Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus

John H. Price; Andrew R. Raduski; Yaniv Brandvain; David L. Van Tassel; Kevin P Smith

doi:10.1038/s41437-022-00530-4

Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus

John H. Price, Andrew R. Raduski, Yaniv Brandvain, David L. Van Tassel, Kevin P Smith

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7 Scopus citations

Abstract

Silphium integrifolium (Asteraceae) has been identified as a candidate for domestication as a perennial oilseed crop and is assumed to have sporophytic self-incompatibility system—the genetic basis of which is not well understood in the Asteraceae. To address this gap, we sought to map the genomic location of the self-recognition locus (S-locus) in this species. We used a biparental population and genotyping-by-sequencing to create the first genetic linkage map for this species, which contained 198 SNP markers and resolved into the correct number of linkage groups. Then we developed a novel crossing scheme and set of analysis methods in order to infer S-locus genotypes for a subset of these individuals, allowing us to map the trait. Finally, we evaluated potential genes of interest using synteny analysis with the annual sunflower (Helianthus annuus) and lettuce (Lactuca sativa) genomes. Our results confirm that S. integrifolium does indeed have a sporophytic self-incompatibility system. Our method is effective and efficient, allowed us to map the S. integrifolium S-locus using fewer resources than existing methods, and could be readily applied to other species.

Original language	English (US)
Pages (from-to)	304-312
Number of pages	9
Journal	Heredity
Volume	128
Issue number	5
DOIs	https://doi.org/10.1038/s41437-022-00530-4
State	Published - May 2022

Bibliographical note

Funding Information:
Funding for this work was provided by The Perennial Agriculture project in conjunction with The Land Institute and the Malone Family Land Preservation Fund, the United States Department of Agriculture’s National Institute of Food and Agriculture Grant no. 2019-67011-29607 to JHP, the Minnesota Department of Agriculture - Forever Green Agricultural Initiative, and NSF grant #1737827 Dimensions US-China to YB. The authors thank Shannon Lee Anderson, Karen Beaubein, and Jill Ekar for their help in completing the controlled crosses for this experiment. In addition, the authors thank Dr. Kevin Dorn for assistance in developing a GBS protocol, Dr. Adam Herman for bioinformatics advice, and Dr. Owen Beisel for inspiring the hill-climbing algorithm method. Finally, the authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing computing resources that contributed to the analysis of this study.

Publisher Copyright:
© 2022, The Author(s), under exclusive licence to The Genetics Society.

Keywords

Asteraceae/genetics
Chromosome Mapping
Domestication
Genetic Linkage
Humans
Synteny

PubMed: MeSH publication types

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

UN SDGs

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10.1038/s41437-022-00530-4

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title = "Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus",

abstract = "Silphium integrifolium (Asteraceae) has been identified as a candidate for domestication as a perennial oilseed crop and is assumed to have sporophytic self-incompatibility system—the genetic basis of which is not well understood in the Asteraceae. To address this gap, we sought to map the genomic location of the self-recognition locus (S-locus) in this species. We used a biparental population and genotyping-by-sequencing to create the first genetic linkage map for this species, which contained 198 SNP markers and resolved into the correct number of linkage groups. Then we developed a novel crossing scheme and set of analysis methods in order to infer S-locus genotypes for a subset of these individuals, allowing us to map the trait. Finally, we evaluated potential genes of interest using synteny analysis with the annual sunflower (Helianthus annuus) and lettuce (Lactuca sativa) genomes. Our results confirm that S. integrifolium does indeed have a sporophytic self-incompatibility system. Our method is effective and efficient, allowed us to map the S. integrifolium S-locus using fewer resources than existing methods, and could be readily applied to other species.",

keywords = "Asteraceae/genetics, Chromosome Mapping, Domestication, Genetic Linkage, Humans, Synteny",

author = "Price, {John H.} and Raduski, {Andrew R.} and Yaniv Brandvain and {Van Tassel}, {David L.} and Smith, {Kevin P}",

note = "Funding Information: Funding for this work was provided by The Perennial Agriculture project in conjunction with The Land Institute and the Malone Family Land Preservation Fund, the United States Department of Agriculture{\textquoteright}s National Institute of Food and Agriculture Grant no. 2019-67011-29607 to JHP, the Minnesota Department of Agriculture - Forever Green Agricultural Initiative, and NSF grant #1737827 Dimensions US-China to YB. The authors thank Shannon Lee Anderson, Karen Beaubein, and Jill Ekar for their help in completing the controlled crosses for this experiment. In addition, the authors thank Dr. Kevin Dorn for assistance in developing a GBS protocol, Dr. Adam Herman for bioinformatics advice, and Dr. Owen Beisel for inspiring the hill-climbing algorithm method. Finally, the authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing computing resources that contributed to the analysis of this study. Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive licence to The Genetics Society.",

year = "2022",

month = may,

doi = "10.1038/s41437-022-00530-4",

language = "English (US)",

volume = "128",

pages = "304--312",

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T1 - Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus

AU - Price, John H.

AU - Raduski, Andrew R.

AU - Brandvain, Yaniv

AU - Van Tassel, David L.

AU - Smith, Kevin P

N1 - Funding Information: Funding for this work was provided by The Perennial Agriculture project in conjunction with The Land Institute and the Malone Family Land Preservation Fund, the United States Department of Agriculture’s National Institute of Food and Agriculture Grant no. 2019-67011-29607 to JHP, the Minnesota Department of Agriculture - Forever Green Agricultural Initiative, and NSF grant #1737827 Dimensions US-China to YB. The authors thank Shannon Lee Anderson, Karen Beaubein, and Jill Ekar for their help in completing the controlled crosses for this experiment. In addition, the authors thank Dr. Kevin Dorn for assistance in developing a GBS protocol, Dr. Adam Herman for bioinformatics advice, and Dr. Owen Beisel for inspiring the hill-climbing algorithm method. Finally, the authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing computing resources that contributed to the analysis of this study. Publisher Copyright: © 2022, The Author(s), under exclusive licence to The Genetics Society.

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N2 - Silphium integrifolium (Asteraceae) has been identified as a candidate for domestication as a perennial oilseed crop and is assumed to have sporophytic self-incompatibility system—the genetic basis of which is not well understood in the Asteraceae. To address this gap, we sought to map the genomic location of the self-recognition locus (S-locus) in this species. We used a biparental population and genotyping-by-sequencing to create the first genetic linkage map for this species, which contained 198 SNP markers and resolved into the correct number of linkage groups. Then we developed a novel crossing scheme and set of analysis methods in order to infer S-locus genotypes for a subset of these individuals, allowing us to map the trait. Finally, we evaluated potential genes of interest using synteny analysis with the annual sunflower (Helianthus annuus) and lettuce (Lactuca sativa) genomes. Our results confirm that S. integrifolium does indeed have a sporophytic self-incompatibility system. Our method is effective and efficient, allowed us to map the S. integrifolium S-locus using fewer resources than existing methods, and could be readily applied to other species.

AB - Silphium integrifolium (Asteraceae) has been identified as a candidate for domestication as a perennial oilseed crop and is assumed to have sporophytic self-incompatibility system—the genetic basis of which is not well understood in the Asteraceae. To address this gap, we sought to map the genomic location of the self-recognition locus (S-locus) in this species. We used a biparental population and genotyping-by-sequencing to create the first genetic linkage map for this species, which contained 198 SNP markers and resolved into the correct number of linkage groups. Then we developed a novel crossing scheme and set of analysis methods in order to infer S-locus genotypes for a subset of these individuals, allowing us to map the trait. Finally, we evaluated potential genes of interest using synteny analysis with the annual sunflower (Helianthus annuus) and lettuce (Lactuca sativa) genomes. Our results confirm that S. integrifolium does indeed have a sporophytic self-incompatibility system. Our method is effective and efficient, allowed us to map the S. integrifolium S-locus using fewer resources than existing methods, and could be readily applied to other species.

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KW - Chromosome Mapping

KW - Domestication

KW - Genetic Linkage

KW - Humans

KW - Synteny

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JO - Heredity

JF - Heredity

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ER -

Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus

Abstract

Bibliographical note

Keywords

PubMed: MeSH publication types

UN SDGs

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