Genetic structure of a small closed population of the New Zealand white rabbit through pedigree analyses

[EN] The genetic structure of a small population of New Zealand White rabbits maintained at the Sheep Breeding and Research Station, Sandynallah, The Nilgiris, India, was evaluated through pedigree analyses. Data on pedigree information (n=2503) for 18 yr (1995-2012) were used for the study. Pedigree analysis and the estimates of population genetic parameters based on the gene origin probabilities were performed. The analysis revealed that the mean values of generation interval, coefficients of inbreeding and equivalent inbreeding were 1.49 yr, 13.23 and 17.59%, respectively. The proportion of population inbred was 100%. The estimated mean values of average relatedness and individual increase in inbreeding were 22.73 and 3.00%, respectively. The percentage increase in inbreeding over generations was 1.94, 3.06 and 3.98 estimated through maximum generations, equivalent generations and complete generations, respectively. The number of ancestors contributing the majority of 50% genes (fa50) to the gene pool of reference population was only 4, which might have led to reduction in genetic variability and increased the amount of inbreeding. The extent of genetic bottleneck assessed by calculating the effective number of founders (fe) and the effective number of ancestors (fa), as expressed by the fe/fa ratio was 1.1, which is indicative of the absence of stringent bottlenecks. Up to 5th generation, 71.29% pedigree was complete, reflecting the well maintained pedigree records. The maximum known generations were 15, with an average of 7.9, and the average equivalent generations traced were 5.6, indicating a fairly good depth in pedigree. The realized effective population size was 14.93, which is very critical, and with the increasing trend of inbreeding the situation has been assessed as likely to become worse in future. The proportion of animals with the genetic conservation index (GCI) greater than 9 was 39.10%, which can be used as a scale to use such animals with higher GCI to maintain balanced contribution from the founders. From the study, it was evident that the herd was completely inbred, with a very high inbreeding coefficient, and the effective population size was critical. Recommendations were made to reduce the probability of deleterious effects of inbreeding and to improve genetic variability in the herd. The present study can help in carrying out similar studies to meet the demand for animal protein in developing countries.The authors acknowledge the support provided by Tamil Nadu Veterinary and Animal Sciences University (TANUVAS) for successful completion of the study.Sakthivel, M.; Balasubramanyam, D.; Kumarasamy, P.; Raja, A.; Anilkumar, R.; Gopi, H.; Devaki, A. (2018). Genetic structure of a small closed population of the New Zealand white rabbit through pedigree analyses. World Rabbit Science. 26(2):101-112. doi:10.4995/wrs.2018.7426SWORD101112262Alderson G.I.H. 1992. A system to maximize the maintenance of genetic variability in small populations. In L. Alderson & I. Bodo (ed). Genetic Conservation of Domestic Livestock II. CABI, Wallingford, UK, 18-29.Boichard D., Maignel L., Verrier E. 1997. The value of using probabilities of gene origin to measure genetic variability in a population. Genet. Sel. Evol., 29: 5-23. https://doi.org/10.1186/1297-9686-29-1-5Cervantes I., Goyache F., Molina A., Valera M., Gutiérrez J.P. 2008. Application of individual increase in inbreeding to estimate realized effective sizes from real pedigrees. J. Anim. Breed. Genet., 125: 301-310. https://doi.org/10.1111/j.1439-0388.2008.00755.xDuchev Z., Distl O., Groeneveld E. 2006. Early warning system for loss of diversity in European livestock breeds. Arch. Anim. Breed., 49: 521-531. https://doi.org/10.5194/aab-49-521-2006Dunner S., Checa M.L., Gutierrez J.P., Martin J.P., Cañon J. 1998. Genetic analysis and management in small populations: the Asturcon pony as an example. Genetics Selection Evolution 30: 397-405. https://doi.org/10.1186/1297-9686-30-4-397Falconer D.S., Mackay T.F.C. 1996. Introduction to Quantitative Genetics. Longmans Green, Harlow, Essex, UK.Fernández J., Toro M.A., Caballero A. 2003. Fixed contributions designs vs. minimization of global conancestry to control inbreeding in small populations. Genetics, 165: 885-894.González-Recio O., López de Maturana E., Gutiérrez J.P. 2007. Inbreeding depression on female fertility and calving ease in Spanish dairy cattle. J. Dairy Sci., 90: 5744-5752. https://doi.org/10.3168/jds.2007-0203Gowane G.R., Chopra A., Misra S.S., Prince L.L.L. 2014. Genetic diversity of a nucleus flock of Malpura sheep through pedigree analyses. Small Ruminant Res., 120: 35-41. https://doi.org/10.1016/j.smallrumres.2014.04.016Goyache F., Gutiérrez J.P., Fernández I., Gomez E., Alvarez I., Díez J., Royo I.J. 2003. Using pedigree information to monitor genetic variability of endangered populations: the Xalda sheep breed of Asturias as an example. J. Anim. Breed. Genet., 120: 95-103. https://doi.org/10.1046/j.1439-0388.2003.00378.xGutiérrez J.P., Altarriba J., Díaz C., Quintanilla A.R., Cañón J., Piedrafita J. 2003. Genetic analysis of eight Spanish beef cattle breeds. Genet. Sel. Evol., 35: 43-64. https://doi.org/10.1051/gse:2002035Gutiérrez J.P., Cervantes I., Goyache F. 2009. Improving the estimation of realized effective population sizes in farm animals. J. Anim. Breed. Genet., 126: 327-332.https://doi.org/10.1111/j.1439-0388.2009.00810.xGutiérrez J.P., Cervantes I., Molina A., Valera M., Goyache F. 2008. Individual increase in inbreeding allows estimating realized effective sizes from pedigrees. Genet. Sel. Evol., 40: 359-378. https://doi.org/10.1051/gse:2008008Gutiérrez J.P., Goyache F. 2005. A note on ENDOG: a computer program for analyzing pedigree information. J. Anim. Breed. Genet., 122: 172-176. https://doi.org/10.1111/j.1439-0388.2005.00512.xHill W.G. 1979. A note on effective population size with overlapping generations. Genetics, 92: 317-322.Lacy R.C. 1989. Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents. Zoo Biol., 8: 111-123. https://doi.org/10.1002/zoo.1430080203Leroy G., Mary-Huard T., Verrier E., Danvy S., Charvolin E., Danchin-Burge C. 2013. Methods to estimate effective population size using pedigree data: examples in dog, sheep, cattle and horse. Genet. Sel. Evol., 45: 1-10. https://doi.org/10.1186/1297-9686-45-1Maignel L., Boichard D., Verrier E. 1996. Genetic variability of French dairy breeds estimated form pedigree information. Interbull Bull., 14: 49-54.Martín de la Rosa A.J., Cervantes I., Gutiérrez J.P. 2016. Equivalent effective population size mating as a useful tool in the genetic management of the Ibicenco rabbit breed (Conill Pages d'Eivissa). Czech J. Anim. Sci., 61: 108-116. https://doi.org/10.17221/8783-CJASMartínez R.A., García D., Gallego J.L., Onofre G., Pérez J., Cañón J. 2008. Genetic variability in Colombian Creole cattle populations estimated by pedigree information. J. Anim. Sci., 86: 545-552. https://doi.org/10.2527/jas.2007-0175Meuwissen T.H.E. 1991. Expectation and variance of genetic gain in open and closed nucleus and progeny testing schemes. Anim. Prod., 53: 133-141. https://doi.org/10.1017/S0003356100020043Meuwissen T.H.E. 2009. Towards consensus on how to measure neutral genetic diversity? J. Anim. Breed. Genet., 126: 333-334. https://doi.org/10.1111/j.1439-0388.2009.00839.xMeuwissen T.I., Luo Z. 1992. Computing inbreeding coefficients in large populations. Genet. Sel. Evol., 24: 305-303. https://doi.org/10.1186/1297-9686-24-4-305Miglior F., Burnside E.B., Dekkers J.C. 1995. Non additive genetic effects and inbreeding depression for somatic cell counts of Holstein cattle. J. Dairy Sci., 78: 1168-1173.https://doi.org/10.3168/jds.S0022-0302(95)76734-0Moura A.S.A.M.T., Polastre R., Wechsler F.S. 2000. Dam and litter inbreeding and environmental effects on litter performances in Botucatu rabbits. World Rabbit Sci., 8: 151-157. https://doi.org/10.4995/wrs.2000.433Nagy I., Curik I., Radnai I., Cervantes I., Gyovai P., Baumung R., Farkas J., Szendrő Zs. 2010. Genetic diversity and population structure of the synthetic Pannon White rabbit revealed by pedigree analyses. J. Anim.Sci., 88: 1267-1275. https://doi.org/10.2527/jas.2009-2273Nagy I., Farkas J., Onika-Szvath S., Radnai I., Szendrő Zs. 2011. Genetic parameters and inbreeding depression of litter weight in Pannon White rabbits. Agric. Conspec. Sci., 76: 231-233.Nagy I., Gyovai P., Farkas J., Radnai I., Eles V., Szendro Zs. 2012. Effects of selection and inbreeding on growth and carcass traits of Pannon terminal line rabbits. In Proc.. 10th World Rabbit Congress, 3-6 September 2012, Sharm El-Sheikh, Egypt, 93-96.Panetto J.C.C., Gutiérrez J.P., Ferraz J.B.S., Cunha D.G., Golden B.L. 2010. Assessment of inbreeding depression in a Guzerat dairy herd: Effects of individual increase in inbreeding coefficients on production and reproduction. J. Dairy Sci., 93: 4902-4912. https://doi.org/10.3168/jds.2010-3197Pedrosa V.B., Santana Jr. M.L., Oliveira P.S., Eler J.P., Ferraz J.B.S. 2010. Population structure and inbreeding effects on growth traits of Santa Ines sheep in Brazil. Small Ruminant Res., 93: 135-139. https://doi.org/10.1016/j.smallrumres.2010.05.012Pérez-Enciso M. 1995. Use of uncertain relationship matrix to compute effective population size. J. Anim. Breed. Genet., 112: 327-332. https://doi.org/10.1111/j.1439-0388.1995.tb00574.xPlaninc M., Kermauner A., Kovac M., Malovrh S. 2012. Pedigree analysis in the Sika rabbits in Slovenia. Acta Agr. Slov., Supplement 3: 171-173.Rafat S.A., Allain D., de Rochambeau H. 2009. Genetic description of a divergent selection experiment in Angora rabbits with overlapping generations. J. Anim. Breed. Genet., 126: 189-197. https://doi.org/10.1111/j.1439-0388.2008.00769.xSantana Jr M.L., Oliveira P.S., Eler J.P., Gutiérrez J.P., Ferraz J.B.S. 2012. Pedigree analysis and inbreeding depression on growth traits in Brazilian Marchigiana and Bonsmara breeds. J. Anim. Sci. 90: 99-108. https://doi.org/10.2527/jas.2011-4079Sorensen A.C., Sorensen M.K., Berg P. 2005. Inbreeding in Danish dairy cattle breed. J. Dairy Sci., 88: 1865-1872. https://doi.org/10.3168/jds.S0022-0302(05)72861-7Valera M., Molina A., Gutiérrez J.P., Gomes I., Goyache F. 2005. Pedigree analyses in the Andalusian horse: population structure, genetic variability and influence of the Carthusian strain. Livest. Prod. Sci., 95: 57-66. https://doi.org/10.1016/j.livprodsci.2004.12.004Venkataramanan R., Subramanian A., Sivaselvam S.N., Sivakumar T., Sreekumar C., Anilkumar R., Iyue M. 2013. Pedigree analysis of the Nilagiri sheep of South India. Anim. Genet. Resour., 53: 11-18. https://doi.org/10.1017/S2078633613000301Wright S. 1931. Evolution in Mendelian populations. Genetics, 16: 97-159

A pilot study on willingness to participate in future preventive HIV vaccine trials

Background & objectives: In India, phase-I human clinical trials for a preventive HIV vaccine are being conducted at Pune and Chennai Centres. In order to find out the willingness of populations at risk to participate in future preventive HIV vaccine trials (HIVVTs) and to assess the factors that enhance or deter them from participation, a study was conducted at Chennai and Madurai in Tamil Nadu. Methods: This cross-sectional study was conducted among transport workers, people attending sexually transmitted infection clinics, injection drug users, men having sex with men, women in sex industry and a representative sample of monogamous married women, by employing measurement scales. A structured questionnaire on knowledge and attitudes about the HIV vaccine was used to measure the participants’ knowledge and attitudes about HIV vaccine and HIVVTs. Results: Of the 112 participants, 67 (60%) were men. Mean age of the respondents was 32 yr; 68 per cent were high school educated. Majority of respondents were willing to participate in a future HIVVT and the reasons were altruism, protection from HIV, and support for the researchers. Major concerns were vaccine efficacy, side effects of the vaccine and the impact of a HIV vaccine on the participants’ lives. Majority (85%) agreed that sex without condom would not be safe despite the availability of an HIV vaccine. Interpretation & conclusion: It is likely that high-risk volunteers will be willing to enroll in HIVVTs. Barriers and concerns should be dealt with carefully by providing correct information. Also there is a need for more education to ensure participants’ understanding of key concepts of HIV vaccine trial

Care Seeking Behavior of Chest Symptomatics: A Community Based Study Done in South India after the Implementation of the RNTCP

INTRODUCTION: With the creation of the Revised National TB Control Programme (RNTCP), tuberculosis services have become decentralized and more accessible. A 1997 study prior to RNTCP implementation reported that most chest symptomatics accessed first private health care facilities and a general dissatisfaction with government health facilities. The study was repeated post-RNTCP implementation to gain insight into the current care seeking behavior of chest symptomatics. METHODOLOGY: A cross-sectional community-based study carried out between March-August 2008 in 4 sites (2 rural [R] and 2 urban [U]) from the same two districts of Chennai and Madurai, southern India, as in the 1997 study. Six hundred and forty chest symptomatics were identified (R 314; U 326), and detailed interviews were done for 606 (R311; U295). RESULTS: Prevalence of chest symptomatics in the urban and rural areas were 2.7% and 4.9% respectively (p<0.01), and was found to increase with age (Chi-square for trend, p<0.01). Longer delays in seeking care were seen amongst symptomatics above 45 years of age (p 0.01), and those who had taken previous TB treatment (p=0.05). Overall, 50% (222/444) of the chest symptomatics approached a government health care facility first (R 142 (61%); U 80 (38%), p=or  <0.001). This was significantly (p<0.001) more than were observed in the 1997 study, where only 38.4% approached a government facility first. Sixty two (28%) of the 222 made a second visit to a government facility (R26%; U31%), while 17% shifted to a private facility (R14%; U21%). Dissatisfaction with the health care facility was one of the major reasons expressed. CONCLUSIONS: It appears that the RNTCP has had an impact in the community with regard to the availability and accessibility of TB services in government health facilities. However the relatively high levels of subsequent shifting to private health facilities calls for urgent action to make government facilities more patients friendly with quality care facilities in the delivery of RNTCP services

Alcohol Use Disorders (AUD) among Tuberculosis Patients: A Study from Chennai, South India

BACKGROUND: Alcohol Use Disorders (AUDs) among tuberculosis (TB) patients are associated with nonadherence and poor treatment outcomes. Studies from Tuberculosis Research Centre (TRC), Chennai have reported that alcoholism has been one of the major reasons for default and mortality in under the DOTS programme in South India. Hence, it is planned to conduct a study to estimate prevalence of alcohol use and AUDs among TB patients attending the corporation health centres in Chennai, India. METHODOLOGY: This is a cross-sectional cohort study covering 10 corporation zones at Chennai and it included situational assessment followed by screening of TB patients by a WHO developed Alcohol Use Disorders Identification Test AUDIT scale. Four zones were randomly selected and all TB patients treated during July to September 2009 were screened with AUDIT scale for alcohol consumption. RESULTS: Out of 490 patients, 66% were males, 66% were 35 years and above, 57% were married, 58% were from the low monthly income group of <Rs 5000 per month. No females reported alcohol use. Overall, out of 490 TB pts, 29% (141) were found to consume alcohol. Among 141 current drinkers 52% (73) had an AUDIT score of >8. Age (>35 years), education (less educated), income (<Rs 5000 per month), marital status (separated/divorced) and treatment category (Category 2) were statistically significant for TB patients with alcohol use than those TB patients without alcohol use. CONCLUSIONS: AUD among TB patients needs to be addressed urgently and the findings suggest the importance of integrating alcohol treatment into TB care

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P &lt; 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

Experimental investigation of cryogenically treated HSS tool in turning on AISI1045 using fuzzy logic – Taguchi approach

This work depicts the effects of deep cryogenically treated high-speed steel on machining. In recent research, cryogenic treatment has been acknowledged for improving the life or performance of tool materials. Hence, tool materials such as the molybdenum-based high-speed tool steel are frequently used in the industry at present. Therefore, it is necessary to observe the tool performance in machining; the present research used medium carbon steel (AISI 1045) under dry turning based on the L9 orthogonal array. The effect of untreated and deep cryogenically treated tools on the turning of medium carbon steel is analyzed using the multi-input-multi-output fuzzy inference system with the Taguchi approach. The cutting speed, feed rate and depth of cut were the selected process parameters with an effect on surface roughness and the cutting tool edge temperature was also observed. The results reveal that surface roughness decreases and cutting tool edge temperature increases on increasing the cutting speed. This is followed by the feed rate and depth of cut. The deep cryogenically treated tool caused a reduction in surface roughness of about 11% while the cutting tool edge temperature reduction was about 23.76% higher than for an untreated tool. It was thus proved that the deep cryogenically treated tool achieved better performance on selected levels of the turning parameters

Stability of impulsive Hopfield neural networks with Markovian switching and time-varying delays

The paper is concerned with stability analysis for a class of impulsive Hopfield neural networks with Markovian jumping parameters and time-varying delays. The jumping parameters considered here are generated from a continuous-time discrete-state homogenous Markov process. By employing a Lyapunov functional approach, new delay-dependent stochastic stability criteria are obtained in terms of linear matrix inequalities (LMIs). The proposed criteria can be easily checked by using some standard numerical packages such as theMatlab LMI Toolbox. A numerical example is provided to show that the proposed results significantly improve the allowable upper bounds of delays over some results existing in the literature

PERFORMANCE COMPARISON OF EG-LDPC CODES WITH MAXIMUM LIKELIHOOD ALGORITHM OVER NON-BINARY LDPC CODES

ABSTRACT Error correcting coding has become one essential part in nearly all the modern data transmission and storage systems. Low density parity check (LDPC) codes are a class of linear block code has the superior performance closer to the Shannon&apos;s limit. In this paper two error correcting codes from the family of LDPC codes specifically Euclidean Geometry Low Density Parity Check (EG-LDPC) codes and Nonbinary low density parity check (NB-LDPC) codes are compared in terms of power consumption, number of iterations and other parameters. For better performance of EG-LDPC codes, Maximum Likelihood (ML) Algorithm was proposed. NB-LDPC codes can provide better error correcting performance with an average of 10 to 30 iterations but has high decoding complexity which can be improve by EG-LDPC code