Episodes of gene flow and selection during the evolutionary history of domesticated barley.
Barley
Exome sequences
Fertile Crescent
Gene flow
Hordeum vulgare
Origins of agriculture
Selection
Selective sweep
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
01 Apr 2021
01 Apr 2021
Historique:
received:
06
07
2020
accepted:
05
03
2021
entrez:
2
4
2021
pubmed:
3
4
2021
medline:
15
5
2021
Statut:
epublish
Résumé
Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is 'non-brittleness' of the rachis (the stem of the inflorescence), which facilitates harvesting of the crop. Other phenotypic differences appear to result from facultative or regional selective pressures. The population structure resulting from these regional events has been interpreted as evidence for multiple domestications or a mosaic ancestry involving genetic interaction between multiple wild or proto-domesticated lineages. However, each of the three mutations that confer non-brittleness originated in the western Fertile Crescent, arguing against multiregional origins for the crop. We examined exome data for 310 wild, cultivated and hybrid/feral barley accessions and showed that cultivated barley is structured into six genetically-defined groups that display admixture, resulting at least in part from two or more significant passages of gene flow with distinct wild populations. The six groups are descended from a single founding population that emerged in the western Fertile Crescent. Only a few loci were universally targeted by selection, the identity of these suggesting that changes in seedling emergence and pathogen resistance could represent crucial domestication switches. Subsequent selection operated on a regional basis and strongly contributed to differentiation of the genetic groups. Identification of genetically-defined groups provides clarity to our understanding of the population history of cultivated barley. Inference of population splits and mixtures together with analysis of selection sweeps indicate descent from a single founding population, which emerged in the western Fertile Crescent. This founding population underwent relatively little genetic selection, those changes that did occur affecting traits involved in seedling emergence and pathogen resistance, indicating that these phenotypes should be considered as 'domestication traits'. During its expansion out of the western Fertile Crescent, the crop underwent regional episodes of gene flow and selection, giving rise to a modern genetic signature that has been interpreted as evidence for multiple domestications, but which we show can be rationalized with a single origin.
Sections du résumé
BACKGROUND
BACKGROUND
Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is 'non-brittleness' of the rachis (the stem of the inflorescence), which facilitates harvesting of the crop. Other phenotypic differences appear to result from facultative or regional selective pressures. The population structure resulting from these regional events has been interpreted as evidence for multiple domestications or a mosaic ancestry involving genetic interaction between multiple wild or proto-domesticated lineages. However, each of the three mutations that confer non-brittleness originated in the western Fertile Crescent, arguing against multiregional origins for the crop.
RESULTS
RESULTS
We examined exome data for 310 wild, cultivated and hybrid/feral barley accessions and showed that cultivated barley is structured into six genetically-defined groups that display admixture, resulting at least in part from two or more significant passages of gene flow with distinct wild populations. The six groups are descended from a single founding population that emerged in the western Fertile Crescent. Only a few loci were universally targeted by selection, the identity of these suggesting that changes in seedling emergence and pathogen resistance could represent crucial domestication switches. Subsequent selection operated on a regional basis and strongly contributed to differentiation of the genetic groups.
CONCLUSIONS
CONCLUSIONS
Identification of genetically-defined groups provides clarity to our understanding of the population history of cultivated barley. Inference of population splits and mixtures together with analysis of selection sweeps indicate descent from a single founding population, which emerged in the western Fertile Crescent. This founding population underwent relatively little genetic selection, those changes that did occur affecting traits involved in seedling emergence and pathogen resistance, indicating that these phenotypes should be considered as 'domestication traits'. During its expansion out of the western Fertile Crescent, the crop underwent regional episodes of gene flow and selection, giving rise to a modern genetic signature that has been interpreted as evidence for multiple domestications, but which we show can be rationalized with a single origin.
Identifiants
pubmed: 33794767
doi: 10.1186/s12864-021-07511-7
pii: 10.1186/s12864-021-07511-7
pmc: PMC8015183
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
227Subventions
Organisme : European Research Council
ID : 339941
Pays : International
Références
Cell. 2015 Jul 30;162(3):527-39
pubmed: 26232223
Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1424-9
pubmed: 17220272
Genome Biol. 2015 Aug 21;16:173
pubmed: 26293830
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Genome Biol. 2019 Dec 18;20(1):284
pubmed: 31849336
Front Plant Sci. 2016 Nov 16;7:1723
pubmed: 27899932
PLoS Genet. 2006 Dec;2(12):e190
pubmed: 17194218
Theor Appl Genet. 2007 Apr;114(6):947-59
pubmed: 17318496
Ann Bot. 2007 Nov;100(5):903-24
pubmed: 17495986
Nature. 2017 Apr 26;544(7651):427-433
pubmed: 28447635
New Phytol. 2018 May;218(3):1247-1259
pubmed: 29528492
Theor Appl Genet. 2007 Apr;114(6):1117-27
pubmed: 17279366
Nat Genet. 2016 Sep;48(9):1024-30
pubmed: 27428750
Sci Rep. 2017 Mar 16;7:44611
pubmed: 28300158
Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3289-94
pubmed: 17360640
Nat Genet. 2016 Sep;48(9):1089-93
pubmed: 27428749
Mol Plant. 2019 Jan 7;12(1):30-43
pubmed: 30472326
PLoS One. 2013 Nov 29;8(11):e81955
pubmed: 24312385
Front Plant Sci. 2015 Sep 30;6:803
pubmed: 26483818
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
BMC Bioinformatics. 2006 Sep 12;7:409
pubmed: 16968531
Plant Cell. 2004 Sep;16(9):2293-306
pubmed: 15308756
Gigascience. 2015 Feb 25;4:7
pubmed: 25722852
J Integr Plant Biol. 2019 Mar;61(3):204-225
pubmed: 30414305
Ann Bot. 2007 Nov;100(5):999-1008
pubmed: 17761690
IEEE Trans Vis Comput Graph. 2014 Dec;20(12):1983-92
pubmed: 26356912
New Phytol. 2017 Apr;214(1):468-472
pubmed: 28092403
Genome Res. 2009 Sep;19(9):1639-45
pubmed: 19541911
Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8641-8
pubmed: 17494757
Genetics. 2012 Nov;192(3):1065-93
pubmed: 22960212
Mol Biol Evol. 2004 Feb;21(2):255-65
pubmed: 14660700
Mol Ecol Resour. 2021 Feb;21(2):584-595
pubmed: 33012121
Science. 1999 Oct 29;286(5441):961-4
pubmed: 10542152
Methods. 2013 Sep 1;63(1):41-9
pubmed: 23816787
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
Genetics. 2014 Apr;196(4):973-83
pubmed: 24496008
PLoS Genet. 2012;8(11):e1002967
pubmed: 23166502
Mol Biol Evol. 2015 Jan;32(1):244-57
pubmed: 25246699
Plant J. 2006 Jan;45(1):83-100
pubmed: 16367956
Bioinformatics. 2014 Mar 1;30(5):614-20
pubmed: 24142950
Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):16969-73
pubmed: 23033493
J Hered. 2014 Mar-Apr;105(2):253-64
pubmed: 24336926
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Genetics. 1989 Nov;123(3):585-95
pubmed: 2513255
Genet Res. 1974 Feb;23(1):23-35
pubmed: 4407212
Nat Plants. 2015 Nov 02;1:15164
pubmed: 27251535
Plant J. 2013 Nov;76(3):494-505
pubmed: 23889683
Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13982-6
pubmed: 18768818