J Appl Genetics DOI 10.1007/s13353-014-0204-2
ANIMAL GENETICS • ORIGINAL PAPER
Linear and threshold analysis of direct and maternal genetic effects for secondary sex ratio in Iranian buffaloes Navid Ghavi Hossein-Zadeh
Received: 1 July 2013 / Revised: 8 November 2013 / Accepted: 3 March 2014 # Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2014
Abstract The objective of this study was to estimate variance components and genetic parameters for secondary sex ratio (SSR) in Iranian buffaloes. Calving records from April 1995 to June 2010 comprising 15,207 calving events from the first three lactations of 1066 buffalo herds of Iran were analyzed using linear and threshold animal models to estimate variance components, heritabilities and genetic correlations between direct and maternal genetic effects for SSR. Linear and threshold animal models included direct and maternal genetic effects with covariance between them and maternal permanent environmental effects were implemented by Gibbs sampling methodology. Posterior means of direct and maternal heritabilities and repeatability for SSR obtained from linear animal model were 0.15, 0.10, and 0.17, respectively. Threshold estimates of direct and maternal heritabilities and repeatability for SSR were 0.48, 0.27, and 0.52, respectively. The results showed that the correlations between direct and maternal genetic effects of SSR were negative and high in both models. In addition, the ratios of maternal permanent environmental variance were low. Exploitable genetic variation in SSR can take advantage of sexual dimorphism for economically important traits which may facilitate greater selection intensity and thus greater response to selection, as well as reducing the replacement costs. Threshold animal model may be applied in selection programs where animals are to be genetically ranked for female rate. Keywords Dairy buffalo . Genetic parameters . Linear model . Maternal effect . Threshold model N. Ghavi Hossein-Zadeh (*) Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran P. O. Box: 41635-1314 e-mail: [email protected] N. Ghavi Hossein-Zadeh e-mail: [email protected]
Introduction There are about 480,000 water buffaloes in Iran. Most of these animals are maintained in the south and northwest. All of the Iranian buffaloes are riverine (Naserian and Saremi 2007; Ghavi Hossein-Zadeh et al. 2012). Based on the theory of Fisher (1930), maternal contribution in male and female progenies is similar, and that secondary sex ratio (SSR; the proportion of males to females at birth) should be 50:50 if one sex does not require greater maternal contribution than the other. Nevertheless, there is compelling evidence to conclude that, under certain conditions, natural selection supports systematic deviations from expected sex ratio of 50:50. From evolutionary perspective, when there is the condition of equilibrium, i.e., the males to females proportion is equal, parental capability could be favorably affected by natural selection to alter sex ratio to the sex that would gain greater benefits of selection (Trivers and Willard 1973). This hypothesis proposed that SSR could be influenced through genotype by environment interaction effects or genetic components (Berry et al. 2011). Attempts to manipulate sex ratio have a long history in animal breeding because it is economically advantageous to increase the proportion of males in meat production breeds or to decrease it in dairy or egg production breeds. A possibility is to practice artificial selection for sex ratio but the extent of response depends crucially on the existence of genetic variance for this trait. If that is not the case, this possibility would be seriously compromised (Toro et al. 2006). Estimation of variance components (VC) has long been important in animal breeding. Accurate estimates of VC are important because genetic parameters are based upon (co) variance components, which must be accurately estimated. Threshold traits, such as SSR, are governed by polygenic inheritance, expressing themselves in two or more phenotypic categories. The genotype of the additive genetic effect is a component of the liability that varies according to the
J Appl Genetics
closeness to the threshold. The first category individuals may differ widely in whether they are near the threshold or far below it. Likewise, some will almost reach the threshold and are genetically close to those just above it (Lush 1994). Even a large change in an individual’s genotype will have no observable phenotypic effect unless the change moves the specific individual across the threshold. If it does, even a small change in the genotype will have a large phenotypic effect. Threshold models assume the existence of an underlying, unobservable normal distribution that is categorized through fixed thresholds. The phenotypes that are observed depend on the underlying tendency to develop in one form rather than the other, depending on where it is situated relative to the threshold (Dempster and Lerner 1950). The results of researches evaluating the genetic variation in SSR are generally variable and inconsistent (Chandler et al. 1998; Xu et al. 2000; Toro et al. 2006). Although estimates of variance components and heritabilities for SSR were available in the scientific literature (Xu et al. 2000; Roche et al. 2006a, b; Berry et al. 2011; Ghavi Hossein-Zadeh 2012), but estimates of variance components and heritabilities for SSR in buffalo are very scarce in the literature. Therefore, the objective of this study was to estimate variance components and genetic parameters for SSR in Iranian buffaloes using Gibbs sampling algorithm in Bayesian methodology. The results of the current study would indicate the possibility of implementing genetic selection for female rate in Iranian buffaloes. Also the current estimates of genetic parameters for SSR could be used for designing future selection schemes in which genetic improvement in SSR might be one of the main parts of selection goals.
Materials and methods Data Calving records from April 1995 to June 2010 comprising 15,207 calving events from the first three lactations of 1066 buffalo herds of Iran were included in the data set. Information for individual calving events, including herd identification, animal identification, sire identification, dam identification, calving date, parity, age of dam at calving, and calf sex were included in the data set. First, second, and third parities accounted for 33.9 %, 33.8 %, and 32.3 % of calving records, respectively. Male births accounted for 54.3 %, 53.8 %, and 53.2 % of the total observations in the first, second, and third parities, respectively. The calf sex was coded as a dichotomous variable (1=male; 2=female). The data were screened several times and defective and doubtful data were deleted. Therefore, records with no information on dam parity number were removed from the dataset. No multiple births were included in the analysis. Calves with no records of their sex
were removed. Also, animal registration numbers lower than the numbers of their parents were left out. Months of calving were grouped into four seasons: January through March (winter), April through June (spring), July through September (summer), and October through December (fall). The buffalo farming system in Iran is based on smallholders (99 percent); most of the herds have an average of five animals; a few herds have between 20 and 50 buffaloes and some of them have 300 buffaloes. Smallholders manage their animals according to the opportunities offered by the environment: on pasture, stubble, shrubs, and grass. Most of them obtain their feeding by grazing along water sources: streams, rivers; ponds, lakes, integrated with the following products: citrus peels and pulp, sugar cane wastage, etc. In Khuzestan, buffaloes are raised outdoors throughout the year; but in the north-west they are housed in the autumn and winter. Buffalo farming in Iran can be considered to be at a good level since the owned or rented properties are of a large size and the land available for buffalo farming is also extensive. Buffalo farming has been a traditional activity for many decades (Kianzad 2000). There are no breeding stations in Iran, but two performance testing/AI stations, one in West Azerbaijan (Jabal station), keeping ten bulls and one in Kuhzestan which will be inaugurated in 2004 with a capacity of 50 bulls (Borghese 2005). Bulls are preselected by provincial experts based on maternal performance and body type and then taken to the station at the age of between 6 and 18 months. Genetic merit of these bulls is estimated against an animal model which includes milk and fat yield, as well as body type parameters. Twenty-thousand semen doses are produced yearly by the Jabal AI station. Artificial insemination is still performed at a low level, since the activity only started in the year 2000; it is estimated that about 200 recorded buffaloes are offered AI yearly; two inseminations at each oestrus are always offered, the conception at the first oestrus being 50 percent (Borghese 2005). In addition to the data file, there was a pedigree file in which the number of animals (in total), sires, dams, inbred animals, founders, and non-founders were 38172, 534, 5652, 162, 28867, and 9305, respectively. Analysis Model specification and the choice of fixed effects to be considered was based on the backward elimination method and the fit of all models was evaluated by using the Hosmer and Lemeshow goodness-of-fit test (Hosmer and Lemeshow 2000) of the LOGISTIC procedure of SAS (2002) by including the “lackfit” option in the model statement. Variables which were significant by the Wald statistic at P0.05), and its corresponding value was −0.13±0.15. Estimates of direct genetic trends from linear and threshold models of analysis were positive and significant (P
ANIMAL GENETICS • ORIGINAL PAPER
Linear and threshold analysis of direct and maternal genetic effects for secondary sex ratio in Iranian buffaloes Navid Ghavi Hossein-Zadeh
Received: 1 July 2013 / Revised: 8 November 2013 / Accepted: 3 March 2014 # Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2014
Abstract The objective of this study was to estimate variance components and genetic parameters for secondary sex ratio (SSR) in Iranian buffaloes. Calving records from April 1995 to June 2010 comprising 15,207 calving events from the first three lactations of 1066 buffalo herds of Iran were analyzed using linear and threshold animal models to estimate variance components, heritabilities and genetic correlations between direct and maternal genetic effects for SSR. Linear and threshold animal models included direct and maternal genetic effects with covariance between them and maternal permanent environmental effects were implemented by Gibbs sampling methodology. Posterior means of direct and maternal heritabilities and repeatability for SSR obtained from linear animal model were 0.15, 0.10, and 0.17, respectively. Threshold estimates of direct and maternal heritabilities and repeatability for SSR were 0.48, 0.27, and 0.52, respectively. The results showed that the correlations between direct and maternal genetic effects of SSR were negative and high in both models. In addition, the ratios of maternal permanent environmental variance were low. Exploitable genetic variation in SSR can take advantage of sexual dimorphism for economically important traits which may facilitate greater selection intensity and thus greater response to selection, as well as reducing the replacement costs. Threshold animal model may be applied in selection programs where animals are to be genetically ranked for female rate. Keywords Dairy buffalo . Genetic parameters . Linear model . Maternal effect . Threshold model N. Ghavi Hossein-Zadeh (*) Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran P. O. Box: 41635-1314 e-mail: [email protected] N. Ghavi Hossein-Zadeh e-mail: [email protected]
Introduction There are about 480,000 water buffaloes in Iran. Most of these animals are maintained in the south and northwest. All of the Iranian buffaloes are riverine (Naserian and Saremi 2007; Ghavi Hossein-Zadeh et al. 2012). Based on the theory of Fisher (1930), maternal contribution in male and female progenies is similar, and that secondary sex ratio (SSR; the proportion of males to females at birth) should be 50:50 if one sex does not require greater maternal contribution than the other. Nevertheless, there is compelling evidence to conclude that, under certain conditions, natural selection supports systematic deviations from expected sex ratio of 50:50. From evolutionary perspective, when there is the condition of equilibrium, i.e., the males to females proportion is equal, parental capability could be favorably affected by natural selection to alter sex ratio to the sex that would gain greater benefits of selection (Trivers and Willard 1973). This hypothesis proposed that SSR could be influenced through genotype by environment interaction effects or genetic components (Berry et al. 2011). Attempts to manipulate sex ratio have a long history in animal breeding because it is economically advantageous to increase the proportion of males in meat production breeds or to decrease it in dairy or egg production breeds. A possibility is to practice artificial selection for sex ratio but the extent of response depends crucially on the existence of genetic variance for this trait. If that is not the case, this possibility would be seriously compromised (Toro et al. 2006). Estimation of variance components (VC) has long been important in animal breeding. Accurate estimates of VC are important because genetic parameters are based upon (co) variance components, which must be accurately estimated. Threshold traits, such as SSR, are governed by polygenic inheritance, expressing themselves in two or more phenotypic categories. The genotype of the additive genetic effect is a component of the liability that varies according to the
J Appl Genetics
closeness to the threshold. The first category individuals may differ widely in whether they are near the threshold or far below it. Likewise, some will almost reach the threshold and are genetically close to those just above it (Lush 1994). Even a large change in an individual’s genotype will have no observable phenotypic effect unless the change moves the specific individual across the threshold. If it does, even a small change in the genotype will have a large phenotypic effect. Threshold models assume the existence of an underlying, unobservable normal distribution that is categorized through fixed thresholds. The phenotypes that are observed depend on the underlying tendency to develop in one form rather than the other, depending on where it is situated relative to the threshold (Dempster and Lerner 1950). The results of researches evaluating the genetic variation in SSR are generally variable and inconsistent (Chandler et al. 1998; Xu et al. 2000; Toro et al. 2006). Although estimates of variance components and heritabilities for SSR were available in the scientific literature (Xu et al. 2000; Roche et al. 2006a, b; Berry et al. 2011; Ghavi Hossein-Zadeh 2012), but estimates of variance components and heritabilities for SSR in buffalo are very scarce in the literature. Therefore, the objective of this study was to estimate variance components and genetic parameters for SSR in Iranian buffaloes using Gibbs sampling algorithm in Bayesian methodology. The results of the current study would indicate the possibility of implementing genetic selection for female rate in Iranian buffaloes. Also the current estimates of genetic parameters for SSR could be used for designing future selection schemes in which genetic improvement in SSR might be one of the main parts of selection goals.
Materials and methods Data Calving records from April 1995 to June 2010 comprising 15,207 calving events from the first three lactations of 1066 buffalo herds of Iran were included in the data set. Information for individual calving events, including herd identification, animal identification, sire identification, dam identification, calving date, parity, age of dam at calving, and calf sex were included in the data set. First, second, and third parities accounted for 33.9 %, 33.8 %, and 32.3 % of calving records, respectively. Male births accounted for 54.3 %, 53.8 %, and 53.2 % of the total observations in the first, second, and third parities, respectively. The calf sex was coded as a dichotomous variable (1=male; 2=female). The data were screened several times and defective and doubtful data were deleted. Therefore, records with no information on dam parity number were removed from the dataset. No multiple births were included in the analysis. Calves with no records of their sex
were removed. Also, animal registration numbers lower than the numbers of their parents were left out. Months of calving were grouped into four seasons: January through March (winter), April through June (spring), July through September (summer), and October through December (fall). The buffalo farming system in Iran is based on smallholders (99 percent); most of the herds have an average of five animals; a few herds have between 20 and 50 buffaloes and some of them have 300 buffaloes. Smallholders manage their animals according to the opportunities offered by the environment: on pasture, stubble, shrubs, and grass. Most of them obtain their feeding by grazing along water sources: streams, rivers; ponds, lakes, integrated with the following products: citrus peels and pulp, sugar cane wastage, etc. In Khuzestan, buffaloes are raised outdoors throughout the year; but in the north-west they are housed in the autumn and winter. Buffalo farming in Iran can be considered to be at a good level since the owned or rented properties are of a large size and the land available for buffalo farming is also extensive. Buffalo farming has been a traditional activity for many decades (Kianzad 2000). There are no breeding stations in Iran, but two performance testing/AI stations, one in West Azerbaijan (Jabal station), keeping ten bulls and one in Kuhzestan which will be inaugurated in 2004 with a capacity of 50 bulls (Borghese 2005). Bulls are preselected by provincial experts based on maternal performance and body type and then taken to the station at the age of between 6 and 18 months. Genetic merit of these bulls is estimated against an animal model which includes milk and fat yield, as well as body type parameters. Twenty-thousand semen doses are produced yearly by the Jabal AI station. Artificial insemination is still performed at a low level, since the activity only started in the year 2000; it is estimated that about 200 recorded buffaloes are offered AI yearly; two inseminations at each oestrus are always offered, the conception at the first oestrus being 50 percent (Borghese 2005). In addition to the data file, there was a pedigree file in which the number of animals (in total), sires, dams, inbred animals, founders, and non-founders were 38172, 534, 5652, 162, 28867, and 9305, respectively. Analysis Model specification and the choice of fixed effects to be considered was based on the backward elimination method and the fit of all models was evaluated by using the Hosmer and Lemeshow goodness-of-fit test (Hosmer and Lemeshow 2000) of the LOGISTIC procedure of SAS (2002) by including the “lackfit” option in the model statement. Variables which were significant by the Wald statistic at P0.05), and its corresponding value was −0.13±0.15. Estimates of direct genetic trends from linear and threshold models of analysis were positive and significant (P
