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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. [ABSTRACT FROM AUTHOR]

• Cold hardy rye genotypes accumulated the highest amounts and diversity of anthocyanins. • Glycosylated cyanidins were preferentially accumulated in cold hardy genotypes. • Delphinidin and pelargonidin glycosides were unrelated to cold hardiness. • A higher accumulation of anthocyanins in leaves than in crowns upon cold acclimation. Fall-seeded rye improve their frost resistance during a cold acclimation period in the fall, which is often associated with an accumulation of red/purple-colored anthocyanins in plant tissues. The pigments provide antioxidant activity and are proposed to scavenge excess reactive oxygen species (ROS) and mitigate light stress occurring during cold exposure. The relationship between anthocyanin and winter hardiness in rye (Secale cereale L.) was assessed by analyzing 96 genotypes with varying levels of winter survival. HPLC-QTOF MS/MS analyses of tissue extracts prepared from cold-acclimated plants revealed presence of accumulated anthocyanins in leaves of 74 genotypes and 51 of these showed low levels of anthocyanins presence in crown tissues. An overall higher abundance and diversity of anthocyanins was noted for the most cold-hardy as compared to the less hardy genotypes. A total of 18 anthocyanins originating from the pelargonidin, cyanidin, and delphinidin precursors were identified, of which the glycosylated cyanidins were accumulated in 37 of the 39 most winter hardy genotypes, but only detected in six of the 38 most tender genotypes. The link between anthocyanin concentration and profiles with winter-hardiness levels for the 96 rye genotypes suggested a role for cyanidin-derived anthocyanins in mediating enhanced winter hardiness in rye. [ABSTRACT FROM AUTHOR]

Overwintering cereals accumulate low temperature tolerance (LTT) during cold acclimation in the autumn. Simultaneously, the plants adjust to the colder season by making developmental changes at the shoot apical meristem. These processes lead to higher winter hardiness in winter rye varieties (Secale cereale L.) adapted to Northern latitudes as compared to other cereal crops. To dissect the winter-hardiness trait in rye, a panel of 96 genotypes of different origins and growth habits was assessed for winter field survival (WFS), LTT, and six developmental traits. Best Linear Unbiased Estimates for WFS determined from five field trials correlated strongly with LTT (r = 0.90, p < 0.001); thus, cold acclimation efficiency was the major contributor to WFS. WFS also correlated strongly (p < 0.001) with final leaf number (r = 0.80), prostrate growth habit (r = 0.61), plant height (r = 0.34), but showed weaker associations with top internode length (r = 0.30, p < 0.01) and days to anthesis (r = 0.25, p < 0.05). The heritability estimates (h2) for WFS-associated traits ranged from 0.45 (prostrate growth habit) to 0.81 (final leaf number) and were overall higher than for WFS (h2 = 0.48). All developmental traits associated with WFS and LTT are postulated to be regulated by phytohormone levels at shoot apical meristem. [ABSTRACT FROM AUTHOR]