Association between dry period length and lactation performance, lactation curve, calf birth weight, and dystocia in Holstein dairy cows in Iran.

peer reviewedIn this study, 65,971 lactations on 41,842 cows in 64 herds were used to determine the association between dry period length (DPL) and lactation performance, lactation curve, calf birth weight, and the incidence of calving difficulty during the subsequent parity in Holstein dairy cows in Iran. The length of the dry period was classified into 7 categories: 0 to 35d, 36 to 50d, 51 to 60d, 61 to 70d, 71 to 85d, 86 to 110d, and 111 to 160d. Cows with the standard DPL (51 to 60d) produced more 305-d milk, fat, and protein over the next lactation compared with those with shorter dry periods. Shorter dry periods (0 to 35d and 36 to 50d) were associated with lower initial milk yield, steeper inclining and declining slopes of the lactation curve, and higher milk persistency compared with dry period length of 51 to 60d. Peak lactation was achieved later in cows with 0- to 35-d and 36- to 50-d dry period length than in those with dry period length of 51 to 60d. We also observed a relationship between DPL and calf birth weight: smaller calf birth weight was recorded with a dry period of 51 to 60d compared with longer dry periods. The incidence of calving difficulty did not differ in cows with 51- to 60-d dry period compared with cows with 0- to 35-d and 36- to 50-d dry periods. In conclusion, the results of this study did not support previous findings that suggested a shorter dry period could be beneficial to dairy production

Genetic relationship of conformation traits with average somatic cell score at 150 and 305 days in milk in Holstein cows of Iran.

peer reviewedGenetic, environmental, and phenotypic correlations among average somatic cell score (SCS) at different stages of lactation and conformation traits were estimated. Data consisted of the lactational average of SCS at 150 (SCS(150)) and 305 (SCS(305)) d in milk and 19 conformation traits recorded on 57,154 primiparous Holstein cows, that calved from 1996 to 2009 in 119 herds in Iran. Variance components were estimated using the restricted maximum likelihood procedure based on multiple-trait animal models. Udder depth (-0.32), fore udder attachment (-0.22), and udder width (0.34) showed moderate genetic correlation with SCS(150). Heart girth (0.17), body depth (0.14), chest width (0.26), and angularity (0.19), showed modest genetic correlation with SCS(150). The estimated heritabilities for SCS(150) and SCS(305) were 0.06 and 0.08, respectively. The heritability of the conformation traits ranged from 0.09 to 0.29. Genetic and environmental correlations between SCS(150) and SCS(305) were very high (means ± SE; 0.99±0.01 and 0.89±0.01, respectively), which indicates that recording SCS over a shorter period of lactation is an alternative approach for involving many herds in SCS data collection. The low heritability of SCS indicated that indirect selection for some of udder and body traits might be helpful to reduce the SCS. Additionally, selection for udder traits may help reduce SCS in developing countries where SCS data are sparsely recorded

Three-dimensional and two-dimensional relationships of gangliogenesis with folliculogenesis in mature mouse ovary: a Golgi–Cox staining approach

The present study was set out to investigate two-dimensional (2D) and three-dimensional (3D) evaluations of ovarian nervous network development and the structural relationship between folliculogenesis and gangliogenesis in mouse ovaries. Adult mice ovarian tissue samples were collected from follicular and luteal phases after cardiac perfusion. Ovarian samples were stained by a Golgi–Cox protocol. Following staining, tissues were serially sectioned for imaging. Neural filaments and ganglia were present in the ovaries. In both 2D and 3D studies, an increase in the number and area of ganglia was seen during the follicular growth. The same pattern was also seen in corpora lutea development. However, in some cases such as ratio of ganglia number to follicle area, the ratio of ganglia area to follicular area, 2D findings were different compared with the 3D results. 3D analysis of ovarian gangliogenesis showed the possible direct effect of them on folliculogenesis. Golgi–Cox staining was used in this study for 3D evaluation in non-brain tissue. The results of 3D analysis of the present study showed that, in some cases, the information provided by 2D analysis does not match the reality of ovarian neuronal function. This confirmed the importance of 3D analysis for evaluation of ovarian functio

Genomic analysis reveals variant association with high altitude adaptation in native chickens

Native chickens are endangered genetic resources that are kept by farmers for different purposes. Native chickens distributed in a wide range of altitudes, have developed adaptive mechanisms to deal with hypoxia. For the first time, we report variants associated with high-altitude adaptation in Iranian native chickens by whole genome sequencing of lowland and highland chickens. We found that these adaptive variants are involved in DNA repair, organs development, immune response and histone binding. Amazingly, signature selection analysis demonstrated that differential variants are adaptive in response to hypoxia and are not due to other evolutionary pressures. Cellular component analysis of variants showed that mitochondrion is the most important organelle for hypoxia adaptation. A total of 50 variants was detected in mtDNA for highland and lowland chickens. High-altitude associated with variant discovery highlighted the importance of COX3, a gene involved in cell respiration, in hypoxia adaptation. The results of study suggest that MIR6644-2 is involved in hypoxia and high-altitude adaptations by regulation of embryo development. Finally, 3877 novel SNVs including the mtDNA ones, were submitted to EBI (PRJEB24944). Whole-genome sequencing and variant discovery of native chickens provided novel insights about adaptation mechanisms and highlights the importance of valuable genomic variants in chickens

Using an incomplete gamma function to quantify the effect of dystocia on the lactation performance of Holstein dairy cows in Iran.

peer reviewedThe aim of the present study was to estimate the effect of dystocia on lactation performance, using an incomplete gamma function. Data from March 2000 to April 2009 comprising 100,628 lactations of 65,421 cows in 204 dairy herds collected by the Animal Breeding Center of Iran were used. Of 100,628 births, 91.8% required no assistance, whereas 8.2% required assistance of some sort. Factors associated with the presence of dystocia were calving season, calving year, herd, calf sex, parity, and age of dam. Peak yield for primiparous cows with dystocia at calving occurred on d 87.2 [standard error (SE) 0.47], and for primiparous cows with easy calving, the peak of lactation was on d 83.3 (0.25). Peak yield was lowered by 0.39 (SE 0.07), 2.20 (SE 0.15), 2.22 (SE 0.21), and 2.54 (SE 0.32) kg for cows with incidence of dystocia compared with normal cows in parity 1 to 4, respectively. Dystocia was associated with decreased 305-d lactation performance in all parities, mostly in early lactation. Although more difficult births occurred in heifer calvings, loss in lactation performance was greater in second or later lactations following a difficult birth

Whole genome re-sequencing reveals adaptation prior to the divergence of buffalo subspecies

The application of high-throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic diversity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran, and Khuzestan provinces, were resequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2× per sample. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain, and 159 stop-loss mutations that might have functional consequences. Genomic diversity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20, and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using resequencing data from other five bovine species as well as the Axiom Buffalo Genotyping Array 90K data of river and swamp buffaloes indicated that these fixation signals persisted across river and swamp buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes

Genetic relationship of conformation traits with average somatic cell score at 150 and 305 days in milk in Holstein cows of Iran

peer reviewedGenetic, environmental, and phenotypic correlations among average somatic cell score (SCS) at different stages of lactation and conformation traits were estimated. Data consisted of the lactational average of SCS at 150 (SCS(150)) and 305 (SCS(305)) d in milk and 19 conformation traits recorded on 57,154 primiparous Holstein cows, that calved from 1996 to 2009 in 119 herds in Iran. Variance components were estimated using the restricted maximum likelihood procedure based on multiple-trait animal models. Udder depth (-0.32), fore udder attachment (-0.22), and udder width (0.34) showed moderate genetic correlation with SCS(150). Heart girth (0.17), body depth (0.14), chest width (0.26), and angularity (0.19), showed modest genetic correlation with SCS(150). The estimated heritabilities for SCS(150) and SCS(305) were 0.06 and 0.08, respectively. The heritability of the conformation traits ranged from 0.09 to 0.29. Genetic and environmental correlations between SCS(150) and SCS(305) were very high (means ± SE; 0.99±0.01 and 0.89±0.01, respectively), which indicates that recording SCS over a shorter period of lactation is an alternative approach for involving many herds in SCS data collection. The low heritability of SCS indicated that indirect selection for some of udder and body traits might be helpful to reduce the SCS. Additionally, selection for udder traits may help reduce SCS in developing countries where SCS data are sparsely recorded