Enhanced flavor strength of broth prepared from chicken following short-term frozen storage.

Genomic characterization of animal genetic resources

Hyperpigmentation of the visceral peritoneum (HVP) has been becoming one of the most challenging problems in yellow-feathered chicken production, which seriously affected chicken carcass quality traits. Detecting which genes dominantly impact pigmentation in the peritoneum tissues is of great benefit to the genetic improvement of HVP. To investigate the genetic mechanism of HVP in yellow-feathered broilers, genome-wide association studies (GWASs) were conducted in the F2 generation of a cross broiler population with 395 birds. A total of 115,706 single-nucleotide polymorphisms (SNPs) of 122,415 were retained to identify quantitative trait loci (QTL) associated to HVP in chicken. The GWAS results based on the logistic mixed model (LMM) revealed that a narrow genomic location on chromosomes 1 (49.2–51.3 Mb) was significantly associated (p ≤ 4.32 × 10−7) with HVP, which contained 23 SNP makers related to 14 functional genes (MFNG, POLDIP3, POLR2F, PICK1, PDXP, SGSM3, RANGAP1, MYH9, RPL3, GALP3, LGALS1, MICALL1, ATF4, and CYP2D6). Four highly associated (p < 10−5) haplotype blocks of 0.80 kb (two SNPs), 0.06 kb (two SNPs), 0.95 kb (two SNPs), and 0.03 kb (two SNPs) were identified with two, two, four, and four distinct haplotypes, respectively. As a melanoma-associated gene, CYP2D6 were also possibly involved in the development of HVP occurring in chicken with two significant variations (rs314284996 and rs317955795) in the promoter regions. Further tests revealed that the expression of CYP2D6 was obviously higher in the visceral peritoneum tissue of chicken with HVP than that in the normal group (p < 0.05). Our results provide a novel clue to understand the genetic mechanism of HVP generation in chicken, and the mapped QTL or candidate genes might serve for genomic selection to improve carcass quality in the yellow-feathered chicken industry.

/pdf/genome-wide-association-studies-provide-insight-into-the-2e5d64i6.pdf

Genome-Wide Association Studies Provide Insight Into the Genetic Determination for Hyperpigmentation of the Visceral Peritoneum in Broilers

Deep learning for genomic selection of aquatic animals

An embodiment of the invention provides a whole-genome predicting method and a device thereof. The method comprises the steps of acquiring genotype data of a to-be-predicted hybrid breed; respectivelypredicting the phenotype data of the hybrid breed according to a plurality of predicting models in a pre-established combined predicting model and the genotype data of the hybrid breed, and obtainingthe phenotype data predicting result of each predicting model; combining a breeding resource and scale, and according to the phenotype data predicting result of each predicting model, determining a hybrid combination with optimal phenotype data predicting results of the plurality of predicting models. By means of the predicting method according to the invention, combined prediction can be performed on the phenotype data through the plurality of established models according to the effect of the genotype on each module mark of the hybrid breed, thereby recommending the hybrid combination with stable high-yield potential.

Whole-genome predicting method and device thereof

The invention discloses a genome breeding value estimation method for integrating dominant effect, which relates to the technical field of livestock and poultry genetic selection. The method comprisessteps identifying a reference group and a candidate group, the phenotype of the target traits of the reference population was determined, Genome-wide marker typing of reference population, quality control of gene marker of reference population, statistics of heterozygous marker deviation of reference population, formulation of genome marker re-coding rules, genome-wide marker typing of candidatepopulation, quality control of gene marker of candidate population, re-coding of genome marker and estimation of genome breeding value, etc. Based on the deviation degree between the phenotype of theheterozygous genotype and the phenotype of the homozygous genotype, the invention formulates coding rules, starts from the genomic marker end, re-codes the heterozygous genotype, causes the gene marker coding to include dominant effect, and then estimates the genomic breeding value. The invention is adapted to the needs of livestock and poultry genetic breeding, and can greatly improve the accuracy of genome estimation breeding value without increasing the complexity of the model.

A method for estimating genomic breeding value integrating dominance effects

The invention discloses a high-uniformity breeding and seed reserving method of yellow-feather chicken and relates to the technical field of poultry breeding. The method includes measuring weight of achicken flock, estimating individual breeding value of the chicken flock, building individual selection index of uniformity, selecting individual chickens reserving as seeds, and the like. Accordingto the method, the breeding value is estimated based on the weight of yellow-feather chicken, the individual selection index model is established, and the individual selection index is calculated fordetermining the individual chicken reserving as seeds. Weight increase can be regulated according to weight regulation parameter, so as to be adaptable to change in market requirement. The high-uniformity breeding and seed reserving method of yellow-feather chicken meets requirements on uniformity breeding and seed reserving of yellow-feather chicken, and can improve the uniformity of the chickenflock on the basis of controlling increase of growth speed.

High-uniformity breeding and seed reserving method of yellow-feather chicken

The choice of a genetic marker genotyping platform is important for genomic prediction in livestock and poultry. High-throughput sequencing can produce more genetic markers, but the genotype quality is lower than that obtained with single nucleotide polymorphism (SNP) chips. The aim of this study was to compare the accuracy of genomic prediction between high-throughput sequencing and SNP chips in broilers. In this study, we developed a new SNP marker screening method, the pre-marker-selection (PMS) method, to determine whether an SNP marker can be used for genomic prediction. We also compared a method which preselection marker based results from genome-wide association studies (GWAS). With the two methods, we analysed body weight at the12th week (BW) and feed conversion ratio (FCR) in a local broiler population. A total of 395 birds were selected from the F2 generation of the population, and 10X specific-locus amplified fragment sequencing (SLAF-seq) and the Illumina Chicken 60K SNP Beadchip were used for genotyping. The genomic best linear unbiased prediction method (GBLUP) was used to predict the genomic breeding values. The accuracy of genomic prediction was validated by the leave-one-out cross-validation method. Without SNP marker screening, the accuracies of the genomic estimated breeding value (GEBV) of BW and FCR were 0.509 and 0.249, respectively, when using SLAF-seq, and the accuracies were 0.516 and 0.232, respectively, when using the SNP chip. With SNP marker screening by the PMS method, the accuracies of GEBV of the two traits were 0.671 and 0.499, respectively, when using SLAF-seq, and 0.605 and 0.422, respectively, when using the SNP chip. Our SNP marker screening method led to an increase of prediction accuracy by 0.089-0.250. With SNP marker screening by the GWAS method, the accuracies of genomic prediction for the two traits were also improved, but the gains of accuracy were less than the gains with PMS method for all traits. The results from this study indicate that our PMS method can improve the accuracy of GEBV, and that more accurate genomic prediction can be obtained from an increased number of genomic markers when using high-throughput sequencing in local broiler populations. Due to its lower genotyping cost, high-throughput sequencing could be a good alternative to SNP chips for genomic prediction in breeding programmes of local broiler populations.

/pdf/high-throughput-sequencing-with-the-preselection-of-markers-2yimofwp07.pdf

High-Throughput Sequencing With the Preselection of Markers Is a Good Alternative to SNP Chips for Genomic Prediction in Broilers

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A method for estimating genomic breeding value integrating dominance effects

High-uniformity breeding and seed reserving method of yellow-feather chicken

High-Throughput Sequencing With the Preselection of Markers Is a Good Alternative to SNP Chips for Genomic Prediction in Broilers