Abstract
Winter field survival (WFS) in autumn-seeded winter cereals is a complex trait associated with low temperature tolerance (LTT), prostrate growth habit (PGH), and final leaf number (FLN). WFS and the three sub-traits were analyzed by a genome-wide association study of 96 rye (Secale cereal L.) genotypes of different origins and winter-hardiness levels. A total of 10,244 single nucleotide polymorphism (SNP) markers were identified by genotyping by sequencing and 259 marker-trait-associations (MTAs; p < 0.01) were revealed by association mapping. The ten most significant SNPs (p < 1.49e-04) associated with WFS corresponded to nine strong candidate genes: Inducer of CBF Expression 1 (ICE1), Cold-regulated 413-Plasma Membrane Protein 1 (COR413-PM1), Ice Recrystallization Inhibition Protein 1 (IRIP1), Jasmonate-resistant 1 (JAR1), BIPP2C1-like protein phosphatase, Chloroplast Unusual Positioning Protein-1 (CHUP1), FRIGIDA-like 4 (FRL4-like) protein, Chalcone Synthase 2 (CHS2), and Phenylalanine Ammonia-lyase 8 (PAL8). Seven of the candidate genes were also significant for one or several of the sub-traits supporting the hypothesis that WFS, LTT, FLN, and PGH are genetically interlinked. The winter-hardy rye genotypes generally carried additional allele variants for the strong candidate genes, which suggested allele diversity was a major contributor to cold acclimation efficiency and consistent high WFS under varying field conditions.
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Claims 8
Claim · model-written summary
Genotyping by sequencing identified 10,244 SNP markers in 96 rye genotypes.
- Taxon
- rye
Secale cerealet0 - Outcome
- single nucleotide polymorphism (SNP) markerse0
- Value
- 10,244e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rye (Secale cereale L.)”
e0“A total of 10,244 single nucleotide polymorphism (SNP) markers were identified by genotyping by sequencing”
Claim · model-written summary
Association mapping revealed 259 marker-trait associations at p < 0.01.
- Taxon
- ryeSecale cerealet0
- Outcome
- marker-trait-associationse0
- Value
- 259e0
- Qualifier
- p < 0.01e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rye (Secale cereale L.)”
e0“259 marker-trait-associations (MTAs; p < 0.01) were revealed by association mapping”
Claim · model-written summary
The most significant SNPs for winter field survival corresponded to the candidate genes ICE1, COR413-PM1 and IRIP1.
- Taxon
- ryeSecale cerealet0
- Gene
- Inducer of CBF Expression 1 (ICE1), Cold-regulated 413-Plasma Membrane Protein 1 (COR413-PM1), Ice Recrystallization Inhibition Protein 1 (IRIP1)e1
- Outcome
- WFSe0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rye (Secale cereale L.)”
e0“SNPs (p < 1.49e-04) associated with WFS”
e1“Inducer of CBF Expression 1 (ICE1), Cold-regulated 413-Plasma Membrane Protein 1 (COR413-PM1), Ice Recrystallization Inhibition Protein 1 (IRIP1)”
Claim · model-written summary
The most significant SNPs for winter field survival corresponded to the candidate genes JAR1, BIPP2C1-like phosphatase and CHUP1.
- Taxon
- ryeSecale cerealet0
- Gene
- Jasmonate-resistant 1 (JAR1), BIPP2C1-like protein phosphatase, Chloroplast Unusual Positioning Protein-1 (CHUP1)e1
- Outcome
- WFSe0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rye (Secale cereale L.)”
e0“SNPs (p < 1.49e-04) associated with WFS”
e1“Jasmonate-resistant 1 (JAR1), BIPP2C1-like protein phosphatase, Chloroplast Unusual Positioning Protein-1 (CHUP1)”
Claim · model-written summary
The most significant SNPs for winter field survival corresponded to the candidate genes FRL4-like, CHS2 and PAL8.
- Taxon
- ryeSecale cerealet0
- Gene
- FRIGIDA-like 4 (FRL4-like) protein, Chalcone Synthase 2 (CHS2), and Phenylalanine Ammonia-lyase 8 (PAL8)e1
- Outcome
- WFSe0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rye (Secale cereale L.)”
e0“SNPs (p < 1.49e-04) associated with WFS”
e1“FRIGIDA-like 4 (FRL4-like) protein, Chalcone Synthase 2 (CHS2), and Phenylalanine Ammonia-lyase 8 (PAL8)”
Claim · model-written summary
Seven of the candidate genes were also significant for one or several of the sub-traits.
- Taxon
- ryeSecale cerealet0
- Outcome
- sub-traitse0
- Value
- Sevene0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rye (Secale cereale L.)”
e0“Seven of the candidate genes were also significant for one or several of the sub-traits”
Claim · model-written summary
Winter-hardy rye genotypes generally carried additional allele variants of the strong candidate genes.
- Taxon
- ryeSecale cerealee0
- Material
- winter-hardy rye genotypese0
- Outcome
- additional allele variantse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rye (Secale cereale L.)”
e0“The winter-hardy rye genotypes generally carried additional allele variants for the strong candidate genes”
Claim · model-written summary
The authors suggest that allele diversity was a major contributor to cold acclimation efficiency and consistently high winter field survival under varying field conditions.
- Taxon
- ryeSecale cerealet0
- Gene
- allele diversitye0
- Outcome
- cold acclimation efficiency and consistent high WFSe0
- Setting
- varying field conditionse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rye (Secale cereale L.)”
e0“allele diversity was a major contributor to cold acclimation efficiency and consistent high WFS under varying field conditions”