Analyse of an experiment of divergent selection for fleece weight in french angora rabbits

Dans cette thèse nous présentons une analyse d'une expérience de sélection divergente chez le lapin Angora français. Les objectifs de l'expérience étaient d'évaluer la réponse à la sélection pour le poids total de toison et pour les caractères corrélés et d'analyser une expérience de sélection sur une population conduite en générations chevauchantes. Nous présentons une vue d'ensemble des facteurs génétiques et non génétiques des caractères quantitatifs et qualitatifs influençant la production de fibre. Parmi des effets fixes, le numéro de récolte est le plus important. Les paramètres génétiques et les tendances génétiques ont été analysés en utilisant un BLUP appliqué à un modèle animal. Pour l'estimation des paramètres génétiques on a employé un modèle avec mesures répétées des mesures dans lequel les récoltes successives ont été considérées comme un caractère répété. Les résultats ont prouvé que la sélection pour le poids total de toison a été efficace et une divergence de trois écarts types génétiques a été observée entre les souches haute et basse après huit années de sélection. La sélection pour le poids total de toison a augmenté de manière significative la longueur de jarres et le rapport entre les nombre de follicules secondaires et primaires (rapport S/P). Dans le même temps, la compression, la résilience, le diamètre de duvets, et le diamètre moyen de fibre ont diminué. Ces changements s'expliquent par des corrélations génétiques moyennes à élevées entre le poids de toison et la longueur des jarres, et entre les dimensions de fibre et le rapport S/P, la compression et la résilience. Ainsi, la sélection pour augmenter le poids total de toison a induit une augmentation des composantes quantitatives et qualitatives de la production delaine du lapin Angora français. La mesure du poids total de toison est simple et facile au niveau de l’élevage. Cette thèse fournit également de nouveaux paramètres génétiques résultant des mesures par l'analyseur de diamètre de ibre optique (OFDA). Il s'agit d'une méthode rapide pour mesurer les caractéristiques de la fibre Angora. Certaines de ces mesures sont intéressantes en raison d'une corrélation génétique élevée avec les caractéristiques du follicule pileux. La méthodologie OFDA est une alternative intéressante pour évaluer des caractéristiques importantes telles que le diamètre de fibre et le coefficient de variation du diamètre des fibres. Nous décrivons les paramètres démographiques et généalogiques de la population étudiée. En outre, nous étudions la différentielle de sélection pour le poids total de toison et le poids corporel. La caractéristique principale de notre approche est la description de la différentielle de sélection en comparant les candidats à la sélection, les parents potentiels et les parents théoriques. La description démographique et génétique a prouvé que dans les deux souches sélectionnées on a appliqué pendant 8 ans une conduite proche. Notre travail apporte des résultats originaux sur les effets de la sélection chez le lapin angora et sur la conduite d'une sélection en générations chevauchantes. Cette thèse a aussi un intérêt pratique pour les sélectionneurs de lapin Angora. Cette thèse est également le dernier projet de recherche de l'INRA après presque 30 ans de recherche sur cet animal. ABSTRACT : In this thesis, we present our research to analyze the efficiency of an experiment of divergent selection in French Angora rabbit. Objectives of the experiment were a) to assess genetic parameter estimatesfor total fleece weight and correlated trait and b) to get an experience on management of a population of angora rabbits under selection with overlapping generations. This thesis is also the last research project of INRA after nearly 30 years of research on this animal. We present an overview of the genetic and non-genetic factors of quantitative and qualitative traits influencing fibre production. Among fixed effects, number of harvest was the most important. The genetic parameters and genetic trends were analysed using a BLUP animal model. For estimation of genetics parameters the repeatability model was used in which wool harvests from third until 12th have been considered as a repeated trait. Results showed that selection for high and low total fleece weight was successfully performed and a divergence of three genetic standard deviations was observed between the high and low lines after eight years of selection. Selection for total fleece weight significantly increased bristle length, secondary to primary follicle ratio and comfort factor and decreased compression, resilience, bristle diameter, and average fibre diameter. These changes resulted from moderate to high genetic correlations between total fleece weight and bristle length, and between fibre dimensions and secondary to primary follicle ratio, comfort factor, compression and resilience. Thus, selection for increasing total fleece weight results in an increase of both quantitative and qualitative traits of wool production in the French Angora rabbit. Measurement of total fleece weight is simple and easy at the farm level. Selection for this trait has positiveeffects on fleece characteristics such as bristle length, follicle population and fibre diameter. This thesis also contains new genetic parameters Angora fibres resulting from measurements by Optical Fibre Diameter Analyser that we provide a rapid method for measuring the characteristics of Angora fibre. Some of these measurements are interesting because of having a high genetic correlation with follicle traits of skin. The OFDA methodology is an interesting alternative to evaluate important characteristics such as fibre diameter, CV of fibre diameter and bristle content through measuring of comfort factor. We describe the demography and genealogy of the studied population. In addition, we study differential of selection for total fleece weight and body weight. The main characteristic of our approach is the use of new method for description of differential of selection in candidates of selection, parent and theoretical parents. Description of demography and the genetic structure in this study showed that in the two divergent lines, the similar management of reproducers has been done successfully during 8 years of selection. Our work contributes to the research in two areas that are estimation of genetic parameters with multivariate models of best linear unbiased prediction of breeding value and theoretical investigation of selection in populations with overlapping generations. This thesis is also of practical interest for Angora rabbit breeders for knowledge of effects of selection for total fleece weight and correlated traits

New Look on an Ancient Fiber of Cashmere

The word cashmere in particular refers to the fine fibers of goats that are grown in high and cold regions of the world. There is not a specific cashmere-producing goat in the world, that is, there are many breeds or ecotypes that produce cashmere fibers. Cashmere-producing goats are grown majorly in areas that are very limited in alternative sources of income, such as agriculture or industry. Therefore, raising goats will encourage the villagers to live in the same rural and nomadic areas and do not migrate to cities. Therefore, the socio-ecological aspects of cashmere goat farming are important and must be notified by animal scientists. Structure of hair and cashmere fibers, physiology, and genetic and nongenetic factors that influence cashmere goats has been mentioned. Challenges and problems facing the cashmere industry reviewed briefly in this chapter: In general, cashmere goat production has some very interesting aspects from interaction of animal science and textile industry’s viewpoint. Cashmere goats are combined with many other human activities in low-density farming. In the world today, it is necessary to pay more attention to raising goats in less developed areas. We declared the importance of cashmere goats in a whole system of animal production, especially in extensive agriculture systems

Study of Population Structure and Genetic Prediction of Buffalo from Different Provinces of Iran using Machine Learning Method

Considering breeding livestock programs to milk production and type traits based on existence two different ecotypes of Iranian’s buffalo, a study carried out to investigate the population structure of Iranian buffalo and validate its classification accuracy according to different ecotypes from Iran (Azerbaijan and North) using data SNP chip 90K by means Support vector Machine (SVM), Random Forest (RF) and Discriminant Analysis Principal Component (DAPC) methods. A total of 258 buffalo were sampled and genotyped. The results of admixture, multidimensional scaling (MDS), and DAPC showed a close relationship between the animals of different provinces. Two ecotypes indicated higher accuracy of 96% that the Area Under Curve (AUC) confirmed the obtained result of the SVM approach while the DAPC and RF approach demonstrated lower accuracy of 88% and 80 %, respectively. SVM method proved high accuracy compared with DAPC and RF methods and assigned animals to their herds with more accuracy. According to these results, buffaloes distributed in two different ecotypes are one breed, and therefore the same breeding program should be used in the future. The water buffalo ecotype of the northern provinces of Iran and Azerbaijan seem to belong to the same population

Large-Scale Mitochondrial DNA Analysis of the Domestic Goat Reveals Six Haplogroups with High Diversity

Background. From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. Methodology/Principal Findings. The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals. Conclusions/Significance. We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species

Global, regional, and national burden of disorders affecting the nervous system, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BackgroundDisorders affecting the nervous system are diverse and include neurodevelopmental disorders, late-life neurodegeneration, and newly emergent conditions, such as cognitive impairment following COVID-19. Previous publications from the Global Burden of Disease, Injuries, and Risk Factor Study estimated the burden of 15 neurological conditions in 2015 and 2016, but these analyses did not include neurodevelopmental disorders, as defined by the International Classification of Diseases (ICD)-11, or a subset of cases of congenital, neonatal, and infectious conditions that cause neurological damage. Here, we estimate nervous system health loss caused by 37 unique conditions and their associated risk factors globally, regionally, and nationally from 1990 to 2021.MethodsWe estimated mortality, prevalence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs), with corresponding 95% uncertainty intervals (UIs), by age and sex in 204 countries and territories, from 1990 to 2021. We included morbidity and deaths due to neurological conditions, for which health loss is directly due to damage to the CNS or peripheral nervous system. We also isolated neurological health loss from conditions for which nervous system morbidity is a consequence, but not the primary feature, including a subset of congenital conditions (ie, chromosomal anomalies and congenital birth defects), neonatal conditions (ie, jaundice, preterm birth, and sepsis), infectious diseases (ie, COVID-19, cystic echinococcosis, malaria, syphilis, and Zika virus disease), and diabetic neuropathy. By conducting a sequela-level analysis of the health outcomes for these conditions, only cases where nervous system damage occurred were included, and YLDs were recalculated to isolate the non-fatal burden directly attributable to nervous system health loss. A comorbidity correction was used to calculate total prevalence of all conditions that affect the nervous system combined.FindingsGlobally, the 37 conditions affecting the nervous system were collectively ranked as the leading group cause of DALYs in 2021 (443 million, 95% UI 378–521), affecting 3·40 billion (3·20–3·62) individuals (43·1%, 40·5–45·9 of the global population); global DALY counts attributed to these conditions increased by 18·2% (8·7–26·7) between 1990 and 2021. Age-standardised rates of deaths per 100 000 people attributed to these conditions decreased from 1990 to 2021 by 33·6% (27·6–38·8), and age-standardised rates of DALYs attributed to these conditions decreased by 27·0% (21·5–32·4). Age-standardised prevalence was almost stable, with a change of 1·5% (0·7–2·4). The ten conditions with the highest age-standardised DALYs in 2021 were stroke, neonatal encephalopathy, migraine, Alzheimer's disease and other dementias, diabetic neuropathy, meningitis, epilepsy, neurological complications due to preterm birth, autism spectrum disorder, and nervous system cancer.InterpretationAs the leading cause of overall disease burden in the world, with increasing global DALY counts, effective prevention, treatment, and rehabilitation strategies for disorders affecting the nervous system are needed

Global burden of 288 causes of death and life expectancy decomposition in 204 countries and territories and 811 subnational locations, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BACKGROUND Regular, detailed reporting on population health by underlying cause of death is fundamental for public health decision making. Cause-specific estimates of mortality and the subsequent effects on life expectancy worldwide are valuable metrics to gauge progress in reducing mortality rates. These estimates are particularly important following large-scale mortality spikes, such as the COVID-19 pandemic. When systematically analysed, mortality rates and life expectancy allow comparisons of the consequences of causes of death globally and over time, providing a nuanced understanding of the effect of these causes on global populations. METHODS The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 cause-of-death analysis estimated mortality and years of life lost (YLLs) from 288 causes of death by age-sex-location-year in 204 countries and territories and 811 subnational locations for each year from 1990 until 2021. The analysis used 56 604 data sources, including data from vital registration and verbal autopsy as well as surveys, censuses, surveillance systems, and cancer registries, among others. As with previous GBD rounds, cause-specific death rates for most causes were estimated using the Cause of Death Ensemble model-a modelling tool developed for GBD to assess the out-of-sample predictive validity of different statistical models and covariate permutations and combine those results to produce cause-specific mortality estimates-with alternative strategies adapted to model causes with insufficient data, substantial changes in reporting over the study period, or unusual epidemiology. YLLs were computed as the product of the number of deaths for each cause-age-sex-location-year and the standard life expectancy at each age. As part of the modelling process, uncertainty intervals (UIs) were generated using the 2·5th and 97·5th percentiles from a 1000-draw distribution for each metric. We decomposed life expectancy by cause of death, location, and year to show cause-specific effects on life expectancy from 1990 to 2021. We also used the coefficient of variation and the fraction of population affected by 90% of deaths to highlight concentrations of mortality. Findings are reported in counts and age-standardised rates. Methodological improvements for cause-of-death estimates in GBD 2021 include the expansion of under-5-years age group to include four new age groups, enhanced methods to account for stochastic variation of sparse data, and the inclusion of COVID-19 and other pandemic-related mortality-which includes excess mortality associated with the pandemic, excluding COVID-19, lower respiratory infections, measles, malaria, and pertussis. For this analysis, 199 new country-years of vital registration cause-of-death data, 5 country-years of surveillance data, 21 country-years of verbal autopsy data, and 94 country-years of other data types were added to those used in previous GBD rounds. FINDINGS The leading causes of age-standardised deaths globally were the same in 2019 as they were in 1990; in descending order, these were, ischaemic heart disease, stroke, chronic obstructive pulmonary disease, and lower respiratory infections. In 2021, however, COVID-19 replaced stroke as the second-leading age-standardised cause of death, with 94·0 deaths (95% UI 89·2-100·0) per 100 000 population. The COVID-19 pandemic shifted the rankings of the leading five causes, lowering stroke to the third-leading and chronic obstructive pulmonary disease to the fourth-leading position. In 2021, the highest age-standardised death rates from COVID-19 occurred in sub-Saharan Africa (271·0 deaths [250·1-290·7] per 100 000 population) and Latin America and the Caribbean (195·4 deaths [182·1-211·4] per 100 000 population). The lowest age-standardised death rates from COVID-19 were in the high-income super-region (48·1 deaths [47·4-48·8] per 100 000 population) and southeast Asia, east Asia, and Oceania (23·2 deaths [16·3-37·2] per 100 000 population). Globally, life expectancy steadily improved between 1990 and 2019 for 18 of the 22 investigated causes. Decomposition of global and regional life expectancy showed the positive effect that reductions in deaths from enteric infections, lower respiratory infections, stroke, and neonatal deaths, among others have contributed to improved survival over the study period. However, a net reduction of 1·6 years occurred in global life expectancy between 2019 and 2021, primarily due to increased death rates from COVID-19 and other pandemic-related mortality. Life expectancy was highly variable between super-regions over the study period, with southeast Asia, east Asia, and Oceania gaining 8·3 years (6·7-9·9) overall, while having the smallest reduction in life expectancy due to COVID-19 (0·4 years). The largest reduction in life expectancy due to COVID-19 occurred in Latin America and the Caribbean (3·6 years). Additionally, 53 of the 288 causes of death were highly concentrated in locations with less than 50% of the global population as of 2021, and these causes of death became progressively more concentrated since 1990, when only 44 causes showed this pattern. The concentration phenomenon is discussed heuristically with respect to enteric and lower respiratory infections, malaria, HIV/AIDS, neonatal disorders, tuberculosis, and measles. INTERPRETATION Long-standing gains in life expectancy and reductions in many of the leading causes of death have been disrupted by the COVID-19 pandemic, the adverse effects of which were spread unevenly among populations. Despite the pandemic, there has been continued progress in combatting several notable causes of death, leading to improved global life expectancy over the study period. Each of the seven GBD super-regions showed an overall improvement from 1990 and 2021, obscuring the negative effect in the years of the pandemic. Additionally, our findings regarding regional variation in causes of death driving increases in life expectancy hold clear policy utility. Analyses of shifting mortality trends reveal that several causes, once widespread globally, are now increasingly concentrated geographically. These changes in mortality concentration, alongside further investigation of changing risks, interventions, and relevant policy, present an important opportunity to deepen our understanding of mortality-reduction strategies. Examining patterns in mortality concentration might reveal areas where successful public health interventions have been implemented. Translating these successes to locations where certain causes of death remain entrenched can inform policies that work to improve life expectancy for people everywhere. FUNDING Bill & Melinda Gates Foundation

Analyse d'une expérience de sélection divergente pour le poids total de la toison chez le lapin angora

In this thesis, we present our research to analyze the efficiency of an experiment of divergent selection in French Angora rabbit. Objectives of the experiment were a) to assess genetic parameter estimatesfor total fleece weight and correlated trait and b) to get an experience on management of a population of angora rabbits under selection with overlapping generations. This thesis is also the last research project of INRA after nearly 30 years of research on this animal. We present an overview of the genetic and non-genetic factors of quantitative and qualitative traits influencing fibre production. Among fixed effects, number of harvest was the most important. The genetic parameters and genetic trends were analysed using a BLUP animal model. For estimation of genetics parameters the repeatability model was used in which wool harvests from third until 12th have been considered as a repeated trait. Results showed that selection for high and low total fleece weight was successfully performed and a divergence of three genetic standard deviations was observed between the high and low lines after eight years of selection. Selection for total fleece weight significantly increased bristle length, secondary to primary follicle ratio and comfort factor and decreased compression, resilience, bristle diameter, and average fibre diameter. These changes resulted from moderate to high genetic correlations between total fleece weight and bristle length, and between fibre dimensions and secondary to primary follicle ratio, comfort factor, compression and resilience. Thus, selection for increasing total fleece weight results in an increase of both quantitative and qualitative traits of wool production in the French Angora rabbit. Measurement of total fleece weight is simple and easy at the farm level. Selection for this trait has positiveeffects on fleece characteristics such as bristle length, follicle population and fibre diameter. This thesis also contains new genetic parameters Angora fibres resulting from measurements by Optical Fibre Diameter Analyser that we provide a rapid method for measuring the characteristics of Angora fibre. Some of these measurements are interesting because of having a high genetic correlation with follicle traits of skin. The OFDA methodology is an interesting alternative to evaluate important characteristics such as fibre diameter, CV of fibre diameter and bristle content through measuring of comfort factor. We describe the demography and genealogy of the studied population. In addition, we study differential of selection for total fleece weight and body weight. The main characteristic of our approach is the use of new method for description of differential of selection in candidates of selection, parent and theoretical parents. Description of demography and the genetic structure in this study showed that in the two divergent lines, the similar management of reproducers has been done successfully during 8 years of selection. Our work contributes to the research in two areas that are estimation of genetic parameters with multivariate models of best linear unbiased prediction of breeding value and theoretical investigation of selection in populations with overlapping generations. This thesis is also of practical interest for Angora rabbit breeders for knowledge of effects of selection for total fleece weight and correlated traitsTOULOUSE-ENSAT-Documentation (315552324) / SudocSudocFranceF

Author Correction: Weighted gene co-expression network analysis identifies modules and functionally enriched pathways in the lactation process (Scientific Reports, (2021), 11, 1, (2367), 10.1038/s41598-021-81888-z)

The Acknowledgements section in the original version of this Article was incomplete. “This research is supported by a research grant from the University of Tabriz (Number 3421).” now reads: “The authors would like to thank the Iran National Science Foundation (INSF, Grant No. 98023162) for financial support. This research is supported by a research grant from the University of Tabriz (Number 3421).” The original Article has been corrected