Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool.
domestication
durum wheat
landraces
nucleotide diversity
polymorphic information content
selection signature
single nucleotide polymorphisms
Journal
Frontiers in plant science
ISSN: 1664-462X
Titre abrégé: Front Plant Sci
Pays: Switzerland
ID NLM: 101568200
Informations de publication
Date de publication:
2023
2023
Historique:
received:
23
03
2023
accepted:
05
07
2023
medline:
7
8
2023
pubmed:
7
8
2023
entrez:
7
8
2023
Statut:
epublish
Résumé
Yanyang Liu, Henan Academy of Agricultural Sciences (HNAAS), China; Landraces are an important genetic source for transferring valuable novel genes and alleles required to enhance genetic variation. Therefore, information on the gene pool's genetic diversity and population structure is essential for the conservation and sustainable use of durum wheat genetic resources. Hence, the aim of this study was to assess genetic diversity, population structure, and linkage disequilibrium, as well as to identify regions with selection signature. Five hundred (500) individuals representing 46 landraces, along with 28 cultivars were evaluated using the Illumina Infinium 25K wheat SNP array, resulting in 8,178 SNPs for further analysis. Gene diversity (GD) and the polymorphic information content (PIC) ranged from 0.13-0.50 and 0.12-0.38, with mean GD and PIC values of 0.34 and 0.27, respectively. Linkage disequilibrium (LD) revealed 353,600 pairs of significant SNPs at a cut-off (
Identifiants
pubmed: 37546270
doi: 10.3389/fpls.2023.1192356
pmc: PMC10400094
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1192356Informations de copyright
Copyright © 2023 Mulugeta, Ortiz, Geleta, Hailesilassie, Hammenhag, Hailu and Tesfaye.
Déclaration de conflit d'intérêts
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.
Références
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
Genetics. 2008 Jan;178(1):489-511
pubmed: 18202390
BMC Genomics. 2021 Apr 5;22(1):233
pubmed: 33820546
Theor Appl Genet. 2019 Sep;132(9):2509-2523
pubmed: 31139853
Proc Natl Acad Sci U S A. 2013 May 14;110(20):8057-62
pubmed: 23630259
Plant Genome. 2020 Jul;13(2):e20031
pubmed: 33016613
Front Plant Sci. 2020 Dec 21;11:569905
pubmed: 33408724
Mol Biol Evol. 2017 Dec 1;34(12):3299-3302
pubmed: 29029172
Bioinformatics. 2012 Oct 1;28(19):2537-9
pubmed: 22820204
Bioinformatics. 2005 May 1;21(9):2128-9
pubmed: 15705655
Proc Natl Acad Sci U S A. 1973 Dec;70(12):3321-3
pubmed: 4519626
Front Genet. 2020 Apr 21;11:217
pubmed: 32373150
PLoS One. 2016 Nov 15;11(11):e0166577
pubmed: 27846306
G3 (Bethesda). 2017 Aug 7;7(8):2461-2471
pubmed: 28611254
Front Plant Sci. 2021 Sep 24;12:671323
pubmed: 34630445
Annu Rev Plant Biol. 2003;54:357-74
pubmed: 14502995
Mol Biol Rep. 2020 Jan;47(1):293-306
pubmed: 31630318
PLoS One. 2017 Jan 18;12(1):e0167821
pubmed: 28099442
Plant Biotechnol J. 2016 Sep;14(9):1800-12
pubmed: 26853077
Mol Ecol. 2005 Jul;14(8):2611-20
pubmed: 15969739
Biochem Genet. 2019 Feb;57(1):98-116
pubmed: 30051349
Gene. 2020 Feb 5;726:144175
pubmed: 31726084
Plant Genome. 2016 Nov;9(3):
pubmed: 27902791
Front Plant Sci. 2019 Jul 17;10:919
pubmed: 31379901
Front Plant Sci. 2017 Aug 29;8:1293
pubmed: 28912785
Plant Biotechnol J. 2019 Jul;17(7):1380-1393
pubmed: 30575264
Int J Mol Sci. 2017 Jun 21;18(6):
pubmed: 28635630
PLoS One. 2019 Feb 27;14(2):e0211718
pubmed: 30811415
Front Genet. 2022 Jun 15;13:900572
pubmed: 35783289
Front Plant Sci. 2022 Jan 05;12:799482
pubmed: 35069657
Bioinformatics. 2007 Oct 1;23(19):2633-5
pubmed: 17586829
Nat Genet. 2010 Nov;42(11):961-7
pubmed: 20972439
J Adv Res. 2023 Jun;48:47-60
pubmed: 36084813
Theor Appl Genet. 2009 Aug;119(3):437-48
pubmed: 19462147
Theor Appl Genet. 2022 Mar;135(3):755-776
pubmed: 34283259
Front Plant Sci. 2016 Jul 06;7:991
pubmed: 27458472
Front Plant Sci. 2017 Apr 20;8:604
pubmed: 28473842
3 Biotech. 2020 Feb;10(2):48
pubmed: 32002339
BMC Genet. 2020 Feb 12;21(1):18
pubmed: 32050895
PLoS One. 2014 Apr 23;9(4):e95211
pubmed: 24759998
Genomics. 1995 Sep 20;29(2):311-22
pubmed: 8666377
Theor Appl Genet. 2010 Aug;121(3):475-87
pubmed: 20364375
PLoS One. 2019 Jul 15;14(7):e0219867
pubmed: 31306459
Mol Ecol Resour. 2010 May;10(3):564-7
pubmed: 21565059
Nat Genet. 2019 May;51(5):885-895
pubmed: 30962619
Plant Cell. 2003 Jul;15(7):1502-6
pubmed: 12837942
PLoS One. 2021 Feb 17;16(2):e0247016
pubmed: 33596260
Int J Mol Sci. 2013 Mar 28;14(4):7061-88
pubmed: 23538839
PLoS One. 2022 Aug 17;17(8):e0273008
pubmed: 35976886
PLoS One. 2019 Jun 28;14(6):e0218562
pubmed: 31251752
Mol Ecol Resour. 2015 Sep;15(5):1179-91
pubmed: 25684545
BMC Genomics. 2020 Jun 26;21(1):434
pubmed: 32586286
Front Genet. 2018 Mar 12;9:76
pubmed: 29593779
Biochem Genet. 2016 Aug;54(4):421-437
pubmed: 27048293
Plant Genome. 2017 Nov;10(3):
pubmed: 29293807
Front Plant Sci. 2017 Jul 18;8:1277
pubmed: 28769970
Nat Genet. 2019 May;51(5):905-911
pubmed: 31043760
Front Plant Sci. 2018 Jan 18;9:8
pubmed: 29403518
BMC Genomics. 2010 Dec 14;11:702
pubmed: 21156062
Mol Breed. 2014;34(4):1629-1645
pubmed: 25506257
Front Plant Sci. 2023 Jan 26;13:1009244
pubmed: 36777537
Plant Biotechnol J. 2018 Jan;16(1):280-291
pubmed: 28635103
Genetics. 2000 Jun;155(2):945-59
pubmed: 10835412
Front Plant Sci. 2017 May 12;8:774
pubmed: 28553306
Euphytica. 2018;214(7):114
pubmed: 30996394
Front Plant Sci. 2020 Jul 17;11:1067
pubmed: 32765555
Evolution. 1984 Nov;38(6):1358-1370
pubmed: 28563791
Front Plant Sci. 2018 Feb 08;9:80
pubmed: 29472936
PLoS One. 2016 Aug 11;11(8):e0160983
pubmed: 27513751
Nat Commun. 2020 Sep 11;11(1):4572
pubmed: 32917907
Genetics. 1989 Nov;123(3):585-95
pubmed: 2513255
J Exp Bot. 2016 Feb;67(4):1161-78
pubmed: 26880749
Genetics. 2008 Oct;180(2):977-93
pubmed: 18780740
Mol Ecol. 2017 Jul;26(14):3594-3602
pubmed: 28544181
Mol Biol Evol. 2014 Jul;31(7):1929-36
pubmed: 24739305