Identification of candidate genes associated with milk production and mastitis based on transcriptome-wide association study.

Genetic research for the assessment of mastitis and milk production traits simultaneously has a long history. The main issue that arises in this context is the known existence of a positive correlation between the risk of mastitis and lactation performance due to selection. The transcriptome-wide association study (TWAS) approach endeavors to combine the expression quantitative trait loci and genome-wide association study summary statistics to decode complex traits or diseases. Accordingly, we used the farmgtex project results as a complete bovine database for mastitis and milk production. The results of colocalization and TWAS approaches were used for the detection of functional associated candidate genes with milk production and mastitis traits on multiple tissue-based transcriptome records. Also, we used the david database for gene ontology to identify significant terms and associated genes. For the identification of interaction networks, the genemania and string databases were used. Also, the available z-scores in TWAS results were used for the calculation of the correlation between tissues. Therefore, the present results confirm that LYNX1, DGAT1, C14H8orf33, and LY6E were identified as significant genes associated with milk production in eight, six, five, and five tissues, respectively. Also, FBXL6 was detected as a significant gene associated with mastitis trait. CLN3 and ZNF34 genes emerged via both the colocalization and TWAS approaches as significant genes for milk production trait. It is expected that TWAS and colocalization can improve our perception of the potential health status control mechanism in high-yielding dairy cows.

Quantifying the effects of the mitochondrial genome on milk production traits in dairy cows: empirical results and modelling challenges.

Significant advances in livestock traits have been achieved primarily through selection strategies targeting variation in the nuclear genome, with little attention given to mitogenome variation. We analyzed the influence of the mitogenome on milk production traits of Holstein cattle in Croatia based on strategically generated next-generation sequencing data for 109 cows pedigree-linked to 7115 milk production records (milk, fat and protein yield) from 3006 cows (first 5 lactations). Since little is known about the biology of the relationship between mitogenome variation and production traits, our quantitative genetic modeling was complex. Thus, the proportion of total variance explained by mitogenome inheritance was estimated using 5 different models: (1) cytoplasmic model with maternal lineages (CYTO), (2) haplotypic model with mitogenome sequences (HAPLO), (3) amino acid model with unique amino acid sequences (AMINO), (4) evolutionary model based on a phylogenetic analysis using Bayesian Evolutionary Analysis Sampling Trees phylogenetic analysis (EVOL), and (5) mitogenome SNP model (SNPmt). The polygenic autosomal and X chromosome additive genetic effects based on pedigree were modeled, together with the effects of herd-year-season interaction, permanent environment, location, and age at first calving. The estimated proportions of phenotypic variance explained by mitogenome in 4 different models (CYTO, HAPLO, AMINO, and SNPmt) were found to be substantial given the size of mitogenome, ranging from 5% to 7% for all 3 milk traits. At the same time, a negligible proportion of the phenotypic variance was explained by mitogenome with the EVOL model. Similarly, in all models, no proportion of phenotypic variance was explained by the X chromosome. Although our results should be confirmed in other dairy cattle populations, including a large number of sequenced mitogenomes and nuclear genomes, the potential of utilizing mitogenome information in animal breeding is promising, especially as the acquisition of complete genome sequences becomes cost-effective.

Genome-wide copy number variant analysis reveals candidate genes associated with milk production traits in water buffalo (Bubalus bubalis).

Buffaloes are vital contributors to the global dairy industry. Understanding the genetic basis of milk production traits in buffalo populations is essential for breeding programs and improving productivity. In this study, we conducted whole-genome resequencing on 387 buffalo genomes from 29 diverse Asian breeds, including 132 river buffaloes, 129 swamp buffaloes, and 126 crossbred buffaloes. We identified 36,548 copy number variants (CNV) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 CNV regions (CNVR), with 1,993 shared CNVR being found within the studied buffalo types. Analyzing CNVR highlighted distinct genetic differentiation between river and swamp buffalo subspecies, verified by evolutionary tree and principal component analyses. Admixture analysis grouped buffaloes into river and swamp categories, with crossbred buffaloes displaying mixed ancestry. To identify candidate genes associated with milk production traits, we employed 3 approaches. First, we used Vst-based population differentiation, revealing 11 genes within CNVR that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci analysis revealed differentially expressed CNVR-derived genes (DECG) associated with milk production traits. Notably, known milk production-related genes were among these DECG, validating their relevance. Last, a GWAS identified 3 CNVR significantly linked to peak milk yield. Our study provides comprehensive genomic insights into buffalo populations and identifies candidate genes associated with milk production traits. These findings facilitate genetic breeding programs aimed at increasing milk yield and improving quality in this economically important livestock species.

Polymorphism of ADAM12, DPP6 and PRKN genes and their associations with milk production traits in Holstein.

Milk production traits as the most important economic traits of dairy cows, they directly reflect the benefits of breeding and the economic benefits of pasture. In this study, A disintegrin and metalloproteinase-12 (ADAM12), Parkinson's disease gene 2 (PRKN) and dipeptidyl peptidase-like protein subtype 6 (DPP6) polymorphism in 384 Chinese Holstein cows were detected by time-of-flight mass spectrometry and through statistical analysis using software such as Popgene 32, SAS 9.4 and Origin 2022, the relationship between single nucleotide polymorphisms (SNPs) of three genes with four milk production traits such as daily milk yield (DMY), milk fat percentage (MFP), milk protein percentage (MPP) and somatic cell score (SCS) was verified at molecular level. The results showed that four polymorphic loci (116,467,133, 116,604,487, 116,618,268 and 116,835,111) of DPP6 gene, two polymorphic loci (97,665,052 and 97,159,837) of PRKN gene and two polymorphic loci (45,542,714 and 45,553,888) of ADAM12 gene were detected. PRKN-97665052, DPP6-116467133, ADAM12-45553888, DPP6-116604487 and DPP6-116835111 were all in Hardy-Weinberg equilibrium state (p > .05). ADAM12-45542714, PRKN-97159837 and PRKN-97665052 were moderately polymorphic (0.25 ≤ PIC <0.50) in Holstein. It is evident that the selection potential and genetic variation of these five loci are relatively large, and the genetic richness is relatively high. The correlation analysis of different genotypes between these eight loci and milk production traits of Holstein showed that ADAM12-45542714 and DPP6-116835111 (p < .01) had an extremely significant effects on the DMY of Chinese Holstein in Ningxia, while PRKN-97665052 had an extremely significant effect on MFP (p < .01). The effect of PRKN-97665052 and DPP6-116467133 on MPP of Holstein were extremely significant (p < .01). DPP6-116618268 had an extremely significant effect on the SCS of Holstein in Ningxia (p < .01), and AA genotype individuals showed a higher SCS than GG genotype individuals; the other two loci (ADAM12-45553888 and DPP6-116604487) had no significant effects on milk production traits of Holstein (p > .05). In addition, through the joint analysis of DPP6, PRKN and ADAM12 gene loci, it was found that the interaction effect between the three gene loci could significantly affect the DMY, SCS (p < .01) and MPP (p < .05). In conclusion, several different loci of DPP6, PRKN and ADAM12 genes can affect the milk production traits of Holstein to different degrees. PRKN, DPP6 and ADAM12 genes can be used as potential candidate genes for milk production traits of Holstein for marker-assisted selection, providing theoretical basis for breeding of Holstein.

Transcriptome-Wide Association Study Reveals Potentially Candidate Genes Responsible for Milk Production Traits in Buffalo.

Identifying key causal genes is critical for unraveling the genetic basis of complex economic traits, yet it remains a formidable challenge. The advent of large-scale sequencing data and computational algorithms, such as transcriptome-wide association studies (TWASs), offers a promising avenue for identifying potential causal genes. In this study, we harnessed the power of TWAS to identify genes potentially responsible for milk production traits, including daily milk yield (MY), fat percentage (FP), and protein percentage (PP), within a cohort of 100 buffaloes. Our approach began by generating the genotype and expression profiles for these 100 buffaloes through whole-genome resequencing and RNA sequencing, respectively. Through comprehensive genome-wide association studies (GWAS), we pinpointed a total of seven and four single nucleotide polymorphisms (SNPs) significantly associated with MY and FP traits, respectively. By using TWAS, we identified 55, 71, and 101 genes as significant signals for MY, FP, and PP traits, respectively. To delve deeper, we conducted protein-protein interaction (PPI) analysis, revealing the categorization of these genes into distinct PPI networks. Interestingly, several TWAS-identified genes within the PPI network played a vital role in milk performance. These findings open new avenues for identifying potentially causal genes underlying important traits, thereby offering invaluable insights for genomics and breeding in buffalo populations.

Whole-Genome Resequencing Analysis of the Camelus bactrianus (Bactrian Camel) Genome Identifies Mutations and Genes Affecting Milk Production Traits.

Milk production is an important trait that influences the economic value of camels. However, the genetic regulatory mechanisms underlying milk production in camels have not yet been elucidated. We aimed to identify candidate molecular markers that affect camel milk production. We classified Junggar Bactrian camels (9-10-year-old) as low-yield (<1.96 kg/d) or high-yield (>2.75 kg/d) based on milk production performance. Milk fat (5.16 ± 0.51 g/100 g) and milk protein (3.59 ± 0.22 g/100 g) concentrations were significantly lower in high-yielding camels than those in low-yielding camels (6.21 ± 0.59 g/100 g, and 3.93 ± 0.27 g/100 g, respectively) (p < 0.01). There were no apparent differences in gland tissue morphology between the low- and high-production groups. Whole-genome resequencing of 12 low- and 12 high-yield camels was performed. The results of selection mapping methods, performed using two methods (FST and θπ), showed that 264 single nucleotide polymorphism sites (SNPs) overlapped between the two methods, identifying 181 genes. These genes were mainly associated with the regulation of oxytocin, estrogen, ErbB, Wnt, mTOR, PI3K-Akt, growth hormone synthesis/secretion/action, and MAPK signaling pathways. A total of 123 SNPs were selected, based on significantly associated genomic regions and important pathways for SNP genotyping, for verification in 521 additional Bactrian camels. This analysis showed that 13 SNPs were significantly associated with camel milk production yield and 18 SNPs were significantly associated with camel milk composition percentages. Most of these SNPs were located in coding regions of the genome. However, five and two important mutation sites were found in the introns of CSN2 (ß-casein) and CSN3 (κ-casein), respectively. Among the candidate genes, NR4A1, ADCY8, PPARG, CSN2, and CSN3 have previously been well studied in dairy livestock. These observations provide a basis for understanding the molecular mechanisms underlying milk production in camels as well as genetic markers for breeding programs aimed at improving milk production.

Whole Genome Scan Uncovers Candidate Genes Related to Milk Production Traits in Barka Cattle.

In this study, our primary aim was to explore the genomic landscape of Barka cattle, a breed recognized for high milk production in a semi-arid environment, by focusing on genes with known roles in milk production traits. We employed genome-wide analysis and three selective sweep detection methods (ZFST, θπ ratio, and ZHp) to identify candidate genes associated with milk production and composition traits. Notably, ACAA1, P4HTM, and SLC4A4 were consistently identified by all methods. Functional annotation highlighted their roles in crucial biological processes such as fatty acid metabolism, mammary gland development, and milk protein synthesis. These findings contribute to understanding the genetic basis of milk production in Barka cattle, presenting opportunities for enhancing dairy cattle production in tropical climates. Further validation through genome-wide association studies and transcriptomic analyses is essential to fully exploit these candidate genes for selective breeding and genetic improvement in tropical dairy cattle.

Transcriptome analysis of the Bactrian camel (Camelus bactrianus) reveals candidate genes affecting milk production traits.

BACKGROUND: Milk production traits are complex traits with vital economic importance in the camel industry. However, the genetic mechanisms regulating milk production traits in camels remain poorly understood. Therefore, we aimed to identify candidate genes and metabolic pathways that affect milk production traits in Bactrian camels. METHODS: We classified camels (fourth parity) as low- or high-yield, examined pregnant camels using B-mode ultrasonography, observed the microscopic changes in the mammary gland using hematoxylin and eosin (HE) staining, and used RNA sequencing to identify differentially expressed genes (DEGs) and pathways. RESULTS: The average standard milk yield over the 300 days during parity was recorded as 470.18 ± 9.75 and 978.34 ± 3.80 kg in low- and high-performance camels, respectively. Nine female Junggar Bactrian camels were subjected to transcriptome sequencing, and 609 and 393 DEGs were identified in the low-yield vs. high-yield (WDL vs. WGH) and pregnancy versus colostrum period (RSQ vs. CRQ) comparison groups, respectively. The DEGs were compared with genes associated with milk production traits in the Animal Quantitative Trait Loci database and in Alashan Bactrian camels, and 65 and 46 overlapping candidate genes were obtained, respectively. Functional enrichment and protein-protein interaction network analyses of the DEGs and candidate genes were conducted. After comparing our results with those of other livestock studies, we identified 16 signaling pathways and 27 core candidate genes associated with maternal parturition, estrogen regulation, initiation of lactation, and milk production traits. The pathways suggest that emerged milk production involves the regulation of multiple complex metabolic and cellular developmental processes in camels. Finally, the RNA sequencing results were validated using quantitative real-time PCR; the 15 selected genes exhibited consistent expression changes. CONCLUSIONS: This study identified DEGs and metabolic pathways affecting maternal parturition and milk production traits. The results provides a theoretical foundation for further research on the molecular mechanism of genes related to milk production traits in camels. Furthermore, these findings will help improve breeding strategies to achieve the desired milk yield in camels.

High resolution melt curve analysis identifies a novel SNP (G21A) in butyrophilin gene having significant association with milk production traits in Holstein Friesian crossbreds of Kerala.

Butyrophilin (BTN1A1) gene is located in the neighborhood of a quantitative trait loci for milk production in bovine autosome 23. We verified the genetic variability of exon-3 in BTN1A1 and its association with milk production traits in Holstein Friesian crossbreds of Kerala. Genomic DNA was isolated and 94 bp fragment enclosing exon-3 was amplified by primers designed using PRIMER 3 based on reference sequence (GenBank NC_037350). Pooled amplicons were sequenced by Sanger's method and a novel single nucleotide polymorphism due to a transversion of guanine to adenine at position 21 of amplicon (G21A) leading to amino acid change arginine to glutamine was detected. The study population was genotyped by high-resolution melt curve analysis and revealed two genotypes with frequencies GG/0.84 and GA/0.14. The allele G was found to be the major one (G/0.93 and A/0.07). Moreover, association analysis of G21A with milk production traits was done using the General linear model-Analysis of Variance considering herd, season, and parity as non-genetic factors and milk production trait as a dependent variable. In analysis, animals with GA genotype were found to be having significantly higher (p ≤ 0.01) 305 day milk (GG:2720.74 ± 122.92 kg; GA:3250.20 ± 183.24 kg), fat (GG:106.55 ± 4.32 kg; GA:126.30 ± 13.35 kg), and SNF yield (GG: 211.52 ± 9.20 kg; GA: 246.90 ± 13.70 kg). However, GG (7.80 ± 0.04) genotype has significantly higher (p ≤ 0.05) SNF percent than GA (7.65 ± 0.07). Butyrophilin gene polymorphism G21A can be suggested as a molecular marker for future breeding programmes of cattle.

Longitudinal genome-wide association studies of milk production traits in Holstein cattle using whole-genome sequence data imputed from medium-density chip data.

Longitudinal traits, such as milk production traits in dairy cattle, are featured by having phenotypic values at multiple time points, which change dynamically over time. In this study, we first imputed SNP chip (50-100K) data to whole-genome sequence (WGS) data in a Chinese Holstein population consisting of 6,470 cows. The imputation accuracies were 0.88 to 0.97 on average after quality control. We then performed longitudinal GWAS in this population based on a random regression test-day model using the imputed WGS data. The longitudinal GWAS revealed 16, 39, and 75 quantitative trait locus regions associated with milk yield, fat percentage, and protein percentage, respectively. We estimated the 95% confidence intervals (CI) for these quantitative trait locus regions using the logP drop method and identified 581 genes involved in these CI. Further, we focused on the CI that covered or overlapped with only 1 gene or the CI that contained an extremely significant top SNP. Twenty-eight candidate genes were identified in these CI. Most of them have been reported in the literature to be associated with milk production traits, such as DGAT1, HSF1, MGST1, GHR, ABCG2, ADCK5, and CSN1S1. Among the unreported novel genes, some also showed good potential as candidate genes, such as CCSER1, CUX2, SNTB1, RGS7, OSR2, and STK3, and are worth being further investigated. Our study provided not only new insights into the candidate genes for milk production traits, but also a general framework for longitudinal GWAS based on random regression test-day model using WGS data.

Fatty acid desaturase 2 affects the milk-production traits in Chinese Holsteins.

As a member of the fatty acid desaturase family, fatty acid desaturase 2 (FADS2) gene is a rate-limiting enzyme in the synthesis of unsaturated fatty acids and within/near to the reported QTL regions for milk-production traits. We previously found that FADS2 is differentially expressed during different lactations of Chinese Holstein cows, and participates in lipid metabolic processes by influencing the insulin, PI3K-Akt, MAPK, AMPK, mTOR and PPAR signaling pathways. Therefore, we considered this gene as a candidate gene for milk-production traits. In this study, we identified 12 SNPs in FADS2 by re-sequencing, including two SNPs in the 5' flanking region, one in the seventh exon, five in introns, two in the 3' untranslated region and two in the 3' flanking region. The 29:g.40378819C>T is a missense mutation that causes alanine (GCG) to be replaced with valine (GTG). Through single marker association analysis, we found that all of the 12 SNPs were significantly associated with 305 day milk yield, fat yield, fat percentage, protein yield or protein percentage (p < 0.0493). The results of the subsequent haplotype association analysis also confirmed the associations between the gene and milk-production traits. In summary, this study suggests that there is a significant genetic association between FADS2 and milk-production traits, and that the SNPs with significant genetic effects can provide important molecular information for the development of a genomic selection chip in dairy cattle.

Devising a selection strategy for the Jamunapari goat for improving lactation performance.

This study aimed to evaluate the genetic potential of the Jamunapari goat and formulate a selection strategy for improving lactation traits. The data set included 4049 phenotypic records for across parity milk yield at 90 days (MY90), 140 days (MY140), total milk yield (TMY), and lactation length (LL) obtained from the progeny of 83 sires and 1643 dams between the period 1990 and 2019. Animal model employing average information restricted maximum likelihood (AIREML) was used to estimate genetic parameters for milk yield traits and LL. The direct additive heritability estimates for across parity lactation traits that used repeatability model were 0.10 ± 0.03, 0.08 ± 0.03, and 0.12 ± 0.02 for MY90, MY140, and TMY, respectively, while it was low for LL (0.06 ± 0.02). The repeatability estimates were moderate ranging from 0.17 to 0.22 for milk yield traits and LL, indicating persistent performance over the parities. Animal permanent environment influence (c2) was significant in milk yield attributes, whereas direct maternal genetic effects were absent. As the early selection criteria based on first parity records are essential, we analyzed the data for the first parity separately and obtained moderate h2 estimates, viz., 0.26 ± 0.05, 0.16 ± 0.06, and 0.25 ± 0.06 for MY90, MY140, and TMY, respectively. These estimates augur further scope of selection in Jamunapari goats for higher milk yield. High and positive genetic correlation of MY90 with MY140 (0.97 ± 0.01) and TMY (0.91 ± 0.05) revealed the scope of using MY90 as the selection criterion. Based on these results, we recommend use of first parity MY90 as a single trait selection criterion for genetic improvement of all lactation traits in Jamunapari goat.

Identification of genetic markers associated with milk production traits in Chinese Holstein cattle based on post genome-wide association studies.

With the rapid development of dairy industry, the breeding process of dairy cows has been accelerated. In previous genome-wide association studies (GWAS), a large number of genetic markers have been reported which may contribute to the selection of Holstein populations with superior milk-producing traits, but they remain to be further verified before practical application. In this study, 90 single nucleotide polymorphisms (SNPs) were selected, which were reported to be significantly associated with five milk production traits, including 305-day milk yield (305MY), 305-day milk fat percent (305FC), 305-day milk protein percent (305PC), 305-day milk fat yield (305FY) and 305-day milk protein yield (305PY). Effective 305-day data and fresh DNA samples were obtained from 295 healthy cows with gestational age of 1-4. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) was used to perform precise genotyping of these loci, followed by site association and haplotype analysis. Results showed that 36 out of 90 loci were supported to be used as genetic markers. In particular, several novel and effective haplotypes were also presented. Overall, our results verified tens of useful markers and provided a basis for further development of breeding strategies.

DGAT1 K232A polymorphism is associated with milk production traits in Chinese cattle.

The production traits of cattle, especially milk trait, are of great significance to human life. A quantitative trait loci (QTL) associated with milk fat content was detected in the centromeric region of cattle chromosome 14. This QTL harbors a strong candidate gene called DGAT1 responsible for the milk quality. A non-conservative substitution of lysine by alanine (K232A) was found in DGAT1 gene producing a strong effect on milk composition and yield. The lysine (K allele) is associated with increased milk fat content, while the decreased milk fat content is linked to the alanine (A allele) amino acid. To estimate the frequencies of the DGAT1 K232A polymorphism in Chinese cattle breeds, PCR and DNA sequencing methods were used to investigate the polymorphism of DGAT1 K232A in a total of 682 individuals, including 655 Chinese cattle and 27 Holstein cattle. The results demonstrated that the frequency of K allele gradually elevated from the northern group to the southern group of native Chinese cattle, whereas the frequency of A allele showed a contrary pattern, displaying a significant geographical difference across native Chinese cattle breeds. Our results confirm that the southern cattle group has higher milk fat content than that of the northern group.

AGPAT3 Gene polymorphisms are associated with milk production traits in Chinese Holstein cows.

The current study reports the identification of previously undiscovered single-nucleotide polymorphisms (SNPs) in the bovine AGPAT3 gene and further investigates their associations with milk production traits. Our results demonstrate that the major allele C of the SNP g.12264 C > T is positively correlated with test-day milk yield, protein percentage and 305-day milk yield. Importantly, in silico analysis showed that the C/T transition at this locus gives rise to two new transcription factor binding sites (TFBS), E2F1 and Nkx3-2. Polymorphism g.18658 G > A was the only SNP associated with milk urea nitrogen (MUN) with the G allele related to an increase in milk urea nitrogen as well as fat percentage. The GG genotype of SNP g.28731 A > G was associated with the highest fat and protein percentage and lowest 305-day milk yield and somatic cell score (SCS). The association between AGPAT3 locus and milk production traits could be utilized in marker-assisted selection for the genetic improvement of milk production traits and, probably in conjunction with other traits, for selection to improve fitness of dairy cattle.

Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle.

Milk production and composition are the most economically important traits affecting profitability in dairy cattle. In this study, we aimed at detecting signatures of positive selection in Kenana, known as one of the high milk production African indigenous zebu cattle, using next-generation sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (FST), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (Pi). Further analysis showed that several candidate genes such as CSN3, IGFBP-2, RORA, ABCG2, B4GALT1 and GHR are positively selected for milk production traits in Kenana cattle. The candidate genes and enriched pathways identified in this study may provide a basis for future genome-wide association studies and investigations into genomic targets of selection in dairy cattle.

Copy number variation analysis reveals variants associated with milk production traits in dairy goats.

Copy number variation (CNV) is a major type of genomic structural variation. We investigated their impacts on goat dairy traits using the CaprineSNP50 array. From 120 samples of five dairy goat breeds, we totally identified 42 CNVs ranging from 56,044 bp to 4,337,625 bp. We found significant associations between two CNVs (CNV5 and CNV25) and two milk production traits (mean of milk fat yield and mean of milk protein yield) after false discovery rate (FDR) correction (P < 0.05). CNV5 overlaps the ADAMTS20 gene, which is involved in the differentiation of mammary cell and plays a crucial role in lactogenic activity of bovine mammary epithelial cells. CNV25 overlaps with PAPPA2, which has been found to be associated with bovine reproduction and milk production traits. Our results revealed that CNVs overlapped with ADAMTS20 and PAPPA2 could be involved in goat dairy traits and function as candidate markers for further genetic selection.

Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping.

The aim of this study was to identify genomic regions underlying milk production traits in the Valle del Belice dairy sheep using regional heritability mapping (RHM). Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY), collected over a period of 6 years (2006-2012) on 481 Valle del Belice ewes, were used for the analysis. Animals were genotyped with the Illumina 50k SNP chip. Variance components, heritabilities and repeatabilities within and across lactations were estimated, fitting parity, litter size, season of lambing and fortnights in milk, as fixed; and additive genetic, permanent environment within and across lactations, flock by test-day interaction and residual as random effects. For the RHM analysis, the model included the same fixed and random effects as before, plus an additional regional genomic additive effect (specific for the region being tested) as random. While the whole genomic additive effect was estimated using the genomic relationship matrix (GRM) constructed from all SNPs, the regional genomic additive effect was estimated from a GRM matrix constructed from the SNPs within each region. Heritability estimates ranged between 0.06 and 0.15, with repeatabilities being between 0.14 and 0.24 across lactations and between 0.23 and 0.39 within lactation for all milk production traits. A substantial effect of flock-test-day on milk production traits was also estimated. Significant genomic regions at either genome-wide (p < .05) or suggestive (i.e., one false positive per genome scan) level were identified on chromosome (OAR) 2, 3 and 20 for F% and on OAR3 for P%, with the regions on OAR3 in common between the two traits. Our results confirmed the role of LALBA and AQP genes, on OAR3, as candidate genes for milk production traits in sheep.

Integrative analysis of genome-wide DNA methylation and gene expression profiles reveals important epigenetic genes related to milk production traits in dairy cattle.

Epigenetic modification plays a critical role in establishing and maintaining cell differentiation, embryo development, tumorigenesis and many complex diseases. However, little is known about the epigenetic regulatory mechanisms for milk production in dairy cattle. Here, we conducted an epigenome-wide study, together with gene expression profiles to identify important epigenetic candidate genes related to the milk production traits in dairy cattle. Whole-genome bisulphite sequencing and RNA sequencing were employed to detect differentially methylated genes (DMG) and differentially expressed genes (DEG) in blood samples in dry period and lactation period between two groups of cows with extremely high and low milk production performance. A total of 10,877 and 6,617 differentially methylated regions were identified between the two groups in the two periods, which corresponded to 3,601 and 2,802 DMGs, respectively. Furthermore, 156 DEGs overlap with DMGs in comparison of the two groups, and 131 DEGs overlap with DMGs in comparison of the two periods. By integrating methylome, transcriptome and GWAS data, some potential candidate genes for milk production traits in dairy cattle were suggested, such as DOCK1, PTK2 and PIK3R1. Our studies may contribute to a better understanding of epigenetic modification on milk production traits of dairy cattle.

Identification of candidate genes for milk production traits by RNA sequencing on bovine liver at different lactation stages.

BACKGROUND: RNA-sequencing was performed to explore the bovine liver transcriptomes of Holstein cows to detect potential functional genes related to lactation and milk composition traits in dairy cattle. The bovine transcriptomes of the nine liver samples from three Holstein cows during dry period (50-d prepartum), early lactation (10-d postpartum), and peak of lactation (60-d postpartum) were sequenced using the Illumina HiSeq 2500 platform. RESULTS: A total of 204, 147 and 81 differentially expressed genes (DEGs, p < 0.05, false discovery rate q < 0.05) were detected in early lactation vs. dry period, peak of lactation vs. dry period, and peak of lactation vs. early lactation comparison groups, respectively. Gene ontology and KEGG pathway analysis showed that these DEGs were significantly enriched in specific biological processes related to metabolic and biosynthetic and signaling pathways of PPAR, AMPK and p53 (p < 0.05). Ten genes were identified as promising candidates affecting milk yield, milk protein and fat traits in dairy cattle by using an integrated analysis of differential gene expression, previously reported quantitative trait loci (QTL), data from genome-wide association studies (GWAS), and biological function information. These genes were APOC2, PPP1R3B, PKLR, ODC1, DUSP1, LMNA, GALE, ANGPTL4, LPIN1 and CDKN1A. CONCLUSION: This study explored the complexity of the liver transcriptome across three lactation periods in dairy cattle by performing RNA sequencing. Integrated analysis of DEGs and reported QTL and GWAS data allowed us to find ten key candidate genes influencing milk production traits.