Genome-wide association study to identify low temperature
resistance-associated loci containing MIRNA genes in B. napus
B. napus is closely related to B. rapa and both areBrassica crops. To identify MIRNA genes associated with low
temperature stress in Brassica crops, we constructed a B.
napus population. Low-temperature resistance was divided into with 5
levels (Grade 1 indicates most cold-resistant, while Grade 5 indicates
most cold-sensitive) and was measured in the field in January of 2017
and 2018, and the phenotypic data of rapeseed population showed a nearly
skewed distribution (Xu et al., 2021). The genome re-sequencing of 220B. napus accessions generated 2.13 Tb clean reads, and single
nucleotide polymorphism (SNP) genotyping of B. napus population
identified 3.80 million highly quality SNPs (MAF > 0.05,
geno < 0.2) (Xu et al., 2021). Overall, the SNPs were not
evenly distributed across the whole genome. The SNP density in the A
sub-genome (5.25/Kb) was higher than that in the C sub-genome (4.74/Kb)
(Figure S3A). A principal component analysis (PCA) was used to assess
the genetic relationship in the association panel. Based on the PCA, theB. napus population was roughly divided into three groups
corresponding to winter (W), semi-winter (SW), and spring (S) ecotypes
(Figure S3B). We further analyzed the linkage disequilibrium (LD)
throughout the genome. The LD was estimated asr2 (the squared Pearson correlation coefficient)
between all pairs of SNP markers. The average distance over which LD
decayed to r2 =0.2 of its maximum value was 100
kb, indicating that SNPs located in the 200-kb genomic region around
each peak SNP represented a GWAS-quantitative trait locus (QTL) (Figure
S3C).
The GWAS was performed using a mixed linear model, and the SNPs
significantly associated with low-temperature resistance were identified
at a threshold of p < 10-6. As a
result, we identified 32 highly credible GWAS-QTLs (Figure 3A). To
discover candidate MIRNA genes within these QTLs, we collected 163
pre-miRNA sequences specific to the Cruciferae family from four species
(B. napus , B. rapa , B. oleracea, andArabidopsis ) according to previous reports (Jones-Rhoades and
Bartel, 2004; Alves-Junior et al., 2009; Yu et al., 2011; He et al.,
2018; Zhang et al., 2018; Li et al., 2019). All the pre-miRNA sequences
were mapped to the B. napus reference to identify their location
(Table S4). We found that four candidate MIRNA genes,bna-MIR166C , bna-MIR1885 , bna-MIR168A andbna-MIR845A, were in the QTLs associated with low-temperature
resistance.
A previous study proved that knock-down of miR165/166 expression
conferred a cold-resistant phenotype in A. thaliana (Yan et al.,
2016). Conserved miR845a was known to be differentially expressed in
leaves of winter turnip rape under cold stress (Zeng et al., 2018). To
further determine whether these four miRNAs were responsive to low
temperature, we measured the abundance of mature miRNAs in B.
napus under cold stress by qRT-PCR. From this analysis, we found that
all four of them were cold-responsive. bna-miR1885 and bna-miR168a were
up-regulated at all these time points, while bna-miR845a and bna-miR166c
were down-regulated (Figure 3B and Figure 4A).
To identify if any genetic variation in cis-regulatory element
contribute to the MIR1885 transcription in the population of
rapeseed, we studied the LD of SNPs in the promoter ofbna-MIR1885 gene locus and found that they exhibited significant
linkage (Figure S3D). We identified 22 SNPs and 7 INDELs inbna-MIR1885 promoter region, which were found to be significant
associated with cold resistance. We further investigated the five
variants located in the 200-bp genomic region around the low
temperature-responsive (LTR: CCGAAA) element identified above. TheB. napus accessions were classified into three haplotype groups
based on the genotypes of these variants (Figure 3C). We found that 179
accessions contained the H1 haplotype, which variants were identical
with the genome reference, and this haplotype was associated with low
temperature-sensitive phenotype. 24 accessions carried H2 haplotype,
which contained mutated LTR cis-element and was associated with low
temperature-resistant phenotype. Consistently, heterozygous H3 haplotype
had an average resistance degree, which less than H1 haplotype, but
higher than H2. Next, we randomly selected 4 accessions with low
temperature-resistant variant alleles and low temperature-sensitive
variant alleles, respectively, to measure their abundance of miR1885
after cold treatment by qRT-PCR. The qRT-PCR data indicated that the
abundance of miR1885 was significantly higher in low
temperature-sensitive accessions with normal LTR in the promoter (H1
haplotype), as compared to low temperature-resistant accessions with
mutated LTR in their promoter (H2 haplotype) (Figure S3E). In total,
these results suggested that genetic variation in the LTR region atMIR1885 promoter in the rapeseed population potentially affected
the miR1885 expression and associated with cold resistance.