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

• Published in: Scientific reports Vol. 12; no. 1; p. 5793
• Main Authors: Båga, Monica, Bahrani, Hirbod, Larsen, Jamie, Hackauf, Bernd, Graf, Robert J., Laroche, Andre, Chibbar, Ravindra N.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06.04.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208; 631/337; 631/449; 704/172; Acclimation; Acclimatization; Alleles; Ammonia; Autumn; Cereals; Chalcone synthase; Chloroplasts; Cold acclimation; Gene mapping; Gene polymorphism; Genetic diversity; Genetic Linkage; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genotypes; Genotyping; Humanities and Social Sciences; Jasmonic acid; Low temperature; Membrane proteins; multidisciplinary; Phenotype; Phenylalanine; Phenylalanine ammonia-lyase; Plant Development; Protein phosphatase; Proteins; Science; Science (multidisciplinary); Secale - metabolism; Single-nucleotide polymorphism; Temperature tolerance; Winter
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-09582-2

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.