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 identifies genomic contexts associated with agriculturally important traits

J Harper, J De Vega, S Swain, D Heavens, D Gasior, A Thomas, C Evans, A Lovatt, S Lister, D Thorogood, L Skot, M Hegarty, T Blackmore, D Kudrna, S Byrne, T Asp, W Powell, N Fernandez-Fuentes, I Armstead

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Abstract

Background and Aims Lolium 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). Methods BAC-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 Results Between ~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. Conclusions Combining 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.
Original languageEnglish
Article numbermcy230
Pages (from-to)977-992
Number of pages16
JournalAnnals of Botany
Volume123
Issue number6
Early online date2 Feb 2019
DOIs
Publication statusPrint publication - 8 May 2019

Fingerprint

bacterial artificial chromosomes
physical chromosome mapping
ecotypes
Lolium
Lolium perenne
genomics
genome
clones
genes
genome-wide association study
heading
ecosystem services
topology
diploidy
forage
grasses
carbohydrates
loci
genotype
crops

Keywords

  • BAC-based physical mapping
  • Lolium perenne
  • Ecotypes
  • FPC
  • LTC
  • GWAS
  • Candidate genes
  • Flowering
  • Heading date
  • Water-soluble carbohydrate
  • Plant width

Cite this

Harper, J ; De Vega, J ; Swain, S ; Heavens, D ; Gasior, D ; Thomas, A ; Evans, C ; Lovatt, A ; Lister, S ; Thorogood, D ; Skot, L ; Hegarty, M ; Blackmore, T ; Kudrna, D ; Byrne, S ; Asp, T ; Powell, W ; Fernandez-Fuentes, N ; Armstead, I. / 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 identifies genomic contexts associated with agriculturally important traits. In: Annals of Botany. 2019 ; Vol. 123, No. 6. pp. 977-992.
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abstract = "Background and Aims Lolium 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). Methods BAC-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 Results Between ~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. Conclusions Combining 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 = "BAC-based physical mapping, Lolium perenne, Ecotypes, FPC, LTC, GWAS, Candidate genes, Flowering, Heading date, Water-soluble carbohydrate, Plant width",
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Harper, J, De Vega, J, Swain, S, Heavens, D, Gasior, D, Thomas, A, Evans, C, Lovatt, A, Lister, S, Thorogood, D, Skot, L, Hegarty, M, Blackmore, T, Kudrna, D, Byrne, S, Asp, T, Powell, W, Fernandez-Fuentes, N & Armstead, I 2019, '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 identifies genomic contexts associated with agriculturally important traits', Annals of Botany, vol. 123, no. 6, mcy230, pp. 977-992. https://doi.org/10.1093/aob/mcy230

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 identifies genomic contexts associated with agriculturally important traits. / Harper, J; De Vega, J; Swain, S; Heavens, D; Gasior, D; Thomas, A; Evans, C; Lovatt, A; Lister, S; Thorogood, D; Skot, L; Hegarty, M; Blackmore, T; Kudrna, D; Byrne, S; Asp, T; Powell, W; Fernandez-Fuentes, N; Armstead, I.

In: Annals of Botany, Vol. 123, No. 6, mcy230, 08.05.2019, p. 977-992.

Research output: Contribution to journalArticle

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 identifies genomic contexts associated with agriculturally important traits

AU - Harper, J

AU - De Vega, J

AU - Swain, S

AU - Heavens, D

AU - Gasior, D

AU - Thomas, A

AU - Evans, C

AU - Lovatt, A

AU - Lister, S

AU - Thorogood, D

AU - Skot, L

AU - Hegarty, M

AU - Blackmore, T

AU - Kudrna, D

AU - Byrne, S

AU - Asp, T

AU - Powell, W

AU - Fernandez-Fuentes, N

AU - Armstead, I

PY - 2019/5/8

Y1 - 2019/5/8

N2 - Background and Aims Lolium 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). Methods BAC-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 Results Between ~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. Conclusions Combining 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 Aims Lolium 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). Methods BAC-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 Results Between ~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. Conclusions Combining 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 - BAC-based physical mapping

KW - Lolium perenne

KW - Ecotypes

KW - FPC

KW - LTC

KW - GWAS

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

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M1 - mcy230

ER -