Is generally known there is antagonistic relationship between production and reproduction traits. We observed this relationship in dataset of 1 197 478 daily milk records of Holstein cows on the ...first lactation only, first time calved during years 2003-2009. We found increased milk production and prolonged calving interval during this period. We observed highest milk production (7604 kg) on standardized 1st lactation for cows with longest calving interval in compare to cows with shortest calving interval (7079 kg). Positive significant correlation (0.56775, P<0.0001) was found between standardized milk production and calving interval. It means that cows with higher milk production have a prolonged calving interval, which confirms antagonist relationship between production and reproduction traits. Significant negative correlation (-0.27695, P<0.0001) observed between percent of protein production on standardized lactation and calving interval suggests that prolonged calving interval has negative effect on daily protein production (%) in milk. Coefficient of determination between breeding values for milk production and length of calving interval was 0.6434. Following these results we should accept relationship between production and reproduction and include it in process of genetic evaluation of cattle.
Growth of the Greenshell™ mussel (Perna canaliculus) industry, New Zealand's most significant aquaculture sector, is limited by spat abundance in the early stages of the aquaculture cycle. However, ...there are few management techniques to improve spat production. Here, we tested the effects of seeding density (low: 257, mid: 515, and high: 1030 mussels per 10 cm of culture rope) – a putative method to manage spat seeding efficiency and yield – on the abundance and size of P. canaliculus spat at four depths at two sites in the Marlborough Sounds. We also recorded the abundance and size of blue mussels, Mytilus galloprovincialis, which are a problematic biofouling species, as well as the biomass and composition of the biofouling accumulating on mussel culture ropes under the same experimental treatments. Although the abundance of P. canaliculus was greatest at the highest seeding density (∼200 mussels per 10 cm of rope at 87 days), this seeding density also experienced the greatest losses. However, while fewer spat were lost from the low-density seeding treatment, the overall number of spat per 10 cm was significantly reduced, resulting in few operational gains in terms of biofouling reduction or spat size. Overall, the seeding density of suggesting that seeding density of ∼1030 spat per 10 cm of rope was the optimal density tested in this study and could be a useful target density for mussel farmers.
•Effects of seeding density (SD) on abundance and growth of mussel spat was tested.•Abundance remained highest at the highest SD over time.•Biofouling accumulation and biomass was generally lowest at the highest SD.•Mussel size and abundance was impacted by SD and additional factors together•Highest SD tested was preferred to optimise mussel abundance and reduce biofouling.
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 variant (CNVs) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 copy number variant regions (CNVRs), with 1,993 shared CNVRs being found within the studied buffalo types. Analyzing CNVRs 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 CNVRs that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci (eQTL) analysis revealed differential expression of CNVR-driven genes (DECGs) associated with milk production traits. Notably, known milk production-related genes were among these DECGs, validating their relevance. Last, a genome-wide association study (GWAS) identified 3 CNVRs 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.
This study investigated genetic correlations of longissimus muscle fatty acid composition with 32 traits related to growth, carcass, fat deposition and meat quality in 2448 pigs from six populations ...using genome wide SNP data. Most of significant loci for saturated (C14:0, C16:0 and C18:0) and mono-saturated fatty acids (C18:1n9 and C16:1n7) identified in GWAS, including those near ELOVL6, SCD and FASN genes, displayed negligible or weak effects on all the 32 traits. Fat deposition traits were the most relevant traits for fatty acid composition in genetic correlations. Backfat thickness and intramuscular fat content consistently showed strong negative genetic correlations with C18:2n6, and positive genetic correlations with C18:1n9 at least five populations. Intramuscular fat content consistently has positive correlations with saturated fatty acids (SFA) in six populations. This study provided insights into shared genetic control of fatty acid composition and the other economic traits, which is helpful in design of breeding strategies to genetically improve fatty acid composition in pork.
Abstract
We estimated heritabilities of semen production traits and their genetic correlations with litter traits and pork production traits in purebred Duroc pigs. Semen production traits were semen ...volume, sperm concentration, proportion of morphologically normal sperms, total number of sperm, and total number of morphologically normal sperm. Litter traits at farrowing were total number born, number born alive, number stillborn, total litter weight at birth, mean litter weight at birth, and piglet survival rate at birth. Litter traits at weaning were litter size at weaning, total litter weight at weaning, mean litter weight at weaning, and piglet survival rate from birth to weaning. Pork production traits were average daily gain, backfat thickness, and loin muscle area. We analyzed 45,913 semen collection records of 896 boars, 6,950 farrowing performance records of 1,400 sows, 2,237 weaning performance records of 586 sows, and individual growth performance records of 9,550 animals measured at approximately 5 mo of age. Heritabilities were estimated using a single-trait animal model. Genetic correlations were estimated using a 2-trait animal model. Estimated heritabilities of semen production traits ranged from 0.20 for sperm concentration to 0.29 for semen volume and were equal to or higher than those of litter traits, ranging from 0.06 for number stillborn and piglet survival rate at birth to 0.25 for mean litter weight at birth, but lower than those of pork production traits, ranging from 0.50 for average daily gain to 0.63 for backfat thickness. In many cases, the absolute values of estimated genetic correlations between semen production traits and other traits were smaller than 0.3. These estimated genetic parameters provide useful information for establishing a comprehensive pig breeding scheme.
Lay Summary
Genetic parameters of 5 semen production traits, 10 litter traits, and 3 pork production traits in purebred Duroc pigs was estimated. Heritabilities of semen production traits ranged from 0.20 for sperm concentration to 0.29 for semen volume and were equal to or higher than those of litter traits, ranging from 0.06 for number stillborn and piglet survival rate at birth to 0.25 for mean litter weight at birth, but lower than those of pork production traits, ranging from 0.50 for average daily gain to 0.63 for backfat thickness. In many cases, the absolute values of genetic correlations between semen production traits and other traits were smaller than 0.3. These estimated genetic parameters provide useful information for establishing a comprehensive pig breeding scheme.
Genetic parameters of 5 semen production traits, 10 litter traits, and 3 pork production traits in purebred Duroc pigs were estimated, providing useful information for establishing a comprehensive pig breeding scheme.
In order to gain insight into the genetic architecture of economically important traits in pigs and to derive suitable genetic markers to improve these traits in breeding programs, many studies have ...been conducted to map quantitative trait loci. Shortcomings of these studies were low mapping resolution, large confidence intervals for quantitative trait loci-positions and large linkage disequilibrium blocks. Here, we overcome these shortcomings by pooling four large F2 designs to produce smaller linkage disequilibrium blocks and by resequencing the founder generation at high coverage and the F1 generation at low coverage for subsequent imputation of the F2 generation to whole genome sequencing marker density. This lead to the discovery of more than 32 million variants, 8 million of which have not been previously reported. The pooling of the four F2 designs enabled us to perform a joint genome-wide association study, which lead to the identification of numerous significantly associated variant clusters on chromosomes 1, 2, 4, 7, 17 and 18 for the growth and carcass traits average daily gain, back fat thickness, meat fat ratio, and carcass length. We could not only confirm previously reported, but also discovered new quantitative trait loci. As a result, several new candidate genes are discussed, among them
(bone morphogenetic protein 2), which we recently discovered in a related study. Variant effect prediction revealed that 15 high impact variants for the traits back fat thickness, meat fat ratio and carcass length were among the statistically significantly associated variants.
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.
The present study explored the association between single nucleotide polymorphisms (SNPs) in leptin gene with various economic traits (body weight at different age, first lactation reproduction and ...production traits) in Sahiwal cows. PCR-RFLP of 522 bp fragment comprising partial intron 2 and exon 3 of leptin gene, carried out using BsaAI restriction endonuclease, revealed three genotypes (GG, AG and AA) at position G93263736A in chromosome 4 with genotypic frequencies of 0.39, 0.52 and 0.09 respectively. The allele frequencies were 0.65 for the G allele and 0.35 for the A allele. General Linear Model (GLM) analysis revealed significant association of SNP G93263736A with growth and first lactation production traits. The present study supports that SNP in leptin gene could be used as an aid to selection for improving different economic traits in Sahiwal cows.
This research aims to estimate heritability and repeatability based on the data on milk production traits (MY – milk yield; FY – milk fat yield; FC – milk fat content; PY – milk protein yield and PC ...– milk protein content) as well as pedigree and genomic information. A total of 6,041 animals were included in the research, while 2,565 of them had data for milk production traits. In order to form a genomic relationship matrix, 58K SNP data were used for a total of 1,491 cows. Several software tools were used in the preparation and analysis of data, which were provided by the Central Breeding Organization, Department of Animal Science, Faculty of Agriculture, University of Novi Sad. PreGSF90, in combination with RENUMF90, was used for quality control of genomic information. Genetic analysis was performed in WOMBAT software by the REML using standard repeatability univariate analysis (BLUPpe) and repeatability models for genomic prediction (GBLUPpe and ssGBLUPpe). In all three analyses, the highest heritability (0.410, 0.378 and 0.389, respectively) and repeatability (0.449, 0.429 and 0.440, respectively) were calculated for FC. Heritability estimates for all other traits were lower. Heritability ranged from 0.158 to 0.185 for MY, from 0.166 to 0.178 for FY, from 0.141 to 0.154 for PY and from 0.135 to 0.221 for PC. Heritability estimates indicate that it is possible to achieve genetic improvement but it is necessary to introduce the best model for prediction of breeding values of cow.
The myostatin gene inhibits skeletal muscle growth in advanced animals, and a mutation in the gene coding region increases muscle formation. Hence, it is accepted to be a candidate gene for the ...selection of some production traits. The objective of the current research was to examine the genotypes of the myostatin gene and reveal the associations between the genotypes and a number of traits, including birth weight, weaning weight, weaning age, average daily weight gain, and productivity, in 110 Morkaraman sheep. Genotypes were determined by the PCR-RFLP method using the HaeIII restriction enzyme, and the genotype frequencies were found to be 9%, 69%, and 22% for MM, Mm, and mm in the myostatin locus, respectively. The M allele frequency was 44%, whereas the m allele frequency was 56%. In the studied population, the myostatin locus was not in Hardy-Weinberg equilibrium. The association analysis revealed no statistically significant impact of the MSTN gene polymorphism in exon 3 on birth weight, weaning weight, and productivity (P>0.05) but found a significant effect on weaning age and average daily weight gain (P<0.05). As a result, the MSTN gene showed polymorphisms in Morkaraman sheep and can be regarded as a genetic marker for sheep selection according to the association analysis results.
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