Genomic variation in Pekin duck populations developed in three
different countries as revealed by whole-genome data
Z. Zhang*, Y. Jia
, Y. Chen
, L. wang
, F. Yang
, Z. Ning* and L. Qu*
*Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and
Technology, China Agricultural University, Beijing, China.
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing,
Beijing Municipal General Station of Animal Science, Beijing, China.
Institute of Pekin Duck, Beijing, China.
Cherry Valley farms
(xianghe) Co., Ltd, Langfang, China.
It is well known that both British and American Pekin ducks originated from China.
However, the populations differ substantially in production performance, but the genetic
changes involved are still poorly understood. Herein, we sequenced 24 individual Pekin
ducks (eight from each population) with an average sequencing depth of more than 459 for
each population (mean coverage of 6.29 per individual). Among these populations from
three different countries, we identiﬁed a large number of SNPs and indels as well as many
unique population variants, which can be used as population-speciﬁc molecular markers.
Genomic comparisons among the three duck populations revealed many candidate genes as
well as pathways and Gene Ontology categories that are putatively associated with meat
yield in the British population, growth in the American population and brain development
in all three populations. These ﬁndings will enable a better understanding of the artiﬁcial
selection history of Pekin ducks and provide a valuable resource for future research on the
breeding of this species.
Keywords molecular marker, selection signature, whole-genome resequencing
Pekin duck (Anas platyrhynchos domestica) is world famous
for its excellent meat quality and fast growth (Xu et al.
2012; Zheng et al. 2014). In 1872, some Chinese Pekin
(PK) ducks were exported to the United Kingdom, where
they gave rise to the Cherry Valley (CV) duck, also named
the British Pekin duck (Cherry & Morris 2008; Ashton
2014). In the following year, ducks of the same breed were
exported to the United States and became the progenitors of
the Maple Leaf (ML) duck, also known as the American
Pekin duck (Cherry & Morris 2008; Ashton 2014). In the
more than 100 years since, CV and ML ducks have been
subjected to intensive selection for higher breast muscle
content and larger body size to cater to the demands for
healthy food (Wu et al. 2008; Zhu et al. 2015b). Conversely,
as the most important raw material of the world famous
Beijing Roast Duck, the PK ducks were instead bred for
greater fat content, as high fat content improves the ﬂavour
of meat (Zheng et al. 2014; Zhu et al. 2015b). Nowadays,
compared with the PK duck, CV and ML ducks differ in
morphology (Fig. 1a) and many aspects of productive
performance, such as body size (Lin et al. 1998), growth
rate (Wu 2013), carcass meat yield (Pang & Lai 2002; Yang
et al. 2013) and fatty content (She et al. 2006). Although
both the CV and ML ducks are commercial table birds, they
have different phenotypes and breed standards. For
instance, the CV duck has a more upright inclination
(Broekman 2009), whereas ML ducks are more horizontal
in stature (Ashton 2014). Additionally, recent selection in
CV ducks has focused primarily on carcass meat yield (Yang
et al. 2013) and lean meat percentage (She et al. 2006),
whereas selection in ML ducks has been more focused on
growth (Wu 2013) and body size (Lin et al. 1998). We used
whole-genome resequencing to characterize the genetic
changes that have occurred in the three Pekin duck
populations over the past century of selection.
We selected 24 ducks representing the three different
Pekin duck populations: eight PK ducks (unselected pure
breed), eight CV ducks (A strain) and eight ML ducks (D
strain). Notably, the unselected pure breed PK population
reproduces primarily via random mating rather than by
Address for correspondence
Y. Jia, Institute of Animal Science, Chinese Academy of Agricultural
Sciences, Beijing, China.
L. Qu and Z. Ning, Department of Animal Genetics and Breeding,
National Engineering Laboratory for Animal Breeding, College of
Animal Science and Technology, China Agricultural University, Beijing,
E-mails: email@example.com, firstname.lastname@example.org and email@example.com
Accepted for publication 06 December 2017
© 2018 Stichting International Foundation for Animal Genetics, 49, 132–136