Abstract
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.
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Claims 14
Claim · model-written summary
RNA sequencing generated 1.3 million candidate Affymetrix SNP probe sets.
- Taxon
- tropical pine tree species
Pinus tropicalist0 - Outcome
- candidate Affymetrix SNP probe setse0
- Value
- 1.3 millione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“resulting in 1.3 million candidate Affymetrix SNP probe sets”
Claim · model-written summary
Capture sequencing generated 563 K candidate SNP probe sets.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Outcome
- candidate SNP probe setse0
- Value
- 563 Ke0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“resulting in 563 K candidate SNP probe sets”
Claim · model-written summary
The screening array tiled 300 K RNA-seq-derived SNP probe sets.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Outcome
- RNA-seq (72%)e0
- Value
- 300 Ke0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“300 K RNA-seq (72%) and 120 K capture-seq (28%) derived SNP probe sets were tiled on a 420 K screening array”
Claim · model-written summary
The screening array tiled 120 K capture-seq-derived SNP probe sets.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Outcome
- capture-seq (28%)e0
- Value
- 120 Ke0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“300 K RNA-seq (72%) and 120 K capture-seq (28%) derived SNP probe sets were tiled on a 420 K screening array”
Claim · model-written summary
A 420 K screening array genotyped 576 trees.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Outcome
- genotype 576 treese0
- Value
- 420 Ke0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“420 K screening array that was used to genotype 576 trees”
Claim · model-written summary
A 50 K SNP array was selected for commercial production.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Outcome
- SNPs were selected for commercial SNP array productione0
- Value
- 50 Ke0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“50 K SNPs were selected for commercial SNP array production”
Claim · model-written summary
20 K polymorphic SNPs were selected for P. patula, P. tecunumanii, P. oocarpa and P. caribaea.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Material
- P. patula, P. tecunumanii, P. oocarpa and P. caribaeae0
- Outcome
- polymorphic SNPse0
- Value
- 20 Ke0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“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”
Claim · model-written summary
15 K polymorphic SNPs were selected for P. greggii and P. maximinoi.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Material
- P. greggii and P. maximinoie0
- Outcome
- polymorphic SNPse0
- Value
- 15 Ke0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“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”
Claim · model-written summary
13 K polymorphic SNPs were selected for P. elliottii.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Material
- P. elliottiie0
- Outcome
- polymorphic SNPse0
- Value
- 13 Ke0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“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”
Claim · model-written summary
8K polymorphic SNPs were selected for P. pseudostrobus.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Material
- P. pseudostrobuse0
- Outcome
- polymorphic SNPse0
- Value
- 8Ke0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“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”
Claim · model-written summary
The array included 9.7 K ancestry-informative SNPs for species and hybrid discrimination.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Outcome
- ancestry informative SNPse0
- Value
- 9.7 Ke0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“9.7 K ancestry informative SNPs that will be valuable for species and hybrid discrimination”
Claim · model-written summary
One quarter of the 50 K SNP markers were polymorphic in only one species.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Outcome
- polymorphic in only one speciese0
- Value
- 25%e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“Of the 50 K SNP markers, 25% are polymorphic in only one species”
Claim · model-written summary
Three quarters of the 50 K SNP markers were shared by at least two species.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Outcome
- shared by two or more speciese0
- Value
- 75%e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“75% are shared by two or more species”
Claim · model-written summary
The authors expect the Pitro50K chip to support population genomics and molecular breeding.
- Taxon
- tropical pine tree speciesPinus tropicalist0
- Outcome
- useful for population genomics and molecular breedinge0
- Comparator
- Pitro50K SNP chipe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“tropical pine tree species”
e0“The Pitro50K SNP chip will be useful for population genomics and molecular breeding”