**2.4. SNP calling**

SNP detection was performed with the widely accepted mutation detection software GATK. SNP. The screening criteria were as follows: The depth of sequencing for each sample was greater than or equal to 4, otherwise the sample was marked as missing. Additionally, the quality value of the comparison must be greater than or equal to 20, and the variation detection quality value must be greater than or equal to 50. If the allele frequency was less than 5% or the absence rate of the sample was greater than 50%, the site was filtered out.

The RIL population contains 105 progeny and two parents; the parent number is "A518\_ LER" and "A518\_SHA." The reads of each sample were compared with the reference genome. The average ratio of the samples was above 95%, and the coverage was greater than 92%. The average sequencing depth was 9.19×. By processing, we obtained 107 samples and 1,023,325 whole genome SNP markers. According to the situation of this population, individuals with heterozygous genotype ratios over 25% and markers indicating that parents possessed heterozygous genotypes were eliminated. Finally, 609,427 SNPs and 80 individuals met the model requirements and could be used to detect the QTLs that affect the growth height of *A. thaliana*.
