In goats, the influence of microRNAs on the post-transcriptional regulation of genes involved in mammary development and remodeling and milk secretion has not been fully elucidated yet. In this study, we have obtained mammary biopsies from five lactating and four dry Murciano-Granadina goats and, subsequently, small RNA has been purified and sequenced, obtaining, on average, 11 million reads per sample with an 85% alignment rate. Bioinformatic analysis of the sequencing data revealed the expression of 342 unique microRNAs in the goat mammary gland, among which 32 were novel miRNAs. Moreover, we have determined that as many as 93 mature microRNAs are differentially expressed (fold-change ≥ 2.7, q-value = 0.05) in lactating vs. dry goats. Of these, 49 and 44 were upregulated and downregulated in lactating goats, respectively, including 13 novel miRNAs. For each one of these differentially expressed miRNAs, we have made a search of scientific literature to find out whether their functional role in lactation has been elucidated, and, if so, we have contrasted the expected (based on function) vs. the observed (inferred from the differential expression analysis) change in gene expression to determine their degree of concordance. About 82% of the miRNAs with functional information that were differentially expressed in lactating vs. dry goats showed concordance between the observed and expected directions of the change in gene expression. By integrating differential expression analysis and functional data generated by others, we have identified a set of 17 miRNAs with converging evidence of being involved in the physiological transformations associated with lactation and mammary involution.

This online survey aimed to gather consumer opinions on dairy products and production and to identify the potential market for A2 milk (milk containing exclusively β-casein A2, which reduces gastrointestinal discomfort after consumption). The questionnaire included seven sections covering the consumption of dairy products, sociodemographic aspects, awareness and purchase intention of A2 milk, questions about milk as a source of nutrients and health benefits, the environmental impact of milk production, and alternatives to cow milk. Responses from 672 Spanish consumers categorized into clusters (according to their milk consumption and their discomfort after drinking it), gender, age, educational level, and milk taste preference were analyzed using a linear multiple regression model. Dairy consumers not experiencing discomfort after drinking milk (62.6%) and those who preferred the taste of milk over plant-based alternatives (64.0%) demonstrated better knowledge of milk nutrients and its health benefits. Participants’ age, gender, and education level also influenced their perceptions, with older participants, women, and those with university education generally showing better results. In conclusion, clusters impact consumers’ milk perceptions as a nutritional source and its health benefits. The positive perception of milk’s nutritional benefits among dairy consumers experiencing discomfort after drinking milk (17.3%) positions them as a strong target market for A2 milk.

Grazing is a natural behaviour of ruminants and when access to pasture is deprivated, a behavioural frustration appears, which can lead to chronic stress. In sheep, no response of stress biomarkers like cortisol has been studied in permanent housed ewes. In the present study, two groups of twenty pregnant Ripollesa ewes were used in a 10-week experiment. The 5h-grazing group (5h-G), had access to pasture five hours daily, and the housed group (H) had no access to pasture and remained permanently in the barn. Hair samples were collected on Weeks 5 and 10 of grazing deprivation (W5, W10), and saliva samples on Weeks 0, 3, 5, 8 and 10 (W0, W3, W5, W8, W10). No significant differences in hair cortisol (HC) or saliva cortisol (SC) were observed between Groups 5h-G and H throughout the study period (P > 0.05). However, significant differences were observed in ewes carrying one or two lambs (PROL1 HC=4.97+0.1, PROL2 HC=7.20+0.1, P < 0.05). No evidence of chronic stress could be detected through cortisol levels in hair and saliva although abnormal behaviours appeared in previous results published from the same experience. Saliva cortisol showed a significant variability over time and it should be used in a combination with other biomarkers. Further research is needed to analyse pregnancy effect, longer periods of grazing deprivation, and the use of wool samples or other body regions.

Milk yield and composition phenotypes are systematically recorded across several lactations in goats, but the majority of genome-wide association studies (GWAS) performed so far have rather ignored the longitudinal nature of such data. Here, we have used two different GWAS approaches to analyse data from three lactations recorded in Murciano-Granadina goats. In Analysis 1, independent GWAS have been carried out for each trait and lactation, while a single longitudinal GWAS, jointly considering all data, has been performed in Analysis 2. In both analyses, genome-wide significant QTL for lactose percentage on chromosome 2 (129.77-131.01 Mb) and for milk protein percentage on the chromosome 6 (74.8-94.6 Mb) casein gene cluster region were detected. In Analysis 1, several QTL were not replicated in all three lactations, possibly due to the existence of lactation-specific genetic determinants. In Analysis 2, we identified several genome-wide significant QTL related to milk yield and protein content that were not uncovered in Analysis 1. The increased number of QTL identified in Analysis 2 suggests that the longitudinal GWAS is particularly well suited for the genetic analysis of dairy traits. Moreover, our data confirm that variability within or close to the casein complex is the main genetic determinant of milk protein percentage in Murciano-Granadina goats.

Sheep production systems are diverse in Europe, and welfare assessment should consider this diversity, including differences in breed type, climatic conditions, and time of the year. The aim of this study was to evaluate welfare in 100 commercial sheep farms in Spain, and therefore in Mediterranean conditions, using a list of 24 indicators, comprising three for good feeding, five for housing, 11 for health, and five for appropriate behavior. The list includes indicators from the AWIN protocol and other suggested indicators. Level of intensification was the main parameter that affected the welfare outcomes of feeding and health, but seasonality and flock size also affected some of the outcomes. Novel indicators included in the list (sternum evaluation, crowding behavior, subcutaneous abscesses, external parasitism, aggressive behaviors, wool pulling, ear posture, and reaction during restraint) were useful to evaluate welfare in Spanish farming conditions, but further studies should be performed to validate these indicators.

Shearing dairy ewes may improve their fitness and heat tolerance during late pregnancy, with positive effects on lambs and lactation performances. To test this hypothesis, two Mediterranean breeds (MN, Manchega, n = 43; LC, Lacaune, n = 28), differing in lactation performances and fleece traits, were submitted to three shearing strategies: (i) shorn before breeding (SBB), (ii) shorn at day 100 of pregnancy (S100) and (iii) unshorn (CO). Ewes were bred in spring and gestated during summer. Fleece traits and respiratory rate were measured on pregnant (107–121 days) resting ewes at different barn temperatures. Blood and colostrum were sampled at lambing. Ewes suckled their lambs (28 days) and were machine-milked until 180 days of lactation. Lamb and ewe weights, and condition score of the ewes, were recorded throughout the experiment. Milk yield was assessed during suckling (fortnightly) and milking (daily), and milk was sampled for composition (fortnightly). Fleece extension and wool weight at S100 were 13 and 45% greater in MN than in LC ewes, respectively, but the ewe’s respiration rate at late pregnancy, between 20 and 25 °C, did not vary among shearing treatments nor breeds. Nevertheless, S100 ewes had a 37% lower respiration rate than SBB and CO ewes at 28 °C. At lambing, SBB and S100 ewes had 86% higher glycaemia than CO in MN, but LC ewes did not vary. Shearing treatment had no effect in plasma insulin, β-hydroxybutyrate or non-esterified fatty acids (NEFAs) at lambing in both breeds. Lamb’s birthweight and growth during suckling did not differ by shearing treatment in both breeds. Colostrum composition and milk yield during suckling were not modified by shearing treatment in either breed, although S100 suckling milk composition increased in MN (protein and casein, 6%) and LC ewes (total solids, 8%; fat, 18%), compared to CO and SBB. No effects were detected in milk yield or composition during milking, but S100 tended to yield 28% more milk than CO in the LC ewes. The S100 treatment improved the body reserves in late pregnancy, when compared to CO and SBB in both breeds. In conclusion, shearing dairy ewes in late pregnancy was a recommendable management practice under summer conditions, because alleviated heat stress and improved the weight of the ewes, without detrimental effects on lambing and lactational performances, the last tending to increase milk yield in high-yielding dairy ewes.

Sheep flocks can be reared in different production systems that differ in the duration of indoor housing and grazing restriction. Indoor housing can lead to aggressive interactions, such as blocking, threats and butts, whereas grazing restriction may cause wool-pulling. Wool-pulling is an abnormal behaviour that appears in confined flocks and affects the wool condition of affected animals. Wool condition has been included in some sheep welfare assessment protocols, but in most cases the causes of wool alteration are not addressed. Therefore, it would be useful to establish whether changes in wool condition may be attributable to wool-pulling behaviour. The aim of this study was to find out the effect of grazing restriction on the prevalence of wool-pulling behaviour, assessing wool cover as an indicator of this behaviour, and to analyse the effect of grazing restriction on the prevalence of aggressive behaviours. Two groups of twenty Ripollesa pregnant ewes were used, a temporary grazing group (G) and a permanently housed group (H). Group G had access to pasture daily from 10:00 h to 15:00 h, while Group H remained in the barn throughout the experimental period (10 weeks). The behaviour of all sheep was video-recorded along a ten-week period, two days per week 45 minutes each day, and an ethogram that included wool-pulling, aggressive behaviours, resting and rumination was developed and used. Wool-pulling was observed exclusively in Group H. On the other hand, a four-scale score of wool cover was used to assess wool pulling behaviour, and the score evolved significantly different in both groups. In Group G, no change in wool-cover was observed whereas in Group H, wool-cover change was observed in eleven out of twenty ewes throughout the experimental period. A positive correlation was found (R=0.98, P=0.01) between wool pulling observed by direct observation and wool-cover assessment, and it was concluded that wool cover is a potentially useful indicator of wool-pulling behaviour. The frequency of aggressive behaviours was higher in Group H than in Group G during the entire experimental period (35 ewes vs. 11, P=0.04), which suggests that it was caused by grazing restriction.

Additional file 9: Table S7. Inbreeding depression estimates (s.e: standard error) for the natural logarithm of the somatic cell count divided by 1000 (lnSCC) in specific regions of goat chromosomes (CHI) 8 and 25 and their 95% confidence intervals (C.I).

Additional file 13: Table S11. Inbreeding depression estimates (s.e: standard error) for milk yield at 210, 240 and 305 days (MY210, MY240 and MY305, measured in kg) in specific regions of goat chromosomes (CHI) 2 and their 95% confidence intervals (C.I).

A total of 72 dairy ewes of 2 breeds (MN, Manchega, 72.4 ± 1.9 kg of body weight, n = 36; LC, Lacaune, 77.7 ± 2.3 kg of body weight; n = 36) were used to evaluate the lactational effects of melatonin implants in early lactation and under the short-day photoperiod conditions of autumn (experiment was centered on the winter solstice). Ewes lambed in autumn and were penned indoors in 12 balanced groups of 6 ewes by breed, body weight, age, and number of lambs, and randomly assigned to a 2 × 2 × 3 factorial design (treatment × breed × replicate). Ewes suckled their lambs for 28 d. Treatments were (1) melatonin (MEL), which received 1 subcutaneous implant of melatonin (18 mg/ewe) in the ear base at 35 ± 1 d (1 wk after lamb weaning), and (2) control, which did not receive any treatment. Ewes were fed ad libitum a total mixed ration (forage:concentrate, 60:40) and machine milked twice daily. Daily milk yield was automatically recorded from d 29 to 105 of lactation and sampled every 2 wk for composition. Jugular blood was sampled for plasma hormone analyses at 30, 50, 80, 110, and 124 d of lactation. Body reserves were assessed every 2 wk. Feed intake was measured by pen during 3 separated periods after the start of the treatments (wk 2 to 3, wk 6 to 7, and wk 10 to 11). Feed intake, and milk yield and composition varied by breed, but no MEL effects were detected on dry matter intake, milk yield, milk composition, or fat and protein standardized milk in either breed. As a result of the unique composition of the implants and the variable body weights of the ewes, the MEL treatment dose (on average, 0.24 mg/kg of body weight) was 6.8% greater in the MN (lighter) than in the LC (heavier) ewes. Plasmatic melatonin markedly increased in the MEL-treated ewes (on average, 111%), but despite the amount of MEL used, the MN responded greatly compared with the LC ewes (150 vs. 63%, respectively). No differences in basal plasmatic melatonin were detected between breeds (6.4 ± 1.1 pg/mL, on average), indicating the greater responsiveness to the implants of the lighter MN ewes. Plasmatic prolactin tended to decrease in the MEL-treated ewes (-35%, on average), but the effect was significant only in the MN ewes (-54%), in agreement with their greater response to MEL. No effects of MEL treatment were detected on plasmatic IGF-I in either breed. Moreover, body reserves did not vary by effect of MEL treatment or breed throughout the experiment. In conclusion, the use of exogenous melatonin as MEL implants, together with the endogenous melatonin naturally produced under short-day photoperiod conditions, had no effects on the early-lactation performances of dairy sheep, despite their breed and level of production.

Additional file 14: Table S12. Genes mapping to goat chromosome (CHI) 2: 22–68 Mb region associated with inbreeding depression for milk yield at 210, 240 and 305 days (MY210, MY240 and MY305).

Background Inbreeding depression can adversely affect traits related to fitness, reproduction and productive performance. Although current research suggests that inbreeding levels are generally low in most goat breeds, the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data. Results We genotyped 1040 goats with the Goat SNP50 BeadChip. This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns. We detected 38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1, 2, 4, 6, 14, 16 and 17. Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes. Four regions on chromosomes 8 and 25 were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count. Notably, these regions contain several genes related with immunity, such as SYK , IL27 , CCL19 and CCL21 . Moreover, one region on chromosome 2 was significantly associated with inbreeding depression for milk yield. Conclusions Although genomic inbreeding levels are low in Murciano-Granadina goats, significant evidence of inbreeding depression for the logarithm of the somatic cell count, a phenotype closely associated with udder health and milk yield, have been detected in this population. Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis, which is one of the main causes of dairy goat culling.

SUMMARYTransmission ratio distortion (TRD) is the preferential transmission of one specific allele to offspring at the expense of the other one. The existence of TRD is mostly explained by the segregation of genetic variants with deleterious effects on the developmental processes that go from the formation of gametes to fecundation and birth. A few years ago, a statistical methodology was implemented in order to detect TRD signals on a genome-wide scale as a first step to uncover the biological basis of TRD and reproductive success in domestic species. In the current work, we have analyzed the impact of SNP calling quality on the detection of TRD signals in a population of Murciano-Granadina goats. Seventeen bucks and their offspring (N=288) were typed with the Goat SNP50 BeadChip, while the genotypes of the dams were lacking. Performance of a genome-wide scan revealed the existence of 36 SNPs showing significant evidence of TRD. When we calculated GenTrain scores for each one of the SNPs, we observed that 25 SNPs showed scores below 0.8. The allele frequencies of these SNPs in the offspring were not correlated with the allele frequencies estimated in the dams with statistical methods, thus evidencing that flawed SNP calling quality might lead to the detection of spurious TRD signals. We conclude that, when performing TRD scans, the GenTrain scores of markers should be taken into account to discriminate SNPs that are truly under TRD from those yielding spurious signals due to technical problems.

An on-line questionnaire was emailed to 1,055 organic farmers from November 2018 to February 2019 to gather information about issues and use of contentious inputs in organic production. A total of 116 responses were retained for the analysis. Characteristics of the participants (68 % men) and participating farms (67 % only had one species) were representatives of the Spanish organic livestock secCarmen L. Manuelian et al. ITEA-Inf. Tec. Econ. Agrar. (en prensa), Vol. xx: 1-25 1 * Autor para correspondencia: carmenloreto.manuelianfuste@unipd.it Cita del artículo: Manuelian CL, Albanell E, Such X, De Marchi M (en prensa). Caracterización parcial del sector ganadero ecológico español y problemática actual. ITEA-Información Técnica Económica Agraria. Vol. xx: 1-25 . https://doi.org/10.12706/itea.2020.044 2 Carmen L. Manuelian et al. ITEA-Inf. Tec. Econ. Agrar. (en prensa), Vol. xx: 1-25

Transmission ratio distortion (TRD) is the preferential transmission of one specific allele to offspring at the expense of the other. The existence of TRD is mostly explained by the segregation of genetic variants with deleterious effects on the developmental processes that go from the formation of gametes to fecundation and birth. A few years ago, a statistical methodology was implemented in order to detect TRD signals on a genome-wide scale as a first step toward uncovering the biological basis of TRD and reproductive success in domestic species. In the current work, we have analyzed the impact of SNP calling quality on the detection of TRD signals in a population of Murciano-Granadina goats. Seventeen bucks and their offspring (N = 288) were typed with the Goat SNP50 BeadChip, whereas the genotypes of the dams were lacking. Performance of a genome-wide scan revealed the existence of 36 SNPs showing significant evidence of TRD. When we calculated GenTrain scores for each of the SNPs, we observed that 25 SNPs showed scores below 0.8. The allele frequencies of these SNPs in the offspring were not correlated with the allele frequencies estimated in the dams with statistical methods, providing evidence that flawed SNP calling quality might lead to the detection of spurious TRD signals. We conclude that, when performing TRD scans, the GenTrain scores of markers should be taken into account to discriminate SNPs that are truly under TRD from those yielding spurious signals owing to technical problems.

An on-line questionnaire was emailed to 1,055 organic farmers from November 2018 to February 2019 to gather information about issues and use of contentious inputs in organic production. A total of 116 responses were retained for the analysis. Characteristics of the participants (68 % men) and participating farms (67 % only had one species) were representatives of the Spanish organic livestock sector. In relation to the use of contentious inputs, participants indicated more difficult to find information about the use of alternatives on antibiotics, antiparasitics, and synthetic vitamins than to find information for animals' bedding; although, they mostly use straw as bedding material. They indicated feeding/nutrition, welfare, and animal health as main concerns nowadays in their farms, and animal health and production cost when moving to organic farming. In the last year, 65 % of the farmers did not administer antibiotics to their animals and the use of alternative therapies depended on the health issue they were facing, although they still relied more on conventional treatments. Based on a multiple-check response, most farmers declared to mainly obtain information about the use of alternatives treatments trough veterinarians and the internet. In conclusion, despite production costs were relevant when deciding becoming an organic farmer, their main concerns as organic producers were related to animal health and welfare. Moreover, there is still a scarce use of alternatives treatments such as phytoterapy, homeopathy, as well as additives such as the probiotics.