived lines and cultivated landraces were pre-selected to form the CBBT. Using the Mean of Transformed Kinships method, we assembled a panel capturing most of the allelic diversity in the GBP. The CBBT (N=250) preserves good balance between row-types and good representation of both phenology allelic combinations and subpopulations of the GBP. The CBBT and its genotypic data is available to researchers worldwide as a collaborative tool to underpin the genetic mechanisms of traits of interest for barley cultivation.
Collapse
Affiliation(s)
- Outmane Bouhlal
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, El-Jadida, Morocco
| | - Andrea Visioni
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | | | - Mostafa Kandil
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, El-Jadida, Morocco
| | | | | | - Miguel Sanchez-Garcia
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| |
Collapse
|
9
|
Yang CJ, Ladejobi O, Mott R, Powell W, Mackay I. Analysis of historical selection in winter wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3005-3023. [PMID: 35864201 PMCID: PMC9482581 DOI: 10.1007/s00122-022-04163-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE Modeling of the distribution of allele frequency over year of variety release identifies major loci involved in historical breeding of winter wheat. Winter wheat is a major crop with a rich selection history in the modern era of crop breeding. Genetic gains across economically important traits like yield have been well characterized and are the major force driving its production. Winter wheat is also an excellent model for analyzing historical genetic selection. As a proof of concept, we analyze two major collections of winter wheat varieties that were bred in Western Europe from 1916 to 2010, namely the Triticeae Genome (TG) and WAGTAIL panels, which include 333 and 403 varieties, respectively. We develop and apply a selection mapping approach, Regression of Alleles on Years (RALLY), in these panels, as well as in simulated populations. RALLY maps loci under sustained historical selection by using a simple logistic model to regress allele counts on years of variety release. To control for drift-induced allele frequency change, we develop a hybrid approach of genomic control and delta control. Within the TG panel, we identify 22 significant RALLY quantitative selection loci (QSLs) and estimate the local heritabilities for 12 traits across these QSLs. By correlating predicted marker effects with RALLY regression estimates, we show that alleles whose frequencies have increased over time are heavily biased toward conferring positive yield effect, but negative effects in flowering time, lodging, plant height and grain protein content. Altogether, our results (1) demonstrate the use of RALLY to identify selected genomic regions while controlling for drift, and (2) reveal key patterns in the historical selection in winter wheat and guide its future breeding.
Collapse
Affiliation(s)
- Chin Jian Yang
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Olufunmilayo Ladejobi
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Richard Mott
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Wayne Powell
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Ian Mackay
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.
- IMplant Consultancy Ltd, Chelmsford, UK.
| |
Collapse
|
10
|
Shorinola O, Simmonds J, Wingen LU, Uauy C. Trend, population structure, and trait mapping from 15 years of national varietal trials of UK winter wheat. G3 GENES|GENOMES|GENETICS 2022; 12:6460332. [PMID: 34897454 PMCID: PMC9210278 DOI: 10.1093/g3journal/jkab415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/22/2021] [Indexed: 11/15/2022]
Abstract
There are now a rich variety of genomic and genotypic resources available to wheat researchers and breeders. However, the generation of high-quality and field-relevant phenotyping data which is required to capture the complexities of gene × environment interactions remains a major bottleneck. Historical datasets from national variety performance trials (NVPT) provide sufficient dimensions, in terms of numbers of years and locations, to examine phenotypic trends and study gene × environment interactions. Using NVPT for winter wheat varieties grown in the United Kingdom between 2002 and 2017, we examined temporal trends for eight traits related to yield, adaptation, and grain quality performance. We show a non-stationary linear trend for yield, grain protein content, Hagberg Falling Number (HFN), and days to ripening. Our data also show high environmental stability for yield, grain protein content, and specific weight in UK winter wheat varieties and high environmental sensitivity for HFN. We also show that UK varieties released within this period cluster into four main population groups. Using the historical NVPT data in a genome-wide association analysis, we uncovered a significant marker-trait association peak on wheat chromosome 6A spanning the NAM-A1 gene that have been previously associated with early senescence. Together, our results show the value of utilizing the data routinely collected during national variety evaluation process for examining breeding progress and the genetic architecture of important traits.
Collapse
Affiliation(s)
- Oluwaseyi Shorinola
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Bioscience Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI), Nairobi 00100, Kenya
| | - James Simmonds
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Luzie U Wingen
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Cristobal Uauy
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| |
Collapse
|
11
|
Sharma R, Cockram J, Gardner KA, Russell J, Ramsay L, Thomas WTB, O'Sullivan DM, Powell W, Mackay IJ. Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:667-678. [PMID: 34778903 PMCID: PMC8866380 DOI: 10.1007/s00122-021-03991-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/02/2021] [Indexed: 05/26/2023]
Abstract
Variety age and population structure detect novel QTL for yield and adaptation in wheat and barley without the need to phenotype. The process of crop breeding over the last century has delivered new varieties with increased genetic gains, resulting in higher crop performance and yield. However, in many cases, the alleles and genomic regions underpinning this success remain unknown. This is partly due to the difficulty of generating sufficient phenotypic data on large numbers of historical varieties to enable such analyses. Here we demonstrate the ability to circumvent such bottlenecks by identifying genomic regions selected over 100 years of crop breeding using age of a variety as a surrogate for yield. Rather than collecting phenotype data, we deployed 'environmental genome-wide association scans' (EnvGWAS) based on variety age in two of the world's most important crops, wheat and barley, and detected strong signals of selection across both genomes. EnvGWAS identified 16 genomic regions in barley and 10 in wheat with contrasting patterns between spring and winter types of the two crops. To further examine changes in genome structure, we used the genomic relationship matrix of the genotypic data to derive eigenvectors for analysis in EigenGWAS. This detected seven major chromosomal introgressions that contributed to adaptation in wheat. EigenGWAS and EnvGWAS based on variety age avoid costly phenotyping and facilitate the identification of genomic tracts that have been under selection during breeding. Our results demonstrate the potential of using historical cultivar collections coupled with genomic data to identify chromosomal regions under selection and may help guide future plant breeding strategies to maximise the rate of genetic gain and adaptation.
Collapse
Affiliation(s)
- Rajiv Sharma
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - James Cockram
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Keith A Gardner
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Luke Ramsay
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, UK
| | - Wayne Powell
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Ian J Mackay
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.
| |
Collapse
|
12
|
Qin Q, Liu J, Hu S, Dong J, Yu J, Fang L, Huang S, Wang L. Comparative proteomic analysis of different barley cultivars during seed germination. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2021.103357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
Morrissy CP, Féchir M, Bettenhausen HM, Van Simaeys KR, Fisk S, Hernandez J, Mathias K, Benson A, Shellhammer TH, Hayes PM. Continued Exploration of Barley Genotype Contribution to Base Malt and Beer Flavor Through the Evaluation of Lines Sharing Maris Otter® Parentage. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2021. [DOI: 10.1080/03610470.2021.1952509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Campbell P. Morrissy
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, U.S.A
| | - Michael Féchir
- Department of Food Science and Technology, Oregon State University, Corvallis, Oregon, U.S.A
| | - Harmonie M. Bettenhausen
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado, USA
| | - Karli R. Van Simaeys
- Department of Food Science and Technology, Oregon State University, Corvallis, Oregon, U.S.A
| | - Scott Fisk
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, U.S.A
| | - Javier Hernandez
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, U.S.A
| | | | | | - Thomas H. Shellhammer
- Department of Food Science and Technology, Oregon State University, Corvallis, Oregon, U.S.A
| | - Patrick M. Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, U.S.A
| |
Collapse
|
14
|
Miricescu A, Byrne T, Doorly CM, Ng CKY, Barth S, Graciet E. Experimental comparison of two methods to study barley responses to partial submergence. PLANT METHODS 2021; 17:40. [PMID: 33849604 PMCID: PMC8045378 DOI: 10.1186/s13007-021-00742-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 03/31/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Crop yield is dependent on climate conditions, which are becoming both more variable and extreme in some areas of the world as a consequence of global climate change. Increased precipitation and flooding events are the cause of important yield losses due to waterlogging or (partial) submergence of crops in the field. Our ability to screen efficiently and quickly for varieties that have increased tolerance to waterlogging or (partial) submergence is important. Barley, a staple crop worldwide, is particularly sensitive to waterlogging. Screening for waterlogging tolerant barley varieties has been ongoing for many years, but methods used to screen vary greatly, from the type of soil used to the time at which the treatment is applied. This variation makes it difficult to cross-compare results. RESULTS Here, we have devised a scoring system to assess barley tolerance to waterlogging and compare two different methods when partial submergence is applied with either water or a starch solution at an early developmental stage, which is particularly sensitive to waterlogging or partial submergence. The use of a starch solution has been previously shown to result in more reducing soil conditions and has been used to screen for waterlogging tolerance. CONCLUSIONS Our results show that the two methods provide similar results to qualitatively rank varieties as tolerant or sensitive, while also affecting plants differently, in that application of a starch solution results in stronger and earlier symptoms than applying partial submergence with water.
Collapse
Affiliation(s)
| | - Tomás Byrne
- Crop Science Department, Teagasc Crops, Environment and Land Use Program, Oak Park, Carlow, R93XE12, Ireland
| | - Catherine M Doorly
- Department of Biology, Maynooth University, Maynooth, Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Kildare, Ireland
| | - Carl K Y Ng
- School of Biology and Environmental Science, Centre for Plant Science, UCD Earth Institute, O'Brien Centre for Science West, University College Dublin, Belfield, Dublin, D04 N2E5, Ireland.
| | - Susanne Barth
- Crop Science Department, Teagasc Crops, Environment and Land Use Program, Oak Park, Carlow, R93XE12, Ireland.
| | - Emmanuelle Graciet
- Department of Biology, Maynooth University, Maynooth, Kildare, Ireland.
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Kildare, Ireland.
| |
Collapse
|