A genome-wide SNP genotyping resource for tropical pine tree species.
Pitro50K
SNP
genotyping array
molecular breeding
tropical pines
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Feb 2022
Feb 2022
Historique:
revised:
10
07
2021
received:
24
12
2020
accepted:
16
07
2021
pubmed:
13
8
2021
medline:
6
1
2022
entrez:
12
8
2021
Statut:
ppublish
Résumé
We performed gene and genome targeted SNP discovery towards the development of a genome-wide, multispecies genotyping array for tropical pines. Pooled RNA-seq data from shoots of seedlings from five tropical pine species was used to identify transcript-based SNPs resulting in 1.3 million candidate Affymetrix SNP probe sets. In addition, we used a custom 40 K probe set to perform capture-seq in pooled DNA from 81 provenances representing the natural ranges of six tropical pine species in Mexico and Central America resulting in 563 K candidate SNP probe sets. Altogether, 300 K RNA-seq (72%) and 120 K capture-seq (28%) derived SNP probe sets were tiled on a 420 K screening array that was used to genotype 576 trees representing the 81 provenances and commercial breeding material. Based on the screening array results, 50 K SNPs were selected for commercial SNP array production including 20 K polymorphic SNPs for P. patula, P. tecunumanii, P. oocarpa and P. caribaea, 15 K for P. greggii and P. maximinoi, 13 K for P. elliottii and 8K for P. pseudostrobus. We included 9.7 K ancestry informative SNPs that will be valuable for species and hybrid discrimination. Of the 50 K SNP markers, 25% are polymorphic in only one species, while 75% are shared by two or more species. The Pitro50K SNP chip will be useful for population genomics and molecular breeding in this group of pine species that, together with their hybrids, represent the majority of fast-growing tropical and subtropical pine plantations globally.
Identifiants
pubmed: 34383377
doi: 10.1111/1755-0998.13484
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
695-710Subventions
Organisme : South Africa Technology Innovation Agency (TIA)
Organisme : South Africa Department of Science and Innovation (DSI)
Organisme : South Africa National Research Foundation (NRF) - Bioinformatics and Functional Genomics (BFG) Programme
ID : 97911
Organisme : United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) project
ID : 2016-67013-24469
Organisme : South Africa Forestry Sector Innovation Fund (FSIF)
Informations de copyright
© 2021 John Wiley & Sons Ltd.
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