Identifying Genetic Differences Between Dongxiang Blue-Shelled and White Leghorn Chickens Using Sequencing Data

Genetic characteristics and selection signatures between Southern Chinese local and commercial chickens

The introduction of exotic breeds and the cultivation of new lines by breeding companies have posed challenges to native chickens in South China, including loss of breed characteristics, decreased genetic diversity, and declining purity. Understanding the population genetic structure and genetic diversity of native chickens in South China is crucial for further advancements in breeding efforts. In this study, we analyzed the population genetic structure and genetic diversity of 321 individuals from 10 different breeds in South China. By comparing commercial chickens with native ones, we identified selection signatures occurring between local chickens and commercial breeds. The analysis of population genetic structure revealed that the native chicken populations in South China exhibited a considerable level of genetic diversity. Moreover, the commercial lines of Xiaobai chicken and Huangma chicken displayed even higher levels of genetic diversity, which distinguished them from other native varieties at the clustering level. However, certain individuals within these commercial varieties showed a discernible genetic relationship with the native populations. Notably, both commercial varieties also retained a significant degree of genetic similarity to their respective native counterparts. In order to investigate the genomic changes occurring during the commercialization of native chickens, we employed 4 methods (Fst, ROD, XPCLR, and XPEHH) to identify potential candidate regions displaying selective signatures in Southern Chinese native chicken population. A total of 168 (identified by Fst and ROD) and 86 (identified by XPCLR and XPEHH) overlapping genes were discovered. Functional annotation analysis revealed that these genes may be associated with reproduction and growth (SAMSN1, HYLS1, ROBO3, FGF14, PRSS23), musculoskeletal development (DNER, MYBPC1, DGKB, ORC1, KLF10), disease resistance and environmental adaptability (PUS3, CRB2, CALD1, USP15, SGCD, LTBP1), as well as egg production (ADGRB3, ACSF3). Overall, native chickens in South China harbor numerous selective sweep regions compared to commercial chickens, enriching valuable genomic resources for future genetic research and breeding conservation.

Genetic parameter estimation and molecular foundation of chicken egg-laying trait

The age of first egg (AFE) in chicken can affect early and even life-time egg production performance to some extent, and therefore is an important economic trait that affects production efficiency. To better understand the genetic patterns of AFE and other production traits including body weight at first egg (BWA), first egg weight (FEW), and total egg number from AFE to 58 wk of age (total-EN), we recorded the production performance of 2 widely used layer breeds, white leghorn (WL) and Rhode Island Red (RIR) and estimated genetic parameters based on pedigree and production data. The results showed that the heritability of AFE in both breeds ranged from 0.4 to 0.6, and AFE showed strong positive genetic and phenotypic correlations to BWA as well as FEW, while showing strong negative genetic and phenotypic correlations with total-EN. Furtherly, by genome-wide association analysis study (GWAS), we identified 12 and 26 significant SNPs to be related to AFE in the 2-layer breeds, respectively. A total of 18 genes were identified that could affect AFE based on the significant SNP annotations obtained, but there were no gene overlapped in the 2 breeds indicating the genetic foundation of AFE could differ from breed to breed. Our results provided a deeper understanding of genetic patterns and molecular basement of AFE in different breeds and could help in the selection of egg production traits.

Genomic insights into shank and eggshell color in Italian local chickens

Eggshell and shank color in poultry is an intriguing topic of research due to the roles in selection, breed recognition, and environmental adaptation. This study delves into the genomics foundations of shank and eggshell pigmentation in Italian local chickens through genome-wide association studies analysis to uncover the mechanisms governing these phenotypes. To this purpose, 483 animals from 20 local breeds (n = 466) and 2 commercial lines (n = 17) were considered and evaluated for shank and eggshell color. All animals were genotyped using the Affymetrix Axiom 600 K Chicken Genotyping Array. As regards shank color, the most interesting locus was detected on chromosome Z, close to the TYRP1 gene, known to play a key role in avian pigmentation. Additionally, several novel loci and genes associated with shank pigmentation, skin pigmentation, UV protection, and melanocyte regulation were identified (e.g., MTAP, CDKN2A, CDKN2B). In eggshell, fewer significant loci were identified, including SLC7A11 and MITF on chromosomes 4 and 12, respectively, associated with melanocyte processes and pigment synthesis. This comprehensive study shed light on the genetic architecture underlying shank and eggshell color in Italian native chicken breeds, contributing to a better understanding of this phenomenon which plays a role in breed identification and conservation, and has ecological and economic implications.

The Construction of ITP Diagnostic Modeling Based on the Expressions of Hub Genes Associated with M1 Polarization of Macrophages

Purpose

Primary immune thrombocytopenia (ITP) is an immune disease with a diagnosis of exclusion, since no validated biomarkers have been identified. In this study, we explored biomarkers associated with the development of ITP from an immune perspective to inform the clinical diagnosis.

Patients and Methods

Differentially expressed genes (DEGs) between normal and ITP samples were analyzed using limma package. Random forest algorithm and LASSO regression were further used to screen for DEGs associated with ITP. The expression of these hub genes was validated by PCR. The relationship between DEGs and immunity was explored by enrichment analysis. Immune cell infiltration in ITP was analyzed by CIBERSORT and ssGSEA, and the relationship between DEGs and infiltrating immune cells was analyzed by Spearman’s rank correlation analysis. Finally, a diagnostic model related to DEGs was constructed by the neural network, and its efficiency was detected by the ROC curve.

Results

After screening the GEO database and validation by PCR analysis, The expression of CTH and TAF8 were higher and while OSBP2 expression was lower in ITP patients compared to normal subjects (P<0.05). GO enrichment analysis showed that these DEGs were associated with inflammatory immune-related diseases, and KEGG analysis showed that they mainly regulated signaling pathways such as JAK-STAT. CIBERSORT and ssGSEA analyses showed that these DEGs were mainly associated with macrophage M1 polarization. The expression of CTH and TAF8 were positively correlated with M1 expression, while OSBP2 was negatively correlated with M1 expression. The ROC curve showed high accuracy of the neural network model [AUC= 0.939, 95% CI (0.8–1)].

Conclusion

Our results suggest that CTH, TAF8, and OSBP2 can be used as effective diagnostic biomarkers of ITP.

Genetic Diversity and Selection Signatures in Synthetic-Derived Wheats and Modern Spring Wheat

Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan.

High-resolution genomic analysis of four local Vietnamese chicken breeds

In Vietnam, local chicken breeds account for over 70% of the national poultry population. Although these breeds are abundant, their productivity is low and their use is threatened by the extensive importation of foreign productive breeds. In this context, conservation programmes targeting several emblematic breeds have been established. The goal of these programmes was to characterize endangered breeds and maintain a pool of characteristic birds for preserving their genetic heritage. To contribute to these programmes, we comprehensively characterized four Vietnamese local chicken breeds (Dong Tao, Ho, Mia and Mong) at the genomic level using high-density single-nucleotide polymorphism (SNP) genotyping. Despite originating in geographically close areas, Dong Tao and Ho were evidently different from each other as well as from Mong and Mia, which shared a more recent common ancestor. The genomic inbreeding coefficient revealed high homozygosity amongst the four breeds (10%-20%). The observation of clear differentiation at the genomic level supported the presence of distinct breeds; nonetheless, the occurrence of crossbred birds in a presumably purebred sample demonstrated the need to apply genomic tools to unambiguously assign the birds to the correct breed. Moreover, the occurrence of substantial inbreeding and the presence of subgroups in certain breeds warranted attention to create future nuclei for use in the conservation of these local breeds.

Genome-wide detection of CNVs and their association with performance traits in broilers

Background

Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age.

Results

We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels.

Conclusions

Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07676-1.

EigenGWAS: An online visualizing and interactive application for detecting genomic signatures of natural selection

Detecting genetic regions under selection in structured populations is of great importance in ecology, evolutionary biology and breeding programmes. We recently proposed EigenGWAS, an unsupervised genomic scanning approach that is similar to F ST but does not require grouping information of the population, for detection of genomic regions under selection. The original EigenGWAS is designed for the random mating population, and here we extend its use to inbred populations. We also show in theory and simulation that eigenvalues, the previous corrector for genetic drift in EigenGWAS, are overcorrected for genetic drift, and the genomic inflation factor is a better option for this adjustment. Applying the updated algorithm, we introduce the new EigenGWAS online platform with highly efficient core implementation. Our online computational tool accepts plink data in a standard binary format that can be easily converted from the original sequencing data, provides the users with graphical results via the R-Shiny user-friendly interface. We applied the proposed method and tool to various data sets, and biologically interpretable results as well as caveats that may lead to an unsatisfactory outcome are given. The EigenGWAS online platform is available at www.eigengwas.com, and can be localized and scaled up via R (recommended) or docker.

Study on the transcriptome for breast muscle of chickens and the function of key gene RAC2 on fibroblasts proliferation

BACKGROUND

Growth performance is significant in broiler production. In the growth process of broilers, gene expression varies at different growth stages. However, limited research has been conducted on the molecular mechanisms of muscle growth and development in yellow-feathered male chickens.

RESULTS

In the study, we used RNA-seq to study the transcriptome of the breast muscle of male Jinghai yellow chickens at 4 (M4F), 8 (M8F) and 12 weeks (M12F) of age. The results showed that 4608 differentially expressed genes (DEGs) were obtained by comparison in pairs of the three groups with Fold Change (FC) ≥ 2 and False Discovery Rate (FDR) ≤ 0.05, and 83, 3445 and 3903 DEGs were obtained separately from M4FvsM8F, M4FvsM12F and M8FvsM12F. Six genes were found as co-differentially expressed in the three age groups, namely SNCG, MYH1A, ARHGDIB, ENSGALG00000031598, ENSGALG00000035660 and ENSGALG00000030559. The GO analysis showed that 0, 304 and 408 biological process (BP) were significantly enriched in M4FvsM8F, M4FvsM12F and M8FvsM12F groups, respectively. KEGG pathway enrichment showed that 1, 2, 4 and 4 pathways were significantly enriched in M4FvsM8F, M4FvsM12F, M8FvsM12F and all DEGs, respectively. They were steroid biosynthesis, carbon metabolism, focal adhesion, cytokine-cytokine receptor interaction, biosynthesis of amino acids and salmonella infection. We constructed short hairpin RNA (shRNA) to interfere the differentially expressed gene RAC2 in DF-1 cells and detected mRNA and protein expression of the downstream genes PAK1 and MAPK8. Results of qPCR showed that RAC2, PAK1 and MAPK8 mRNA expression significantly decreased in the shRAC2-2 group compared with the negative control (NC) group. Western Blot (WB) results showed that the proteins of RAC2, PAK1 and MAPK8 also decreased in the shRAC2-2 group. Cell Counting Kit-8 (CCK-8) and 5-Ethynyl-2'-deoxyuridine (EdU) assay both showed that the proliferation of DF-1 cells was significantly inhibited after transfection of shRAC2-2.

CONCLUSIONS

The results of RNA-seq revealed genes, BP terms and KEGG pathways related to growth and development of male Jinghai yellow chickens, and they would have important guiding significance to our production practice. Further research suggested that RAC2 might regulate cell proliferation by regulating PAKs/MAPK8 pathway and affect growth of chickens.

Identifying the unique characteristics of the Chinese indigenous pig breeds in the Yangtze River Delta region for precise conservation

Background

China is the country with the most abundant swine genetic resources in the world. Through thousands of years of domestication and natural selection, most of pigs in China have developed unique genetic characteristics. Finding the unique genetic characteristics and modules of each breed is an essential part of their precise conservation.

Results

In this study, we used the partial least squares method to identify the significant specific SNPs of 19 local Chinese pig breeds and 5 Western pig breeds. A total of 37,514 significant specific SNPs (p < 0.01) were obtained from these breeds, and the Chinese local pig breed with the most significant SNPs was Hongdenglong (HD), followed by Jiaxing black (JX), Huaibei (HB), Bihu (BH), small Meishan (SMS), Shengxian Hua (SH), Jiangquhai (JQ), Mi (MI), Chunan (CA), Chalu (CL), Jinhualiangtouwu (JHL), Fengjing (FJ), middle Meishan (MMS), Shanzhu (SZ), Pudong white (PD), Dongchuan (DC), Erhualian (EH), Shawutou (SW) and Lanxi Hua (LX) pig.

Furthermore, we identified the breeds with the most significant genes, GO terms, pathways, and networks using KOBAS and IPA and then ranked them separately. The results showed that the breeds with the highest number of interaction networks were Hongdenglong (12) and Huaibei (12) pigs. In contrast, the breeds with the lowest interaction networks were Shawutou (4) and Lanxi Hua pigs (3), indicating that Hongdenglong and Huaibei pigs might have the most significant genetic modules in their genome, whereas Shawutou and Lanxi Hua pigs may have the least unique characteristics. To some degree, the identified specific pathways and networks are related to the number of genes and SNPs linked to the specific breeds, but they do not appear to be the same. Most importantly, more significant modules were found to be related to the development and function of the digestive system, regulation of diseases, and metabolism of amino acids in the local Chinese pig breeds, whereas more significant modules were found to be related to the growth rate in the Western pig breeds.

Conclusion

Our results show that each breed has some relatively unique structural modules and functional characteristics. These modules allow us to better understand the genetic differences among local Chinese and Western pig breeds and therefore implement precise conservation methods. This study could provide a basis for formulating more effective strategies for managing and protecting these genetic resources in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07476-7.

Discovery of selection-driven genetic differences of Duroc, Landrace, and Yorkshire pig breeds by EigenGWAS and Fst analyses

Pigs are one of the earliest domesticated animals and multiple breeds have been developed to meet the various demands of consumers. EigenGWAS is a novel strategy to identify candidate genes that underlying population genetic differences and to infer candidate regions under selection as well. In this study, EigenGWAS and F_st analyses were performed using the public re-sequencing data of three typical commercial pig breeds, Duroc, Landrace and Yorkshire. The intersection of genome-wide significant SNPs detected by EigenGWAS and top-ranked 1% SNPs of F_st results were treated as signals under selection. Using the data of all three breeds, 3062 signals under selection were detected and the nearby genomic regions within 300 kb upstream and downstream covered 6.54% of whole genome. Pairs of breeds were analysed along with the pathway analysis. The gene function enrichment results indicated that many candidate genes located in the genomic regions of the signals under selection were associated with biological processes related to growth, metabolism, reproduction, sensory perception, etc. Among the candidate genes, the FSHB, AHR, PTHLH, KDR and FST genes were reported to be associated with reproductive performance; the KIT, KITLG, MITF, MC1R and EDNRB genes were previously identified to affect coat colour; the RETREG1, TXNIP, BMP5, PPARD and RBP4 genes were reported to be associated with lipid metabolism and growth traits. The identified genetic differences across the three commercial breeds will advance understanding of the artificial selection history of pigs and the signals under selection will suggest potential uses in pig genomic breeding programmes.