Abstract: The present invention relates to the field of plant molecular breeding, and provides methods for estimating additive and dominant genetic effects of single methylation polymorphisms (SMPs) on quantitative traits. The method comprises the following steps: 1) collecting samples and measuring phenotype in a natural population, and extracting genomic DNA from the samples; 2) constructing MethylC-seq libraries using the sample genomic DNA, and sequencing; 3) identifying the SMPs from the DNA methylation sequencing reads, and performing genotyping; and 4) performing epigenome-wide association study on the SMPs and the phenotypic data using a Mixed Linear Model (MLM), identifying SMPs that are significantly associated with the phenotype, and estimating the additive and dominant genetic effects. The method can provide a new technical guidance for gene marker-assisted breeding, and has important theoretical and breeding values.

Abstract: The invention relates to the technical field of gene expression detection, and provides methods for high-throughput detection of differential expression of plant circRNA allelic loci. The method comprises the following steps: 1) extracting total RNA of a plant sample, and constructing a strand-specific library; 2) performing paired-end sequencing on the strand-specific library with Illumina HiSeq; 3) screening circRNAs data from raw sequencing data; 4) extracting reverse splicing reads at a circRNAs looping position to form the circRNAs data; 5) performing single nucleotide variation detection on the reverse splicing reads; and 6) collecting statistics about the number of reads of different genotypes, which are aligned to SNP loci, in the reverse splicing reads, to align the proportion of the number of reads of different genotypes to the proportion of expression quantities of different genotypes. The methods can accurately detect differential expression of circRNA allelic loci with high throughput.

Abstract: The present invention relates to the technical field of genetics and provides a method for detecting activity change of a transposon in a plant before and after stress treatment. The method includes the following steps: 1) respectively extracting total RNAs of samples before and after stress treatment; 2) respectively constructing cDNA libraries of the samples before and after stress treatment by using the total RNAs; 3) sequencing the cDNA libraries; 4) respectively screening siRNAs from raw sequencing data, and combining the screened siRNAs to obtain a total siRNA, and performing cluster clustering on the total siRNA; 5) extracting repeat in whole genome data by using repeatmasker software to obtain positional information of the plant whole genome transposon; and 6) obtaining activity change in the transposon of the plant before and after treatment by means of change in siRNA cluster expression quantity. The method fills the technical gap in the field of plant transposon activity detections.