Production Traits Research Articles

Gene expression profiles in specific skeletal muscles and meat quality characteristics of sheep and goats

Lamb meat is highly valued across various cultures and regions due to its unique flavor and nutritional benefits. As the primary component of edible meat, skeletal muscle holds significant economic value and research importance. However, previous studies have largely focused on a limited array of muscle groups, overlooking the differences between various types. Therefore, a comprehensive transcriptomic and meat quality analysis of the skeletal muscles of sheep and goats is essential to improve meat production traits. In this study, we performed RNA sequencing and assessed meat quality in 10 different skeletal muscles from 2-year-old Liangshan Black sheep and Meigu Black goats. We generated 803.16 Gb of high-quality bulk RNA sequencing data with six biological replicates for each muscle. This dataset provides a deeper understanding of the gene expression profiles and meat quality characteristics of different muscle tissues in sheep and goats, laying the foundation for broader comparative research.

Benchmarking performance in Targhee sheep in development of a genetic reference flock

Abstract The Targhee breed is important to range sheep production in the Western U.S. The objective of this research was to integrate industry sires participating in national genetic evaluation through the National Sheep Improvement Program (NSIP) into the U.S. Sheep Experiment Station (USSES) flock, where the breed originated, to benchmark sire performance. Estimated breeding values (EBV) of industry sires (n = 16) and USSES sires (n = 12) from the 2023 NSIP Targhee genetic evaluation differed (P < 0.05) only for the NSIP Number Born EBV. This difference, and small (nonsignificant) differences favoring industry sires for maternal weaning weight, yearling fiber diameter, and yearling staple length EBV also resulted in greater (P < 0.05) Western Range Index scores for industry sires. The performance of sires’ direct progeny born 2016 to 2018 was compared for 17 traits. After data cleaning, there were 664 progeny (417 from industry sires and 247 from USSES sires) with 146 to 664 records per trait. Least squares means differed (P < 0.05) for grease fleece weight, side fiber diameter, and britch fiber diameter in favor of the industry sires. Production traits were measured from the progeny and other retained descendants of both sire genetic groups from 2016 through 2022. After data cleaning, there was a range of 1,138 to 1,493 records per trait. A three-generation pedigree was constructed and the proportional assignment of each lamb to each genetic group (e.g., 0.5 industry, 0.5 USSES) was included in an augmented relationship matrix. A univariate animal model was fitted for each lamb trait and a repeated measures model for each of the three ewe traits was fitted to estimate variance components and predict breeding values. Genetic group solutions did not differ (P > 0.05) for any of these traits but provided a means by which to compare the two groups. Establishment of a Targhee genetic reference flock at USSES has been initiated, which can be used to address issues of importance to the industry.

Frequencies of β-casein variants and their influence on genetic merit for production traits in Holstein cows

Context Traits considered for selection are influenced by social, consumer, and breeder demands. In the past decades, there has been increasing global interest in producing milk free from the β-casein (CSN2) A1 allele because of the health benefits it may have. This has encouraged many breeders to select A2A2 cows in their dairy cattle herds. Aims This study aimed to evaluate the genetic variation in the bovine CSN2 gene regarding A1-like and A2-like variants and to assess the potential association between these variants and production traits in Holstein cows. Methods In total, 2600 Holstein cows from three commercial dairy farms with different breeding objectives and phenotypic records taken over different seasons, periods, and lactations were genotyped for single-nucleotide polymorphism rs43703011, which distinguishes A1-like from A2-like β-casein variants. Allele and genotype frequencies were determined and their breeding values for milk, fat, and protein yields, and fat and protein percentages were estimated. The influence of CSN2 genotypes on these breeding values was studied through a one-way ANOVA. For the significant CSN2 genotype–breeding value associations, allele substitution effects were estimated. Key results We found allele frequencies for A1-like and A2-like alleles in the ranges 0.262–0.366 and 0.634–0.738 respectively, and genotype frequencies in the ranges of 0.043–0.125, 0.43–0.537, and 0.393–0.523 for A1A1, A1A2 and A2A2 genotypes respectively. We demonstrated that the A2-like CSN2 variant correlates with higher estimated breeding values (EBVs) for milk, protein, and fat yields, and lower EBVs for fat and protein percentages. Conclusions These results are valuable to visualize the trends in CSN2 allele and genotype frequency changes over the years and to analyze the effect of the different variants of β-casein on production performance. Implications Our findings contribute to evaluating the consequences on dairy performance of selection for the A2-like variant.

Single nucleotide polymorphisms of GYS2 gene and its association with milk production traits of dairy cows

Glycogen synthase 2 (GYS2) encodes liver glycogen synthase, a rate limiting enzyme in glycogen metabolism. Our preliminary work suggested that GYS2 was a candidate gene affecting milk production traits by analyzing the liver proteome of dairy cows. Herein, this research identified single nucleotide polymorphisms (SNPs) of GYS2, analyzed their genetic effects on traits of dairy cattle, and speculated the pathogenic mechanism through functional prediction of key mutation sites. Seven SNPs were found by resequencing and the association analysis showed that these SNPs were significantly associated with 305-day milk yield, fat yield, protein yield or fat percentage (p-value ≤ 0.0488). Six SNPs among them formed two haplotype blocks and they were associated with 305-day milk yield, fat yield, protein yield or fat percentage (p-value ≤ 0.0349). Furthermore, 5:g.88602007G > A and 5:g.88602026G > A were predicted to change the transcription factor binding sites (TFBSs), which might regulate the expression of GYS2. The missense mutation site, 5:g.88602535G > T, changed the secondary structure of mRNA and the secondary and tertiary structure of protein. In summary, the GYS2 was proved to have genetic effect on milk production traits, and its valuable seven SNPs, could provide more useful genetic information for molecular breeding of dairy cows.

Породата Ил дьо Франс в Молдова – проява на основни продуктивни признаци

The aim of the study is to analyze the manifestation of the main selection traits of Ile de France sheep, introduced for the first time in 2023, in the Republic of Moldova. The object of the study is 180 female animals and their offspring, raised on two farms in the geographical and economic conditions of Moldova. The manifestation of the main selection traits at the first birth of the ewes was monitored - live weight and average daily gain of lambs, fertility and fecundity of the ewes. The growth intensity of the lambs was analyzed in two age periods. As a result of the study, it can be concluded that Ile de France sheep breed adapt well to the geographical and economic conditions in the Republic of Moldova, maintain excellent physiological status and realize their potential for high productivity. The monitored animals have an excellent expression of two of the main productive traits – live weight and average daily gain. The established average daily gain of lambs in the period from birth to 30 days is from 250 to 280 g/day for singletons; from 210 to 220 g/day for twins and from 170 to 180 g/day for triplets and more born lambs. The results obtained are below the average for the population in Bulgaria. The results for the average daily gain in the next age category – from 30 to 70 days of age, respectively, 295 to 305 g/ day for singletons; from 301 to 309 g/day for twins and from 288 to 315 g/day for triplets and more lambs. The average fertility of ewes at first birth is 1.5 lambs per ewe, and the fertility rate for a total of 180 ewes is 91%.

The impact of genetic variants related to the fatty acid metabolic process pathway on milk production traits in Jersey cows

The synthesis of fatty acids plays a critical role in shaping milk production characteristics in dairy cattle. Thus, identifying effective haplotypes within the fatty acid metabolism pathway will provide novel and robust insights into the genetics of dairy cattle. This study aimed to comprehensively examine the individual and combined impacts of fundamental genes within the fatty acid metabolic process pathway in Jersey cows. A comprehensive phenotypic dataset was compiled, considering milk production traits, to summarize a cow’s productivity across three lactations. Genotyping was conducted through PCR-RFLP and Sanger sequencing, while the association between genotype and phenotype was quantified using linear mixed models. Moderate biodiversity and abundant variation suitable for haplotype analysis were observed across all examined markers. The individual effects of the FABP3, LTF and ANXA9 genes significantly influenced both milk yield and milk fat production. Additionally, this study reveals novel two-way interactions between genes in the fatty acid metabolism pathway that directly affect milk fat properties. Notably, we identified that the GGAAGG haplotype in FABP3×LTF×ANXA9 interaction may be a robust genetic marker concerning both milk fat yield and percentage. Consequently, the genotype combinations highlighted in this study serve as novel and efficient markers for assessing the fat content in cow’s milk.

Nutritional Composition and Productivity of Panicum maximum cv. “Mombasa” Under Different Levels of Nitrogen Fertilization and Water Deficit

This study investigates the production and nutritional quality of Panicum maximum cv. Mombasa grass under varying levels of water stress and nitrogen (N) fertilization, aiming to enhance forage production in harsh environments. Four irrigation levels (5760, 6912, 4608, and 3456 m3 ha−1 year−1) and three N fertilizer doses (115, 57.5, and 0 kg ha−1 year−1) were tested. The results indicate that Mombasa grass produced higher fresh and dry weights under higher irrigation levels (I1 and I2) compared to water deficit conditions across all cuts. Interestingly, under moderate water stress (I3), the dry weight was not significantly different from that under higher irrigation for the sixth harvest in the first season. Water deficit conditions led to a significant reduction in protein content across all treatments. However, under lower irrigation levels (I3 and I4), there was a significant increase in phosphorus (P), potassium (K₊), iron (Fe2₊), and zinc (Zn) concentrations. A heatmap analysis of shape descriptors grouped the productivity and nutritional traits into two clusters based on their response to combined fertilization and drought stress. This analysis revealed that the dry weight, number of leaves, and Fe and Zn contents were positively affected under moderate water stress (80% of control; 4608 m3 ha−1 year−1) with recommended N fertilization. The study concludes that Panicum maximum cv. Mombasa is tolerant to moderate water stress and is suitable for forage production in the Qassim region, Saudi Arabia.

Genetic variation of HPA axis activity in farm animals and beyond.

Many experimental data in several species clearly demonstrate the important genetic contribution to variations in HPA axis activity. The influence of corticosteroid hormones on adaptive processes and on production traits such as growth rate, feed efficiency, carcass composition and meat quality is a strong impetus to the search for the molecular bases of these differences for efficient genetic selection. Three main sources of genetic variability have been documented so far in farm animal species, the adrenal cortex sensitivity to ACTH regulating corticosteroid hormone production, the bioavailability of corticosteroid hormones and especially corticosteroid-binding globulin capacity, and glucocorticoid receptor function. The effect of single mutations may be dependent on the genetic background and genetic variation of cortisol levels may have different functional consequences depending on the molecular mechanisms responsible for this change. Understanding the genetic basis of HPA axis activity allows the development of genomic tools and breeding technologies aimed at improving adaptive capacity and stress tolerance in farm animals and their use as valuable models for the genetic study of the HPA axis and the correlation with adaptation, metabolism and other functions regulated by adrenal hormones, and associated pathologies (obesity, cardiovascular, etc.). The next step will be to explore HPA axis variability from a system genetics perspective including the multiple sources of variation and their interactions. This multifactorial approach is a prerequisite to the use of the HPA axis phenotypes in the genetic selection for more productive and robust animals, with a high level of production of quality products.

Estimates of Heritability, Repeatability and Correlation of Some Productive and Reproductive Traits of Holstein Cows in Egypt

Estimates of Heritability, Repeatability and Correlation of Some Productive and Reproductive Traits of Holstein Cows in Egypt

Association of Microsatellite Markers on Chromosome Seven with Milk Production and Fertility Traits in Egyptian Buffalo

Association of Microsatellite Markers on Chromosome Seven with Milk Production and Fertility Traits in Egyptian Buffalo

A PLIN1 polymorphism is associated with fat production in male emus

The emu (Dromaius novaehollandiae) is a novel poultry species that produces meat, eggs, and fat. Although emus have recently been domesticated, genetic improvements to establish strains have scarcely progressed. In this study, we investigated the relationship between production traits and perilipin 1-encoding gene (PLIN1) polymorphisms in the emus. We determined the partial complementary DNA (cDNA) sequence of the PLIN1, which is involved in lipid droplet formation. We identified four nucleotide substitution sites (c.270C>T, c.321T>C, c.587A>T, and c.639C>T) in the PLIN1 gene of emus. Of these, c.587A>T is a non-synonymous substitution that converts lysine to methionine at the 196th codon (p.K196M). Although p.K196M was predicted to affect the production traits of emus, a large deflection in genotype frequency was observed in this study; thus, we could not investigate the relationship between genotypes and phenotypes. In males, the fat yields of the CC, CT, and TT genotypes in c.270C>T were 0.25 ± 0.06, 0.22 ± 0.06, and 0.21 ± 0.07 kg, respectively, while the meat yields of the CC, CT, and TT genotypes in c.270C>T were 0.15 ± 0.01, 0.16 ± 0.02, and 0.16 ± 0.03 kg, respectively. These results indicate that male emus with the CC genotype had a significantly higher fat content and lower meat productivity than male emus with the other genotypes (P < 0.05). Therefore, c.270C>T in PLIN1 affects fat and meat production in males. Our findings may contribute to the effective genetic improvement of the emus.

Genotypic adaptation to soil water deficit in rice - a comparison of desirable traits for aerobic production and lowland drought resistance

Genotypic adaptation to soil water deficit in rice - a comparison of desirable traits for aerobic production and lowland drought resistance

The Bisulphite-Sequencing PCR for the Bovine Gstp1, Gsta4, and Ache Gene Methylation Study

Abstract Modifying cytosine by adding a methyl group in CpG dinucleotides within DNA sequence has several functions, but acts primarily as an important regulatory mechanism of mammalian gene expression. This consequently affects the phenotypic characteristics of the organism. The methylation profiles can be altered as a consequence of various environmental influences, age, disease, or diet, and can serve as biomarkers of important production and health traits. In this regard, the methylation profile analysis techniques are important. In the present study, we proposed and tested specific oligonucleotide primers for the bisulphite-sequencing polymerase chain reaction (BSP) analysis of the bovine GSTP1, GSTA4, and AChE genes, to optimize this approach for future studies of the methylation status of these genes. BSP can be used, for example, to study the effect of different pesticides and their combinations on the methylation of these and other bovine genes.

Association of CXCR1 Gene Polymorphism With Clinical Mastitis and Performance Traits in Murrah Buffalo.

This study revealed the presence of single nucleotide polymorphisms in the CXCR1 gene and their association with performance traits and mastitis incidence in Murrah buffalo. The targeted SNP rs211042414 (T > C) at the g.106216468 locus in partial exon 2 of the CXCR1 gene was genotyped using PCR amplification and restriction enzyme digestion by Alu I, Bsa I, Dde I, Ava I, Hind III, EcoRV, Hae III, and Hae II restriction enzymes. The genotypic frequencies revealed three genotypes: CC, CT, and TT, with the C allele being the most prevalent (0.79) compared to the T allele (0.21). Targeted SNP showed significant association with the incidence of clinical mastitis incidence, and the study revealed that the TT genotyped animals showed a higher incidence of clinical mastitis compared to the TT and CT genotyped animals in the targeted population. Furthermore, least squares analysis revealed that targeted performance traits, viz. 305 days milk yield, total milk yield, and lactation length, were significantly associated with the genetic variants of the CXCR1 gene. TT genotyped animals exhibited higher milk yield than CT and CC genotyped animals, indicating a positive association between the T allele and increased milk production. These findings revealed that there is a scope for the genetic improvement of Murrah buffalo. Incorporating the identified CXCR1 gene polymorphisms into existing selection criteria can help to improve disease resistance and milk production traits in Murrah buffalo. However, further validation with a larger sample size is necessary to strengthen the observed associations and ensure their practical applicability.

Genetic parameters for milk production traits of Simmental cows with random regression test-day model

Genetic parameters for milk production traits of Simmental cows with random regression test-day model

Determination of growth potentials of two chicken strains using day old phenotypic markers

This study focused on assessing one day old effect of some phenotypic markers on production traits in Ross broiler chickens (ROBROS) and Southern ecotype breeds of chicken (SEC) as an alternative for genetic markers. The study was conducted at the Akenten Appiah Menka University of Skills Training and Entrepreneurial Development (AAMUSTED) Animal farm unit in Asante Mampong Campus of Ghana from June to December, 2022. One hundred and eighty (180) Ross broiler and 180 Southern ecotype breeds of chicks were used for the research. For each breed, the chicks were put into four groups with 45 chicks in each group. Breast length (BRL), Back length (BL), Circumference of the head (CH) and day-old body weight (DOBW) were taken on the chicks at one day old in group 1, 2, 3, and 4 respectively using a tailor’s tape and a weighing scale. Chicks within each group were classified into three (3) sub groups and considered as treatments (T) 1, 2 and 3. The treatments were described as higher (T1), medium (T2), and lower (T3) ranges based on the values obtained from the measurement and reared under randomised completely block design (RCBD). Data on production traits were taken up to week 8 for the Ross broiler and 18 weeks for the Southern ecotype chicken. The results from ANOVA using Statistix indicated that for the Ross broiler chickens, T1 in all the groups were significantly (P &lt; 0.05) superior over T3 for feed intake, body weight, body weight gain and feed conversion ratio. T2 were significantly better than T3 in terms of body weight. For the Southern ecotype chickens, T1 were significantly (P &lt; 0.05) better than T3 for feed intake, body weight, and body weight gain. However, for feed intake and body weight gain, T2 were significantly (P &lt; 0.05) better than T3. Pearson correlation analysis also indicated a high, strong and significant (P &lt; 0.05) correlation between day-old phenotypic markers with body weight. Regression equations of day-old phenotypic markers with body weight were positive and significant (P &lt; 0.05) with coefficient of determination (R2) ranging from 0.64 to 0.76 for Ross broilers and 0.81 to 0.95 for Southern ecotype chickens. CH and DOBW had the highest R2 values and thus the best predictors of body weight. Breast length, back length, circumference of the head, and day-old body weight taken on the chicks at one day old were effective in predicting final body weight. It was concluded that, the four (4) phenotypic markers could be used for selection purposes efficiently.

Adaptive capacity and ecological stability of some bean varieties in the conditions of the western forest-steppe of the Priobie region

Relevance. Crop productivity is determined by genotype, environmental effects and their interactions. Comprehensive evaluation of crop varieties based on their adaptability, plasticity and stability makes it possible to select the most promising varieties, high-yielding and adapted to many environmental conditions to improve productivity.Materials and Methods. Fourteen common bean varieties were tested in a randomized complete block design with three replications during two years (2022 and 2023) in the experimental field “Michurintsev Garden” of Novosibirsk State Agrarian University. Productivity traits were taken into account: number and weight of beans per plant, weight of 1000 seeds, yield. The purpose of the work was to evaluate bean samples for adaptive capacity and ecological stability in the conditions of the forest-steppe Priobie.Results. The article provides an assessment of the adaptability and stability of bean varieties in order to identify varieties with high productivity and adapted to climatic and farming conditions in the Siberian region. The results of the tests showed that the highest average net yields of Rubin, Krasnopestraya, Zolotistaya and Muhranula varieties were in the range of 0.41-0.64 kg/m2. Analysis of genotype-environment interaction (GxE) according to the mathematical model of Eberhart and Russel shows that varieties Rubin, Krasnopestraya, Zolotistaya and Muhranula have high indices of general adaptability and breeding value of genotype, Among them, varieties Rubin and Zolotistaya have stable productivity and high adaptability to environmental conditions.

Additive and Non-additive Genetic Effects on Growth and Egg Production Performance of Crossbred Chicken in Ethiopia

The present review article aims to provide an overview of the additive and non-additive genetic effects of crossbreeding and their contribution to the improvement of growth and egg production traits in chickens. It discusses the advancement in crossbreeding effects and mating design contribution to a significant rate of genetic progress in indigenous chicken. In Ethiopia, crossbreeding practice may be used to enhance the performance of local chicken ecotypes. The article extensively reviews various papers related to crossbreeding trials conducted in Ethiopia, evaluating their effectiveness in improving growth and egg production. It discusses the mating design and breeds used in these programs, such as exotic breeds like Rhode Island Red, Fayoumi, White Leghorn, Koekoek, Sasso, Kuroiler, and local Ethiopian chicken ecotypes. Among the exotic breeds involved in crossbreeding, Rhode Island Red and Sasso are considered more favorable for improving growth rate and color preference, while White Leghorn is preferred for enhancing egg production traits. In opposite to these indigenous chickens are preferred for disease resistance and product quality. Additive genetic effects are typically responsible for the genetic improvement of traits over generations through selection. In egg production, additive genetic effects influence the overall capacity of a chicken to lay eggs, affecting traits like egg number and egg size. Whereas, In growth performance, additive genetic effects influence traits like body weight gain, feed conversion efficiency, and overall growth rate. Non-additive genetic effects include dominance and epistatic interactions between genes. These effects can lead to genetic heterogeneity and can impact traits like egg production and growth performance besides playing a role in hybrid vigor or heterosis. In conclusion, both additive and non-additive genetic effects play a crucial role in determining egg production and growth performance in chickens. Additive effects drive genetic improvement over generations, while non-additive effects provide immediate benefits like hybrid vigor. Understanding and utilizing both types of genetic effects is essential for enhancing these traits in poultry breeding programs. Chicken crossbreeding programs are highly important in the poultry industry as they continuously improve the genetic potential of chickens, leading to more efficient production systems and higher profitability for producers.

Genomic Diversity of U.S. Katahdin Hair Sheep.

In the late 1950s, Katahdin hair sheep were developed as a composite breed of medium size and moderate prolificacy, with potential to express resistance to gastrointestinal nematodes. With increasing popularity and the recent adoption of genomic prediction in their genetic evaluation, there is a risk of decreasing variation with selection based on genomically enhanced estimated breeding values. While Katahdin pedigrees are readily available for monitoring diversity, they may not capture the entirety of genetic relationships. We aimed to characterise the genomic population structure and diversity present in the breed, and how these impact the size of a reference population necessary to achieve accurate genomic predictions. Genotypes of Katahdin sheep from 81 member flocks in the National Sheep Improvement Program (NSIP) were used. After quality control, there were 9704 animals and 31,984 autosomal single nucleotide polymorphisms analysed. Population structure was minimal as a single ancestral population explained 99.9% of the genetic variation among animals. The current Ne was estimated to be 150, and despite differences in trait heritabilities, the effect of Ne on the accuracy of genomic predictions suggested the breed should aim for a reference population size of 15,000 individuals. The average degree of inbreeding estimated from runs of homozygosity (ROH) was 16.6% ± 4.7. Four genomic regions of interest, previously associated with production traits, contained ROH shared among > 50% of the breed. Based on four additional methods, average genomic inbreeding coefficients ranged from 0.011 to 0.012. The current population structure and diversity of the breed reflects genetic connectedness across flocks due to the sharing of animals. Shared regions of ROH should be further explored for incorporation of functional effects into genomic predictions to increase selection gains. Negative impacts on genetic diversity due to genomic selection are not of immediate concern for Katahdin sheep engaged in NSIP.

DUS testing characteristics relation with agro-morphological and quality traits of winter wheat

In a field trial, a database of qualitative traits associated with agromorphological and quality traits of winter wheat (Triticum aestivum L.) has been collected. The present study aimed to determine the relationships between the winter wheat traits of productivity and quality with traits of Distinctness, Uniformity and Stability (DUS) testing. In addition, according to grain yield and significantly correlated traits, investigated genotypes will be clustered. Grain yield was significantly positively correlated with the number of days to heading, time of ear emergence, and plant growth habit. Based on the grouping of the winter wheat genotypes using the Euclidean distance algorithm, wheat genotypes were separated into five main clusters according to the similarity of those four traits. The grouping pattern was very origin homogeneous in each group, and the grouping pattern of genotypes appeared to be associated. The highest contributor to a grouping of genotypes was grain yield. The established result pertain to the potential for increasing the grain yield of winter wheat.