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

Dataset type: Genomic
Data released on June 11, 2021

Yang R; Guo X; Zhu D; Tan C; Bian C; Ren J; Huang Z; Zhao Y; Cai G; Liu D; Wu Z; Wang Y; Li N; Hu X (2021): Supporting data for "Accelerated Deciphering of the Genetic Architecture of Agricultural Economic Traits in Pigs Using the Low Coverage Whole-genome Sequencing Strategy" GigaScience Database. http://dx.doi.org/10.5524/100894

DOI10.5524/100894

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.
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.
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.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 34282453)

Accessions (data generated as part of this study):

BioProject: PRJNA681437
BioProject: PRJNA712489





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
WD02289823PigpigSus scrofa Description (unique to each sample):DNA extracted ...
Analyte type:DNA
Alternative accession-BioSample:SAMN18236793
...
+
WD02389823PigpigSus scrofa Description (unique to each sample):DNA extracted ...
Analyte type:DNA
Alternative accession-BioSample:SAMN18236794
...
+
WD02849823PigpigSus scrofa Description (unique to each sample):DNA extracted ...
Analyte type:DNA
Alternative accession-BioSample:SAMN18236795
...
+
WD03189823PigpigSus scrofa Description (unique to each sample):DNA extracted ...
Analyte type:DNA
Alternative accession-BioSample:SAMN18236796
...
+
WD03659823PigpigSus scrofa Description (unique to each sample):DNA extracted ...
Analyte type:DNA
Alternative accession-BioSample:SAMN18236797
...
+
WD04399823PigpigSus scrofa Description (unique to each sample):DNA extracted ...
Analyte type:DNA
Alternative accession-BioSample:SAMN18236798
...
+
WD04549823PigpigSus scrofa Description (unique to each sample):DNA extracted ...
Analyte type:DNA
Alternative accession-BioSample:SAMN18236810
...
+
WD04779823PigpigSus scrofa Description (unique to each sample):DNA extracted ...
Analyte type:DNA
Alternative accession-BioSample:SAMN18236799
...
+
WD05319823PigpigSus scrofa Description (unique to each sample):DNA extracted ...
Analyte type:DNA
Alternative accession-BioSample:SAMN18236800
...
+
WD05889823PigpigSus scrofa Description (unique to each sample):DNA extracted ...
Analyte type:DNA
Alternative accession-BioSample:SAMN18236801
...
+
Displaying 1-10 of 2906 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
otherBED172.68 MB2021-05-15
otherUNKNOWN7.18 MB2021-05-15
otherUNKNOWN62.82 KB2021-05-15
Tabular DataUNKNOWN6.69 MB2021-05-15
Tabular DataUNKNOWN2.81 KB2021-05-15
Tabular DataUNKNOWN2.85 KB2021-05-15
Tabular DataUNKNOWN6.69 MB2021-05-15
Tabular DataUNKNOWN2.86 KB2021-05-15
Tabular DataUNKNOWN6.69 MB2021-05-15
Tabular DataUNKNOWN2.83 KB2021-05-15
Displaying 1-10 of 108 File(s).
Funding body Awardee Award ID Comments
MOST Xiaoxiang Hu 2016ZX08009003-006 National Transgenic Grand Project
Ministry of Agriculture of China Xiaoxiang Hu 2012-G1(4) Program 948
Guangdong Province Xiaoxiang Hu 2019B020203002 Science and Technology Innovation Strategy Project
Guangdong Province Ning Li 2011A090700016 Academician Workstation
Date Action
June 11, 2021 Dataset publish
June 28, 2021 Manuscript Link added : 10.1093/gigascience/giab048
November 29, 2021 Manuscript Link updated : 10.1093/gigascience/giab048