Abstract Phosphoenolpyruvate carboxykinase 1 (Soluble) (PCK1) encodes the rate-limiting enzyme (phosphoenolpyruvate carboxykinase, cytosolic，PEPCK-C) in gluconeogenesis, and is the key gene at controlling the overall level of glucose. Several studies have reported that PCK1 had experienced selective adaption to environment changes. In this research, in order to study the expression differentiation of PCK1 during duck (Anas platyrhynchos domesticus) domestication, and analyze whether it had signature of selection adapted to the domestication, mallard (Anas platyrhynchos), Shaoxing ducks and Peking ducks were chosen as the representative of the wild breed, egg-type and meat-type ducks, respectively. Expression analysis found that PCK1 was down regulated in the 2 domesticated breeds. In comparison to the mallard, PCK1 was down-regulated 3- and 10- folds in the liver of Shaoxing ducks and Peking ducks, respectively and down-regulated 3- and 26- folds in the abdominal fat of Shaoxing ducks and Peking ducks, respectively. To identify whether PCK1 was selected during duck domestication, we performed whole-genome resequencing of mallards (n=27), Shaoxing ducks (n=27) and Peking ducks (n=27), and 12179415 SNP were obtained for genome wide analysis of selection signals, including analysis of the heterozygosity (Hp) and genetic distance (Fst). Z transformed whole-genome Hp (Z(Hp)) and Fst (Z(Fst)) distribution showed that Z(Hp)＜ -3 and Z(Fst)＞2 represented the extreme end of the distribution, and thus were described as the threshold of putatively selected signals. In this study, we only focus on selection signals in scaffold KB742479.1 which containing PCK1. And to reduce the interference of fixation due to genetic drift within populations, we combined results from Shaoxing ducks and Peking ducks and only chosen regions with reduced heterozygosity and increased genetic distance in both of the 2 breeds relative to Anas platyrhynchos. By using these thresholds KB742479.1:2 200 091~2 239 938 bp and KB742 479.1: 2 220 079~2 259 967 bp were identified. Comparing to KB742479.1:2 200 091~2 239 938 bp, the region of KB742479.1: 2 220 079~2 259 967 bp was found with lower Z(Hp) (-3.92 in Shaoxing ducks and -3.63 in Peking ducks) and higher Z(Fst) (3.91 in Shaoxing ducks and 2.54 in Peking ducks ), suggesting stronger selection signal was found in this region. KB742479.1: 2 220 079~2 259 967 bp was a genetic region, and further expression analysis of genes adjacent to this region, including an unknown downstream gene (Ensembl ID: ENSAPLG00000002901), upstream C20orf85 gene (chromosome 20 open reading frame 85), and PCK1, found that only PCK1 displayed differential expression during duck domestication. Then, to describe the extract distance between this region and PCK1, the full-length cDNA of PCK1 was cloned and blast against the duck genome. Results showed that PCK1 was mapped to the region of KB742479.1:2 342 320~2 350 143 bp which was 82.4 kb upstream from KB742 479.1: 2 220 079~2 259 967 bp. Based on these results we speculated that the selection signals happened at KB742479.1:2 342 320~2 350 143 bp might induce the differential expression of PCK1 during duck domestication. In summary, we presented the genetic mechanism of duck domestication for the first time, and the different expression of PCK1 and the selection signal 82.4 kb downstream from this gene obtained in this study will provide clues for the further function analysis of PCK1.
Axelsson E, Ratnakumar A, Arendt M L, et al. The genomic signature of dog domestication reveals adaptation to a starch-rich diet [J]. Nature, 2013, 495 (7441): 360-364. Croniger C M, Olswang Y, Reshef L, et al. Phosphoenolpyruvate Carboxykinase Revisited, Insights into its metabolic role [J]. Biochemistry and Molecular Biology Education, 2002, 30 (1): 14–20. Devine J H, Eubank D W, Clouthier D E, et al. Adipose expression of the phosphoenolpyruvate carboxykinase promoter requires peroxisome proliferator-activated receptor gamma and 9-cis-retinoic acid receptor binding to an adipocyte-specific enhancer in vivo [J]. The Journal of Biological Chemistry, 1999, 274(19): 13604–13612. Franckhauser S, Mu?oz S, Pujol A, et al. Increased fatty acid re-esterification by PEPCK overexpression in adipose tissue leads to obesity without insulin resistance [J]. Diabetes, 2002, 51(3): 624–630. Goto M, Yoshioka T, Battelino T, et al. Decreases Gluconeogenesis in Hepatocytes Isolated from 10-Day-Old Rats [J]. Pediatric Research, 2001, 49(4): 552–557. Li H F, Zhu W Q, Song W T, et al. Origin and genetic diversity of Chinese domestic ducks [J]. Molecular Phylogenetics and Evolution, 2010, 57: 634–640. McCracken K G, Bulgarella M, Johnson K P, et al. Gene Flow in the Face of Countervailing Selection: Adaptation to High-Altitude Hypoxia in the β-Hemoglobin Subunit of Yellow-Billed Pintails in the Andes [J]. Molecular Biology and Evolution, 2009, 26(4): 815–827. Pinheiro E C, Taddei V A, Migliorini R H, et al. Effect of fasting on carbohydrate metabolism in frugivorous bats (Artibeus lituratus and Artibeus jamaicensis) [J]. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 2006, 143: 279–284. Pinheiro E C, Taddei V A, Migliorini R H, et al. Effect of fasting on carbohydrate metabolism in frugivorous bats (Artibeus lituratus and Artibeus jamaicensis) [J]. Comparative Biochemistry and Physiology, Part B, 2006, 143: 279–284. Rubin C J, Zody M C, Eriksson J, et al. Whole-genome resequencing reveals loci under selection during chicken domestication [J]. Nature, 2010, 464: 587-591. Sartori D R S, Garófalo M A R, Kettelhut I C, et al. Gluconeogenesis and P-enolpyruvate carboxykinase in liver and kidney of long-term fasted quails [J]. Journal of Comparative Physiology B, 2000, 170: 373-377. She P, Shiota M, Shelton K D, et al. Phosphoenolpyruvate carboxykinase is necessary for the integration of hepatic energy metabolism [J]. Molecular and Cellular Biology, 2000, 20: 6508–6517. Valera A, Pujol M, Pelegrin F, et al. Transgenic mice overexpressing phosphoenolpyruvate carboxykinase develop noninsulin-dependent diabetes mellitus [J]. Proceedings of the National Academy of Sciences of the United States of America, 1994, 91: 9151–9154. Zhu L, Yin Q Y, Irwin D M, et al. 2015. Phosphoenolpyruvate Carboxykinase 1 Gene (PCK1) Displays Parallel Evolution between Old World and New World Fruit Bats [J]. Plos One, 25: DOI:10.1371
