Fine mapping of genes on sheep chromosome 1 and their association with milk traits

On the basis of comparative mapping between cattle/sheep and human for milk trait quantitative trait loci (QTL) on BTA3/OAR1, annexin A9 (ANXA9) and solute carrier family 27 (fatty acid transporter), member 3 (SLC27A3) were selected as candidate genes for fat content (FC) in sheep milk. Two other genes in the same region, cingulin (CGN) and acid phosphatase 6, lysophosphatidic (ACP6), were also considered. DNA fragments of 1931 and 2790 bp corresponding to ANXA9 and SLC27A3 respectively were isolated, and 14 and 6 single nucleotide polymorphisms (SNPs) respectively were found in each gene. ANXA9, SLC27A3, CGN and ACP6 were localized to chromosome 1 between INRA006 and AE57 by linkage mapping using the International Mapping Flock. Across-family analyses of a daughter design comprising 13 sire families revealed significant sire and SLC27A3 genotype-nested-within-sire effects for FC. Within-family analyses indicated significant regression coefficients for FC in four of six heterozygous sires. These results could reflect the existence of a QTL for FC linked to SLC27A3 in sheep.     

Ovine alpha-amylase genes: isolation, linkage mapping and association analysis with milk traits

On the basis of comparisons between cattle and sheep genome mapping information the ovine alpha-amylase gene was examined as a possible genetic marker for milk traits in sheep. The objective of the present study was to isolate, map and determine whether this gene is a candidate gene for milk traits. DNA fragments (832 and 2360 bp) corresponding to two different AMY genes were isolated, and one SNP in intron 3 and one GTG deletion in exon 3 of the 2360 bp DNA fragment were found. The 2360 bp ovine AMY DNA fragment was located on chromosome 1 by linkage mapping using the International Mapping Flock. No association was found between estimated breeding values for milk yield, protein and fat contents and AMY genotypes in a daughter design comprising 13 Manchega families with an average of 29 daughters (12-62) per sire.     

A mammary gland EST showing linkage disequilibrium to a milk production QTL on bovine Chromosome 14

As part of a genome scan, ESTs derived from mammary gland tissue of a lactating cow were used as candidate genes for quantitative trait loci (QTL), affecting milk production traits. Resource families were genotyped with 247 microsatellite markers and 4 polymorphic ESTs. It was shown by linkage analysis that one of these ESTs, KIEL_E8, mapped to the centromeric region of bovine Chromosome (Chr) 14. Regression analysis revealed the presence of a QTL, with significant effect on milk production, in this chromosome region, and analysis of variance showed no significant interaction of marker genotype and family. The estimated significant differences between homozygous marker genotypes were 140 kg milk, −5.02 kg fat yield, and 2.58 kg protein yield for the first 100 days of lactation. Thus, there was strong evidence for a complete or nearly complete linkage disequilibrium between KIEL_E8 and the QTL. To identify the biological function of KIEL_E8, we extended the sequence for 869 bp by 5′-RACE. A 560-bp fragment of this shows a 90.9% similarity to a gene encoding a cysteine- and histidine-rich cytoplasmic protein in mouse. Although such a protein may have a regulatory function for lactation and a linkage disequilibrium between the EST marker and the QTL has been observed, it remains to be elucidated whether they are identical or not. Nevertheless, KIEL_E8 will be an efficient marker to perform marker-assisted selection in the Holstein-Friesian population. Received 20 October 2000 / Accepted: 11 April 2001     

Genome wide association studies for milk production traits in Chinese Holstein population

Genome-wide association studies (GWAS) based on high throughput SNP genotyping technologies open a broad avenue for exploring genes associated with milk production traits in dairy cattle. Motivated by pinpointing novel quantitative trait nucleotide (QTN) across Bos Taurus genome, the present study is to perform GWAS to identify genes affecting milk production traits using current state-of-the-art SNP genotyping technology, i.e., the Illumina BovineSNP50 BeadChip. In the analyses, the five most commonly evaluated milk production traits are involved, including milk yield (MY), milk fat yield (FY), milk protein yield (PY), milk fat percentage (FP) and milk protein percentage (PP). Estimated breeding values (EBVs) of 2,093 daughters from 14 paternal half-sib families are considered as phenotypes within the framework of a daughter design. Association tests between each trait and the 54K SNPs are achieved via two different analysis approaches, a paternal transmission disequilibrium test (TDT)-based approach (L1-TDT) and a mixed model based regression analysis (MMRA). In total, 105 SNPs were detected to be significantly associated genome-wise with one or multiple milk production traits. Of the 105 SNPs, 38 were commonly detected by both methods, while four and 63 were solely detected by L1-TDT and MMRA, respectively. The majority (86 out of 105) of the significant SNPs is located within the reported QTL regions and some are within or close to the reported candidate genes. In particular, two SNPs, ARS-BFGL-NGS-4939 and BFGL-NGS-118998, are located close to the DGAT1 gene (160bp apart) and within the GHR gene, respectively. Our findings herein not only provide confirmatory evidences for previously findings, but also explore a suite of novel SNPs associated with milk production traits, and thus form a solid basis for eventually unraveling the causal mutations for milk production traits in dairy cattle.     

FABP5 is a critical regulator of methionine- and estrogen-induced SREBP-1c gene expression in bovine mammary epithelial cells

The intracellular fatty acid-binding proteins (FABPs) are a well-conserved family that function as lipid chaperones. Ongoing studies are focused on identification of the mechanistic complexity and vast biological diversity of different isoforms of FABPs. However, the molecular mechanism of FABP5 in the regulation of milk fat synthesis in the mammary gland of dairy cows is still largely unknown. Here, we report that FABP5 acts as a critical regulator of terol response element-binding protein-1c (SREBP-1c) gene expression induced by methionine (Met) and estrogen (E2) in bovine mammary epithelial cells (BMECs). We observed that the expression of FABP5 was markedly higher in dairy cow mammary tissue during the lactating period than the puberty period and the dry period. FABP5 is located in the cytoplasm, and Met and E2 significantly increase the protein levels of FABP5 in BMECs. Using gene function study approaches, we revealed that FABP5 positively regulates SREBP-1c gene expression and promotes milk fat synthesis. We confirmed that FABP5 is required for Met- and E2-induced SREBP-1c gene expression and milk fat synthesis. We further uncovered that fatty acids are needed for FABP5-mediated SREBP-1c gene expression. Thus, our study demonstrates that FABP5 is a critical regulator of Met- and E2-induced SREBP-1c gene expression leading to milk fat synthesis.     

QTL and gene expression analyses identify genes affecting carcass weight and marbling on BTA14 in Hanwoo (Korean Cattle)

Causal mutations affecting quantitative trait variation can be good targets for marker-assisted selection for carcass traits in beef cattle. In this study, linkage and linkage disequilibrium analysis (LDLA) for four carcass traits was undertaken using 19 markers on bovine chromosome 14. The LDLA analysis detected quantitative trait loci (QTL) for carcass weight (CWT) and eye muscle area (EMA) at the same position at around 50?cM and surrounded by the markers FABP4SNP2774C>G and FABP4_??sat3237. The QTL for marbling (MAR) was identified at the midpoint of markers BMS4513 and RM137 in a 3.5-cM marker interval. The most likely position for a second QTL for CWT was found at the midpoint of tenth marker bracket (FABP4SNP2774C>G and FABP4_??sat3237). For this marker bracket, the total number of haplotypes was 34 with a most common frequency of 0.118. Effects of haplotypes on CWT varied from a ?5-kg deviation for haplotype 6 to +8?kg for haplotype 23. To determine which genes contribute to the QTL effect, gene expression analysis was performed in muscle for a wide range of phenotypes. The results demonstrate that two genes, LOC781182 (p?=?0.002) and TRPS1 (p?=?0.006) were upregulated with increasing CWT and EMA, whereas only LOC614744 (p?=?0.04) has a significant effect on intramuscular fat (IMF) content. Two genetic markers detected in FABP4 were the most likely QTL position in this QTL study, but FABP4 did not show a significant effect on both traits (CWT and EMA) in gene expression analysis. We conclude that three genes could be potential causal genes affecting carcass traits CWT, EMA, and IMF in Hanwoo.     

GWA Analysis for Milk Production Traits in Dairy Sheep and Genetic Support for a QTN Influencing Milk Protein Percentage in the LALBA Gene

In this study, we used the Illumina OvineSNP50 BeadChip to conduct a genome-wide association (GWA) analysis for milk production traits in dairy sheep by analyzing a commercial population of Spanish Churra sheep. The studied population consisted of a total of 1,681 Churra ewes belonging to 16 half-sib families with available records for milk yield (MY), milk protein and fat yields (PY and FY) and milk protein and fat contents (PP and FP). The most significant association identified reached experiment-wise significance for PP and FP and was located on chromosome 3 (OAR3). These results confirm the population-level segregation of a previously reported QTL affecting PP and suggest that this QTL has a significant pleiotropic effect on FP. Further associations were detected at the chromosome-wise significance level on 14 other chromosomal regions. The marker on OAR3 showing the highest significant association was located at the third intron of the alpha-lactalbumin (LALBA) gene, which is a functional and positional candidate underlying this association. Sequencing this gene in the 16 Churra rams of the studied resource population identified additional polymorphisms. One out of the 31 polymorphisms identified was located within the coding gene sequence (LALBA_g.242T>C) and was predicted to cause an amino acid change in the protein (Val27Ala). Different approaches, including GWA analysis, a combined linkage and linkage disequilibrium study and a concordance test with the QTL segregating status of the sires, were utilized to assess the role of this mutation as a putative QTN for the genetic effects detected on OAR3. Our results strongly support the polymorphism LALBA_g.242T>C as the most likely causal mutation of the studied OAR3 QTL affecting PP and FP, although we cannot rule out the possibility that this SNP is in perfect linkage disequilibrium with the true causal polymorphism.     

Cytogenetic mapping of eight genes encoding fatty acid binding proteins (FABPs) in the pig genome

In the present study cytogenetic localization of eight fatty acid binding protein genes in the pig genome was shown. BAC clones, containing sequences of selected genes (FABP1, FABP2, FABP3, FABP4, FABP5, FABP6, FABP7 and FABP8) were derived from porcine BAC libraries and mapped by FISH to porcine chromosomes (SSC) 3q12, 8q25, 6q26, 4q12, 4q12, 16q22, 1p22 and 4q12, respectively. Detailed analyses of regions containing gene clusters (FABP4, FABP5, FABP8) in chromosome 4 were performed and their order was established. It was shown that these three genes are located beyond the FAT1 region. Assignment of the FABP genes to chromosome regions harboring quantitative trait loci (QTL) for fat deposition is discussed.     

Detection of loci affecting milk production and health traits in an elite US Holstein population using microsatellite markers

Quantitative trait loci (QTL) affecting health and milk production traits were studied in seven large half-sib US Holstein families by using the granddaughter design. Genotyping for 16 markers was completed and marker allele differences within and pooled-across families were analysed. Potential QTL were identified for somatic cell score (SCS), fat yield, fat percentage, protein yield and protein percentage. Three markers (BM203, BM4505 and BM2078) were associated with significant effects for different traits and, after further analysis, may be useful in marker-assisted selection in specific families. Comparisons between these data and previously identified QTL support the location of a QTL for milk yield and protein yield on chromosome 21.     

Characterization,genetic variation and chromosomal assignment to sheep chromosome 2 of the ovine heart fatty acid-binding protein gene (FABP3)

The purpose of this study was to locate and detect genetic variation in the sheep FABP3 gene, a candidate gene for milk and meat quality traits in sheep. We have obtained an almost complete sequence (4,689 bp, excluding a part of intron 1) of the sheep FABP3 gene using PCR-based comparative genome walking. Sheep FABP3 has been located to chromosome 2 by sheep sequence-specific PCR on DNA from a sheep/rodent cell hybrid panel, and confirmed by linkage mapping using the International Mapping Flock. Direct sequencing of PCR products amplified from different DNA samples of Manchega breed sheep over the complete sheep FABP3 gene revealed 13 SNPs, one CTC insertion/deletion and a variable polyA tract. This poly A tract was found in association with a SINE/artiodactyls repeat. In addition, two SNPs were screened in different sheep breeds.     

FABP3, FABP4 and ANXA9 SNP genotypes in relation to breeding values for milk production traits in Polish Holstein-Friesian cows

The aim of this study is to estimate the associations between the ANXA9, FABP3, and FABP4 genotypes and the breeding value for milk production traits (yields of milk, protein, and fat, as well as protein and fat percentage) in 975 Polish Holstein-Friesian cows. The frequencies of genotypes and alleles were determined. Statistically significant relations between the ANXA9 SNP and the breeding value for fat content, as well as the FABP4 SNP and the breeding value for protein content were found. The results indicated that selection for the ANXA9 GG and FABP4 GG animals might contribute to an decreased fat content and increased protein content in milk, respectively, in Polish Holstein-Friesian cows. Although verification in the further studies is needed.     

Identification of genetic polymorphisms in FABP3 and FABP4 and putative association with back fat thickness in Korean native cattle

The aim of this study was to determine whether single nucleotide polymorphisms (SNP) in the beef cattle adipocyte fatty-acid binding protein 3 and 4 (FABP3 and FABP4) genes are associated with carcass weight (CW) and back fat thickness (BF) of beef cattle. By direct DNA sequencing in 24 unrelated Korean native cattle, we identified 20 SNPs in FABP3 and FABP4. Among them, 10 polymorphic sites were selected for genotyping in our beef cattle. We performed SNP, haplotype and linkage disequilibrium studies on 419 Korean native cattle with the 10 SNPs in the FABP genes. Statistical analysis revealed that 220AG (I74V) and 348+303TC polymorphisms in FABP4 showed putative associations with BF traits (P=0.02 and 0.01, respectively). Our findings suggest that the polymorphisms in FABP4 may play a role in determining one of the important genetic factors that influence BF in beef cattle.     

Casein haplotypes and their association with milk production traits in the Finnish Ayrshire cattle

Polymorphism of casein genes was studied in half-sib families of artificial insemination bulls of the Finnish Ayrshire dairy breed. Ten grandsires and 300 of their sons were genotyped for the following polymorphisms: α_S1-casein (B, C), β-casein (A¹, A²), the microsatellite within the K-casein gene (ms⁵, ms⁴) and K-casein (A, B, E). Nine different combinations of these alleles, casein haplotypes, were found. Associations between casein haplotypes and milk production traits (milk and protein yield, fat and protein percentage and milking speed) were studied with ordinary least-squares analysis to find a direct effect of the haplotypes or an association within individual grandsire families using the granddaughter design. Estimated breeding values of sons were obtained from cow evaluation by animal model. No direct effect of the casein haplotypes on the traits was found. Within grandsire families, in one out of four families the chromosomal segment characterized by haplotype 3 (B-A²-ms⁴-A) was associated with an increase in milk yield ( P <0.01) and a decrease in fat percentage ( P < 0.01) when contrasted with haplotype 8 (B-A¹-ms⁴-E). The results provide evidence that in the Finnish Ayrshire breed at least one quantitative trait locus affecting the genetic variation in yields traits is segregating linked to either haplotype 3 (B-A²-ms⁴-A) or 8 (B-A¹-ms⁴-E).     

A novel polymorphism of the lactoferrin gene and its association with milk composition and body traits in dairy goats

Milk composition and body measurement traits, influenced by genes and environmental factors, play important roles in value assessments of efficiency and productivity in dairy goats. Lactoferrin (LF), involved in the efficient expression of protein in milk, is also an anabolic factor in skeletal tissue and a potent osteoblast survival factor. Therefore, it is an important candidate gene for milk composition and body measurement trait selection in marker-assisted selection. We employed PCR-SSCP and DNA sequencing to screen the genetic variations of the LF gene in 549 Chinese dairy goats. A novel single-nucleotide polymorphism (SNP) (G198A in exon II) of the LF gene was detected. The frequencies of the AA genotype were 0.0285 and 0.0261 in GZ and SN populations, respectively. Both populations were found to have low levels of polymorphism and were in Hardy-Weinberg disequilibrium (P < 0.05). We found significant (P < 0.05) associations of the SNP marker with milk protein and acidity in the total population; animals with the AA genotype had higher mean values for milk protein than those with the GA genotype. Animals with genotype AA had higher mean values for withers height than those with genotype GG (P < 0.05). We concluded that this SNP of the LF gene has potential as a genetic marker for milk composition and body traits in dairy goat breeding.     

Detection of QTL for milk production traits in cattle by application of a specifically developed marker map of BTA6

Interval mapping was carried out to identify quantitative trait loci (QTL) for milk production traits in five granddaughter design families of the German Holstein population. Fourteen randomly generated markers spanning the whole of BTA6 and six targeted microsatellite markers from BTA6q21-31 were included in the analysis. In one family a QTL with effects on milk fat yield and milk protein yield was mapped to the interval TGLA37-FBN13 (3 CM proximal to FBN13, lodscore 3.22) in the middle part of the chromosome. Although there are several reports about QTL with effects on milk production traits on BTA6 in the literature, a QTL with effects on milk fat and milk protein yield has not been previously described.     

Paratuberculosis: decrease in milk production of German Holstein dairy cows shedding Mycobacterium avium ssp. paratuberculosis depends on within-herd prevalence

Paratuberculosis impairs productivity of infected dairy cows because of reduced milk production and fertility and enhanced risk of culling. The magnitude of the milk yield depression in individual cows is influenced by factors such as parity, the stage of the disease and the choice of test used. The objectives of this case–control study were to substantiate the influence of the different levels of the within-herd prevalence (WHP) on individual milk yield of fecal culture (FC)-positive cows (FC+) compared with FC-negative herd-mates (FC−), and to estimate the magnitude of the deviation of the milk yield, milk components and somatic cell count (SCC) in an FC-based study. Of a total of 31 420 cows from 26 Thuringian dairy herds tested for paratuberculosis by FC, a subset of 1382 FC+ and 3245 FC− with milk recording data were selected as cases and controls, respectively. The FC− cows were matched for the same number and stage of lactation (±10 days in milk) as one FC+ from the same herd. Within a mixed model analysis using the fixed effects of Mycobacterium avium ssp. paratuberculosis (MAP) status, lactation number, days in milk, prevalence class of farm and the random effect of farm on milk yield per day (kg), the amount of fat and protein (mg/dl) and lactose (mg/dl) as well as the SCC (1000/ml) were measured. On the basis of least square means, FC+ cows had a lower test-day milk yield (27.7±0.6 kg) compared with FC− (29.0±0.6 kg), as well as a lower milk protein content and a slightly diminished lactose concentration. FC status was not associated with milk fat percentage or milk SCC. In FC+ cows, reduction in milk yield increased with increasing WHP. An interaction of FC status and farm was found for the test-day milk yield, and milk protein percentage, respectively. We conclude that the reduction in milk yield of FC+ cows compared with FC− herd-mates is significantly influenced by farm effects and depends on WHP class. Owners of MAP-positive dairy herds may benefit from the reduction in WHP not only by reducing number of infected individuals but also by diminishing the individual losses in milk production per infected cow, and therefore should establish control measures.     

Variants located upstream of CHRNB4 on chromosome 15q25.1 are associated with age at onset of daily smoking and habitual smoking

Several genome-wide association and candidate gene studies have linked chromosome 15q24-q25.1 (a region including the CHRNA5-CHRNA3-CHRNB4 gene cluster) with alcohol dependence, nicotine dependence and smoking-related illnesses such as lung cancer and chronic obstructive pulmonary disease. To further examine the impact of these genes on the development of substance use disorders, we tested whether variants within and flanking the CHRNA5-CHRNA3-CHRNB4 gene cluster affect the transition to daily smoking (individuals who smoked cigarettes 4 or more days per week) in a cross sectional sample of adolescents and young adults from the COGA (Collaborative Study of the Genetics of Alcoholism) families. Subjects were recruited from families affected with alcoholism (either as a first or second degree relative) and the comparison families. Participants completed the SSAGA interview, a comprehensive assessment of alcohol and other substance use and related behaviors. Using the Quantitative trait disequilibrium test (QTDT) significant association was detected between age at onset of daily smoking and variants located upstream of CHRNB4. Multivariate analysis using a Cox proportional hazards model further revealed that these variants significantly predict the age at onset of habitual smoking among daily smokers. These variants were not in high linkage disequilibrium (0.28相似文献