WGS data analysis

High-quality SNPs were identified using the Sentieon pipeline [34]. First, BAM files were obtained by Burrows-Wheeler Alignment (BWA) mem algorithm mapping to the current standard reference genome ZS11 [35]. SAMtools was then used to filter the BAM files with quality of >10 [36]. SNPs were collected from all the samples using the Haplotyper algorithm from Sentieon. The VCF files from all samples were merged using the Sentieon GVCFtyper algorithm. To obtain high-quality SNPs, the raw SNPs were filtered using the GATK VariantFiltration module with the parameter --filterExpression ‘QUAL < 30.0 || MQ < 50.0 || QD < 2′ --clusterSize 3 --clusterWindowSize 10. Next, the paternal SNPs were compared with maternal SNPs to identify different SNPs of the parents with a bin size of 50 kb. Subsequently, to identify SVs in the parents, VCF files were used by paragraph with default settings [37]. Finally, paternal SVs were compared with maternal SVs to identify different SVs of the parents with a bin size of 50 kb.