PMID- 37235014
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20230528
IS  - 1664-462X (Print)
IS  - 1664-462X (Electronic)
IS  - 1664-462X (Linking)
VI  - 14
DP  - 2023
TI  - A genome-wide association study of freezing tolerance in red clover (Trifolium 
      pratense L.) germplasm of European origin.
PG  - 1189662
LID - 10.3389/fpls.2023.1189662 [doi]
LID - 1189662
AB  - Improvement of persistency is an important breeding goal in red clover (Trifolium 
      pratense L.). In areas with cold winters, lack of persistency is often due to 
      poor winter survival, of which low freezing tolerance (FT) is an important 
      component. We conducted a genome wide association study (GWAS) to identify loci 
      associated with freezing tolerance in a collection of 393 red clover accessions, 
      mostly of European origin, and performed analyses of linkage disequilibrium and 
      inbreeding. Accessions were genotyped as pools of individuals using 
      genotyping-by-sequencing (pool-GBS), generating both single nucleotide 
      polymorphism (SNP) and haplotype allele frequency data at accession level. 
      Linkage disequilibrium was determined as a squared partial correlation between 
      the allele frequencies of pairs of SNPs and found to decay at extremely short 
      distances (< 1 kb). The level of inbreeding, inferred from the diagonal elements 
      of a genomic relationship matrix, varied considerably between different groups of 
      accessions, with the strongest inbreeding found among ecotypes from Iberia and 
      Great Britain, and the least found among landraces. Considerable variation in FT 
      was found, with LT50-values (temperature at which 50% of the plants are killed) 
      ranging from -6.0 degrees C to -11.5 degrees C. SNP and haplotype-based GWAS identified eight and 
      six loci significantly associated with FT (of which only one was shared), 
      explaining 30% and 26% of the phenotypic variation, respectively. Ten of the loci 
      were found within or at a short distance (<0.5 kb) from genes possibly involved 
      in mechanisms affecting FT. These include a caffeoyl shikimate esterase, an 
      inositol transporter, and other genes involved in signaling, transport, lignin 
      synthesis and amino acid or carbohydrate metabolism. This study paves the way for 
      a better understanding of the genetic control of FT and for the development of 
      molecular tools for the improvement of this trait in red clover through genomics 
      assisted breeding.
CI  - Copyright (c) 2023 Zanotto, Ruttink, Pegard, Skot, Grieder, Kolliker and Ergon.
FAU - Zanotto, Stefano
AU  - Zanotto S
AD  - Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), As, Norway.
FAU - Ruttink, Tom
AU  - Ruttink T
AD  - Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and 
      Food (ILVO), Melle, Belgium.
FAU - Pegard, Marie
AU  - Pegard M
AD  - INRAE P3F, Lusignan, France.
FAU - Skot, Leif
AU  - Skot L
AD  - IBERS, Aberystwyth University, Aberystwyth, United Kingdom.
FAU - Grieder, Christoph
AU  - Grieder C
AD  - Group of Fodder Plant Breeding, Agroscope, Zurich, Switzerland.
FAU - Kolliker, Roland
AU  - Kolliker R
AD  - Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, 
      Switzerland.
FAU - Ergon, Ashild
AU  - Ergon A
AD  - Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), As, Norway.
LA  - eng
PT  - Journal Article
DEP - 20230510
PL  - Switzerland
TA  - Front Plant Sci
JT  - Frontiers in plant science
JID - 101568200
PMC - PMC10208120
OTO - NOTNLM
OT  - GWAS
OT  - LT50
OT  - cold stress
OT  - forage legumes
OT  - haplotypes
OT  - linkage disequilibrium
OT  - pool-GBS
OT  - winter survival
COIS- The authors declare that the research was conducted in the absence of any 
      commercial or financial relationships that could be construed as a potential 
      conflict of interest.
EDAT- 2023/05/26 19:14
MHDA- 2023/05/26 19:15
PMCR- 2023/01/01
CRDT- 2023/05/26 12:21
PHST- 2023/03/19 00:00 [received]
PHST- 2023/04/13 00:00 [accepted]
PHST- 2023/05/26 19:15 [medline]
PHST- 2023/05/26 19:14 [pubmed]
PHST- 2023/05/26 12:21 [entrez]
PHST- 2023/01/01 00:00 [pmc-release]
AID - 10.3389/fpls.2023.1189662 [doi]
PST - epublish
SO  - Front Plant Sci. 2023 May 10;14:1189662. doi: 10.3389/fpls.2023.1189662. 
      eCollection 2023.