PMID- 29869355
OWN - NLM
STAT- Publisher
LR  - 20240227
IS  - 1439-0388 (Electronic)
IS  - 0931-2668 (Linking)
DP  - 2018 Jun 5
TI  - Accurate genomic predictions for BCWD resistance in rainbow trout are achieved 
      using low-density SNP panels: Evidence that long-range LD is a major contributing 
      factor.
LID - 10.1111/jbg.12335 [doi]
AB  - Previously accurate genomic predictions for Bacterial cold water disease (BCWD) 
      resistance in rainbow trout were obtained using a medium-density single 
      nucleotide polymorphism (SNP) array. Here, the impact of lower-density SNP panels 
      on the accuracy of genomic predictions was investigated in a commercial rainbow 
      trout breeding population. Using progeny performance data, the accuracy of 
      genomic breeding values (GEBV) using 35K, 10K, 3K, 1K, 500, 300 and 200 SNP 
      panels as well as a panel with 70 quantitative trait loci (QTL)-flanking SNP was 
      compared. The GEBVs were estimated using the Bayesian method BayesB, single-step 
      GBLUP (ssGBLUP) and weighted ssGBLUP (wssGBLUP). The accuracy of GEBVs remained 
      high despite the sharp reductions in SNP density, and even with 500 SNP accuracy 
      was higher than the pedigree-based prediction (0.50-0.56 versus 0.36). 
      Furthermore, the prediction accuracy with the 70 QTL-flanking SNP (0.65-0.72) was 
      similar to the panel with 35K SNP (0.65-0.71). Genomewide linkage disequilibrium 
      (LD) analysis revealed strong LD (r(2)  >/= 0.25) spanning on average over 1 Mb 
      across the rainbow trout genome. This long-range LD likely contributed to the 
      accurate genomic predictions with the low-density SNP panels. Population 
      structure analysis supported the hypothesis that long-range LD in this population 
      may be caused by admixture. Results suggest that lower-cost, low-density SNP 
      panels can be used for implementing genomic selection for BCWD resistance in 
      rainbow trout breeding programs.
CI  - (c) 2018 The Authors. This article is a U.S. Government work and is in the public 
      domain in the USA. Journal of Animal Breeding and Genetics published by Blackwell 
      Verlag GmbH.
FAU - Vallejo, Roger L
AU  - Vallejo RL
AUID- ORCID: 0000-0002-5399-3531
AD  - National Center for Cool and Cold Water Aquaculture, United States Department of 
      Agriculture, Agricultural Research Service, Kearneysville, West Virginia.
FAU - Silva, Rafael M O
AU  - Silva RMO
AD  - Animal and Dairy Science Department, University of Georgia, Athens, Georgia.
FAU - Evenhuis, Jason P
AU  - Evenhuis JP
AD  - National Center for Cool and Cold Water Aquaculture, United States Department of 
      Agriculture, Agricultural Research Service, Kearneysville, West Virginia.
FAU - Gao, Guangtu
AU  - Gao G
AD  - National Center for Cool and Cold Water Aquaculture, United States Department of 
      Agriculture, Agricultural Research Service, Kearneysville, West Virginia.
FAU - Liu, Sixin
AU  - Liu S
AD  - National Center for Cool and Cold Water Aquaculture, United States Department of 
      Agriculture, Agricultural Research Service, Kearneysville, West Virginia.
FAU - Parsons, James E
AU  - Parsons JE
AD  - Troutlodge, Inc, Sumner, Washington.
FAU - Martin, Kyle E
AU  - Martin KE
AD  - Troutlodge, Inc, Sumner, Washington.
FAU - Wiens, Gregory D
AU  - Wiens GD
AD  - National Center for Cool and Cold Water Aquaculture, United States Department of 
      Agriculture, Agricultural Research Service, Kearneysville, West Virginia.
FAU - Lourenco, Daniela A L
AU  - Lourenco DAL
AUID- ORCID: 0000-0003-3140-1002
AD  - Animal and Dairy Science Department, University of Georgia, Athens, Georgia.
FAU - Leeds, Timothy D
AU  - Leeds TD
AD  - National Center for Cool and Cold Water Aquaculture, United States Department of 
      Agriculture, Agricultural Research Service, Kearneysville, West Virginia.
FAU - Palti, Yniv
AU  - Palti Y
AD  - National Center for Cool and Cold Water Aquaculture, United States Department of 
      Agriculture, Agricultural Research Service, Kearneysville, West Virginia.
LA  - eng
PT  - Journal Article
DEP - 20180605
PL  - Germany
TA  - J Anim Breed Genet
JT  - Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und 
      Zuchtungsbiologie
JID - 100955807
OTO - NOTNLM
OT  - bacterial cold water disease
OT  - genomic breeding value
OT  - genomic selection
OT  - linkage disequilibrium
OT  - progeny performance
OT  - reduced SNP array
OT  - salmonids
EDAT- 2018/06/06 06:00
MHDA- 2018/06/06 06:00
CRDT- 2018/06/06 06:00
PHST- 2018/02/06 00:00 [received]
PHST- 2018/04/27 00:00 [revised]
PHST- 2018/05/01 00:00 [accepted]
PHST- 2018/06/06 06:00 [entrez]
PHST- 2018/06/06 06:00 [pubmed]
PHST- 2018/06/06 06:00 [medline]
AID - 10.1111/jbg.12335 [doi]
PST - aheadofprint
SO  - J Anim Breed Genet. 2018 Jun 5. doi: 10.1111/jbg.12335.