LAUSR

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.