Supporting data for "Accelerated Deciphering of the Genetic Architecture of Agricultural Economic Traits in Pigs Using the Low Coverage Whole-genome Sequencing Strategy"

Uncovering the genetic architecture of economic traits in pigs is important for agricultural breeding. However, high-density haplotype reference panels are unavailable in most agricultural species, limiting accurate genotype imputation in large populations. Moreover, the infinitesimal model of quantitative traits implies that weak association signals tend to be spread across most of the genome, further complicating the genetic analysis. Hence, there is a need to develop new methods for sequencing large cohorts without large reference panels. <br>We described a Tn5-based highly accurate, cost- and time-efficient, low coverage sequencing (LCS) method to obtain 11.3 M whole-genome SNPs in 2,869 Duroc boars at an average depth of 0.73x. Based on these SNPs, a genome-wide association study (GWAS) detected 14 quantitative trait loci (QTLs) for seven of 21 important agricultural traits in pigs, such as ABCD4 for total teat number and HMGA1 for backfat thickness, and provided a starting point for further investigation. The inheritance models of the different traits varied greatly. Most follow the minor-polygene model, but this can be attributed to different reasons, such as the shaping of genetic architecture by artificial selection for this population and sufficiently interconnected minor gene regulatory networks. <br>GWAS results for 21 important agricultural traits identified 14 QTLs/genes and showed their various genetic architectures, providing promising guidance for genetic improvement harnessing genomic features. The Tn5-based LCS method can be applied to large-scale genome studies for any species without a good reference panel and can be widely used for agricultural breeding.