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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.
Highlights
Based on Fisher’s theory of natural selection in 1930, traits are associated with evolutionary fitness, such as morphology and complex physiology [1]
The current duck genome lacks the linkage information to align scaffolds at the chromosome level, which impedes the identification of continuous genomic signatures under selection and genes overlapping these signatures
Comparative genomics analysis has revealed that ducks have the closest genetic relationship with chickens and turkeys, whose genomes have been assembled with assigned chromosomes [21]
Summary
Based on Fisher’s theory of natural selection in 1930, traits are associated with evolutionary fitness, such as morphology and complex physiology [1]. To investigate the genetic signatures underlying artificial selection in these new duck breeds, genomic sequences of all three breeds (LTPD, FTPD, and CMD, referred to collectively as the artificial selection population (AS)) were compared with their ancestor (mallard, M). 99 genes were found to be under selection between the FTPD and LTPD populations (S8 Table), 16 of which are involved in skeletal muscle development and fat deposition (S8 Table).
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