Projects per year
Abstract
Survivor populations of red clover (Trifolium pratense L.) from plots in a field experiment in southern Norway were genetically characterized using genotyping by sequencing, and compared with the original population and each other. Genetic differentiation between populations was characterized on the basis of allele frequencies of single nucleotide polymorphisms (SNPs), using principal component analysis. SNPs that had been under selection, i.e., SNPs with significantly different allele frequencies in survivor populations relative to the original population, or between survivor populations that had received different treatments, were identified by analysis of F ST values, using BayeScan and a simple and stringent F ST-based test utilizing replicate populations from the field experiment. In addition, we tested the possibility of pooling DNA samples prior to sequencing, and pooling leaf samples prior to DNA extraction and sequencing, followed by allele frequency estimation on the basis of number of variant reads. Overall, survivor populations were more different from each other than from the original population, indicating random changes in allele frequency, selection in response to local variation in conditions between plots in the field experiment, or sampling error. However, some differentiation was observed between plots sown as pure stands or species mixtures, plots sown at different densities, and plots subjected to different harvesting regimes. Allele frequencies could be accurately estimated from pooled DNA, and SNPs under selection could be identified when leaf samples were pooled prior to DNA extraction. However, substantial sampling error required replicate populations and/or a high number of sampled individuals. We identified a number of chromosomal loci that had been under selection in pure stand plots relative to the original sown population, and loci that had been under differential selection in pure stands of red clover vs. red clover grown in species mixtures. These are all candidate loci for establishment success or persistence in red clover.
Original language | English |
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Article number | 718 |
Journal | Frontiers in Plant Science |
Volume | 10 |
DOIs | |
Publication status | Published - 11 Jun 2019 |
Keywords
- genetic shift
- SNP
- GBS
- Fst
- pool
- population genomics
- establishment success
- persistence
- F
- Establishment success
- Genetic shift
- Persistence
- Population genomics
- Pool
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Dive into the research topics of 'Allele frequency changes provide evidence for selection and identification of candidate loci for survival in red clover (Trifolium pratense L)'. Together they form a unique fingerprint.Projects
- 2 Finished
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BBSRC Core Strategic Programme in Resilient Crops: Grasslands Gogerddan
Armstead, I. (PI), Donnison, I. (CoI), Jones, H. (CoI), Skot, L. (CoI), Fernandez Fuentes, N. (CoI), Phillips, D. (PI), Kingston-Smith, A. (CoI) & Bosch, M. (CoI)
Biotechnology and Biological Sciences Research Council
01 Apr 2017 → 31 Mar 2020
Project: Externally funded research
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Multi species swards and multi scale strategies for multifunctional grassland based ruminant production systems (MULTISWARD)
Collins, R. (PI)
01 Mar 2010 → 28 Feb 2014
Project: Externally funded research