Association mapping of autumn-seeded rye (Secale cereale L.) reveals genetic linkages between genes controlling winter hardiness and plant development

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.

Figure 1

Principal component analysis (PCA) score plot. Plot generated from analysis of 10,244 SNP markers identified in rye population of 96 accessions. The x axis represents the eigenvalue for principal component 1 (PC1) and the y axis for PC2. Genotypes with highest WFS are encircled and arrows refer to less cold hardy Petkus and Carsten, respectively. Data for the individual genotypes is listed in Table S1.

Figure 2

Box-whisker plots showing the allele effects for the most significant (p < 1.49 e−04) MTAs. The plots show median (horizontal bar), interquartile ranges (boxes), ranges (whiskers), and outliers (dots) for marker allele frequencies among the 96 rye genotypes.

Figure 3

PCA bi-plot visualizing SNP effects on four traits analyzed for rye population of 96 genotypes.

Figure 4

Location of significant MTAs identified on rye physical map. Locations refers to the Lo7 v1 pseudomolecules 2021. Most significant markers (p < 1.49e−04; Table 2) are indicated in bold. Location of FR-R2, VRN1, and discussed candidate genes are shown.