Effective Population Size in Field Pea Article Swipe
Josephine Princy Johnson
,
Lisa Piche
,
Hannah Worral
,
Sikiru Adeniyi Atanda
,
Clarice J. Coyne
,
Rebecca J. McGee
,
Kevin McPhee
,
Nonoy Bandillo
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.02.19.581041
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.02.19.581041
Background Effective population size ( N e ) is a pivotal parameter in population genetics as it can provide information on the rate of inbreeding and the contemporary status of genetic diversity in breeding populations. The population with smaller N e can lead to faster inbreeding, with little potential for genetic gain making selections ineffective. The importance of N e has become increasingly recognized in plant breeding, which can help breeders monitor and enhance the genetic variability or redesign their selection protocols. Here, we present the first N e estimates based on linkage disequilibrium (LD) in the pea genome. Results We calculated and compared N e using SNP markers from North Dakota State University (NDSU) modern breeding lines and United States Department of Agriculture (USDA) diversity panel. The extent of LD was highly variable not only between populations but also among different regions and chromosomes of the genome. Overall, NDSU had a higher and longer-range LD than the USDA that could extend up to 500Kb, with a genome-wide average r 2 of 0.57 (vs 0.34), likely due to its lower recombination rates and the selection background. The estimated N e for the USDA was nearly three-fold higher ( N e = 174) than NDSU ( N e = 64), which can be confounded by a high degree of population structure due to the selfing nature of pea. Conclusions Our results provided insights into the genetic diversity of the germplasm studied, which can guide plant breeders to actively monitor N e in successive cycles of breeding to sustain viability of the breeding efforts in the long term.
Related Topics
Concepts
Selfing
Biology
Genetic diversity
Inbreeding
Effective population size
Population
Germplasm
Linkage disequilibrium
Selection (genetic algorithm)
Breeding program
Population size
Runs of Homozygosity
Genetics
Demography
Agronomy
Haplotype
Allele
Single-nucleotide polymorphism
Genotype
Computer science
Cultivar
Gene
Artificial intelligence
Sociology
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- http://dx.doi.org/10.1101/2024.02.19.581041
- https://www.biorxiv.org/content/biorxiv/early/2024/02/21/2024.02.19.581041.full.pdf
- OA Status
- green
- References
- 62
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4392201367
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4392201367Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2024.02.19.581041Digital Object Identifier
- Title
-
Effective Population Size in Field PeaWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-02-21Full publication date if available
- Authors
-
Josephine Princy Johnson, Lisa Piche, Hannah Worral, Sikiru Adeniyi Atanda, Clarice J. Coyne, Rebecca J. McGee, Kevin McPhee, Nonoy BandilloList of authors in order
- Landing page
-
https://dx.doi.org/10.1101/2024.02.19.581041Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2024/02/21/2024.02.19.581041.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
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-
greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2024/02/21/2024.02.19.581041.full.pdfDirect OA link when available
- Concepts
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Selfing, Biology, Genetic diversity, Inbreeding, Effective population size, Population, Germplasm, Linkage disequilibrium, Selection (genetic algorithm), Breeding program, Population size, Runs of Homozygosity, Genetics, Demography, Agronomy, Haplotype, Allele, Single-nucleotide polymorphism, Genotype, Computer science, Cultivar, Gene, Artificial intelligence, SociologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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62Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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