Genomic diversity and signatures of selection in meat and fancy rabbit breeds based on high-density marker data

open6noThe study was funded by the PSRN (Programma di Sviluppo Rurale Nazionale) Cun-Fu and Cun-Fu 2 projects (co-funded by the European Agricultural Fund for Rural Development of the European Union and by the Italian Ministry of Agriculture, Food and Forestry—MiPAAF) and by the University of Bologna RFO 2019 programme.Background: Domestication of the rabbit (Oryctolagus cuniculus) has led to a multi-purpose species that includes many breeds and lines with a broad phenotypic diversity, mainly for external traits (e.g. coat colours and patterns, fur structure, and morphometric traits) that are valued by fancy rabbit breeders. As a consequence of this human-driven selection, distinct signatures are expected to be present in the rabbit genome, defined as signatures of selection or selective sweeps. Here, we investigated the genome of three Italian commercial meat rabbit breeds (Italian Silver, Italian Spotted and Italian White) and 12 fancy rabbit breeds (Belgian Hare, Burgundy Fawn, Champagne d’Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex, Rhinelander and Thuringian) by using high-density single nucleotide polymorphism data. Signatures of selection were identified based on the fixation index (FST) statistic with different approaches, including single-breed and group-based methods, the latter comparing breeds that are grouped based on external traits (different coat colours and body sizes) and types (i.e. meat vs. fancy breeds). Results: We identified 309 genomic regions that contained signatures of selection and that included genes that are known to affect coat colour (ASIP, MC1R and TYR), coat structure (LIPH), and body size (LCORL/NCAPG, COL11A1 and HOXD) in rabbits and that characterize the investigated breeds. Their identification proves the suitability of the applied methodologies for capturing recent selection events. Other regions included novel candidate genes that might contribute to the phenotypic variation among the analyzed breeds, including genes for pigmentation-related traits (EDNRA, EDNRB, MITF and OCA2) and body size, with a strong candidate for dwarfism in rabbit (COL2A1). Conclusions: We report a genome-wide view of genetic loci that underlie the main phenotypic differences in the analyzed rabbit breeds, which can be useful to understand the shift from the domestication process to the development of breeds in O. cuniculus. These results enhance our knowledge about the major genetic loci involved in rabbit external traits and add novel information to understand the complexity of the genetic architecture underlying body size in mammals.openBallan, Mohamad; Bovo, Samuele; Schiavo, Giuseppina; Schiavitto, Michele; Negrini, Riccardo; Fontanesi, LucaBallan, Mohamad; Bovo, Samuele; Schiavo, Giuseppina; Schiavitto, Michele; Negrini, Riccardo; Fontanesi, Luc

Comparative analysis of genomic inbreeding parameters and runs of homozygosity islands in several fancy and meat rabbit breeds

Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (~150) and the lowest in Italian Silver (~106). The average length of ROH ranged from 4.001 ± 0.556 Mb in Italian White to 6.268 ± 1.355 Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome

De sangre y leche: Raza y religión en el mundo ibérico moderno

Sangre y leche fueron símbolos omnipresentes en los territorios de la «Monarquía Católica», en España y su Imperio colonial. Situados a medio camino entre la naturaleza y la cultura, a lo largo de las edades Media y Moderna, la sangre y la leche tejieron una poderosa analogía entre la reproducción fisiológica y la reproducción cultural. Como exploran los artículos de este libro, estos símbolos desempeñaron un papel determinante en los procesos de ordenación, jerarquización, y por supuesto también, de exclusión social dentro de la monarquía. Partiendo de perspectivas tan diversas como la religiosa, la social, la jurídica o la antropológica, los autores de este libro analizan esta privilegiada encrucijada simbólica para interrogarse sobre el origen y desarrollo del discurso de la «raza» en la España altomoderna.Índice: Introducción, por Mercedes García-Arenal y Felipe Pereda. SANGRE. LA POLÍTICA DEL LINAJE Y LA SANGRE. -Genealogía, linaje e identidad etnocultural en la Granada nazarí, por Mohamad Ballan. -Religión y raza en la Edad Media cristiana e islámica, por David Nirenberg. -Linaje, conversión y naturalezas inestables en el Atlántico ibérico: comparación entre la incorporación y la exclusión de los moriscos y de los pueblos indígenas, por Karoline P. Cook. -Limpieza de sangre: la batalla por la reforma desde Salucio hasta Quevedo, por Francisco Bethencourt. LA SANGRE, VEHÍCULO DE LA NATURALEZA INMUTABLE. -Sangre de mi sangre: lo que no se podía adquirir, o casi no, por Jean-Frédéric Schaub. -Demonios, estrellas e imaginación. El cuerpo a principios de la modernidad en los trópicos, por Jorge Cañizares-Esguerra. -«Sua malicia vem-se a conaturizar»: Sangre, color de piel y conversión en el mundo ibérico moderno, por Giuseppe Marcocci. -Los «judíos menstruantes». Sangre, bautismo y la retórica de la evidencia en un tratado de Juan de Quiñones (1632), por Stefania Pastore. SANGRE & LECHE. EL DISCURSO SIMBÓLICO DE LOS FLUIDOS SACROS .-Líquidos sagrados y la formación de protestantes (españoles), por James S. Amelang. -Divinos pechos, como cántaros: estética, política y género de las imágenes del Barroco español, por Felipe Pereda. -La puesta en escena de la limpieza de sangre en la España del siglo XVII, por Rachel Burk. REPRESENTACIONES Y FICCIONES. -Saberes médicos e ideología esencialista: sangre, esperma, leche y construcción del ser, por Christine Orobitg. -Ficciones genealógicas. El morisco Román Ramírez y los libros de caballerías, por Miguel Martínez. -Del morisco real al imaginado. Construcciones de la alteridad en la Península Ibérica moderna, por Francisco J. Moreno Díaz del Campo y Borja Franco Llopis. A MODO DE COLOFÓN. -De sangre y leche: debates y categorías sobre racialización. Una lectura retrospectiva, por Max S. Hering Torres. -¿Eran racistas los europeos de la modernidad temprana?, por Joan Pau Rubiès.Peer reviewe

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a ?One Health? perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identifed in the four candidate genes: 26% of them were not previously described; 29 variants afected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a frst step towards a ?One Health? perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the describedFE1B-06B2-126F | Jos? Pedro Pinto de Ara?joN/

The Scribe of the Alhambra: Lisān al-Dīn ibn al-Khaṭīb, Sovereignty and History in Nasrid Granada

This dissertation explores the relationship between intellectual networks, royal patronage and developments in political thought in late medieval Islamic Spain and North Africa. It proposes a new reading of the history of the Nasrid Kingdom of Granada (635/1238–897/1492) that examines these broader issues by closely studying the life and works of Lisān al-Dīn Muḥammad b. al-Khaṭīb (713/1313–776/1374), the most prominent Spanish Muslim historian, chancellor and philosopher during the 8th/14th century, situating this figure within a larger network of scholars, statesmen and functionaries in the late medieval Islamic West. This dissertation illustrates the manner in which the crisis and transformation that characterized the territorial fragmentation of Islamic Spain and North Africa contributed to the rise of a distinct class of scholar-officials who reshaped the intellectual and political culture of the Western Mediterranean. It argues that the gradual concentration of executive political authority in the hands of scholar-officials, such as Ibn al-Khaṭīb, was part of the process of the consolidation of royal power at the expense of the nobility during the late Middle Ages. For their part, these scholar-officials composed works across a variety of genres that sought to legitimate and rationalize the centralization of royal authority. To examine this phenomenon, this dissertation draws upon a corpus of Arabic, Castilian and Aragonese manuscripts, as well as coinage and epigraphy. It investigates the lives of those individuals who existed in close proximity to royal power during the late medieval period in order to explore how their own experiences and ideas fashioned discourses about sovereignty, governmentality and the craft of history during the 14th century. The rise of a distinct class of scholar-officials, whose members included Christians, Muslims and Jews working for different (often competing) dynasties, was underpinned by similar networks of patronage, intellectual interests and a shared geography. These highly-educated individuals rose to prominence as chancellors, treasurers, and councilors within the royal courts in Iberia and were responsible for producing a multitude of works, while patronizing pieces of art and architecture that embodied their particular worldview. Lisān al-Dīn b. al-Khaṭīb provides us with an illustrative example of this class of individuals during the 8th/14th century. This figure followed in the footsteps of leading Spanish Muslim scholar-officials such as Abū Bakr b. al-Khaṭṭāb, Ibn ‘Amīra, Ibn Sa‘īd and Ibn al-Abbār, individuals who had exercised significant administrative and political authority while also being deeply involved in various intellectual and literary pursuits during the 7th/13th century. Ibn al-Khaṭīb authored over 50 works, including historical chronicles, epistolography, biographical dictionaries, poetry, medical texts, and political treatises, throughout his career. This dissertation illustrates his role at the intersection of intellectual and political developments and demonstrates how his literary production was closely intertwined with his function as a statesman. It provides the first comprehensive study in English of Ibn al-Khaṭīb’s life, from his birth into a minor family in the small town of Loja in 713/1313 to his rise as a physician and scribe in the Nasrid court, his transformation from a client and servant of the Nasrid dynasty into an itinerant scholar-official who sought to establish his own individual power and influence across the Islamic West, to his controversial assassination in Fez in 776/1374. It looks particularly closely at the letters that he exchanged with his broader network of scholars, nobles, functionaries and kings across the Mediterranean world to think about the question of loyalty, ties of obligation and individual strategies of survival in the Islamic West during this period

Applied genomics in livestock: genome-wide association studies and population genomics analysis in pig and rabbit breeds

The domestication and selection processes in pigs and rabbits have resulted in the constitution of multiple breeds with broad phenotypic diversity. Population genomics analysis and Genome-wide association study analysis can be utilized to gain insights into the ancestral origins, genetic diversity, and the presence of lethal mutations across these diverse breeds. In this thesis, we analysed the dataset obtained from three Italian Pig breeds to detect deleterious alleles. We screened the dataset for genetic markers showing homozygous deficiency using two approaches single marker and haplotype-based approach. Moreover, Genome-wide association study analyses were performed to detect genetic markers associated with pigs' reproductive traits. In rabbits, we investigated the application of SNP bead chip for detection signatures of selection in rabbits using different methods. This analysis was implemented for the first time in different fancy and meet rabbit breeds. Multiple approaches were utilized for the detection of the selection of signatures including Fst analysis, ROH analysis, PCAdapt analysis, and haplotype-based analysis. The analysis in pigs was able to identify five putative deleterious SNPs and nine putative deleterious haplotypes in the analysed Italian Pig breeds. The genomic regions of the detected putative deleterious genomic markers harboring loss of function variants such as the Frameshift variant, start lost, and splice donor variant. Those variants are close to important candidate genes such as IGF2BP1, ADGRL4, and HGF. In rabbits, multiple genomic regions were detected to be under selection of signature. These genomic regions harbor candidate genes associated with coat color phenotype (MC1R, TYR, and ASIP), hair structure (LIPH), and body size (HMGA2 and COL2A1). The described results in rabbits and pigs could be used to improve breeding programs by excluding the deleterious genetic markers carriers and incorporating candidate genes for coat color, body size, and meat production in rabbit breeding programs to enhance desired trait

Signatures of selection are present in the genome of two close autochthonous cattle breeds raised in the North of Italy and mainly distinguished for their coat colours

Autochthonous cattle breeds are genetic resources that, in many cases, have been fixed for inheritable exterior phenotypes useful to understand the genetic mechanisms affecting these breed‐specific traits. Reggiana and Modenese are two closely related autochthonous cattle breeds mainly raised in the production area of the well‐known Protected Designation of Origin Parmigiano‐Reggiano cheese, in the North of Italy. These breeds can be mainly distinguished for their standard coat colour: solid red in Reggiana and solid white with pale shades of grey in Modenese. In this study we genotyped with the GeneSeek GGP Bovine 150k single nucleotide polymorphism (SNP) chip almost half of the extant cattle populations of Reggiana (n = 1109 and Modenese (n = 326) and used genome‐wide information in comparative F(ST) analyses to detect signatures of selection that diverge between these two autochthonous breeds. The two breeds could be clearly distinguished using multidimensional scaling plots and admixture analysis. Considering the top 0.0005% F(ST) values, a total of 64 markers were detected in the single‐marker analysis. The top F(ST) value was detected for the melanocortin 1 receptor (MC1R) gene mutation, which determines the red coat colour of the Reggiana breed. Another coat colour gene, agouti signalling protein (ASIP), emerged amongst this list of top SNPs. These results were also confirmed with the window‐based analyses, which included 0.5‐Mb or 1‐Mb genome regions. As variability affecting ASIP has been associated with white coat colour in sheep and goats, these results highlighted this gene as a strong candidate affecting coat colour in Modenese breed. This study demonstrates how population genomic approaches designed to take advantage from the diversity between local genetic resources could provide interesting hints to explain exterior traits not yet completely investigated in cattle

Successful management of late stage of acute compartment syndrome after 72 h snake bite in 8-year-old female. A case report

One of the most serious complications of snakebite is compartment syndrome (CS), Signs of CS include paresthesia in the distal part and pain that is out of proportion to the severity of the injury, Management involves improving the general condition, and fasciotomy has been found to be effective. An 8-year-old girl was referred to the internal emergency department in our hospital 72 h after a snake bite. She was unconscious, in poor general condition, and had a high fever. Edema was present throughout the right lower limb, extending to the abdomen, with signs of cellular necrosis (blackening with bubbles) on the right foot. The diagnosis of CS was made, and the patient underwent fasciotomy after improving the general condition. Although snake bites are rare, surgeons should be concerned about life-threatening and limb-threatening complications. CS can be effectively treated with fasciotomy. Additionally, it is important to emphasize the significance of daily dressing and regular follow-up for achieving the best results

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a “One Health” perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a “One Health” perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resource