Identification of new single nucleotide polymorphisms affecting total number born and candidate genes related to ovulation rate in Chinese Erhualian pigs.
The Chinese Erhualian pig has the highest record for litter size in the world. However, the genetic mechanism of its high prolificacy remains poorly understood. In our study, large phenotypic variations in litter size were found among Erhualian sows. Significant differences in total number born (TNB) and corpora lutea numbers were observed between sows with high and low estimated breeding values (EBVs) for TNB. To identify single nucleotide polymorphisms (SNPs) associated with TNB, a selective genomic scan was conducted on 18 sows representing the top 10% and 18 sows representing the bottom 10% of EBVs of 177 sows using Illumina Porcine SNP60 genotype data. Genome-wide fixation coefficient (FST) values were calculated for each SNP between the high- and low-EBV groups. A total of 154 SNPs were significantly differentiated loci between the two groups. Of the top 10 highest FSTSNPs, rs81399474, rs81400131 and rs81405013 on SSC8 and rs81434499 and rs81434489 on SSC 12 corresponded to previously reported QTL for litter size. The other five SNPs, rs81367039 on SSC2, rs80891106 on SSC7, rs81477883 on SSC12 and rs80938898 and rs80971725 on SSC14, appeared to be novel QTL for TNB. Significant associations between rs81399474 on SSC8 and TNB were confirmed in 313 Erhualian sows. Forty genes were identified around the top 10 highest FSTSNPs, of which UCHL1, adjacent to rs81399474, and RPS6KB1 and CLTC, adjacent to rs81434499, have been reported to affect the ovulation rate in pig. The findings can advance understanding of the genetic variations in litter size of pigs.
Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.
L C
LC
He
Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.
P H
PH
Li
Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.
X
X
Ma
Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.
S P
SP
Sui
Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.
S
S
Gao
Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA.
S W
SW
Kim
Changzhou Jiaoxi Cooperatives of Erhualian pigs, Changzhou, 213116, China.
Y Q
YQ
Gu
Changzhou Jiaoxi Cooperatives of Erhualian pigs, Changzhou, 213116, China.
Y
Y
Huang
College of Animal Science and Veterinary Medicine, Jiangxi Agricultural University, Nanchang, 330045, China.
N S
NS
Ding
Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.
R H
RH
Huang
D000818:Animals; D001947:Breeding; D002681:China; D005260:Female; D005838:Genotype; D008098:Litter Size / Q000235:genetics*; D010060:Ovulation / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D034421:Sus scrofa / Q000235:genetics*

SNP
; FST value; genetic differentiation; litter size; prolificacy