Analysis of Anasplatyrhynchos genome resequencing data reveals genetic signatures of artificial selection

Abstract

Three artificially selected duck populations (AS), higher lean meat ratios (LTPD), higher fat ratios (FTPD) and higher quality meat (CMD), have been developed in China, providing excellent populations for investigation of artificial selection effects. However, the genetic signatures of artificial selection are unclear. In this study, we sequenced the genome sequences of these three artificially selected populations and their ancestral population (mallard, M). We then compared the genome sequences between AS and M and between LTPD and FTPD using integrated strategies such as anchoring scaffolds to pseudo-chromosomes, mutation detection, selective screening, GO analysis, qRT-PCR, and protein multiple sequences alignment to uncover genetic signatures of selection. We anchored duck scaffolds to pseudo-chromosomes and obtained 28 pseudo-chromosomes, accounting for 84% of duck genome in length. Totally 78 and 99 genes were found to be under selection between AS and M and between LTPD and FTPD. Genes under selection between AS and M mainly involved in pigmentation and heart rates, while genes under selection between LTPD and FTPD involved in muscle development and fat deposition. A heart rate regulator (HCN1), the strongest selected gene between AS and M, harbored a GC deletion in AS and displayed higher mRNA expression level in M than in AS. IGF2R, a regulator of skeletal muscle mass, was found to be under selection between FTPD and LTPD. We also found two nonsynonymous substitutions in IGF2R, which might lead to higher IGF2R mRNA expression level in FTPD than LTPD, indicating the two nonsynonymous substitutions might play a key role for the regulation of duck skeletal muscle mass. Taken together, these results of this study provide valuable insight for the genetic basis of duck artificial selection.

Genetic characteristics of Jiaji Duck by whole genome re-sequencing

“…These results indicated that the majority of the identified mutations were located in non-coding sequences (intergenic regions or intronic regions), and only a small proportion of them fell in exon sequence, showing that only very few variants along with duck genome could exert functional effects on protein function. Our results were consistent with those of Xu et al [8] in ducks and Carneiro et al in rabbits [6].…”

“…Subsequently, the highquality data were mapped to the A. platyrhynchos genome (BGI_duck_1.0), resulting in an average mapping rate of 93.14% and an average coverage rate of 95.63% for each individual (Table 1). The average mapping rate of this study (93.14%) was higher compared with our previous report (89.71%) [8], indicating a better quality of sequencing data used in this study.…”

“…A phylogenetic tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or subspecies based on the similarities and differences of their genetic characteristics [8]. In this study, we constructed the phylogenetic tree to illustrate the genetic relationships among the five duck populations (Fig 3A).…”

“…For ducks, the genome sequences have been constructed in 2013 [7], providing a platform for the research of ducks using WGRS method and promoting the related exploration of ducks. Xu et al have explored the genetic signatures of artificial selection using genome WGRS data [8]. Zhang et al have indicated the genomic variation in Peking duck populations using WGRS data [9].…”

Population analysis of the Korean native duck using whole-genome sequencing data

“…As a result, various genetic studies have been conducted to discover economically valuable genetic characteristics of duck breeds. For example, three duck breeds, which were artificially selected in China, were analyzed to identify the genetic features related to artificial selection based on whole-genome sequencing data [ 12 ]. Positively selected genes and differentially expressed genes involved with muscle growth and lipid deposition were identified by comparing native Pekin duck and Cherry Valley Pekin duck using whole-genome and transcriptome sequencing data [ 13 ].…”