广东省现有5个地方猪种基于SNP芯片的遗传多样性分析

本研究以广东省现有的5个地方猪品种为对象,利用SNP芯片进行SNP分型,对比欧洲野猪、亚洲野猪以及4个西方商业猪种,对广东省现有地方猪品种的遗传多样性、遗传距离以及群体结构进行分析。结果表明:两广小耳花猪、大花白猪和蓝塘猪的遗传多样性低于西方商业猪种以及粤东黑猪和梅花猪;广东省地方猪与亚洲野猪遗传距离较近,与西方猪种遗传距离较远;作为大花白猪一个类群的梅花猪与大花白猪遗传距离较远,主成分分析以及Structure分析表明梅花猪与大花白猪遗传差异较大,梅花猪具有独特的遗传结构并存在西方猪血液的渗入;粤东黑猪与西方猪种遗传距离较近,粤东黑猪也存在西方猪种血液的渗入。综上所述,两广小耳花猪、大花白猪和蓝塘猪的遗传多样性较低,梅花猪和粤东黑猪存在西方猪种血液的渗入。

Genetic parameters and trends for production and reproduction traits of a Landrace herd in China

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.

Identifying the complex genetic architecture of growth and fatness traits in a Duroc pig population

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 1067 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,VPS4 B,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.

Exploring the genetic features and signatures of selection in South China indigenous pigs

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.

Genome-wide detection of selective signatures in a Duroc pig population

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 FGFI. 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.

MicroRNA-34c regulates porcine granulosa cell function by targeting forkhead box O3a

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 Ed U assays to demonstrate that miR-34c exerted pro-apoptotic and anti-proliferative effects in porcine GCs. Dual-luciferase reporter assays, quantitative real-time PCR（q RT-PCR） and Western blotting identified Forkhead box O3a（Fox O3a） 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.

p53 and NFκB regulate microRNA-34c expression in porcine ovarian granulosa cells

supported by the National Natural Science Foundation of China （31201771）;the earmarked fund for the China Agriculture Research System （CARS-36）