Fig 1.
Genetic polymorphism of the 289 core accessions revealed by genome resequencing.
(a) principal component analysis (PCA) plot of two components (PC1, PC2) using single-nucleotide polymorphisms (SNPs). (b) Single nucleotide polymorphism (SNP) density within a 0.1Mb window size on the 19 chromosomes of 289 resequenced genomes.
Fig 2.
The frequency distributions map of phenotypic BLUE values in 289 core accessions at different locations.
(a) The BLUE value of REL. (b) The BLUE value of POD. (c) The BLUE value of SP. (d) The BLUE value of MDA.
Fig 3.
Box plot of phenotypic BLUE values in 289 core accessions at different locations.
(a) The BLUE value of REL.(b) The BLUE value of POD. (c)The BLUE value of SP. (d) The BLUE value of MDA.
Fig 4.
Manhattan plots and QQ plots of GWAS for BLUE.
(a, e) the BLUE of REL among three locations. (b, f) the BLUE of POD among three locations. (c, g) the BLUE of SP among three locations. (d, h) the BLUE of MDA among three locations.
Fig 5.
The pathway enriched of 4,998 neighboring genes.
(a) the KEGG pathways of neighboring genes. (b) the GO classification annotation of neighboring genes.
Fig 6.
Differentially expressed genes (DEGs) in the freezing-sensitive and freezing-resistant cultivars revealed by RNA-seq analysis.
(a) the Venn plot of DEGs under freezing stress treatment. (b) the Venn plot of genes between GWAS and RNA-seq. (c) the Heat map of overlapped genes between GWAS and RNA-seq.
Table 1.
Candidate genes narrowed down by GWAS and RNA-seq experiments and their annotations.
Fig 7.
The transcription factors identified of neighboring genes.
(a)Total number of transcription factors in neighboring genes. (b) Number of transcription factors identified in both cultivar after freezing stress.