Environmental Genome-Wide Association Reveals Climate Adaptation Is Shaped by Subtle to Moderate Allele Frequency Shifts in Loblolly Pine.
GEA
climate adaptation
loblolly pine
ultradense linkage map
Journal
Genome biology and evolution
ISSN: 1759-6653
Titre abrégé: Genome Biol Evol
Pays: England
ID NLM: 101509707
Informations de publication
Date de publication:
01 10 2019
01 10 2019
Historique:
accepted:
07
10
2019
pubmed:
11
10
2019
medline:
28
3
2020
entrez:
11
10
2019
Statut:
ppublish
Résumé
Understanding the genomic basis of local adaptation is crucial to determine the potential of long-lived woody species to withstand changes in their natural environment. In the past, efforts to dissect the genomic architecture in gymnosperms species have been limited due to the absence of reference genomes. Recently, the genomes of some commercially important conifers, such as loblolly pine, have become available, allowing whole-genome studies of these species. In this study, we test for associations between 87k SNPs, obtained from whole-genome resequencing of loblolly pine individuals, and 270 environmental variables and combinations of them. We determine the geographic location of significant loci and identify their genomic location using our newly constructed ultradense 26k SNP linkage map. We found that water availability is the main climatic variable shaping local adaptation of the species, and found 821 SNPs showing significant associations with climatic variables or combinations of them based on the consistent results of three different genotype-environment association methods. Our results suggest that adaptation to climate in the species might have occurred by many changes in the frequency of alleles with moderate to small effect sizes, and by the smaller contribution of large effect alleles in genes related to moisture deficit, temperature and precipitation. Genomic regions of low recombination and high population differentiation harbored SNPs associated with groups of environmental variables, suggesting climate adaptation might have evolved as a result of different selection pressures acting on groups of genes associated with an aspect of climate rather than on individual environmental variables.
Identifiants
pubmed: 31599932
pii: 5585006
doi: 10.1093/gbe/evz220
pmc: PMC6821164
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
2976-2989Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Philos Trans R Soc Lond B Biol Sci. 2012 Feb 5;367(1587):451-60
pubmed: 22201174
Genetics. 1999 Jan;151(1):321-30
pubmed: 9872970
Am Nat. 1998 Mar;151(3):283-92
pubmed: 18811359
Am Nat. 2015 Oct;186 Suppl 1:S24-36
pubmed: 26656214
Int J Plant Sci. 2010 Nov 1;171(9):1059-1071
pubmed: 21218185
Proc Natl Acad Sci U S A. 2013 May 7;110(19):E1743-51
pubmed: 23610436
Mol Ecol. 2014 Apr;23(8):2046-59
pubmed: 24597663
Genetics. 2014 Apr;196(4):1263-75
pubmed: 24443444
Mol Ecol. 2010 Sep;19(17):3789-805
pubmed: 20723060
Am Nat. 2015 Oct;186 Suppl 1:S74-89
pubmed: 26656219
PLoS Genet. 2014 Sep 25;10(9):e1004622
pubmed: 25255320
New Phytol. 2019 Mar;221(4):1789-1801
pubmed: 30318590
Mol Biol Evol. 2017 Jun 1;34(6):1363-1377
pubmed: 28333233
Annu Rev Plant Biol. 2017 Apr 28;68:457-483
pubmed: 28226237
Bioinformatics. 2003 May 1;19(7):889-90
pubmed: 12724300
Nat Rev Genet. 2010 Oct;11(10):665-7
pubmed: 20838407
Science. 2011 Oct 7;334(6052):83-6
pubmed: 21980108
Mol Ecol. 2018 May;27(9):2215-2233
pubmed: 29633402
Genome Biol. 2018 Oct 5;19(1):157
pubmed: 30290843
PLoS Genet. 2014 Aug 07;10(8):e1004412
pubmed: 25102153
Bioinformatics. 2014 Jun 1;30(11):1623-4
pubmed: 24532720
Mol Ecol. 2013 Feb;22(3):699-708
pubmed: 22420446
Mol Biol Evol. 2013 Jul;30(7):1687-99
pubmed: 23543094
Front Plant Sci. 2017 Jun 15;8:1041
pubmed: 28663754
PLoS One. 2016 Jun 08;11(6):e0156720
pubmed: 27275583
Mol Ecol. 2011 Apr;20(8):1702-16
pubmed: 21375634
Proc R Soc Lond B Biol Sci. 1966 Mar 22;164(995):362-79
pubmed: 4379525
Genetics. 2010 Aug;185(4):1411-23
pubmed: 20516501
Evolution. 2011 Jul;65(7):1897-911
pubmed: 21729046
Genome Res. 2009 Sep;19(9):1639-45
pubmed: 19541911
Mol Biol Evol. 2016 Jul;33(7):1754-67
pubmed: 26983554
Nat Rev Genet. 2011 Feb;12(2):111-22
pubmed: 21245829
Bioinformatics. 2011 Nov 1;27(21):3070-1
pubmed: 21926124
Genetics. 2010 Jul;185(3):969-82
pubmed: 20439779
Mol Ecol. 2014 Oct;23(19):4696-708
pubmed: 25156570
G3 (Bethesda). 2019 May 7;9(5):1623-1632
pubmed: 30898899
Genetics. 2005 Apr;169(4):2335-52
pubmed: 15716498
Mol Ecol Resour. 2015 Sep;15(5):1179-91
pubmed: 25684545
Genetics. 2013 Sep;195(1):205-20
pubmed: 23821598
Bioinformatics. 2012 Sep 15;28(18):2397-9
pubmed: 22796960
Genetics. 2006 Mar;172(3):1915-26
pubmed: 16387885
Mol Ecol. 2012 Apr;21(7):1548-66
pubmed: 22332667
Curr Biol. 2010 Feb 23;20(4):R208-15
pubmed: 20178769
Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2459-68
pubmed: 20643735
Bioinformatics. 2008 Jun 1;24(11):1403-5
pubmed: 18397895
New Phytol. 2016 Feb;209(3):1240-51
pubmed: 26372471
Genome Biol Evol. 2015 Nov 11;7(12):3269-85
pubmed: 26560341
Science. 2011 Oct 7;334(6052):86-9
pubmed: 21980109
Tree Physiol. 1987 Mar;3(1):41-61
pubmed: 14975834
Genetics. 2014 Jun;197(2):573-89
pubmed: 24700103
Genetics. 2003 Jul;164(3):1205-19
pubmed: 12871925
J Comput Biol. 2000 Feb-Apr;7(1-2):203-14
pubmed: 10890397
Nat Genet. 2010 Apr;42(4):355-60
pubmed: 20208535
Nat Commun. 2013;4:1827
pubmed: 23652015
Plant Physiol. 2014 Dec;166(4):1724-32
pubmed: 25349325
Genet Res. 1974 Feb;23(1):23-35
pubmed: 4407212
Brief Funct Genomics. 2014 Jul;13(4):268-75
pubmed: 24759704
Mol Ecol. 2017 Nov;26(22):6253-6269
pubmed: 28977721
Mol Biol Evol. 2014 Jul;31(7):1929-36
pubmed: 24739305
Mol Ecol. 2006 Dec;15(14):4261-93
pubmed: 17107465
G3 (Bethesda). 2015 Jun 11;5(8):1685-94
pubmed: 26068575