Livestock Fish Flagship: Animal Genetics

Permanent URI for this collectionhttps://hdl.handle.net/10568/16628

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From farmyard to the lab
(Journal Article, 2012-11-23) Lawler, A.
Chinese biologist Jianlin Han is attempting to breed better red jungle fowl to benefit the rural poor and gather a massive data set to understand the genetic underpinnings of the domestic chicken.
In search of the wild chicken
(Journal Article, 2012-11-23) Lawler, A.
Researchers are melding genetics and archaeology to close in on the origin of the world's most common bird—and potentially help protect a major source of animal protein.
Genetic evaluation of growth and survival at 6 weeks old fry of Egyptian Nile Tilapia (Oreochromis niloticus) between improved Abbassa and commercial Manzala strains in a diallel crossing
(Journal Article, 2016) Said, M.M.; Mekkawy, Wagdy
GnRH and prostaglandin- based synchronization protocols as alternatives to progestogen- based treatments in sheep
(Journal Article, 2016-12) Rekik, Mourad; Haile, Aynalem; Abebe, A.; Muluneh, D.; Goshme, Shenkute; Ben Salem, I.; Hilali, M. El-Dine; Lassoued, N.; Chanyalew, Y.; Rischkowsky, Barbara A.
The study investigated, for cycling sheep, synchronizing protocols simultaneously to the standard “P” protocol using progestogens priming with intravaginal devices and gonadotropin. In November 2014, 90 adult Menz ewes were assigned to either the “P” protocol, “PGF” treatment where oestrus and ovulation were synchronized using two injections of prostaglandin 11 days apart or a “GnRH” treatment where the ewes had their oestrus and ovulation synchronized with GnRH (day 0)–prostaglandin (day 6)–GnRH (day 9) sequence. The ewes were naturally mated at the induced oestrus and the following 36 days. Plasma progesterone revealed that 92% of the ewes were ovulating before synchronization and all, except one, ovulated in response to the applied treatments. All “P” ewes exhibited oestrus during the 96‐hr period after the end of the treatments in comparison with only 79.3% and 73.3% for “PGF” and “GnRH” ewes, respectively (p < .05). Onset and duration of oestrus were affected by the hormonal treatment (p < .05); “GnRH” ewes showed oestrus earliest and had the shortest oestrous duration. Lambing rate from mating at the induced oestrus was lower for “P” than for “PGF” ewes (55.6% and 79.3%, respectively; p < .05). The same trait was also lower for “P” than for “PGF” and “GnRH” ewes (70.4%, 89.7% and 86.7%, respectively; p < .05) following the 36‐day mating period. Prostaglandin and GnRH analogue‐based protocols are promising alternatives for both controlled natural mating and fixed insemination of Menz sheep after the rainy season when most animals are spontaneously cycling.
Do Texas Angora bucks improve mohair weight and quality traits of Tajik Angora goats? Short communication
(Journal Article, 2016-01) Mueller, J.P.; Kosimov, M.A.; Kosimov F.F.; Brent, L.; Nishanov, N.; Rischkowsky, Barbara A.
With the main objective of improving Tajik mohair quantity and quality, frozen semen from eight top performance tested Texan Angora bucks was imported and used on 459 selected local goats from 11 farmers in two insemination seasons. Conception rates in both seasons were very low. Sixty six Texan x Tajik crossbred progeny were compared with 308 contemporary Tajik controls. Early live body weights, mohair quantity and mohair quality data were collected and genotypes compared after correcting for season, farm and sex of progeny, fitting age as a co-variable. Body weights at birth were higher in crossbreds (2.39 vs. 2.19 kg, P < 0.001) but body weights at 6 weeks, 6 months and 12 months were similar. Fleece weights at first shearing were much higher in crossbreds (1.16 vs. 0.68 kg, P < 0.001) as well as staple length (19.6 vs. 16.3 cm, P < 0.001). Fibre diameter at first shearing tended to be lower in crossbreds (24.2 vs. 25.9 μm, P = 0.088) and was lower at second shearing (29.2 vs. 31.5 μm, P < 0.05). Med fibre percentage (proportion of fibres with a medulla less than 60% of its diameter) was lower in crossbreds at first (1.70 vs. 4.12%, P < 0.05) and second shearing (1.86 vs. 3.01%, P < 0.05). Kemp fibre percentages (proportion of fibres with a medulla equal or larger than 60% of its diameter) were very low and not significantly different between genotypes. There was no difference in visual assessment of fibre fineness but the proportion of progeny classed as superior for overall quality was much higher in crossbreds (39/52 vs. 99/290, P < 0001). It was suggested to monitor later life performance of crossbreds and it is concluded that the introduction of Texan Angora bucks improved Tajik goats. Further improvement may be based on cooperative breeding of Texan progeny and outstanding local goats on one site and distribution to multipliers in different communities.
Genetic diversity and structure of goats within an early livestock dispersal area in Eastern North Africa
(Journal Article, 2016-03-15) Elbeltagy, A.R.; Aboul-Naga, A.M.; Hassen, H.; Solouma, G.M.; Rischkowsky, Barbara A.; Wacharo, J.M.
In this study we genotyped 14 microsatellites to assess genetic diversity, population stratification and demographic dynamics using Egyptian local goats (Zaraibi, Baladi, Saidi and Barki) and the Shami (Damascus) goat from the Middle East and West Asia close to the geographic center of goat domestication. We observed high levels of allelic and genetic diversity that was partitioned into six gene pools. Cluster analyses separated Zaraibi and Shami, which were identified with independent gene pools of potential ancestral backgrounds. The analyses provided further evidence for extensive sharing of genetic variation, revealing, varying levels of admixture among the study populations. This finding was supported by AMOVA analysis, which indicated that the proportion of genetic variation due to differences among populations was 7.06%. Our results most likely indicate that multiple waves of introduction of diverse gene pools and recent flock intermixing has created and maintained a unique set of caprine biodiversity in Eastern North Africa emphasizing the importance of the region as one of the hotbeds of African animal biodiversity.
Combining revealed and stated preferences to define goat breeding objectives in Ethiopia
(Journal Article, 2016-09) Woldu, T.; Markemann, A.; Reiber, Christoph; Girma T. K.; Zárate, Anne Valle
Participatory definition of trait preference and pastorals’ indigenous knowledge on goat breeding strategy around Aysaita district, Ethiopia
(Journal Article, 2015) Misbah, F.; Belay, B.; Haile, Aynalem
Goat production systems in Punjab, Pakistan
(Journal Article, 2015-06-15) Muhammad, M.S.; Abdullah, M.; Javed, K.; Khan, M.S.; Jabbar, M.A.
The present study was conducted to explore the rural goat production system and know the involvement of rural families in this enterprise by using household surveys. The survey was conducted in six villages at two experimental sites (Bahawalpur and Faisalabad). Fifty five households from each village were interviewed using stratified random sampling method. Information about livestock inventory, production of goat, type of production systems and parameters, management of goat, and breeding strategies were recorded. Household heads were the incharge of farm activities at both sites in most of the cases (91.40% vs 91.97%). Interests in goat keeping were similar at both sites (83.11% & 80.15%). Flock sizes averaged 7.14 and 4.87 at both sites, respectively. Majority of the farmers kept goats mainly for home consumption (23.03% and 17.93% at Sites I and II, respectively). Main production system adopted in the spring (58.5% and 55.4%), summer (52.9% & 51.2%), rainy (57.7% & 52.9%) and winter (60.2% & 56.3%) seasons were intensive and semi-intensive at Sites I and II, respectively. Types of housing during day time were free range (47.9% & 35.3%) and during night confinement in sheds (87.0% & 72.9%) at Sites I and II, respectively. Most of the farmers' time was spent on marketing goats at Sites I and II (1.15 vs 1.95 Hrs), respectively. Main feeding regime was grazing and more farmers used grazing at Site-I (45.45%) as compared to Site-II (5.80%) while feed ingredients were used by the majority of farmers at Site-II (26.81%) as compared to Site-I (14.94%). Twice a day watering was common practice at both sites. It is suggested that long term policies should be made in the light of present findings to improve the productivity of rural production systems and facilitate the farmers to the maximum for improved goat production.
Differences in sexual size dimorphism among farmed tilapia species and strains undergoing genetic improvement for body weight
(Journal Article, 2015-05) Lind, C.E.; Safari, A.; Agyakwah, Seth K.; Attipoe, F.Y.K.; El-Naggar, G.O.; Hamzah, A.; Hulata, G.; Ibrahim, N.A.; Khaw, H.L.; Nguyen, N.H.; Maluwa, A.O.; Zaid, M.; Zak, T.; Ponzoni, R.W.
Many tilapia (Oreochromis spp.) farmers produce all-male populations because of the superior growth rate of males compared to females. To investigate differences in body weight at harvest of males and females among different tilapia strains, we analyzed data from 62,787 individuals collected from pedigreed breeding programs of O. niloticus (GIFT from Malaysia, the Abbassa line from Egypt, and the Akosombo line from Ghana), O. shiranus (the Bunda College-Domasi selection line), O. aureus (a selection line under development in Abbassa, Egypt, and a selection line from Israel) and a synthetic selection line of Red tilapia under development in Jitra, Malaysia, derived from stock from Malaysia, Taiwan and Thailand (O. sp.). Mixed models were separately fitted to the data from each selection line. There was a significant sex effect in all strains (P < 0.001). A significant (P < 0.001) sex by generation interaction was observed in all strains (scale effect, not reversal of rankings), except Red tilapia and O. shiranus. Least squares means showed a large range in the magnitude of body weight differences between sexes across the seven strains. The largest percentage difference between females and males was in O. aureus from Egypt (female body weight was 52.2% that of males at harvest), whereas the smallest difference was observed in the GIFT strain of O. niloticus (female body weight 84.7% that of males). Female to male body weight percentages for Red tilapia, O. shiranus, Egypt O. niloticus, Israeli O. aureus and Ghana O. niloticus were 81.3, 81.0, 69.1, 61.7 and 61.0, respectively. We discuss the results in relation to the potential productivity improvements due to superior growth rates of all-male culture compared to mixed-sex culture in tilapia populations differing in the female to male body weight ratio.
Genetic parameters for survival during the grow-out period in the GIFT strain of Nile tilapia (Oreochromis niloticus) and correlated response to selection for harvest weight
(Journal Article, 2017-01) Hamzah, A.; Mekkawy, Wagdy; Hooi Ling Khaw; Nguyen Hong Nguyen; Hoong Yip Yee; Abu Bakar, Khairul Rizal; Nor, S.A.M.; Ponzoni, R.W.
The aims of this study were the estimation of genetic parameters for survival rate from tagging until harvest and the evaluation of the correlated response in survival rate to selection for harvest weight in the genetically improved farmed tilapia (GIFT) strain. The heritability for survival rate was low (0.038), and so was its genetic correlation with harvest weight (0.065), suggesting that selecting for the latter trait would have had no effect on survival. The calculation of the probability of survival by spawning season and line, fitting a model that included the random effects of individual animal and common environment, confirmed this prediction. There were very small and variable between line differences in the probability of survival, which generally favoured the selection line. We conclude that the focus of the GIFT programme on improving harvest weight was not detrimental to the survival of the fish during the grow-out phase.
Survival, male morphotypes, female and male proportion, female reproductive status and tag loss in crosses among three populations of freshwater prawn Macrobrachium rosenbergii (de Man) in India
(Journal Article, 2015-11) Pillai, B.R.; Mahapatra, K.D.; Ponzoni, R.W.; Sahoo, L.; Lalrinsanga, P.L.; Mekkawy, Wagdy; Khaw, H.L.; Nguyen, N.H.; Mohanty, Samarendu; Sahu, S.; Patra, G.
The present study examined the variation in survival, proportion of male morphotypes, female and male proportion, female reproductive status and tag losses in nine crosses from a complete (3 × 3) diallel mating of three populations of Macrobrachium rosenbergii in India. The populations originated from Gujarat (north-west), Kerala (south-west) and Odisha (east), representing different agro-ecological regions in India. Progeny from 60 families (4773 juveniles) were individually tagged and reared for 16–17 weeks in earthen ponds. Binary logistic regression was used to analyse the data. Survival rate was greatest (0.88) for Kerala × Odisha (KO; the first letter represents the sire), whereas it was lowest (0.75) for both Kerala × Kerala (KK) and Gujarat × Kerala (GK). Significantly greater proportions of large male morphotypes were observed in KK cross and in combinations involving Kerala population. The highest proportion of immature females, as well as of non-berried females, was observed in the Odisha × Odisha (OO) cross. Tag loss was greatest for KK (0.35) and lowest for GG (0.19). We found significant variations among crosses for all studied traits suggesting the possibility of including them in genetic improvement programmes of this species.
Genetic variance for uniformity of harvest weight in Nile tilapia (Oreochromis niloticus)
(Journal Article, 2016-01) Hooi Ling Khaw; Ponzoni, R.W.; Hoong Yip Yee; Aziz, M.A.; Mulder, H.A.; Marjanovic, J.; Bijma, P.
Competition for resources is common in aquaculture, which inflates the variability of fish body weight. Selective breeding is one of the effective approaches that may enable a reduction of size variability (or increase in uniformity) for body weight by genetic means. The genetic variance of uniformity is commonly known as genetic heterogeneity of environmental variance for particular traits. The data collected from a social interaction experiment were used to investigate the presence of genetic variation in heterogeneity of environmental variance for harvest weight in the GIFT strain. A total of 944 records pooled (by family-group) from 6330 individual harvest weights were used in the analysis. For the estimation of genetic parameters we fitted a bivariate sire–dam model to harvest weight and its standard deviation. To normalize the residuals, individual harvest weight was Box–Cox transformed. The heritability (at the family by group level) and genetic coefficient of variation for standard deviation of Box–Cox transformed harvest weight (0.23 and 0.17, respectively) indicated that uniformity of harvest weight was partly under genetic control. In addition, we found a very low genetic relationship between Box–Cox transformed harvest weight and its standard deviation, rA = 0.095 ± 0.183. Hence, these two traits are unrelated and can be selected in different directions using index selection, namely, aiming to increase growth rate while decreasing size variation. We conclude that there is potential to increase harvest weight and its uniformity by selective breeding in the GIFT strain of farmed tilapia.
Effect of female weight on reproductive performance of Nile tilapia (Oreochromis niloticus)
(Journal Article, 2014) Mohammed, W.O.; Shehata, S.M.A.; El-Naggar, G.O.; Khater, A.M.M.; Mahmoud, M.K.
Genetic parameter estimates for growth and reproductive trait of sheep for genetic improvement and designing breeding program in Ethiopia: A review
(Journal Article, 2014) Mekuriaw, S.; Haile, Aynalem
Small ruminants in general and sheep in particular are important investments in the highlands of Ethiopia. Genetic and environmental improvements offer an opportunity to increase production from existing animal resources. Development of effective genetic evaluation and improvement programs requires knowledge of the genetic parameters (genetic variance of each trait and covariance among traits) for economically important production traits. Direct heritability estimates for birth weight of Afar sheep (0.13 to 0.38) and BHS (0.20 to 0.58) using univariate analysis; for Horro sheep (0.18 - 0.32) and Menz sheep (0.46) by fitting a multi-trait individual animal model. The weaning weight direct heritability estimates for sheep in Ethiopia, Afar sheep (0.11 - 0.37) and BHS (0.00 - 0.29), Horro sheep (0.10 - 0.26) and Menz sheep (0.48). Fertility, litter size and lamb survival are the components of the overall ewe reproduction traits. It appears that heritability estimates of these traits are rather low and reflect the generally small genetic variance for most reproductive traits. Moreover, litter size has a higher heritability (0.16 - 0.19) than the other components traits like fertility (0.10) and survival rate (0.07 - 0.09) for Awassi sheep breed. Genetic correlations among most pairs of traits were higher than the corresponding phenotypic correlations. Live weights measured at successive ages were highly correlated, ranging from 0.61 to 0.98 for Menz sheep. Genetic correlations were also high between pre-weaning daily gain and weaning weight for Afar and BHS sheep. Except for Blackhead Somali sheep breed which has high genetic correlation between birth weight and weaning weight, Horro, Menz and Afar sheep have high genetic correlation between post-weaning weight traits. This indicates that selection for one trait improves the other trait in those sheep breeds. In order to develop alternative improvement program for sheep breeds in Ethiopia, estimates of genetic parameters for economical growth and reproduction traits should be done by designing experiments since the information on most sheep breed is nonexistence.
Genetic diversity and population structure of the indigenous sheep in Kenya based on microsatellite analysis: Implications for their conservation
(Journal Article, 2014-07-20) Mukhongo, D.M.; Okeyo Mwai, Ally; Tapio, M.; Muigai, Anne W.T.
Optimizing the use of breed types in developing country livestock production systems: A neglected research area
(Journal Article, 2014-10) Marshall, Karen
Developing country livestock production systems are diverse and dynamic, and include those where existing indigenous breeds are currently optimal and likely to remain so, those where non-indigenous breed types are already in common use, and systems that are changing, such as by intensification, where the introduction of new breed types represents significant opportunities. These include opportunities to improve the livelihood of the world's poor, increase food and nutrition security and enhance environmental sustainability. At present, very little research has focused on this issue, such that significant knowledge gaps in relation to breed-change interventions remain. The purpose of this study is to raise awareness of this issue and suggests strategic research areas to begin filling these knowledge gaps. Such strategic research would include (i) assessing the impact of differing breed types in developing country livestock productions systems, from a range of viewpoints including intrahousehold livelihood benefit, food and nutrition security at different scales, and environmental sustainability; (ii) identification of specific livestock production systems within developing countries, and the type of livestock keepers within these system, that are most likely to benefit from new breed types; and (iii) identification of new breed types as candidates for in-situ testing within these systems, such as through the use of spatial analysis to identify similar production environments combined with community acceptance studies. Results of these studies would primarily assist stakeholders in agriculture, including both policy makers and livestock keepers, to make informed decisions on the potential use of new breed types.
Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia
(Journal Article, 2014-10) Edea, Zewdu; Dadi, H.; Kim, S.W.; Park, J.H.; Shin, G.H.; Dessie, Tadelle; Kim, K.S.
Despite the wide range of observed phenotypic diversities and adaptation to different ecological conditions, little has been studied regarding the genetics of adaptation in the genome of indigenous cattle breeds of developing countries. Here, we investigated the linkage disequilibrium (LD) and identified the subset of outlier loci that are highly differentiated among cattle populations adapted to different ecological conditions in Ethiopia. Specifically, we genotyped 47 unrelated animals sampled from high- versus low-altitude environments using a Bovine 50K SNP BeadChip. Linkage disequilibrium was assessed using both D′ and r2 between adjacent SNPs. We calculated FST and heterozygosity at different significance levels as measures of genetic differentiation for each locus between high- and low-altitude populations following the hierarchical island model approach. We identified 816 loci (p < 0.01) showing selection signals and are associated with genes that might have roles in local adaptation. Some of them are associated with candidate genes that are involved in metabolism (ATP2A3, CA2, MYO18B, SIK3, INPP4A, and IREB2), hypoxia response (BDNF, TFRC, and PML) and heat stress (PRKDC, CDK1, and TFDC). Average r2 and D′ values were 0.14 ± 0.21 and 0.57 ± 0.34, respectively, for a minor allele frequency (MAF) ≥ 0.05 and were found to increase with increasing MAF value. The outlier loci identified in the studied Ethiopian cattle populations indicate the presence of genetic variation produced/shaped by adaptation to different environmental conditions and provide a basis for further validation and functional analysis using a reasonable sample size and high-density markers.
A training manual on artificial insemination in goats
(Manual, 2015-03-30) Tsuma, V.T.; Khan, M.S.; Okeyo Mwai, Ally; Ibrahim, Mohamed N.M.
Breeding programs for smallholder sheep farming systems: I. Evaluation of alternative designs of breeding schemes
(Journal Article, 2014-10) Gizaw, Solomon; Rischkowsky, Barbara A.; Valle-Zárate, A.; Haile, Aynalem; Arendonk, Johan A.M. van; Okeyo Mwai, Ally; Dessie, Tadelle
Village- and central nucleus-based schemes were simulated and evaluated for their relative bio-economic efficiencies, using Ethiopia's Menz sheep as example. The schemes were: village-based 2-tier (Scheme-1) and 1-tier (Scheme-2) cooperative village breeding schemes, dispersed village-based nuclei scheme (Scheme-3), conventional 2-tier central nucleus-based scheme (Scheme-4), and schemes linking a central nucleus and village multiplier nuclei with selection in central nucleus (Scheme-5) or in both central and village nuclei (Scheme-6). Among village-based schemes, Scheme-1 gave the highest genetic progress, while Scheme-2 was economically the most efficient with genetic gain in the breeding objective of Birr 5.6 and a profit of Birr 37.2/ewe/year. The central nucleus schemes were more efficient than the village schemes. Scheme-4 was the most efficient with genetic gain in the breeding objective of Birr 13.5 and a profit of Birr 71.2, but is operationally more difficult as it requires a very large central nucleus. The choice between village and central nucleus-based schemes would depend on local conditions (availability of infrastructure, logistics and technical knowhow and support). Linking central nucleus with village-based nuclei (Scheme-6) would be a feasible option to overcome the operational difficulties of the conventional central nucleus scheme. If a village-based breeding program is envisaged as should be the 1st step in most low-input systems, then Scheme-2 is the most efficient. To scale out to an entire Menz breed level, Scheme-3 would be recommended.

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