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Identifying the complex genetic architecture of growth and fatness traits in a Duroc pig population
ZHANG Zhe, CHEN Zi-tao, DIAO Shu-qi, YE Shao-pan, WANG Jia-ying, GAO Ning, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi
2021, 20 (6): 1607-1614.   DOI: 10.1016/S2095-3119(20)63264-6
Abstract185)      PDF in ScienceDirect      
In modern pig breeding programs, growth and fatness are vital economic traits that significantly influence porcine production.  To identify underlying variants and candidate genes associated with growth and fatness traits, a total of 1 067 genotyped Duroc pigs with de-regressed estimated breeding values (DEBV) records were analyzed in a genome wide association study (GWAS) by using a single marker regression model.  In total, 28 potential single nucleotide polymorphisms (SNPs) were associated with these traits of interest.  Moreover, VPS4B, PHLPP1, and some other genes were highlighted as functionally plausible candidate genes that compose the underlying genetic architecture of porcine growth and fatness traits.  Our findings contribute to a better understanding of the genetic architectures underlying swine growth and fatness traits that can be potentially used in pig breeding programs. 
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Exploring the genetic features and signatures of selection in South China indigenous pigs
DIAO Shu-qi, XU Zhi-ting, YE Shao-pan, HUANG Shu-wen, TENG Jin-yan, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi, ZHANG Zhe
2021, 20 (5): 1359-1371.   DOI: 10.1016/S2095-3119(20)63260-9
Abstract152)      PDF in ScienceDirect      
To explore the genetic features and signatures of selection in indigenous pigs from South China and Duroc pigs, 259 pigs from six populations were genotyped using single-nucleotide polymorphism (SNP) BeadChips.  Principal component analysis (PCA), effective population size (Ne), linkage disequilibrium (LD), and signatures of selection were explored and investigated among the six pig populations.  The results showed the Ne of five South China indigenous pig populations has been decreasing rapidly since 100 generations ago.  The LD between pairwise SNP distance at 100 kb ranged from 0.16 to 0.20 for the five indigenous pig populations, while it was 0.32 for the Duroc population.  However, the LD of all six pig populations showed the opposite order at long distances (>5 Mb).  Furthermore, 15 potential signatures of selection associated with meat quality and age at puberty were exclusively detected in South China indigenous pigs, while eight potential signatures of selection associated with growth traits were detected in Duroc pigs.  Our work provides valuable insights for the utilization and conservation of South China indigenous pigs.
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Genome-wide detection of selective signatures in a Duroc pig population
DIAO Shu-qi, LUO Yuan-yu, MA Yun-long, DENG Xi, HE Ying-ting, GAO Ning, ZHANG Hao, LI Jia-qi, CHEN Zan-mou, ZHANG Zhe
2018, 17 (11): 2528-2535.   DOI: 10.1016/S2095-3119(18)61984-7
Abstract429)      PDF in ScienceDirect      
The Duroc pig has high adaptability and feeding efficiency, making it one of the most popular pig breeds worldwide.  Over long periods of natural and artificial selection, genetic footprints, i.e., selective signatures, were left in the genome.  In this study, a Duroc pig population (n=715) was genotyped with the Porcine SNP60K Bead Chip and the GeneSeek Genomic Profiler (GGP) Porcine Chip.  The relative extended haplotype homozygosity (REHH) method was used for selective signature detection in a subset of the population (n=368), selected to represent a balanced family structure.  In total, 154 significant core regions were detected as selective signatures (P<0.01), some of which overlap with previously reported quantitative trait loci associated with several economically important traits, including average daily gain and backfat thickness.  Genome annotation for these significant core regions revealed a variety of interesting candidate genes including GATA3, TAF3, ATP5C1, and FGF1.  These genes were functionally related to anterior/posterior pattern specification, phosphatidylinositol 3-kinase signaling, embryonic skeletal system morphogenesis, and oxidation-reduction processes.  This research provides knowledge for the study of selection mechanisms and breeding practices in Duroc and other pigs.
 
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MicroRNA-34c regulates porcine granulosa cell function by targeting forkhead box O3a
XU Yuan, ZHANG Ai-ling, ZHANG Zhe, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi
2017, 16 (09): 2019-2028.   DOI: 10.1016/S2095-3119(16)61582-4
Abstract880)      PDF in ScienceDirect      
Granulosa cells (GCs) are somatic cells of ovary, the behaviors of GCs are important for ovarian function.  MicroRNAs (miRNAs) are a class of endogenous 18–24 nucleotide (nt) non-coding RNAs, some of which have been shown to be important regulators of GCs function.  miR-34c involved in the regulation of various biological processes and was identified to be a pro-apoptotic and anti-proliferative factor in many cell types.  However, the roles of miR-34c in GCs function remain unknown.  In this study, we used Annexin V-FITC and EdU assays to demonstrate that miR-34c exerted pro-apoptotic and anti-proliferative effects in porcine GCs.  Dual-luciferase reporter assays, quantitative real-time PCR (qRT-PCR) and Western blotting identified Forkhead box O3a (FoxO3a) as a direct target gene of miR-34c.  The overexpression of FoxO3a rescued the phenotypic change caused by miR-34c in porcine GCs.  In conclusion, miR-34c regulate the function of porcine GCs by targeting FoxO3a.
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p53 and NFκB regulate microRNA-34c expression in porcine ovarian granulosa cells
XU Yuan, ZHANG Ai-ling, XIAO Guang, ZHANG Zhe, CHEN Zan-mou, ZHANG Hao, LI Jia-qi
2016, 15 (8): 1816-1824.   DOI: 10.1016/S2095-3119(15)61178-9
Abstract1514)      PDF in ScienceDirect      
   MicroRNAs (miRNAs) are endogenous 18–24 nucleotide (nt) non-coding RNAs, some of which have been indicated to play key roles in granulosa cells (GCs) function. However, little is known about how the miRNA gene expression itself is regulated in the GCs. Our previous study showed that miR-34c, identified to be a pro-apoptotic and anti-proliferative factor in many cell types, exerted the same effects in porcine GCs. Here, the transcriptional regulation of miR-34c expression in GCs was further investigated. 5´ rapid amplification of cDNA ends (RACE) assay indicated that the pri-miR-34c transcription start site was located in 1 556 bp upstream of pre-miR-34c. With dual-luciferase reporter assay, we confirmed a 69 bp core promoter region (–1 799 bp/–1 730 bp) was indispensable for the transcription of miR-34c. Chromatin immunoprecipitation (ChIP) assay demonstrated that p53, p50, and p65 could bind to the transcription factor binding sites within the 69 bp core promoter region. In addition, deletion of transcripition factor binding sites resulted in obvious change of the miR-34c promoter activity. Finally, using overexpression and knockdown of p53, p50, and p65 strategies, we showed that p53 and p50 could positively regulated miR-34c expression, whereas p65 neletively regulated miR-34c expression in GCs. Our results provide new data about the transcription regulatory mechanism of miRNA genes in GCs.
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Genetic parameters and trends for production and reproduction traits of a Landrace herd in China
ZHANG Zhe, ZHANG Hao, PAN Rong-yang, WU Long, LI Ya-lan, CHEN Zan-mou, CAI Geng-yuan, LI Jia-qi, WU Zhen-fang
2016, 15 (05): 1069-1075.   DOI: 10.1016/S2095-3119(15)61105-4
Abstract1677)      PDF in ScienceDirect      
    The objectives of this study were to estimate the genetic parameters and the breeding progress in a Landrace herd in China, and to predict the potential benefits by applying new breeding technology. Hereby, the performance records from a Landrace swine herd in China, composing over 33 000 pigs born between 2001 and 2013, were collected on six economically important traits, i.e., average daily gain between 30–100 kg (ADG), adjusted backfat thickness at 100 kg (BF), adjusted days to 30 kg (D30), adjusted days to 100 kg (D100), number born alive (NBA), and total number born (TNB). The genetic parameters were estimated by restricted maximum likelihood via DMU, and realized genetic trends were analyzed. Based on the real population structure and genetic parameters obtained from this herd, the potential genetic trends by applying genomic selection (GS) were predicted via a computer simulation study. Results showed that the heritability estimates in this Landrace herd were 0.55 (0.02), 0.42 (0.01), and 0.12 (0.01), for BF, D100, and TNB, respectively. Favorable genetic trends were obtained for D100, BF, and TNB due to direct selection, for ADG and NBA due to indirect selection. Long-term selection against D100 did not improve D30, though they are highly genetically correlated (0.64). Appling GS in such a swine herd, the genetic gain can be increased by 25%, or even larger for traits with low heritability or individuals without phenotypes before selection. It can be concluded that conventional breeding strategy was effective in the herd studied, while applying GS is promising and hence the road ahead in swine breeding.
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