Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle

Comparative Study of Bacterial Microbiota Differences in the Rumen and Feces of Xinjiang Brown and Holstein Cattle

Xinjiang Brown cattle are a unique and widely distributed breed of dual-purpose cattle in the Xinjiang area of China, whose milk production performance differs from Holstein cattle. It has been known that variations in bacterial species of the gastrointestinal tract influence milk protein, fat, and lactose synthesis. However, the microbiota differences between Xinjiang Brown and Holstein cattle are less known. This study aims to compare the bacterial community composition of the rumen and feces of these two cattle breeds under the same dietary and management conditions. The 16s rRNA sequencing data and milk production of 18 Xinjiang Brown cows and 20 Holstein cows on the same farm were obtained for analysis. The results confirmed differences in milk production between Xinjiang Brown and Holstein cattle. Microbiota with different relative abundance between these two cattle breeds were identified, and their biological functions might be related to milk synthesis. This study increases the understanding of the differences in microbiota between Xinjiang Brown and Holstein cattle and might provide helpful information for microbiota composition optimization of these dairy cattle.

Genome-wide association study identifies genomic regions associated with key reproductive traits in Korean Hanwoo cows

BACKGROUND

Conducting genome-wide association studies (GWAS) for reproductive traits in Hanwoo cattle, including age at first calving (AFC), calving interval (CI), gestation length (GL), and number of artificial inseminations per conception (NAIPC), is of paramount significance. These analyses provided a thorough exploration of the genetic basis of these traits, facilitating the identification of key markers for targeted trait improvement. Breeders can optimize their selection strategies, leading to more efficient and sustainable breeding programs, by incorporating genetic insights. This impact extends beyond individual traits and contributes to the overall productivity and profitability of the Hanwoo beef cattle industry. Ultimately, GWAS is essential in ensuring the long-term genetic resilience and adaptability of Hanwoo cattle populations. The primary goal of this study was to identify significant single nucleotide polymorphisms (SNPs) or quantitative trait loci (QTLs) associated with the studied reproductive traits and subsequently map the underlying genes that hold promise for trait improvement.

RESULTS

A genome-wide association study of reproductive traits identified 68 significant single nucleotide polymorphisms (SNPs) distributed across 29 Bos taurus autosomes (BTA). Among them, BTA14 exhibited the highest number of identified SNPs (25), whereas BTA6, BTA7, BTA8, BTA10, BTA13, BTA17, and BTA20 exhibited 8, 5, 5, 3, 8, 2, and 12 significant SNPs, respectively. Annotation of candidate genes within a 500 kb region surrounding the significant SNPs led to the identification of ten candidate genes relevant to age at first calving. These genes were: FANCG, UNC13B, TESK1, TLN1, and CREB3 on BTA8; FAM110B, UBXN2B, SDCBP, and TOX on BTA14; and MAP3K1 on BTA20. Additionally, APBA3, TCF12, and ZFR2, located on BTA7 and BTA10, were associated with the calving interval; PAX1, SGCD, and HAND1, located on BTA7 and BTA13, were linked to gestation length; and RBM47, UBE2K, and GPX8, located on BTA6 and BTA20, were linked to the number of artificial inseminations per conception in Hanwoo cows.

CONCLUSIONS

The findings of this study enhance our knowledge of the genetic factors that influence reproductive traits in Hanwoo cattle populations and provide a foundation for future breeding strategies focused on improving desirable traits in beef cattle. This research offers new evidence and insights into the genetic variants and genome regions associated with reproductive traits and contributes valuable information to guide future efforts in cattle breeding.

Transcriptomic Changes and Regulatory Networks Associated with Resistance to Mastitis in Xinjiang Brown Cattle

Xinjiang brown cattle are highly resistant to disease and tolerant of roughage feeding. The identification of genes regulating mastitis resistance in Xinjiang brown cattle is a novel means of genetic improvement. In this study, the blood levels of IL-1β, IL-6, IL-10, TNF-α, and TGF-β in Xinjiang brown cattle with high and low somatic cell counts (SCCs) were investigated, showing that cytokine levels were higher in cattle with high SCCs. The peripheral blood transcriptomic profiles of healthy and mastitis-affected cattle were constructed by RNA-seq. Differential expression analysis identified 1632 differentially expressed mRNAs (DE-mRNAs), 1757 differentially expressed lncRNAs (DE-lncRNAs), and 23 differentially expressed circRNAs (DE-circRNAs), which were found to be enriched in key pathways such as PI3K/Akt, focal adhesion, and ECM-receptor interactions. Finally, ceRNA interaction networks were constructed using the differentially expressed genes and ceRNAs. It was found that keynote genes or mRNAs were also enriched in pathways such as PI3K-Akt, cholinergic synapses, cell adhesion molecules, ion binding, cytokine receptor activity, and peptide receptor activity, suggesting that the key genes and ncRNAs in the network may play an important role in the regulation of bovine mastitis.

Identification of genetic variants affecting reproduction traits in Vrindavani cattle

Genome-wide association studies (GWAS) are one of the best ways to look into the connection between single-nucleotide polymorphisms (SNPs) and the phenotypic performance. This study aimed to identify the genetic variants that significantly affect the important reproduction traits in Vrindavani cattle using genome-wide SNP chip array data. In this study, 96 randomly chosen Vrindavani cows were genotyped using the Illumina Bovine50K BeadChip platform. A linear regression model of the genome-wide association study was fitted in the PLINK program between genome-wide SNP markers and reproduction traits, including age at first calving (AFC), inter-calving period (ICP), dry days (DD), and service period (SP) across the first three lactations. Information on different QTLs and genes, overlapping or adjacent to genomic coordinates of significant SNPs, was also mined from relevant databases in order to identify the biological pathways associated with reproductive traits in bovine. The Bonferroni correction resulted in total 39 SNP markers present on different chromosomes being identified that significantly affected the variation in AFC (6 SNPs), ICP (7 SNPs), DD (9 SNPs), and SP (17 SNPs). Novel potential candidate genes associated with reproductive traits that were identified using the GWAS methodology included UMPS, ITGB5, ADAM2, UPK1B, TEX55, bta-mir-708, TMPO, TDRD5, MAPRE2, PTER, AP3B1, DPP8, PLAT, TXN2, NDUFAF1, TGFA, DTNA, RSU1, KCNQ1, ADAM32, and CHST8. The significant SNPs and genes associated with the reproductive traits and the enriched genes may be exploited as candidate biomarkers in animal improvement programs, especially for improved reproduction performance in bovines.

Genome-Wide Analysis of Milk Production Traits and Selection Signatures in Serbian Holstein-Friesian Cattle

To improve the genomic evaluation of milk-related traits in Holstein-Friesian (HF) cattle it is essential to identify the associated candidate genes. Novel SNP-based analyses, such as the genetic mapping of inherited diseases, GWAS, and genomic selection, have led to a new era of research. The aim of this study was to analyze the association of each individual SNP in Serbian HF cattle with milk production traits and inbreeding levels. The SNP 60 K chip Axiom Bovine BovMDv3 was deployed for the genotyping of 334 HF cows. The obtained genomic results, together with the collected phenotypic data, were used for a GWAS. Moreover, the identification of ROH segments was performed and served for inbreeding coefficient evaluation and ROH island detection. Using a GWAS, a polymorphism, rs110619097 (located in the intron of the CTNNA3 gene), was detected to be significantly (p < 0.01) associated with the milk protein concentration in the first lactation (adjusted to 305 days). The average genomic inbreeding value (FROH) was 0.079. ROH islands were discovered in proximity to genes associated with milk production traits and genomic regions under selection pressure for other economically important traits of dairy cattle. The findings of this pilot study provide useful information for a better understanding of the genetic architecture of milk production traits in Serbian HF dairy cows and can be used to improve lactation performances in Serbian HF cattle breeding programs.

Genome-wide survey reveals the genetic background of Xinjiang Brown cattle in China

Introduction: Xinjiang Brown cattle are a famous dual-purpose (dairy-beef) cultivated breed in China that occupy a pivotal position within the cattle breeding industry in Xinjiang, China. However, little information is available on the genetic background of this breed. To fill this research gap, we conducted a whole-genome screen using specific-locus amplified fragment sequencing to examine the genetic structure and diversity of 130 Xinjiang Brown cattle-grazing type (XBG, traditional type) cattle. Methods: A subsequent joint analysis incorporating two ancestral breeds, specifically 19 Brown Swiss (BS) foreign and nine Kazakh (KZ) Chinese cattle, as well as 20 Xinjiang Brown cattle-housing type (XBH) cattle, was used to explore the genetic background of the Xinjiang Brown cattle. Results: The results showed that, after nearly a century of crossbreeding, XBG cattle formed a single population with a stable genetic performance. The genetic structure, genetic diversity, and selection signature analysis of the two ancestral types showed highly different results compared to that of XBH cattle. Local ancestry inference showed that the average proportions of XGB cattle within the BS and KZ cattle lineages were 37.22% and 62.78%, respectively, whereas the average proportions of XBH cattle within the BS and KZ cattle lineages were 95.14% and 4.86%, respectively. Thus, XGB cattle are more representative of all Xinjiang Brown cattle, in line with their breeding history, which involves crossbreeding. Two complementary approaches, fixation index and mean nucleotide diversity, were used to detect selection signals in the four aforementioned cattle breeds. Finally, the analysis of 26 candidate genes in Xinjiang Brown cattle revealed significant enrichment in 19 Gene Ontology terms, and seven candidate genes were enriched in three pathways related to disease resistance (CDH4, SIRPB1, and SIRPα) and the endocrine system (ADCY5, ABCC8, KCNJ11, and KCNMA1). Finally, development of the core SNPs in XBG cattle yielded 8,379 loci. Conclusion: The results of this study detail the evolutionary process of crossbreeding in Xinjiang Brown cattle and provide guidance for selecting and breeding new strains of this species.

Genomic association using principal components of morphometric traits in horses: identification of genes related to bone growth

The measurement of morphometric traits in horses is important for determining breed qualification and is one of the main selection criteria for the species. The development of an index (HPC) that consists of principal components weighted by additive genetic values allows to explore the most relevant relationships using a reduced number of variables that explain the greatest amount of variation in the data. Genome-wide association studies (GWAS) using HPC are a relatively new approach that permits to identify regions related to a set of traits. The aim of this study was to perform GWAS using HPC for 15 linear measurements as the explanatory variable in order to identify associated genomic regions and to elucidate the biological mechanisms linked to this index in Campolina horses. For GWAS, weighted single-step GBLUP was applied to HPC. The eight genomic windows that explained the highest proportion of additive genetic variance were identified. The sum of the additive variance explained by the eight windows was 95.89%. Genes involved in bone and cartilage development were identified (SPRY2, COL9A2, MIR30C, HEYL, BMP8B, LTBP1, FAM98A, and CRIM1). They represent potential positional candidates for the HPC of the linear measurements evaluated. The HPC is an efficient alternative to reduce the 15 usually measured traits in Campolina horses. Moreover, candidate genes inserted in region that explained high additive variance of the HPC were identified and might be fine-mapped for searching putative mutation/markers.

Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data

The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.

Genome-wide identification and analysis of TMT-based proteomes in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle

With the gradual completion of the human genome project, proteomes have gained extremely important value in the fields of human disease and biological process research. In our previous research, we performed transcriptomic analyses of longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle and conducted in-depth studies on the muscles of both species through epigenetics. However, it is unclear whether differentially expressed proteins in Kazakh cattle and Xinjiang brown cattle regulate muscle production and development. In this study, a proteomic analysis was performed on Xinjiang brown cattle and Kazakh cattle by using TMT markers, HPLC classification, LC/MS and bioinformatics analysis. A total of 13,078 peptides were identified, including 11,258 unique peptides. We identified a total of 1874 proteins, among which 1565 were quantifiable. Compared to Kazakh cattle, Xinjiang brown cattle exhibited 75 upregulated proteins and 44 downregulated proteins. These differentially expressed proteins were enriched for the functions of adrenergic signaling in cardiomyocytes, fatty acid degradation and glutathione metabolism. In our research, we found differentially expressed proteins in longissimus dorsi tissue between Kazakh cattle and Xinjiang brown cattle. We predict that these proteins regulate muscle production and development through select enriched signaling pathways. This study provides novel insights into the roles of proteomes in cattle genetics and breeding.

Methylation Levels in the Promoter Region of FHIT and PIAS1 Genes Associated with Mastitis Resistance in Xinjiang Brown Cattle

Mastitis causes serious economic losses in the dairy industry, but there are no effective treatments or preventive measures. In this study, the ZRANB3, PIAS1, ACTR3, LPCAT2, MGAT5, and SLC37A2 genes in Xinjiang brown cattle, which are associated with mastitis resistance, were identified using a GWAS. Pyrosequencing analysis showed that the promoter methylation levels of the FHIT and PIAS1 genes in the mastitis group were higher and lower, respectively, than those in the healthy group (65.97 ± 19.82% and 58.00 ± 23.52%). However, the methylation level of the PIAS1 gene promoter region in the mastitis group was lower than that in the healthy group (11.48 ± 4.12% and 12.17 ± 4.25%). Meanwhile, the methylation levels of CpG3, CpG5, CpG8, and CpG15 in the promoter region of the FHIT and PIAS1 genes in the mastitis group were significantly higher than those in the healthy group (p < 0.01), respectively. RT-qPCR showed that the expression levels of the FHIT and PIAS1 genes were significantly higher in the healthy group than those in the mastitis group (p < 0.01). Correlation analysis showed that the promoter methylation level of the FHIT gene was negatively correlated with its expression. Hence, increased methylation in the promoter of the FHIT gene reduces the mastitis resistance in Xinjiang brown cattle. Finally, this study provides a reference for the molecular-marker-assisted selection of mastitis resistance in dairy cattle.

Whole-genome selective scans detect genes associated with important phenotypic traits in goat (Capra hircus)

Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. In this study, we focused on the worldwide goat breeds with outstanding traits and used whole-genome resequencing data in 361 samples from 68 breeds to detect genomic selection sweep regions. We identified 210-531 genomic regions with six phenotypic traits, respectively. Further gene annotation analysis revealed 332, 203, 164, 300, 205, and 145 candidate genes corresponding with dairy, wool, high prolificacy, poll, big ear, and white coat color traits. Some of these genes have been reported previously (e.g., KIT, KITLG, NBEA, RELL1, AHCY, and EDNRA), while we also discovered novel genes, such as STIM1, NRXN1, LEP, that may be associated with agronomic traits like poll and big ear morphology. Our study found a set of new genetic markers for genetic improvement in goats and provided novel insights into the genetic mechanisms of complex traits.

A 67-bp variable duplication in the promoter region of the ADIPOQ is associated with milk traits in Xinjiang brown cattle

Adiponectin, also known as ADIPOQ, is a hormone protein secreted by adipocytes. The ADIPOQ gene is expressed primarily in adipose tissue, and the encoded protein circulates in the bloodstream and has the potential to regulate both animal fat metabolism and hormone production. Our previous work uncovered a 67-bp variable duplication in the promoter region of ADIPOQ, which reduced the basal transcriptional activity of ADIPOQ in the 3T3_L1 cell and also inhibits the ADIPOQ mRNA expression in adipose tissue. Accordingly, the present study aimed to identify the relationship between the 67-bp structural variations in ADIPOQ promoter region and the milk traits of Xinjiang brown cattle (XJBC). The results revealed two genotypes, DD and ID, in the XJBC, and minor allelic frequency (MAF) for the 'I' allele was more than 1%. Moreover, the association analysis revealed that the 67-bp duplication in the promoter region of the ADIPOQ gene was significantly correlated with the 305 days of milk production volume, fat yield, and milk fat percentage in the XJBC (p < 0.05). These results obtained in this study suggested that the identified variable duplication could be considered as the potential genetic marker for improving milk traits of XJBC.

Genome-wide association study for reproduction-related traits in Chinese domestic goose

1. This study measured six reproduction traits in a Sichuan white goose population (209 individuals), including fertility, qualified egg rate, plasma concentrations of progesterone (P), follicle-stimulating hormone (FSH), prolactin (PRL) and oestrogen (E2).2. Whole-genome resequencing data from the same goose population (209 individuals) were used in a genome-wide association study (GWAS) utilising a mixed linear model to investigate the genes and genetic markers associated with reproduction traits. The frequency of the selected SNPs and haplotypes were determined using the Matrix-Assisted Laser Desorption Ionisation Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) method.3. In total, 42 SNPs significantly associated with these traits were identified. A haplotype block was constructed based on five SNPs that were significantly associated with qualified egg rate, with individuals having the haplotype CCTTAAGGAA having the lowest qualified egg rate.4. In conclusion, these results provided potential markers for marker-assisted selection to improve goose reproductive performance and a basis for elucidating the genetics of goose reproduction.

Genome-wide association analysis of milk production, somatic cell score, and body conformation traits in Holstein cows

Milk production and body conformation traits are critical economic traits for dairy cows. To understand the basic genetic structure for those traits, a genome wide association study was performed on milk yield, milk fat yield, milk fat percentage, milk protein yield, milk protein percentage, somatic cell score, body form composite index, daily capacity composite index, feed, and leg conformation traits, based on the Illumina Bovine HD100k BeadChip. A total of 57, 12 and 26 SNPs were found to be related to the milk production, somatic cell score and body conformation traits in the Holstein cattle. Genes with pleiotropic effect were also found in this study. Seven significant SNPs were associated with multi-traits and were located on the PLEC, PLEKHA5, TONSL, PTGER4, and LCORL genes. In addition, some important candidate genes, like GPAT3, CEBPB, AGO2, SLC37A1, and FNDC3B, were found to participate in fat metabolism or mammary gland development. These results can be used as candidate genes for milk production, somatic cell score, and body conformation traits of Holstein cows, and are helpful for further gene function analysis to improve milk production and quality.

Discovering Copy Number Variation in Dual-Purpose XinJiang Brown Cattle

Copy number variants (CNVs), which are a class of structural variant, can be important in relating genomic variation to phenotype. The primary aims of this study were to discover the common CNV regions (CNVRs) in the dual-purpose XinJiang-Brown cattle population and to detect differences between CNVs inferred using the ARS-UCD 1.2 (ARS) or the UMD 3.1 (UMD) genome assemblies based on the 150K SNP (Single Nucleotide Polymorphisms) Chip. PennCNV and CNVPartition methods were applied to calculate the deviation of the standardized signal intensity of SNPs markers to detect CNV status. Following the discovery of CNVs, we used the R package HandyCNV to generate and visualize CNVRs, compare CNVs and CNVRs between genome assemblies, and identify consensus genes using annotation resources. We identified 38 consensus CNVRs using the ARS assembly with 1.95% whole genome coverage, and 33 consensus CNVRs using the UMD assembly with 1.46% whole genome coverage using PennCNV and CNVPartition. We identified 37 genes that intersected 13 common CNVs (>5% frequency), these included functionally interesting genes such as GBP4 for which an increased copy number has been negatively associated with cattle stature, and the BoLA gene family which has been linked to the immune response and adaption of cattle. The ARS map file of the GGP Bovine 150K Bead Chip maps the genomic position of more SNPs with increased accuracy compared to the UMD map file. Comparison of the CNVRs identified between the two reference assemblies suggests the newly released ARS reference assembly is better for CNV detection. In spite of this, different CNV detection methods can complement each other to generate a larger number of CNVRs than using a single approach and can highlight more genes of interest.

Genomic Selection for Milk Production Traits in Xinjiang Brown Cattle

One-step genomic selection is a method for improving the reliability of the breeding value estimation. This study aimed to compare the reliability of pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP), single-trait and multitrait models, and the restricted maximum likelihood (REML) and Bayesian methods. Data were collected from the production performance records of 2207 Xinjiang Brown cattle in Xinjiang from 1983 to 2018. A cross test was designed to calculate the genetic parameters and reliability of the breeding value of 305 daily milk yield (305 dMY), milk fat yield (MFY), milk protein yield (MPY), and somatic cell score (SCS) of Xinjiang Brown cattle. The heritability of 305 dMY, MFY, MPY, and SCS estimated using the REML and Bayesian multitrait models was approximately 0.39 (0.02), 0.40 (0.03), 0.49 (0.02), and 0.07 (0.02), respectively. The heritability and estimated breeding value (EBV) and the reliability of milk production traits of these cattle calculated based on PBLUP and ssGBLUP using the multitrait model REML and Bayesian methods were higher than those of the single-trait model REML method; the ssGBLUP method was significantly better than the PBLUP method. The reliability of the estimated breeding value can be improved from 0.9% to 3.6%, and the reliability of the genomic estimated breeding value (GEBV) for the genotyped population can reach 83%. Therefore, the genetic evaluation of the multitrait model is better than that of the single-trait model. Thus, genomic selection can be applied to small population varieties such as Xinjiang Brown cattle, in improving the reliability of the genomic estimated breeding value.

Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data

Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.

Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs

The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMI_CL, BMI_BL, and BMI_BH, respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMI_CL, and BMI_BL and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs.

Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle

Mastitis is one of the most frequently encountered diseases in dairy cattle, negatively affecting animal welfare and milk production. For this reason, contributions to understanding its genomic architecture are of great interest. Genome-wide association studies (GWAS) have identified multiple loci associated with somatic cell score (SCS) and mastitis in cattle. However, most of the studies have been conducted in different parts of the world on various breeds, and none of the investigations have studied the genetic architecture of mastitis in Romanian dairy cattle breeds up to this point in time. In this study, we report the first GWAS for SCS in dairy cattle breeds from Romania. For GWAS, we used an Axiom Bovine v3 SNP-chip (>63,000 Single Nucleotide Polymorphism -SNPs) and 33,330 records from 690 cows belonging to Romanian Spotted (RS) and Romanian Brown (RB) cattle. The results found one SNP significantly associated with SCS in the RS breed and 40 suggestive SNPs with -log₁₀ (p) from 4 to 4.9 for RS and from 4 to 5.4 in RB. From these, 14 markers were located near 12 known genes (AKAP8, CLHC1, MEGF10, SATB2, GATA6, SPATA6, COL12A1, EPS8, LUZP2, RAMAC, IL12A and ANKRD55) in RB cattle, 3 markers were close to ZDHHC19, DAPK1 and MMP7 genes, while one SNP overlapped the HERC3 gene in RS cattle. Four genes (HERC3, LUZP2, AKAP8 and MEGF10) associated with SCS in this study were previously reported in different studies. The most significant SNP (rs110749552) associated with SCS was located within the HERC3 gene. In both breeds, the SNPs and position of association signals were distinct among the three parities, denoting that mastitis is controlled by different genes that are dependent according to parity. The current results contribute to an expansion in the body of knowledge regarding the proportion of genetic variability explained by SNPs for SCS in dairy cattle.

Genome-Wide Association Study on Reproduction-Related Body-Shape Traits of Chinese Holstein Cows

Reproduction is an important production activity for dairy cows, and their reproductive performance can directly affect the level of farmers' income. To better understand the genomic regions and biological pathways of reproduction-related traits of dairy cows, in the present study, three body shape traits-Loin Strength (LS), Rump Angle (RA), and Pin Width (PW)-were selected as indicators of the reproductive ability of cows, and we conducted genome-wide association analyses on them. The heritability of these three traits was medium, ranging from 0.20 to 0.38. A total of 11 significant single-nucleotide polymorphisms (SNPs) were detected associated with these three traits. Bioinformatics analysis was performed on genes close to the significant SNPs (within 200 Kb) of LS, RA, and PW, and we found that these genes were totally enriched in 20 gene ontology terms and six KEGG signaling pathways. Finally, the five genes CDH12, TARP, PCDH9, DTHD1, and ARAP2 were selected as candidate genes that might affect LS. The six genes LOC781835, FSTL4, ATG4C, SH3BP4, DMP1, and DSPP were selected as candidate genes that might affect RA. The five genes USP6NL, CNTN3, LOC101907665, UPF2, and ECHDC3 were selected as candidate genes that might affect the PW of Chinese Holstein cows. Our results could provide useful biological information for the improvement of body shape traits and contribute to the genomic selection of Chinese Holstein cows.

Combined transcriptome and proteome analyses reveal differences in the longissimus dorsi muscle between Kazakh cattle and Xinjiang brown cattle

Objective

With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects.

Methods

Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3).

Results

In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results.

Conclusion

Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.

Mutation differences in circulating tumor DNAs from non-small cell lung cancer patients between Uygur and Han populations

BACKGROUND

The incidence of non-small cell lung cancer (NSCLC) in Uygur population is gradually increasing recently. In view of the great diagnostic and prognostic values of cell-free DNAs (cfDNA) detection, this study focus on a liquid biopsy to explore the value of cfDNA mutation in healthy and NSCLC patients in 2 ethnicities.

METHODS

The concentration and sequencing of cfDNA in NSCLC and healthy subjects was assessed with a standard information analysis procedure, including detection, annotation, and statistical analysis. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted to analyze the function of mutant genes and related pathways. Totally, 133 subjects, including 35 Uygur NSCLC patients, 10 Uygur healthy subjects, 63 cases of Han NSCLC patients and 25 Han health control, were admitted to the hospital.

RESULTS

There were a lower proportion of adenocarcinoma and higher percentage of smoking rate for Uygur patients. For cfDNA level between NSCLC and healthy subjects, Han patients exhibited sharp increase while there was no statistical difference in Uygur population. In addition, the mutation frequency of cfDNA in Han patients (72.6%) was significantly higher than Uygur patients (45.7%). There were 5 gene mutations only found in Han patients and ABCC11 showed a higher mutation frequency in Uygur population as a common one. Finally, Go and Kyoto Encyclopedia of Genes and Genomes analysis showed apprent functional enrichments and pathway changes between 2 ethnicities.

CONCLUSION

There existed distinct distributions of cancer subtypes, smoking proportion, cfDNA level, and mutation patterns between Han and Uygur patients. The results may be a useful tool in NSCLC patients' diagnosis as well as individualized therapy between ethnicities in future.

Determination of genetic variation within the DYRK2 gene and its associations with milk traits in cattle

To speed up the progress of marker-assisted selection (MAS) in cattle breeding, the dual-specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2), cadherin 2 (CDH2), and kinesin family member 1A (KIF1A) genes were chosen based on our pervious genome-wide association study (GWAS) analysis results. DYRK2 is a kinase that may participate in cell growth and/or development; it shows phosphorylation activity toward serine, threonine, and tyrosine fragments of proteins, and it is different from other protein kinases. The CDH2 gene encodes a classic cadherin, which is a member of the cadherin superfamily. The protein encoded by KIF1A is a member of the kinesin family and plays a role in the transportation of membrane organelles along axon microtubules. We detected insertion/deletion (InDel) variation in these three candidate genes in 438 individual cattle (Xinjiang Brown cattle and Wagyu × Luxi crossbreed cattle). Only DYRK2-P3-11 bp was polymorphic and genotyped. The polymorphism information content of DYRK2-P3-11 bp was 0.336. Correlation analyses showed that InDel polymorphism was significantly associated with six different milk traits. These findings may aid future analyses of InDel genotypes in cattle breeds, and speed up the progress of MAS in cattle breeding.

Effects of eight InDel variants in FHIT on milk traits in Xinjiang brown cattle

In our previous genome-wide association study (GWAS), we identified the fragile histidine triad diadenosine triphosphatase (FHIT) gene in Xinjiang brown cattle (XJBC) as a candidate gene associated with cattle productive traits, with potential application in mark-assisted selection (MAS) in cattle breeding. FHIT is a prototype of a class of tumor suppressor genes that contain genomic loci mapped to common fragile loci. Here, 388 healthy and unrelated XJBC were selected to identify insertion/deletion (InDel) variants in the bovine FHIT and assess their effects on milk traits. Eight of the thirteen InDel loci were found to be polymorphic in FHIT. The polymorphism information content of the eight loci ranged from 0.061 to 0.375. The correlation analysis showed that all the new InDel variants were significantly related to six different milk traits (p < 0.05). The following variants presented a significant relationship with productive traits: P2-23bp with the 305 milk yield (p = 0.005) in the sixth parity; P3-24bp with the milk fat yield (p = 0.009) in the third parity; P5-21bp with the somatic cell score (p = 0.001) in the first parity and with the milk protein percentage (p = 0.002) in the sixth parity; and P7-26bp with the somatic cell score (p = 0.003) in the sixth parity. These findings will help evaluate InDel genotypes, within and between cattle breeds and identify potential target loci to accelerate progress in MAS in cattle breeding.