Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identified genomic contexts associated with agriculturally important traits

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Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identified genomic contexts associated with agriculturally important traits. / Harper, John; de Vega, J.; Swain, Suresh; Heavens, D.; Gasior, Dagmara; Thomas, Ann; Evans, Caron; Lovatt, Alan; Lister, Sue; Thorogood, Danny; Skot, Leif; Hegarty, Matthew; Blackmore, Tina; Kudrna, Dave; Byrne, S.; Asp, T.; Powell, Wayne; Fernandez-Fuentes, Narcis; Armstead, Ian.

Yn: Annals of Botany, Cyfrol 123, Rhif 6, mcy230, 02.02.2019, t. 977-992.

Allbwn ymchwil: Cyfraniad at gyfnodolynErthygladolygiad gan gymheiriaid

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@article{93ac4086f1b54f67b36efc829d4e7efa,
title = "Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identified genomic contexts associated with agriculturally important traits",
abstract = "Background and AimsLolium perenne (perennial ryegrass) is the most widely cultivated forage and amenity grass species in temperate areas worldwide and there is a need to understand the genetic architectures of key agricultural traits and crop characteristics that deliver wider environmental services. Our aim was to identify genomic regions associated with agriculturally important traits by integrating a bacterial artificial chromosome (BAC)-based physical map with a genome-wide association study (GWAS).MethodsBAC-based physical maps for L. perenne were constructed from ~212 000 high-information-content fingerprints using Fingerprint Contig and Linear Topology Contig software. BAC clones were associated with both BAC-end sequences and a partial minimum tiling path sequence. A panel of 716 L. perenne diploid genotypes from 90 European accessions was assessed in the field over 2 years, and genotyped using a Lolium Infinium SNP array. The GWAS was carried out using a linear mixed model implemented in TASSEL, and extended genomic regions associated with significant markers were identified through integration with the physical map.Key ResultsBetween ~3600 and 7500 physical map contigs were derived, depending on the software and probability thresholds used, and integrated with ~35 k sequenced BAC clones to develop a resource predicted to span the majority of the L. perenne genome. From the GWAS, eight different loci were significantly associated with heading date, plant width, plant biomass and water-soluble carbohydrate accumulation, seven of which could be associated with physical map contigs. This allowed the identification of a number of candidate genes.ConclusionsCombining the physical mapping resource with the GWAS has allowed us to extend the search for candidate genes across larger regions of the L. perenne genome and identified a number of interesting gene model annotations. These physical maps will aid in validating future sequence-based assemblies of the L. perenne genome.",
keywords = "Lolium perenne, BAC-based physical map, FPC, LTC, GWAS, ecotypes, candidate genes, flowering, heading date, water-soluble carbohydrate, plant width",
author = "John Harper and {de Vega}, J. and Suresh Swain and D. Heavens and Dagmara Gasior and Ann Thomas and Caron Evans and Alan Lovatt and Sue Lister and Danny Thorogood and Leif Skot and Matthew Hegarty and Tina Blackmore and Dave Kudrna and S. Byrne and T. Asp and Wayne Powell and Narcis Fernandez-Fuentes and Ian Armstead",
note = "UK Biotechnology and Biological Sciences Research Council through Responsive Mode, Institute Strategic Programme and Core Strategic Programme grants (grants BB/J004405/1, BB/CSP1730/1 and BB/G012342/1) with financial contributions from Germinal Holdings (UK), Syngenta (UK) and Vialactia Biosciences (NZ)",
year = "2019",
month = feb,
day = "2",
doi = "10.1093/aob/mcy230",
language = "English",
volume = "123",
pages = "977--992",
journal = "Annals of Botany",
issn = "0305-7364",
publisher = "Oxford University Press",
number = "6",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identified genomic contexts associated with agriculturally important traits

AU - Harper, John

AU - de Vega, J.

AU - Swain, Suresh

AU - Heavens, D.

AU - Gasior, Dagmara

AU - Thomas, Ann

AU - Evans, Caron

AU - Lovatt, Alan

AU - Lister, Sue

AU - Thorogood, Danny

AU - Skot, Leif

AU - Hegarty, Matthew

AU - Blackmore, Tina

AU - Kudrna, Dave

AU - Byrne, S.

AU - Asp, T.

AU - Powell, Wayne

AU - Fernandez-Fuentes, Narcis

AU - Armstead, Ian

N1 - UK Biotechnology and Biological Sciences Research Council through Responsive Mode, Institute Strategic Programme and Core Strategic Programme grants (grants BB/J004405/1, BB/CSP1730/1 and BB/G012342/1) with financial contributions from Germinal Holdings (UK), Syngenta (UK) and Vialactia Biosciences (NZ)

PY - 2019/2/2

Y1 - 2019/2/2

N2 - Background and AimsLolium perenne (perennial ryegrass) is the most widely cultivated forage and amenity grass species in temperate areas worldwide and there is a need to understand the genetic architectures of key agricultural traits and crop characteristics that deliver wider environmental services. Our aim was to identify genomic regions associated with agriculturally important traits by integrating a bacterial artificial chromosome (BAC)-based physical map with a genome-wide association study (GWAS).MethodsBAC-based physical maps for L. perenne were constructed from ~212 000 high-information-content fingerprints using Fingerprint Contig and Linear Topology Contig software. BAC clones were associated with both BAC-end sequences and a partial minimum tiling path sequence. A panel of 716 L. perenne diploid genotypes from 90 European accessions was assessed in the field over 2 years, and genotyped using a Lolium Infinium SNP array. The GWAS was carried out using a linear mixed model implemented in TASSEL, and extended genomic regions associated with significant markers were identified through integration with the physical map.Key ResultsBetween ~3600 and 7500 physical map contigs were derived, depending on the software and probability thresholds used, and integrated with ~35 k sequenced BAC clones to develop a resource predicted to span the majority of the L. perenne genome. From the GWAS, eight different loci were significantly associated with heading date, plant width, plant biomass and water-soluble carbohydrate accumulation, seven of which could be associated with physical map contigs. This allowed the identification of a number of candidate genes.ConclusionsCombining the physical mapping resource with the GWAS has allowed us to extend the search for candidate genes across larger regions of the L. perenne genome and identified a number of interesting gene model annotations. These physical maps will aid in validating future sequence-based assemblies of the L. perenne genome.

AB - Background and AimsLolium perenne (perennial ryegrass) is the most widely cultivated forage and amenity grass species in temperate areas worldwide and there is a need to understand the genetic architectures of key agricultural traits and crop characteristics that deliver wider environmental services. Our aim was to identify genomic regions associated with agriculturally important traits by integrating a bacterial artificial chromosome (BAC)-based physical map with a genome-wide association study (GWAS).MethodsBAC-based physical maps for L. perenne were constructed from ~212 000 high-information-content fingerprints using Fingerprint Contig and Linear Topology Contig software. BAC clones were associated with both BAC-end sequences and a partial minimum tiling path sequence. A panel of 716 L. perenne diploid genotypes from 90 European accessions was assessed in the field over 2 years, and genotyped using a Lolium Infinium SNP array. The GWAS was carried out using a linear mixed model implemented in TASSEL, and extended genomic regions associated with significant markers were identified through integration with the physical map.Key ResultsBetween ~3600 and 7500 physical map contigs were derived, depending on the software and probability thresholds used, and integrated with ~35 k sequenced BAC clones to develop a resource predicted to span the majority of the L. perenne genome. From the GWAS, eight different loci were significantly associated with heading date, plant width, plant biomass and water-soluble carbohydrate accumulation, seven of which could be associated with physical map contigs. This allowed the identification of a number of candidate genes.ConclusionsCombining the physical mapping resource with the GWAS has allowed us to extend the search for candidate genes across larger regions of the L. perenne genome and identified a number of interesting gene model annotations. These physical maps will aid in validating future sequence-based assemblies of the L. perenne genome.

KW - Lolium perenne

KW - BAC-based physical map

KW - FPC

KW - LTC

KW - GWAS

KW - ecotypes

KW - candidate genes

KW - flowering

KW - heading date

KW - water-soluble carbohydrate

KW - plant width

U2 - 10.1093/aob/mcy230

DO - 10.1093/aob/mcy230

M3 - Article

C2 - 30715119

VL - 123

SP - 977

EP - 992

JO - Annals of Botany

JF - Annals of Botany

SN - 0305-7364

IS - 6

M1 - mcy230

ER -

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