A pan-genome of commercial pig breeds

M.F.L. Derks; A. Boshove; B. Harlizius; E. Sell-Kubiak; M.S. Lopes; E. Grindflek; E. Knol; M.A.M. Groenen; A.B. Gjuvsland

doi:10.3920/978-90-8686-940-4_564

A pan-genome of commercial pig breeds

M.F.L. Derks, A. Boshove, B. Harlizius, E. Sell-Kubiak, M.S. Lopes, E. Grindflek, E. Knol, M.A.M. Groenen, A.B. Gjuvsland

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic

Abstract

Genomics related research in animal breeding is usually performed by comparing genomic information to an existing reference genome. However, even if the reference genome is of high quality, the use of a single reference genome has clear drawbacks. Therefore, the breeding community is shifting towards the construction of a pan-genome for important agricultural species. In this study we produced a pig pangenome based on four different breeds (Landrace, Large White, Synthetic, Duroc) using the nanopore long read sequencing technology. We produced chromosome arm level assemblies comparable to the current Sus scrofa 11.1 reference genome. We identified between breed structural variation, which gives a unique insight in the genomic structural variation that define and differentiates breeds. The pig pan-genome will facilitate the discovery of novel variation providing a unique fundamental insight into breed genomic characteristics, which can subsequently be utilized for breeding.

Original language	English
Title of host publication	Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)
Subtitle of host publication	Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges
Editors	R.F. Veerkamp, Y. de Haas
Place of Publication	Wageningen
Publisher	Wageningen Academic Publishers
Pages	2337-2341
ISBN (Electronic)	9789086869404
DOIs	https://doi.org/10.3920/978-90-8686-940-4_564
Publication status	Published - 2022
Event	World Congress on Genetics Applied to Livestock Production: WCGALP 2022 - Rotterdam, Netherlands Duration: 3 Jul 2022 → 8 Jul 2022

Conference

Conference	World Congress on Genetics Applied to Livestock Production: WCGALP 2022
Country/Territory	Netherlands
City	Rotterdam
Period	3/07/22 → 8/07/22

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10.3920/978-90-8686-940-4_564Licence: CC BY

https://edepot.wur.nl/588165Licence: CC BY

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Derks, M. F. L., Boshove, A., Harlizius, B., Sell-Kubiak, E., Lopes, M. S., Grindflek, E., Knol, E., Groenen, M. A. M., & Gjuvsland, A. B. (2022). A pan-genome of commercial pig breeds. In R. F. Veerkamp, & Y. de Haas (Eds.), Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges (pp. 2337-2341). Article 564 Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-940-4_564

Derks, M.F.L. ; Boshove, A. ; Harlizius, B. et al. / A pan-genome of commercial pig breeds. Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. editor / R.F. Veerkamp ; Y. de Haas. Wageningen : Wageningen Academic Publishers, 2022. pp. 2337-2341

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title = "A pan-genome of commercial pig breeds",

abstract = "Genomics related research in animal breeding is usually performed by comparing genomic information to an existing reference genome. However, even if the reference genome is of high quality, the use of a single reference genome has clear drawbacks. Therefore, the breeding community is shifting towards the construction of a pan-genome for important agricultural species. In this study we produced a pig pangenome based on four different breeds (Landrace, Large White, Synthetic, Duroc) using the nanopore long read sequencing technology. We produced chromosome arm level assemblies comparable to the current Sus scrofa 11.1 reference genome. We identified between breed structural variation, which gives a unique insight in the genomic structural variation that define and differentiates breeds. The pig pan-genome will facilitate the discovery of novel variation providing a unique fundamental insight into breed genomic characteristics, which can subsequently be utilized for breeding.",

author = "M.F.L. Derks and A. Boshove and B. Harlizius and E. Sell-Kubiak and M.S. Lopes and E. Grindflek and E. Knol and M.A.M. Groenen and A.B. Gjuvsland",

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doi = "10.3920/978-90-8686-940-4_564",

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pages = "2337--2341",

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Derks, MFL, Boshove, A, Harlizius, B, Sell-Kubiak, E, Lopes, MS, Grindflek, E, Knol, E, Groenen, MAM & Gjuvsland, AB 2022, A pan-genome of commercial pig breeds. in RF Veerkamp & Y de Haas (eds), Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges., 564, Wageningen Academic Publishers, Wageningen, pp. 2337-2341, World Congress on Genetics Applied to Livestock Production: WCGALP 2022, Rotterdam, Netherlands, 3/07/22. https://doi.org/10.3920/978-90-8686-940-4_564

A pan-genome of commercial pig breeds. / Derks, M.F.L.; Boshove, A.; Harlizius, B. et al.
Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. ed. / R.F. Veerkamp; Y. de Haas. Wageningen: Wageningen Academic Publishers, 2022. p. 2337-2341 564.

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic

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AU - Derks, M.F.L.

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AU - Harlizius, B.

AU - Sell-Kubiak, E.

AU - Lopes, M.S.

AU - Grindflek, E.

AU - Knol, E.

AU - Groenen, M.A.M.

AU - Gjuvsland, A.B.

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N2 - Genomics related research in animal breeding is usually performed by comparing genomic information to an existing reference genome. However, even if the reference genome is of high quality, the use of a single reference genome has clear drawbacks. Therefore, the breeding community is shifting towards the construction of a pan-genome for important agricultural species. In this study we produced a pig pangenome based on four different breeds (Landrace, Large White, Synthetic, Duroc) using the nanopore long read sequencing technology. We produced chromosome arm level assemblies comparable to the current Sus scrofa 11.1 reference genome. We identified between breed structural variation, which gives a unique insight in the genomic structural variation that define and differentiates breeds. The pig pan-genome will facilitate the discovery of novel variation providing a unique fundamental insight into breed genomic characteristics, which can subsequently be utilized for breeding.

AB - Genomics related research in animal breeding is usually performed by comparing genomic information to an existing reference genome. However, even if the reference genome is of high quality, the use of a single reference genome has clear drawbacks. Therefore, the breeding community is shifting towards the construction of a pan-genome for important agricultural species. In this study we produced a pig pangenome based on four different breeds (Landrace, Large White, Synthetic, Duroc) using the nanopore long read sequencing technology. We produced chromosome arm level assemblies comparable to the current Sus scrofa 11.1 reference genome. We identified between breed structural variation, which gives a unique insight in the genomic structural variation that define and differentiates breeds. The pig pan-genome will facilitate the discovery of novel variation providing a unique fundamental insight into breed genomic characteristics, which can subsequently be utilized for breeding.

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A2 - Veerkamp, R.F.

A2 - de Haas, Y.

PB - Wageningen Academic Publishers

CY - Wageningen

T2 - World Congress on Genetics Applied to Livestock Production: WCGALP 2022

Y2 - 3 July 2022 through 8 July 2022

ER -

Derks MFL, Boshove A, Harlizius B, Sell-Kubiak E, Lopes MS, Grindflek E et al. A pan-genome of commercial pig breeds. In Veerkamp RF, de Haas Y, editors, Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. Wageningen: Wageningen Academic Publishers. 2022. p. 2337-2341. 564 doi: 10.3920/978-90-8686-940-4_564

A pan-genome of commercial pig breeds

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