Inbreeding affected differently on observations distribution of a growth trait in Iranian Baluchi sheep

Binabaj Fateme Bahri,Farhangfar Seyyed Homayoun,Jafari Majid 아세아·태평양축산학회 2021 Animal Bioscience Vol.34 No.4

Objective: Initial consequence of inbreeding is inbreeding depression which impairs the performance of growth, production, health, fertility and survival traits in different animal breeds and populations. The effect of inbreeding on economically important traits should be accurately estimated. The effect of inbreeding depression on growth traits in sheep has been reported in many breeds. Based on this, the main objective of the present research was to evaluate the impact of inbreeding on some growth traits of Iranian Baluchi sheep breed using quantile regression model. Methods: Pedigree and growth traits records of 13,633 Baluchi lambs born from year 1989 to 2016 were used in this research. The traits were birth weight, weaning weight, six-month weight, nine-month weight, and yearling weight. The contribution, inbreeding and co-ancestry software was used to calculate the pedigree statistics and inbreeding coefficients. To evaluate the impact of inbreeding on different quantiles of each growth trait, a series of quantile regression models were fitted using QUANTREG procedure of SAS software. Annual trend of inbreeding was also estimated fitting a simple linear regression of lamb’s inbreeding coefficient on the birth year. Results: Average inbreeding coefficient of the population was 1.63 percent. Annual increase rate of inbreeding of the flock was 0.11 percent (p<0.01). The results showed that the effect of inbreeding in different quantiles of growth traits is not similar. Also, inbreeding affected differently on growth traits, considering lambs’ sex and type of birth. Conclusion: Quantile regression revealed that inbreeding did not have similar effect on different quantiles of growth traits in Iranian Baluchi lambs indicating that at a given age and inbreeding coefficient, lambs with different sex and birth type were not equally influenced by inbreeding. Objective: Initial consequence of inbreeding is inbreeding depression which impairs the performance of growth, production, health, fertility and survival traits in different animal breeds and populations. The effect of inbreeding on economically important traits should be accurately estimated. The effect of inbreeding depression on growth traits in sheep has been reported in many breeds. Based on this, the main objective of the present research was to evaluate the impact of inbreeding on some growth traits of Iranian Baluchi sheep breed using quantile regression model.Methods: Pedigree and growth traits records of 13,633 Baluchi lambs born from year 1989 to 2016 were used in this research. The traits were birth weight, weaning weight, six-month weight, nine-month weight, and yearling weight. The contribution, inbreeding and co-ancestry software was used to calculate the pedigree statistics and inbreeding coefficients. To evaluate the impact of inbreeding on different quantiles of each growth trait, a series of quantile regression models were fitted using QUANTREG procedure of SAS software. Annual trend of inbreeding was also estimated fitting a simple linear regression of lamb’s inbreeding coefficient on the birth year.Results: Average inbreeding coefficient of the population was 1.63 percent. Annual increase rate of inbreeding of the flock was 0.11 percent (p<0.01). The results showed that the effect of inbreeding in different quantiles of growth traits is not similar. Also, inbreeding affected differently on growth traits, considering lambs’ sex and type of birth.Conclusion: Quantile regression revealed that inbreeding did not have similar effect on different quantiles of growth traits in Iranian Baluchi lambs indicating that at a given age and inbreeding coefficient, lambs with different sex and birth type were not equally influenced by inbreeding.

교수임용쿼터제가 교수 내적 충원에 미치는 영향 분석

임용순,유훼 한국교육학회 2013 敎育學硏究 Vol.51 No.1

While the negative thoughts on the faculty inbreeding have spread, not much academic interest and studies on this issue have been conducted. In order to know the effects of the faculty recruiting quarter system on faculty inbreeding, it is better to study the change of faculty inbreeding rates according to types of categorized universities than to analyze the change of faculty inbreeding rates for all universities. So, this study categorized universities into 4 kinds: traditional type, open type, closed type, and newly-established type. The purpose of this study is to analyze the effects of the faculty recruiting quarter system and to understand faculty inbreeding phenomenon deeply by analyzing how faculty inbreeding rates changed in each university type after the introduction of the faculty recruiting quarter system. In this respect, 20 universities which rank high on the professor occupation market were classified into 4 types according to faculty inbreeding rate and faculty external-supply rate. Each type's faculty inbreeding rate was then analyzed. As a result, the decreasing trend in faculty inbreeding rates resulting from the faculty recruiting quarter system is comprehensive; especially, it proved effective in the case of closed-type universities which showed unreasonably high faculty inbreeding rates. In conclusion, the faculty recruiting quarter system had positive effects on closed-type universities by regulating unreasonable faculty inbreeding. 한국고등교육에서 교수의 내적충원현상에 대한 부정적인 인식은 1999년에 교수임용쿼터제가 도입될 정도로 강한 편이라고 할 수 있다. 그러나 교수의 내적충원에 대한 강한 부정적 인식에 비해서 이에 대한 학문적 관심은 매우 낮은 것이 현실이다. 교수임용쿼터제가 대학 교수의 내적 충원에 어떤 영향을 미쳤는지를 연구하려면 단순히 모든 대학의 내적 충원율의 변화를 분석하는 것보다 대학들을 유형화하여 그 유형에 따른 내적 충원율의 변화를 연구할 필요가 있다. 본 연구는 대학들을 전통형, 개방형, 폐쇄형, 그리고 신설형으로 유형화하여 그 유형별로 대학의 교수 내적 충원율이 교수임용쿼터제가 도입 후에 어떻게 변화하는지를 분석함으로써 교수의 내적충원현상을 보다 심층적으로 이해하여 교수임용쿼터제의 영향을 의미 있게 분석하는데 그 목적을 두었다. 이런 점에서 출발하여 본 연구는 교수시장 점유율 상위 20개 대학을 내적 충원율과 외적 공급율을 기준으로 하여 네 가지 유형으로 분류한 다음 각 유형별로 대학의 내적 충원율 변화를 분석하였다. 분석 결과는 교수쿼터제의 도입으로 인한 교수 내적 충원율의 감소경향은 전반적으로 나타나지만, 경계해야할 연고성 내적 충원의 비율이 상대적으로 높은 폐쇄형 대학의 경우에서 그 감소경향이 더욱 뚜렷하게 나타났다. 이러한 결과를 통해 교수임용쿼터제가 폐쇄형 대학의 내적 충원을 억제하는데 긍정적인 영향을 미쳤음을 알 수 있다.

Academic inbreeding: exploring its characteristics and rationale in Japanese universities using a qualitative perspective

Hugo Duarte Alves Horta,Machi Sato,Akiyoshi Yonezawa 서울대학교 교육연구소 2011 Asia Pacific Education Review Vol.12 No.1

This study analyses why and how academic inbreeding as a recruitment practice continues to prevail in Japan, a country with a mature higher education system, where high rates of academic inbreeding endure in most of the research-oriented universities in spite of several higher education reforms. Based on a qualitative analysis, we disclose three characteristics that lead academics to become inbred at Japanese universities. One characteristic-the adoption of "open recruitment processes" in detriment of "closed recruitment processes"—changed over time, limiting academic inbreeding practices, but two other characteristics remained unchanged over time: the "one university learning experience" and the "concentration of doctoral supervisors at the same university". These latter characteristics represent difficult challenges to be tackled as they are also traditional characteristics of the Japanese higher education system. The research also shows that academic inbreeding practices are a means to assure organizational stability and institutional identity, features perceived as important by Japanese universities. A central challenge for the Japanese universities is then to guarantee these features without needing to rely on academic inbreeding practices to obtain them. However, devising policies to meet this challenge calls for institutional will to change, proactive strategies and time.

Inbreeding and Genetic Diversity in Three Imported Swine Breeds in China Using Pedigree Data

Tang, G.Q.,Xue, J.,Lian, M.J.,Yang, R.F.,Liu, T.F.,Zeng, Z.Y.,Jiang, A.A.,Jiang, Y.Z.,Zhu, L.,Bai, L.,Wang, Z.,Li, X.W. Asian Australasian Association of Animal Productio 2013 Animal Bioscience Vol.26 No.6

The accumulation of inbreeding and the loss of genetic diversity is a potential problem in the modern swine breeds in China. Therefore, the purpose of this study was to analyze the pedigrees of Chinese Duroc (CD), Landrace (CL) and Yorkshire (CY) swine to estimate the past and current rates of inbreeding, and to identify the main causes of genetic diversity loss. Pedigree files from CD, CL and CY containing, 4529, 16,776 and 22,600 records, respectively, were analyzed. Pedigree completeness indexes of the three breeds, accounting for one generation back, were 83.72, 93.93 and 93.59%, respectively. The estimated average annual inbreeding rates for CD, CL and CY in recent three years were 0.21, 0.19 and 0.13%, respectively. The estimated average percentage of genetic diversity loss within each breed in recent three years was about 8.92, 2.19, and 3.36%, respectively. The average relative proportion of genetic diversity loss due to unequal contributions of founders in CD, CL and CY was 69.09, 57.95 and 60.57%, and due to random genetic drift was 30.91, 42.05 and 39.43%, respectively. The estimated current effective population size for CD, CL and CY was 76, 117 and 202, respectively. Therefore, CD has been found to have lost considerable genetic diversity, demanding priority for optimizing the selection and mating to control future coancestry and inbreeding. Unequal contribution of founders was a major cause of genetic diversity loss in Chinese swine breeds and random genetic drift also showed substantial impact on the loss of diversity.

Academic inbreeding: local challenge, global problem

Philip G. Altbach,Maria Yudkevich,Laura E. Rumbley 서울대학교 교육연구소 2015 Asia Pacific Education Review Vol.16 No.3

‘‘Academic inbreeding’’—involving the appointment of faculty members who graduated from the institution employing them—is considered a small and peripheral aspect of the academic profession but is quite widespread globally. This paper analyzes the nature of inbreeding and its impact on universities. Data from eight countries where inbreeding is widespread are analyzed in order to examine the perceived impact of the phenomenon on academics and universities. Our analysis reveals that while inbreeding has deleterious effects on universities, it is widely perceived as a ‘‘normal’’ part of academic life— and some positive aspects are evident.

Maximizing the Selection Response by Optimal Quantitative Trait Loci Selection and Control of Inbreeding in a Population with Different Lifetimes between Sires and Dams

Tang, G.Q.,Li, X.W.,Zhu, L.,Shuai, S.R.,Bai, L. Asian Australasian Association of Animal Productio 2008 Animal Bioscience Vol.21 No.11

A rule was developed to constrain the annual rate of inbreeding to a predefined value in a population with different lifetimes between sires and dams, and to maximize the selection response over generations. This rule considers that the animals in a population should be divided into sex-age classes based on the theory of gene flow, and restricts the increase of average inbreeding coefficient for new offspring by limiting the increase of the mean additive genetic relationship for parents selected. The optimization problem of this rule was formulated as a quadratic programming problem. Inputs for the rule were the BLUP estimated breeding values, the additive genetic relationship matrix of all animals, and the long-term contributions of sex-age classes. Outputs were optimal number and contributions of selected animals. In addition, this rule was combined with the optimization of emphasis given to QTL, and further increased the genetic gain over the planning horizon. Stochastic simulations of closed nucleus schemes for pigs were used to investigate the potential advantages obtained from this rule by combining the standard QTL selection, optimal QTL selection and conventional BLUP selection. Results showed that the predefined rates of inbreeding were actually achieved by this rule in three selection strategies. The rule obtained up to 9.23% extra genetic gain over truncation selection at the same rates of inbreeding. The combination of the extended rule and the optimization of emphasis given to QTL allowed substantial increases in selection response at a fixed annual rate of inbreeding, and solved substantially the conflict between short-term and long-term selection response in QTL-assisted selection schemes.

Performance Evaluation of Karan Fries and Karan Swiss Cattle under Closed Breeding System

Singh, M.K.,Gurnani, M. Asian Australasian Association of Animal Productio 2004 Animal Bioscience Vol.17 No.1

The 490 and 380 performance records of Karan Fries and Karan Swiss cows developed through crossbreeding followed by inter-se mating were evaluated for production, reproduction performance and disposal rate. Duration of study (1982-92) was grouped into five periods (1982-83; 1984-85; 1986-87; 1988-89; 1990-92) and each year was divided into four seasons (Winter: Dec.-Jan.; Spring: Feb.-March; Summer: April-June; Rainy: July-Sept.; Autumn: Oct.-Nov). Data were also classified according to sire and level of inbreeding. The least squares means of FLY (first lactation yield -305 days), FLL (first lactation length), FSP (first service period), FDP (first dry period), FCI (first calving interval ), MY/FLL (milk yield per day of first lactation length), MY/FCI (milk yield per day of first calving interval), EBV (expected breeding value) and EBE (expected breeding efficiency) were $3,173{\pm}82$ kg, $34611{\pm}$days, $143{\pm}11$ days, $75{\pm}6$ days, $423{\pm}11$ days, $10.6{\pm}0.2$ kg, $8.9{\pm}0.2$ kg, $3,380{\pm}26$ kg, and $88.2{\pm}1.3$% respectively in Karan Fries. Corresponding estimates in Karan Swiss cows were $2,616{\pm}82$ kg, $328{\pm}8$ days, $148{\pm}12$ days, $103{\pm}9$ days, $435{\pm}13$ days, $8.9{\pm}0.2$ kg, $7.2{\pm}0.3$ kg, $2,924{\pm38}$ kg and $86.0{\pm}3.8$% respectively. The effect of sire was significant on FLY, MY/FLL, MY/FCI and EBV in both the herd (p<0.01). The 10 and 15% sires showed superiority (FLY) over herd average of 11 and 7% in Karan Fries and 32 and 21% in Karan Swiss cattle respectively. Inbreeding has adversely and significantly (p<0.05) affected the FLY, MY/FLL, MY/FCI and survivability of Karan Fries females; FDP and disposal through culling of Karan Swiss heifers. The Karan Fries heifers with inbreeding above 12.5% performed 16% lower FLY to herd average. The effect of season of calving was significant on FLL, FSP and FCI (p<0.05) in Karan Fries. Summer calvers ($361{\pm}12$) were have higher lactation length and autumn calvers ($329{\pm}14$) had minimum. Period of calving significantly influenced the FSP, FCI, MY/FLL and MY/FCI in Karan Fries and FLY, MY/FLL and MY/FCI in Karan Swiss. Production efficiency traits in Karan Fries herd witnessed higher yield in the last two periods whereas, Karan Swiss heifers showed fluctuating performance. The findings suggested judicious use of available genetic variability, keeping of inbreeding under safer level and managemental interventions for the consistent improvement of both herds.

Animal Breeding: What Does the Future Hold?

Eisen, E.J. Asian Australasian Association of Animal Productio 2007 Animal Bioscience Vol.20 No.3

An overview of developments important in the future of animal breeding is discussed. Examples from the application of quantitative genetic principles to selection in chickens and mice are given. Lessons to be learned from these species are that selection for production traits in livestock must also consider selection for reproduction and other fitness-related traits and inbreeding should be minimized. Short-term selection benefits of best linear unbiased predictor methodology must be weighed against long-term risks of increased rate of inbreeding. Different options have been developed to minimize inbreeding rates while maximizing selection response. Development of molecular genetic methods to search for quantitative trait loci provides the opportunity for incorporating marker-assisted selection and introgression as new tools for increasing efficiency of genetic improvement. Theoretical and computer simulation studies indicate that these methods hold great promise once genotyping costs are reduced to make the technology economically feasible. Cloning and transgenesis are not likely to contribute significantly to genetic improvement of livestock production in the near future.

Fine-scale genetic structure in populations of the spring ephemeral herb <i>Megaleranthis saniculifolia</i> (Ranunculaceae)

Chung, Mi Yoon,Nason, John D.,Ló,pez-Pujol, Jordi,Chung, Jae Min,Kim, Ki-Joong,Maki, Masayuki,Chung, Myong Gi GUSTAV FISCHER VERLAG 2018 FLORA -JENA- Vol.240 No.-

<P><B>Abstract</B></P> <P>Fine-scale genetic structure (FSGS) in plants occurs primarily through restricted seed dispersal. Analyses of FSGS have been used retrospectively to infer seed dispersal and other ecological processes. The spring ephemeral <I>Megaleranthis saniculifolia</I>, endemic to Korea, is insect-pollinated and has no special seed dispersal mechanism, and its seedling recruitment is quite low. Given these ecological and life-history traits, we expect that there would be significant FSGS in juveniles, which would persist into adult stage. Since <I>M. saniculifolia</I> is self-compatible and many adults produce 2–3 inflorescences, we expect considerable inbreeding. To test these predictions, we used allozyme-based <I>Sp</I> statistics to compare two undisturbed populations on Mt. Deogyu (DEO) and Mt. Taebaek (TAE), as well as between juveniles (J) and adults (A) stages. We also measured genetic diversity and inbreeding in each population. The two populations exhibited significant FSGS in both life stages. Although the strength of FSGS was reduced with increasing stage (J, <I>Sp</I> = 0.0313; A, <I>Sp</I> = 0.0178 in DEO and J, <I>Sp</I> = 0.0502; A, <I>Sp</I> = 0.0286 in TAE), differences in FSGS between stages and between populations were not significant. Within-population genetic diversity (mean <I>%P</I> = 27.0, <I>A</I> = 1.27, <I>H</I> <SUB>e</SUB> = 0.116) was relatively low and comparable to reference values for both endemic and narrowly-distributed plant species. Genetic differentiation between sites, however, was high (<I>F</I> <SUB>ST</SUB> = 0.465), and the two populations exhibited a significant deficit of heterozygotes (mean <I>F</I> <SUB>IS</SUB> = 0.289), primarily due to selfing and biparental inbreeding (effective selfing rate was ∼0.40). Our results revealed that the magnitude and spatial scale of FSGS in <I>M. saniculifolia</I> is strong and does not differ significantly with life-history stage. The strong FSGS, low within-population genetic variation, high between-population genetic differentiation, and high inbreeding are consistent with the species’ limited seed dispersal and a mixed mating system.</P> <P><B>Highlights</B></P> <P> <UL> <LI> We studied change of fine-scale genetic structure (FSGS) with life stage in two populations of <I>Megaleranthis saniculifolia</I>. </LI> <LI> The two populations exhibited significant FSGS in both life stages. </LI> <LI> However, differences in FSGS between stages and between populations were not significant. </LI> <LI> Low population densities of adults and juveniles would attribute to the similar magnitude and spatial extent of FSGS between stages. </LI> </UL> </P>

The Effect of Sub-division (Two or Three Sub-populations) of a Population on Genetic Gain and Genetic Diversity

Oikawa, T.,Matsui, H.,Sato, K. Asian Australasian Association of Animal Productio 2002 Animal Bioscience Vol.15 No.6

Breeding efficiencies were compared among three population schemes: a single population, a population with two subpopulations and a population with three sub-populations. A simulation experiment of selection was carried out for 10 generations with 20 replications each by comparing average breeding values and inbreeding coefficients among the three population schemes. Phenotypes of three traits were generated with a model comprising 36 loci, each with additive genetic effects and residuals distributed normally. Among the three population schemes, the single population scheme was definitely superior to the other two with regards to selection response and inbreeding. The multiple sub-population scheme was, however, considered to be an alternative population scheme when the difference in economic weights of the traits was small among the sub-populations, assuming moderate inbreeding depression for traits and crossbreeding. The scheme with two sub-populations had a higher genetic value than that with three subpopulations; however, the genetic values of the schemes were comparable when maternal heterosis was taken into account. The choice of population schemes may depend on the cost-sharing policy between the breeding population and the commercial population rather than just the breeding efficiency.