High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 740 pigs, combine with 149 of our previously published resequencing data, retrieve 207 resequencing datasets, and form a panel of worldwide distributed wild boars, aboriginal and highly selected pigs with pedigree structures, amounting to 1096 genomes from 43 breeds. Combining with their haplotype-informative reads and pedigree structure, we accurately construct a panel of 1874 haploid genomes with 41,964,356 genetic variants. We further demonstrate its valuable applications in GWAS by identifying five novel loci for intramuscular fat content, and in genomic selection by increasing the accuracy of estimated breeding value by 36.7%. In evolutionary selection, we detect MUC13 gene under a long-term balancing selection, as well as NPR3 gene under positive selection for pig stature. Our study provides abundant genomic variations for robust selection-signature detection and accurate haplotypes for deciphering complex traits in pigs.
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