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Together with phenological and genomic approaches, gel-based and label-free proteomic as well metabolomic procedures were separately applied to plants to highlight differences between ecotypes, to estimate genetic variability within/between organism populations, or to characterize specific mutants/genetically modified lines at metabolic level. To investigate the possible use of tandem mass tag (TMT)-based quantitative proteomics in the above-mentioned contexts and based on the absence of combined proteo-metabolomic studies on Diospyros kaki cultivars, we here applied integrated proteomic and metabolomic approaches to fruits from Italian persimmon ecotypes with the aim to characterize plant phenotypic diversity at molecular level. We identified 2255 proteins in fruits, assigning 102 differentially represented components between cultivars, including some related to pomological, nutritional and allergenic characteristics. Thirty-three polyphenols were also identified and quantified, which belong to hydroxybenzoic acid, flavanol, hydroxycinnamic acid, flavonol, flavanone and dihydrochalcone sub-classes. Heat-map representation of quantitative proteomic and metabolomic results highlighted compound representation differences in various accessions, whose elaboration through Euclidean distance functions and other linkage methods defined dendrograms establishing phenotypic relationships between cultivars. Principal component analysis of proteomic and metabolomic data provided clear information on phenotypic differences/similarities between persimmon accessions. Coherent cultivar association results were observed between proteomic and metabolomic data, emphasizing the utility of integrating combined omic approaches to identify and validate phenotypic relationships between ecotypes, and to estimate corresponding variability and distance. Accordingly, this study describes an original, combined approach to outline phenotypic signatures in persimmon cultivars, which may be used for a further characterization of other ecotypes of the same species and an improved description of nutritional characteristics of corresponding fruits. [ABSTRACT FROM AUTHOR]

Together with phenological and genomic approaches, gel-based and label-free proteomic as well metabolomic procedures were separately applied to plants to highlight differences between ecotypes, to estimate genetic variability within/between organism populations, or to characterize specific mutants/genetically modified lines at metabolic level. To investigate the possible use of tandem mass tag (TMT)-based quantitative proteomics in the above-mentioned contexts and based on the absence of combined proteo-metabolomic studies on Diospyros kaki cultivars, we here applied integrated proteomic and metabolomic approaches to fruits from Italian persimmon ecotypes with the aim to characterize plant phenotypic diversity at molecular level. We identified 2255 proteins in fruits, assigning 102 differentially represented components between cultivars, including some related to pomological, nutritional and allergenic characteristics. Thirty-three polyphenols were also identified and quantified, which belong to hydroxybenzoic acid, flavanol, hydroxycinnamic acid, flavonol, flavanone and dihydrochalcone sub-classes. Heat-map representation of quantitative proteomic and metabolomic results highlighted compound representation differences in various accessions, whose elaboration through Euclidean distance functions and other linkage methods defined dendrograms establishing phenotypic relationships between cultivars. Principal component analysis of proteomic and metabolomic data provided clear information on phenotypic differences/similarities between persimmon accessions. Coherent cultivar association results were observed between proteomic and metabolomic data, emphasizing the utility of integrating combined omic approaches to identify and validate phenotypic relationships between ecotypes, and to estimate corresponding variability and distance. Accordingly, this study describes an original, combined approach to outline phenotypic signatures in persimmon cultivars, which may be used for a further characterization of other ecotypes of the same species and an improved description of nutritional characteristics of corresponding fruits.

Japanese black Wagyu cattle are renowned for producing some of the world's most highly valued and recognized beef with exceptional marbling. Therefore, the primary focus of genetic selection for Wagyu cattle has historically been on meat quality, particularly achieving high marbling levels. However, even when the price of the final product is high, production costs also remain high, especially considering that most of the feed has to be imported. The objective of this study was to evaluate phenotypic relationships between feed efficiency, specifically residual feed intake (RFI), as the most utilized efficiency index in cattle, and various meat quality parameters in Japanese black cattle in order to determine if a common phenotypic selection for these parameters could be feasible. For this, a total of 39 Wagyu cattle were evaluated for feed efficiency over their entire fattening period (900 d), with a focus on RFI as a key indicator. Animals were fed high-starch diets with vitamin A deprivation to achieve the desired marbling. Results revealed positive correlations between feed efficiency and meat quality in Wagyu cattle. Specifically, animals with higher feed efficiency exhibited superior meat quality traits, including firmness, marbling, and overall meat rating. When comparing the 20 most extreme RFI individuals (10 most and 10 least efficient), we observed that efficient RFI animals showed increased marbling levels (+13.2%, P = 0.05) and ranking quality (+12%, P = 0.06) of the meat. In conclusion, this research contributes to understanding the interplay between feed efficiency and meat quality in Japanese black Wagyu cattle. Phenotypic correlations observed suggest the possibility of incorporating RFI criteria into genetic selection programs without compromising the prized meat quality traits of Wagyu beef., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

The study was conducted to determine the production characteristics and to find out the phenotypic relationships between udder and milk production traits in Hair goats. A total of 403 Hair Goats under extensive conditions of Çine town of Aydin province of Turkey were constituted the animal material of the study. The live weights of all goats were recorded just before breeding season. Milk was measured in every month according to the basis of morning or evening milking in a day to estimation of milk yields. Live weights of kids were recorded monthly intervals. Measurements for udder characteristics were determined for two times at 30th and at 180th of the lactation period. Average lactation length, lactation milk yield and daily milk yield of goats were 192.4 days, 139.1 kg and 0.7 kg, respectively. The live weights at birth, 30th, 60th, 90th and 120th days of goat kids were 3.1, 8.6, 13.9, 19.1 and 24.5 kg, respectively. Mean values of withers height, body length and live weight of goats were measured as 73.2 cm, 71.3 cm and 54.5 kg, respectively. Udder and teat characteristics of goats were found positively correlated with milk production characteristics both 30th and 180th days of the lactation period. It can be concluded that Hair goats in extensive conditions had a substantial level of milk yield and their kids had sufficient levels of live weight gains. Furthermore, the udder measurements at the beginning of the lactation could be used for identifying the differences among does. [ABSTRACT FROM AUTHOR]

Background: Several types of genetic interactions in humans can be directly or indirectly associated with the causal effects of mutations. These interactions are usually based on their co-associations to biological processes, coexistence in cellular locations, coexpression in cell lines, physical interactions and so on. In addition, pathological processes can present similar phenotypes that have mutations either in the same genomic location or in different genomic regions. Therefore, integrative resources for all of these complex interactions can help us prioritize the relationships between genes and diseases that are most deserving to be studied by researchers and physicians. Results: PhenUMA is a web application that displays biological networks using information from biomedical and biomolecular data repositories. One of its most innovative features is to combine the benefits of semantic similarity methods with the information taken from databases of genetic diseases and biological interactions. More specifically, this tool is useful in studying novel pathological relationships between functionally related genes, merging diseases into clusters that share specific phenotypes or finding diseases related to reported phenotypes. Conclusions: This framework builds, analyzes and visualizes networks based on both functional and phenotypic relationships. The integration of this information helps in the discovery of alternative pathological roles of genes, biological functions and diseases. PhenUMA represents an advancement toward the use of new technologies for genomics and personalized medicine. [ABSTRACT FROM AUTHOR]

Abstract: A total of 436 young bulls from fifteen Western European breeds, including beef, dairy and local types from five countries, were studied to assess variability in live weight, live weight gain, body measurements and carcass traits. Animals were logged indoors, and fed a diet based on concentrate and straw offered ad libitum from 9 months of age to slaughter at 15 months of age. The weight, body length, height at withers and pelvis width, of the animals were recorded at 9, 12 and 15 months of age. After slaughter, 15 carcass variables were recorded, including carcass weight, EU classification scores, morphological measurements and dissection data. Data were analysed by GLM, regression and principal component analysis procedures. Significant differences were found between breeds for all variables studied, however, the body size measurements and the carcass traits were more useful to discriminate among cattle breeds, than either live weight or daily gain. With respect to the body size and carcass traits the studied breeds could be grouped as: [–] Specialized beef breeds, comprising Piemontese, Asturiana de los Valles, Pirenaica, Limousin, South Devon, Charolais and Aberdeen Angus, all of which were characterized by high muscularity, wide pelvis and medium height and a low to medium level of fatness. [–] Local and dairy breeds, comprising Jersey, Casina, Highland, Holstein and Danish Red, the latter two breeds were tall animals, while the former three breeds were small in size. In general the group was poorly muscled and tended to have a high or medium level of fat. [–] Intermediate group, Avileña, Marchigiana and Simmental: these breeds were characterized by an intermediate muscle conformation and fatness level and were relatively tall. This study provides a detailed assessment or a wide range of variables in the major breeds, and several minor breeds, that are used in breeding programmes across Europe and elsewhere, and will provide information that will be of use to define breeding strategies to meet the demands of the European beef market. [Copyright &y& Elsevier]

A sample of about 70 young bulls of each of 10 beef cattle breeds from France and Spain, reared in their typical production systems, was studied regarding growth and carcass quality traits. There were large differences between and within breed-systems. The animals slaughtered in Spain weighed between 444 and 551 kg, whereas the range in France was from 610 to 750 kg. Growth showed a linear tendency; the daily weight gain ranging from 1.03 to 1.65 kg/day. Asturiana de los Valles and Pirenaica were, among the Spanish populations, the breed-systems with more muscle (around 75%) and less fat (8–10%) in the carcass, whereas Avilen˜a-Negra Ibe´rica, Morucha and Retinta showed opposite characteristics (60–65% muscle and 17–19% total fat at the 6th rib). Bruna dels Pirineus and Asturiana de la Montan˜a occupied an intermediate position. All of the French breed-systems, Aubrac, Gasconne and Salers surpassed 73% muscle, while the percentage of total fat ranged from 7.6 to 10%. Salers breed-system also showed the longest and thinnest hind-limb. In the wide range of carcass weights studied in this paper, the general relationships among carcass traits were confirmed. Animals with the better conformation were also leaner. Longer carcasses tended to be associated with poor conformation and fatness. Bone content was clearly opposed to carcass conformation and muscle content. [Copyright &y& Elsevier]