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Coombes B, Fellers JP, Grewal S, Rusholme‐Pilcher R, Hubbart‐Edwards S, Yang C, Joynson R, King IP, King J, Hall A. Whole-genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines. Plant Biotechnol J 2023; 21:482-496. [PMID: 35598169 PMCID: PMC9946142 DOI: 10.1111/pbi.13859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/28/2022] [Accepted: 05/15/2022] [Indexed: 05/29/2023]
Abstract
Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat's wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterize introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilization of introgression pre-breeding material in wheat breeding programmes.
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Affiliation(s)
| | - John P. Fellers
- USDA–ARS Hard Winter Wheat Genetics Research UnitManhattanKansas66506USA
| | - Surbhi Grewal
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | | | - Stella Hubbart‐Edwards
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | - Cai‐yun Yang
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | | | - Ian P. King
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | - Julie King
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
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Sales CRG, Molero G, Evans JR, Taylor SH, Joynson R, Furbank RT, Hall A, Carmo-Silva E. Phenotypic variation in photosynthetic traits in wheat grown under field versus glasshouse conditions. J Exp Bot 2022; 73:3221-3237. [PMID: 35271722 PMCID: PMC9126738 DOI: 10.1093/jxb/erac096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/08/2022] [Indexed: 05/19/2023]
Abstract
Recognition of the untapped potential of photosynthesis to improve crop yields has spurred research to identify targets for breeding. The CO2-fixing enzyme Rubisco is characterized by a number of inefficiencies, and frequently limits carbon assimilation at the top of the canopy, representing a clear target for wheat improvement. Two bread wheat lines with similar genetic backgrounds and contrasting in vivo maximum carboxylation activity of Rubisco per unit leaf nitrogen (Vc,max,25/Narea) determined using high-throughput phenotyping methods were selected for detailed study from a panel of 80 spring wheat lines. Detailed phenotyping of photosynthetic traits in the two lines using glasshouse-grown plants showed no difference in Vc,max,25/Narea determined directly via in vivo and in vitro methods. Detailed phenotyping of glasshouse-grown plants of the 80 wheat lines also showed no correlation between photosynthetic traits measured via high-throughput phenotyping of field-grown plants. Our findings suggest that the complex interplay between traits determining crop productivity and the dynamic environments experienced by field-grown plants needs to be considered in designing strategies for effective wheat crop yield improvement when breeding for particular environments.
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Affiliation(s)
- Cristina R G Sales
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster LA1 4YQ, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- Correspondence: or
| | - Gemma Molero
- International Maize and Wheat Improvement Centre (CIMMYT), Int. Apdo. Postal 6-641, 06600 Mexico, DF, Mexico
- KWS Momont Recherche, 7 rue de Martinval, 59246 Mons-en-Pévèle, France
| | - John R Evans
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Samuel H Taylor
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster LA1 4YQ, UK
| | - Ryan Joynson
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UG, UK
- Limagrain Europe, CS 3911, 63720 Chappes, France
| | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Anthony Hall
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UG, UK
| | - Elizabete Carmo-Silva
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster LA1 4YQ, UK
- Correspondence: or
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3
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Grewal S, Coombes B, Joynson R, Hall A, Fellers J, Yang CY, Scholefield D, Ashling S, Isaac P, King IP, King J. Chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines. Plant Genome 2022; 15:e20193. [PMID: 35102721 DOI: 10.1002/tpg2.20193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/20/2021] [Indexed: 05/23/2023]
Abstract
Many wild-relative species are being used in prebreeding programs to increase the genetic diversity of wheat (Triticum aestivum L.). Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterize wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based Kompetitive allele-specific polymerase chain reaction (KASP) markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and polymerase chain reaction (PCR)-amplicon-based sequencing of the wild species. But chromosome-specific KASP assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum (Boiss.) Eig and development of a de novo SNP discovery pipeline that generated ∼38,000 SNPs in unique wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as diagnostic for Am. muticum in a wheat background. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome-specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | | | - Ryan Joynson
- Earlham Institute, Norwich Research Park, Norwich, UK
- Current address: Limagrain Europe, Clermont-Ferrand, France
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - John Fellers
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Cai-Yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Peter Isaac
- iDna Genetics Ltd., Norwich Research Park, Norwich, UK
| | - Ian P King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
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Lyra DH, Griffiths CA, Watson A, Joynson R, Molero G, Igna AA, Hassani-Pak K, Reynolds MP, Hall A, Paul MJ. Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel. Food Energy Secur 2021; 10:e292. [PMID: 34594548 PMCID: PMC8459250 DOI: 10.1002/fes3.292] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Trehalose 6‐phosphate (T6P) signalling regulates carbon use and allocation and is a target to improve crop yields. However, the specific contributions of trehalose phosphate synthase (TPS) and trehalose phosphate phosphatase (TPP) genes to source‐ and sink‐related traits remain largely unknown. We used enrichment capture sequencing on TPS and TPP genes to estimate and partition the genetic variation of yield‐related traits in a spring wheat (Triticum aestivum) breeding panel specifically built to capture the diversity across the 75,000 CIMMYT wheat cultivar collection. Twelve phenotypes were correlated to variation in TPS and TPP genes including plant height and biomass (source), spikelets per spike, spike growth and grain filling traits (sink) which showed indications of both positive and negative gene selection. Individual genes explained proportions of heritability for biomass and grain‐related traits. Three TPS1 homologues were particularly significant for trait variation. Epistatic interactions were found within and between the TPS and TPP gene families for both plant height and grain‐related traits. Gene‐based prediction improved predictive ability for grain weight when gene effects were combined with the whole‐genome markers. Our study has generated a wealth of information on natural variation of TPS and TPP genes related to yield potential which confirms the role for T6P in resource allocation and in affecting traits such as grain number and size confirming other studies which now opens up the possibility of harnessing natural genetic variation more widely to better understand the contribution of native genes to yield traits for incorporation into breeding programmes.
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Affiliation(s)
- Danilo H Lyra
- Computational & Analytical Sciences Rothamsted Research Harpenden UK
| | | | - Amy Watson
- Plant Sciences Rothamsted Research Harpenden UK
| | | | - Gemma Molero
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT) Texcoco Mexico
| | | | | | - Matthew P Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT) Texcoco Mexico
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5
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Joynson R, Molero G, Coombes B, Gardiner L, Rivera‐Amado C, Piñera‐Chávez FJ, Evans JR, Furbank RT, Reynolds MP, Hall A. Uncovering candidate genes involved in photosynthetic capacity using unexplored genetic variation in Spring Wheat. Plant Biotechnol J 2021; 19:1537-1552. [PMID: 33638599 PMCID: PMC8384606 DOI: 10.1111/pbi.13568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/26/2021] [Indexed: 05/10/2023]
Abstract
To feed an ever-increasing population we must leverage advances in genomics and phenotyping to harness the variation in wheat breeding populations for traits like photosynthetic capacity which remains unoptimized. Here we survey a diverse set of wheat germplasm containing elite, introgression and synthetic derivative lines uncovering previously uncharacterized variation. We demonstrate how strategic integration of exotic material alleviates the D genome genetic bottleneck in wheat, increasing SNP rate by 62% largely due to Ae. tauschii synthetic wheat donors. Across the panel, 67% of the Ae. tauschii donor genome is represented as introgressions in elite backgrounds. We show how observed genetic variation together with hyperspectral reflectance data can be used to identify candidate genes for traits relating to photosynthetic capacity using association analysis. This demonstrates the value of genomic methods in uncovering hidden variation in wheat and how that variation can assist breeding efforts and increase our understanding of complex traits.
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Affiliation(s)
| | - Gemma Molero
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT)TexcocoMexico
| | | | | | - Carolina Rivera‐Amado
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT)TexcocoMexico
| | | | - John R. Evans
- ARC Centre of Excellence for Translational PhotosynthesisAustralian National UniversityCanberraAustralia
| | - Robert T. Furbank
- ARC Centre of Excellence for Translational PhotosynthesisAustralian National UniversityCanberraAustralia
| | - Matthew P. Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT)TexcocoMexico
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6
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Li Y, Leveau A, Zhao Q, Feng Q, Lu H, Miao J, Xue Z, Martin AC, Wegel E, Wang J, Orme A, Rey MD, Karafiátová M, Vrána J, Steuernagel B, Joynson R, Owen C, Reed J, Louveau T, Stephenson MJ, Zhang L, Huang X, Huang T, Fan D, Zhou C, Tian Q, Li W, Lu Y, Chen J, Zhao Y, Lu Y, Zhu C, Liu Z, Polturak G, Casson R, Hill L, Moore G, Melton R, Hall N, Wulff BBH, Doležel J, Langdon T, Han B, Osbourn A. Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals. Nat Commun 2021; 12:2563. [PMID: 33963185 PMCID: PMC8105312 DOI: 10.1038/s41467-021-22920-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Non-random gene organization in eukaryotes plays a significant role in genome evolution. Here, we investigate the origin of a biosynthetic gene cluster for production of defence compounds in oat-the avenacin cluster. We elucidate the structure and organisation of this 12-gene cluster, characterise the last two missing pathway steps, and reconstitute the entire pathway in tobacco by transient expression. We show that the cluster has formed de novo since the divergence of oats in a subtelomeric region of the genome that lacks homology with other grasses, and that gene order is approximately colinear with the biosynthetic pathway. We speculate that the positioning of the late pathway genes furthest away from the telomere may mitigate against a 'self-poisoning' scenario in which toxic intermediates accumulate as a result of telomeric gene deletions. Our investigations reveal a striking example of adaptive evolution underpinned by remarkable genome plasticity.
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Affiliation(s)
- Yan Li
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | | | - Qiang Zhao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Qi Feng
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hengyun Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jiashun Miao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Zheyong Xue
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Eva Wegel
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Jing Wang
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Miroslava Karafiátová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Ryan Joynson
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - James Reed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Lei Zhang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xuehui Huang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Tao Huang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Danling Fan
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Congcong Zhou
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Qilin Tian
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Wenjun Li
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yiqi Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jiaying Chen
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yan Zhao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Ying Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Chuanrang Zhu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guy Polturak
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Lionel Hill
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Rachel Melton
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Bin Han
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China.
| | - Anne Osbourn
- John Innes Centre, Norwich Research Park, Norwich, UK.
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Rees H, Joynson R, Brown JKM, Hall A. Naturally occurring circadian rhythm variation associated with clock gene loci in Swedish Arabidopsis accessions. Plant Cell Environ 2021; 44:807-820. [PMID: 33179278 PMCID: PMC7986795 DOI: 10.1111/pce.13941] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 05/25/2023]
Abstract
Circadian clocks have evolved to resonate with external day and night cycles. However, these entrainment signals are not consistent everywhere and vary with latitude, climate and seasonality. This leads to divergent selection for clocks which are locally adapted. To investigate the genetic basis for this circadian variation, we used a delayed fluorescence imaging assay to screen 191 naturally occurring Swedish Arabidopsis accessions for their circadian phenotypes. We demonstrate that the period length co-varies with both geography and population sub-structure. Several candidate loci linked to period, phase and relative amplitude error (RAE) were revealed by genome-wide association mapping and candidate genes were investigated using TDNA mutants. We show that natural variation in a single non-synonymous substitution within COR28 is associated with a long-period and late-flowering phenotype similar to that seen in TDNA knock-out mutants. COR28 is a known coordinator of flowering time, freezing tolerance and the circadian clock; all of which may form selective pressure gradients across Sweden. We demonstrate the effect of the COR28-58S SNP in increasing period length through a co-segregation analysis. Finally, we show that period phenotypic tails remain diverged under lower temperatures and follow a distinctive "arrow-shaped" trend indicative of selection for a cold-biased temperature compensation response.
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Affiliation(s)
- Hannah Rees
- Organisms and EcosystemsEarlham Institute, Norwich Research ParkNorwichUK
- Institute of Integrative Biology, University of LiverpoolLiverpoolUK
| | - Ryan Joynson
- Organisms and EcosystemsEarlham Institute, Norwich Research ParkNorwichUK
| | | | - Anthony Hall
- Organisms and EcosystemsEarlham Institute, Norwich Research ParkNorwichUK
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8
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Molero G, Joynson R, Pinera‐Chavez FJ, Gardiner L, Rivera‐Amado C, Hall A, Reynolds MP. Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential. Plant Biotechnol J 2019; 17:1276-1288. [PMID: 30549213 PMCID: PMC6576103 DOI: 10.1111/pbi.13052] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/20/2018] [Accepted: 11/25/2018] [Indexed: 05/22/2023]
Abstract
One of the major challenges for plant scientists is increasing wheat (Triticum aestivum) yield potential (YP). A significant bottleneck for increasing YP is achieving increased biomass through optimization of radiation use efficiency (RUE) along the crop cycle. Exotic material such as landraces and synthetic wheat has been incorporated into breeding programmes in an attempt to alleviate this; however, their contribution to YP is still unclear. To understand the genetic basis of biomass accumulation and RUE, we applied genome-wide association study (GWAS) to a panel of 150 elite spring wheat genotypes including many landrace and synthetically derived lines. The panel was evaluated for 31 traits over 2 years under optimal growing conditions and genotyped using the 35K wheat breeders array. Marker-trait association identified 94 SNPs significantly associated with yield, agronomic and phenology-related traits along with RUE and final biomass (BM_PM) at various growth stages that explained 7%-17% of phenotypic variation. Common SNP markers were identified for grain yield, BM_PM and RUE on chromosomes 5A and 7A. Additionally, landrace and synthetic derivative lines showed higher thousand grain weight (TGW), BM_PM and RUE but lower grain number (GM2) and harvest index (HI). Our work demonstrates the use of exotic material as a valuable resource to increase YP. It also provides markers for use in marker-assisted breeding to systematically increase BM_PM, RUE and TGW and avoid the TGW/GM2 and BM_PM/HI trade-off. Thus, achieving greater genetic gains in elite germplasm while also highlighting genomic regions and candidate genes for further study.
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Affiliation(s)
- Gemma Molero
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT)TexcocoMexico
| | | | | | | | - Carolina Rivera‐Amado
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT)TexcocoMexico
| | | | - Matthew P. Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT)TexcocoMexico
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9
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Gardiner LJ, Wingen LU, Bailey P, Joynson R, Brabbs T, Wright J, Higgins JD, Hall N, Griffiths S, Clavijo BJ, Hall A. Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol 2019; 20:69. [PMID: 30982471 PMCID: PMC6463664 DOI: 10.1186/s13059-019-1675-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/13/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations. RESULTS We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high-frequency crossover sites are shared between populations and that closely related parents lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We identify quantitative trait loci for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. CONCLUSIONS This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage drag utilizing widespread gene conversions.
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Affiliation(s)
| | | | | | | | | | | | - James D. Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH UK
| | - Neil Hall
- Earlham Institute, Norwich, NR4 7UZ UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | | | | | - Anthony Hall
- Earlham Institute, Norwich, NR4 7UZ UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
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Singh S, Vikram P, Sehgal D, Burgueño J, Sharma A, Singh SK, Sansaloni CP, Joynson R, Brabbs T, Ortiz C, Solis-Moya E, Govindan V, Gupta N, Sidhu HS, Basandrai AK, Basandrai D, Ledesma-Ramires L, Suaste-Franco MP, Fuentes-Dávila G, Moreno JI, Sonder K, Singh VK, Singh S, Shokat S, Arif MAR, Laghari KA, Srivastava P, Bhavani S, Kumar S, Pal D, Jaiswal JP, Kumar U, Chaudhary HK, Crossa J, Payne TS, Imtiaz M, Sohu VS, Singh GP, Bains NS, Hall A, Pixley KV. Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security. Sci Rep 2018; 8:12527. [PMID: 30131572 PMCID: PMC6104032 DOI: 10.1038/s41598-018-30667-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/02/2018] [Indexed: 12/03/2022] Open
Abstract
The value of exotic wheat genetic resources for accelerating grain yield gains is largely unproven and unrealized. We used next-generation sequencing, together with multi-environment phenotyping, to study the contribution of exotic genomes to 984 three-way-cross-derived (exotic/elite1//elite2) pre-breeding lines (PBLs). Genomic characterization of these lines with haplotype map-based and SNP marker approaches revealed exotic specific imprints of 16.1 to 25.1%, which compares to theoretical expectation of 25%. A rare and favorable haplotype (GT) with 0.4% frequency in gene bank identified on chromosome 6D minimized grain yield (GY) loss under heat stress without GY penalty under irrigated conditions. More specifically, the ‘T’ allele of the haplotype GT originated in Aegilops tauschii and was absent in all elite lines used in study. In silico analysis of the SNP showed hits with a candidate gene coding for isoflavone reductase IRL-like protein in Ae. tauschii. Rare haplotypes were also identified on chromosomes 1A, 6A and 2B effective against abiotic/biotic stresses. Results demonstrate positive contributions of exotic germplasm to PBLs derived from crosses of exotics with CIMMYT’s best elite lines. This is a major impact-oriented pre-breeding effort at CIMMYT, resulting in large-scale development of PBLs for deployment in breeding programs addressing food security under climate change scenarios.
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Affiliation(s)
- Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico.
| | - Prashant Vikram
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Juan Burgueño
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Achla Sharma
- Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, 141004, India
| | - Sanjay K Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Carolina P Sansaloni
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Ryan Joynson
- Earlham Institute, Norwich, Norfolk, NR4 7UG, UK
| | | | - Cynthia Ortiz
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Ernesto Solis-Moya
- Carretera Celaya-San Miguel de Allende, Km 0.6.5, C.P., 38110, Celaya, Guanajuato, Mexico
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Naveen Gupta
- Borlaug Institute for South Asia (BISA), CIMMYT, Ladhowal, Punjab, 141004, India
| | - Harminder S Sidhu
- Borlaug Institute for South Asia (BISA), CIMMYT, Ladhowal, Punjab, 141004, India
| | - Ashwani K Basandrai
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, Himachal Pradesh, 176062, India
| | - Daisy Basandrai
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, Himachal Pradesh, 176062, India
| | | | - Maria P Suaste-Franco
- Carretera Celaya-San Miguel de Allende, Km 0.6.5, C.P., 38110, Celaya, Guanajuato, Mexico
| | - Guillermo Fuentes-Dávila
- INIFAP-CIRNO, Campo Experimental Norman E. Borlaug, Apdo. Postal 155, Km 12 Norman E. Borlaug, Cd. Obregon, Sonora, C.P., 85000, Mexico
| | - Javier I Moreno
- INIFAP, Interior Parque Los Colomos S/N, Colonia Providencia, CP, 44660, Guadalajara, Jalisco, Mexico
| | - Kai Sonder
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Vaibhav K Singh
- ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110 012, India
| | - Sanjay Singh
- National Research Center for Plant Biotechnology, New Delhi, 110 012, India
| | - Sajid Shokat
- Nuclear Institute for Agriculture and Biology, Faislabad, 38000, Pakistan.,Department of Plant and Environmental Sciences, Crop Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630, Taastrup, Denmark
| | - Mian A R Arif
- Nuclear Institute for Agriculture and Biology, Faislabad, 38000, Pakistan
| | - Khalil A Laghari
- Nuclear Institute of Agriculture, Tando Jam, Sindh, 70050, Pakistan
| | - Puja Srivastava
- Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, 141004, India
| | - Sridhar Bhavani
- CIMMYT - World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri. P.O. Box 1041-00621, Nairobi, Kenya
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Dharam Pal
- ICAR-Indian Agricultural Research Institute, Regional Station, Shimla, 171004, India
| | - Jai P Jaiswal
- Department of Genetics and Plant Breeding, G.B. Pant University of Agriculture & Technology, Pantnagar, 263145, Uttarakhand, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), CIMMYT, Ladhowal, Punjab, 141004, India
| | - Harinder K Chaudhary
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, Himachal Pradesh, 176062, India
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Thomas S Payne
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Muhammad Imtiaz
- CIMMYT - Pakistan, NARC CSI Complex, Park Road, Islamabad, 44000, Pakistan
| | - Virinder S Sohu
- Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, 141004, India
| | - Gyanendra P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Navtej S Bains
- Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, 141004, India
| | - Anthony Hall
- Earlham Institute, Norwich, Norfolk, NR4 7UG, UK.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Kevin V Pixley
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico.
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Gardiner LJ, Joynson R, Omony J, Rusholme-Pilcher R, Olohan L, Lang D, Bai C, Hawkesford M, Salt D, Spannagl M, Mayer KFX, Kenny J, Bevan M, Hall N, Hall A. Hidden variation in polyploid wheat drives local adaptation. Genome Res 2018; 28:1319-1332. [PMID: 30093548 PMCID: PMC6120627 DOI: 10.1101/gr.233551.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/16/2018] [Indexed: 12/20/2022]
Abstract
Wheat has been domesticated into a large number of agricultural environments and has the ability to adapt to diverse environments. To understand this process, we survey genotype, repeat content, and DNA methylation across a bread wheat landrace collection representing global genetic diversity. We identify independent variation in methylation, genotype, and transposon copy number. We show that these, so far unexploited, sources of variation have had a significant impact on the wheat genome and that ancestral methylation states become preferentially "hard coded" as single nucleotide polymorphisms (SNPs) via 5-methylcytosine deamination. These mechanisms also drive local adaption, impacting important traits such as heading date and salt tolerance. Methylation and transposon diversity could therefore be used alongside SNP-based markers for breeding.
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Affiliation(s)
| | - Ryan Joynson
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
| | - Jimmy Omony
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany
| | | | - Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Daniel Lang
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany
| | - Caihong Bai
- Rothamsted Research, Harpenden, AL5 2JQ, United Kingdom
| | | | - David Salt
- University of Nottingham, Sutton Bonington Campus, Sutton Bonington, LE12 5RD, United Kingdom
| | - Manuel Spannagl
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany
| | - Klaus F X Mayer
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany.,Wissenschaftszentrum Weihenstephan (WZW), Technical University Munich, Freising, 85354, Germany
| | - John Kenny
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | | | - Neil Hall
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Anthony Hall
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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12
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Joynson R, Pritchard L, Osemwekha E, Ferry N. Metagenomic Analysis of the Gut Microbiome of the Common Black Slug Arion ater in Search of Novel Lignocellulose Degrading Enzymes. Front Microbiol 2017; 8:2181. [PMID: 29167663 PMCID: PMC5682323 DOI: 10.3389/fmicb.2017.02181] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/24/2017] [Indexed: 11/24/2022] Open
Abstract
Some eukaryotes are able to gain access to well-protected carbon sources in plant biomass by exploiting microorganisms in the environment or harbored in their digestive system. One is the land pulmonate Arion ater, which takes advantage of a gut microbial consortium that can break down the widely available, but difficult to digest, carbohydrate polymers in lignocellulose, enabling them to digest a broad range of fresh and partially degraded plant material efficiently. This ability is considered one of the major factors that have enabled A. ater to become one of the most widespread plant pest species in Western Europe and North America. Using metagenomic techniques we have characterized the bacterial diversity and functional capability of the gut microbiome of this notorious agricultural pest. Analysis of gut metagenomic community sequences identified abundant populations of known lignocellulose-degrading bacteria, along with well-characterized bacterial plant pathogens. This also revealed a repertoire of more than 3,383 carbohydrate active enzymes (CAZymes) including multiple enzymes associated with lignin degradation, demonstrating a microbial consortium capable of degradation of all components of lignocellulose. This would allow A. ater to make extensive use of plant biomass as a source of nutrients through exploitation of the enzymatic capabilities of the gut microbial consortia. From this metagenome assembly we also demonstrate the successful amplification of multiple predicted gene sequences from metagenomic DNA subjected to whole genome amplification and expression of functional proteins, facilitating the low cost acquisition and biochemical testing of the many thousands of novel genes identified in metagenomics studies. These findings demonstrate the importance of studying Gastropod microbial communities. Firstly, with respect to understanding links between feeding and evolutionary success and, secondly, as sources of novel enzymes with biotechnological potential, such as, CAZYmes that could be used in the production of biofuel.
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Affiliation(s)
- Ryan Joynson
- School of Environment and Life Science, University of Salford, Greater Manchester, United Kingdom.,Earlham Institute, Norwich, United Kingdom
| | - Leighton Pritchard
- Information and Computational Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Ekenakema Osemwekha
- School of Environment and Life Science, University of Salford, Greater Manchester, United Kingdom
| | - Natalie Ferry
- School of Environment and Life Science, University of Salford, Greater Manchester, United Kingdom
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13
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Gardiner LJ, Bansept-Basler P, Olohan L, Joynson R, Brenchley R, Hall N, O'Sullivan DM, Hall A. Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat. Plant J 2016; 87:403-19. [PMID: 27144898 PMCID: PMC5026171 DOI: 10.1111/tpj.13204] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 05/20/2023]
Abstract
Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat-Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo-chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo-chromosomes allow us to demonstrate the application of mapping-by-sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub-genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a smaller genic region than was previously possible; associate the interval with one wheat sub-genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user-friendly community resource for phenotype mapping.
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Affiliation(s)
- Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | | | - Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Ryan Joynson
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Rachel Brenchley
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, PO Box 237, Whiteknights, Reading, RG6 6AR, UK
| | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
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