Genomic signatures reveal selection of characteristics within and
between Meishan pig populations
H. Sun*, Z. Wang*, Z. Zhang*, Q. Xiao*, S. Mawed*, Z. Xu*, X. Zhang*
, H. Yang
, M. Zhu
, X. Liu
, W. Zhang
, Y. Zhen
, Q. Wang*
and Y. Pan*
*Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
Laboratory of Veterinary Biotechnology, Shanghai 200240, China.
National Station of Animal Husbandry, Beijing 100125, China.
Station of Animal Husbandry, Nanjing 210036, China.
The Chinese Meishan pig breed is well known for its high proliﬁcacy. Moreover, this breed
can be divided into three types based on their body size: big Meishan, middle Meishan
(MMS) and small Meishan (SMS) pigs. Few studies have reported on the genetic signatures
of Meishan pigs, particularly on a genome-wide scale. Exploring for genetic signatures
could be quite valuable for revealing the genetic architecture of phenotypic variation.
Thus, we performed research in two parts based on the genome reducing and sequencing
data of 143 Meishan pigs (74 MMS pigs, 69 SMS pigs). First, we detected the selection
signatures among all Meishan pigs studied using the relative extended haplotype
homozygosity test. Second, we detected the selection signatures between MMS and SMS
pigs using the cross-population extended haplotype homozygosity and F
methods. A total
of 111 398 SNPs were identiﬁed from the sequenced genomes. In the population analysis,
the most signiﬁcant genes were associated with the mental development (RGMA),
reproduction (HDAC4, FOXL2) and lipid metabolism (ACACB). From the cross-population
analysis, we detected genes related to body weight (SPDEF, PACSIN1) in both methods. We
suggest that rs341373351, located within the PACSIN1 gene, might be the causal variant.
This study may have achieved consistency between selection signatures and characteristics
within and between Meishan pig populations. These ﬁndings can provide insight into
investigating the molecular background of high proliﬁcacy and body size in pig.
Keywords genome reducing and sequencing, SNP, population structure, selection
Pigs (Sus scrofa domesticus) have gone through intensive
domestication and selection to improve pork productivity.
As a result of the selection pressure, dramatic phenotypic
changes have occurred in domestic pigs with regard to a
number of economically important traits such as reproduc-
tion, growth rate and meat quality (Rubin et al. 2012). The
Chinese Meishan pig breed is renowned for its high
proliﬁcacy (Haley & Lee 1993). Moreover, this pig breed
can be divided into three subgroups based on their body
size: big Meishan, middle Meishan (MMS) and small
Meishan (SMS) pigs. In the latter part of the last century,
the population size of Meishan pigs rapidly decreased due to
the importation of the Western commercial pigs, and the big
Meishan pigs have become extinct.
There are four different state-owned conservation farms
in the Taihu Lake region in eastern China that are used for
preserving MMS and SMS pigs. Every subgroup of Meishan
pig breeds are raised on two different farms respectively. On
average, the body weight of mature MMS pigs is about
50 kg more than that of SMS (Chen 2014). It has been
reported that there is an obvious genetic distance between
MMS and SMS pigs (Wang et al. 2015). Thus, given the
interest in the characteristics of Meishan pigs, associated
selection signatures might be detected. The Meishan pig
population might be good subjects for revealing the
selection signatures for reproduction and body size.
Address for correspondence
Y. Pan and Q. Wang, School of Agriculture and Biology, Shanghai Jiao
Tong University, Shanghai 200240, China.
E-mail: firstname.lastname@example.org; email@example.com
Accepted for publication 18 December 2017
© 2018 Stichting International Foundation for Animal Genetics, 49, 119–126