Classification of the southern African sanga and east African shorthorned zebu

Is neutral genetic diversity related to quantitative variation in semen traits in bulls?

Conservation decisions based on neutral genetic diversity have been observed to promote retention of useful quantitative variation in biological populations. An experiment was undertaken to determine the association between microsatellite marker polymorphisms and phenotypic variation in semen production and cryosurvival traits in bulls. Thirty-five ejaculates were collected from ten bulls of two breeds and evaluated before and after cryopreservation for several semen traits. The bulls were also genotyped using a set of sixteen bovine-specific microsatellite marker loci. Fixation indices (F_ST ), heterozygosity and Nei's genetic distance measures were computed from allele frequency data for each of the bulls. Molecular and phenotypic data were used to compute tri-distance matrices for the ten bulls and correlated using Mantel's test in GenAIEx 6.5. The study revealed extensive heterogeneity in semen traits, heterozygosity and F_ST values among the bulls. Large pairwise phenotypic and genetic distances were also observed. Correlation between pairwise genetic distances and phenotypic distances was significant and highly positive for sperm viability (r = .61, p < .001) and moderately positive for sperm motility (r = .40-42, p < .05) variables. For sperm morphology, ejaculate volume and sperm concentration, correlation with genetic distances was positive, low and not significantly different from zero (p > .05). A tendency for a triangular-shaped relationship between genetic and phenotypic distances for post-thaw motility and viability traits was also observed. Accordingly, association with neutral genetic diversity was absent for semen production traits and moderate to highly positive for sperm cryosurvival traits. Given these findings, conservation decisions based on neutral genetic diversity may capture variation in some adaptive traits, but not others.

Strategies for Sustainable Use of Indigenous Cattle Genetic Resources in Southern Africa

Indigenous cattle breeds are the most important livestock species in the Southern African Development Community (SADC) region owing to their role in human food, nutrition, income, and social security. Despite the role of these breeds in the household and national economies, they are currently underutilised, their productivity remains low, and populations are faced with extinction. In addition, there are insufficient measures taken to secure their present and future value. The current review highlights strategies for sustainable use of indigenous cattle genetic resources in the region, including the use of novel production and marketing practices, women and youth empowerment, and development of the appropriate capacity building, legislative, and policy structures. At present, the lack of coordination among the different stakeholders still poses a challenge to the implementation of these strategies. To this end, partnerships, collaboration, and stakeholders’ participation are recommended to effectively implement strategies for sustainable use of indigenous cattle breeds.

Towards a new phenotype for tick resistance in beef and dairy cattle: a review

About 80% of the world’s cattle are affected by ticks and tick-borne diseases, both of which cause significant production losses. Cattle host resistance to ticks is the most important factor affecting the economics of tick control, but it is largely neglected in tick-control programs due to technical difficulties and costs associated with identifying individual-animal variation in resistance. The present paper reviews the scientific literature to identify factors affecting resistance of cattle to ticks and the biological mechanisms of host tick resistance, to develop alternative phenotype(s) for tick resistance. If new cost-effective phenotype(s) can be developed and validated, then tick resistance of cattle could be genetically improved using genomic selection, and incorporated into breeding objectives to simultaneously improve cattle productive attributes and tick resistance. The phenotype(s) could also be used to improve tick control by using cattle management. On the basis of the present review, it is recommended that three possible phenotypes (haemolytic analysis; measures of skin hypersensitivity reactions; simplified artificial tick infestations) be further developed to determine their practical feasibility for consistently, cost-effectively and reliably measuring cattle tick resistance in thousands of individual animals in commercial and smallholder farmer herds in tropical and subtropical areas globally. During evaluation of these potential new phenotypes, additional measurements should be included to determine the possibility of developing a volatile-based resistance phenotype, to simultaneously improve cattle resistance to both ticks and biting flies. Because the current measurements of volatile chemistry do not satisfy the requirements of a simple, cost-effective phenotype for use in commercial cattle herds, consideration should also be given to inclusion of potentially simpler measures to enable indirect genetic selection for volatile-based resistance to ticks.

Genetic tests for estimating dairy breed proportion and parentage assignment in East African crossbred cattle

BACKGROUND

Smallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. Pedigree recording is rare in such systems which means that it is impossible to make informed breeding decisions. High-density single nucleotide polymorphism (SNP) assays allow accurate estimation of breed composition and parentage assignment but are too expensive for routine application. Our aim was to determine the level of accuracy achieved with low-density SNP assays.

METHODS

We constructed subsets of 100 to 1500 SNPs from the 735k-SNP Illumina panel by selecting: (a) on high minor allele frequencies (MAF) in a crossbred population; (b) on large differences in allele frequency between ancestral breeds; (c) at random; or (d) with a differential evolution algorithm. These panels were tested on a dataset of 1933 crossbred dairy cattle from Kenya/Uganda and on crossbred populations from Ethiopia (N = 545) and Tanzania (N = 462). Dairy breed proportions were estimated by using the ADMIXTURE program, a regression approach, and SNP-best linear unbiased prediction, and tested against estimates obtained by ADMIXTURE based on the 735k-SNP panel. Performance for parentage assignment was based on opposing homozygotes which were used to calculate the separation value (sv) between true and false assignments.

RESULTS

Panels of SNPs based on the largest differences in allele frequency between European dairy breeds and a combined Nelore/N'Dama population gave the best predictions of dairy breed proportion (r² = 0.962 to 0.994 for 100 to 1500 SNPs) with an average absolute bias of 0.026. Panels of SNPs based on the highest MAF in the crossbred population (Kenya/Uganda) gave the most accurate parentage assignments (sv = -1 to 15 for 100 to 1500 SNPs).

CONCLUSIONS

Due to the different required properties of SNPs, panels that did well for breed composition did poorly for parentage assignment and vice versa. A combined panel of 400 SNPs was not able to assign parentages correctly, thus we recommend the use of 200 SNPs either for breed proportion prediction or parentage assignment, independently.

A Genomic Approach for Distinguishing between Recent and Ancient Admixture as Applied to Cattle

Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We developed a metric, scaled block size (SBS), which uses the nonrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient types of admixture, and applied it to the reconstruction of admixture in cattle. Cattle are descendants of 2 independently domesticated lineages, taurine and indicine, which diverged more than 200 000 years ago. Several breeds have hybrid ancestry between these divergent lineages. Using 47 506 single-nucleotide polymorphisms, we analyzed the genomic architecture of the ancestry of 1369 individuals. We focused on 4 groups with admixed ancestry, including 2 anciently admixed African breeds (n = 58; n = 43), New World cattle of Spanish origin (n = 51), and known recent hybrids (n = 46). We estimated the ancestry of chromosomal regions for each individual and used the SBS metric to differentiate the timing of admixture among groups and among individuals within groups. By comparing SBS values of test individuals with standards with known recent hybrid ancestry, we were able to differentiate individuals of recent hybrid origin from other admixed cattle. We also estimated ancestry at the chromosomal scale. The X chromosome exhibits reduced indicine ancestry in recent hybrid, New World, and western African cattle, with virtually no evidence of indicine ancestry in New World cattle.

Comparative evaluation of beef cattle breeds of African, European and Indian origins. 1. Live weights and heterosis at birth, weaning and 18 months

Cattle breeds of African, European and Indian origins are being evaluated at Rockhampton for their suitability for beef production in northern Australia. In the current study, Belmont Adaptaur (HS), Belmont Red (AX) and Belmont BX (BX) dams were mated to produce straightbreds and crossbred progeny by Brahman (B), Boran (Bo) and Tuli (Tu) sires. B dams were mated to produce straightbreds and crossbred progeny by AX, BX, Bo, Charolais (Ch), HS and Tu sires. This paper reports values for heterosis for some crosses and live weights on pasture for some straightbred and crossbred genotypes at birth, at weaning and at 18 months.

Heterosis for birth weights was greatest for taurine dam breed × indicine sire breed, generally negative for the reciprocal cross and markedly less for Tu-sired than for B- or Bo-sired progeny. Heterosis was not estimated for Bo and Tu crosses at weaning or at 18 months. At these ages, heterosis for growth includes a component related to resistance to environmental stresses. Thus, heterosis was then greater for B crossbreds derived from the less resistant HS than from the more resistant AX.

There were significant differences between genotypes in live weights at each age. Progeny by B sires from taurine dams had higher live weights than progeny by Bo or Tu sires. Evidence is presented that strongly indicates that the difference in growth rates between the B- and Bo-sired progeny arose entirely from differences in mature live weights of the B and Bo, not from differences in efficiency of growth of their crossbred progeny. Similarly, live weights of progeny by taurine sires from B dams ranked according to the mature live weights of the sire breeds. Thus, the Ch- and Tu-sired progeny had the highest and lowest live weights at all ages respectively. Comparative growth potentials of the indicine sire breeds were estimated by comparing 18-month live weights of progeny from HS dams. Relative to Bo = 100, growth potential of B = 205. Similarly, growth potentials of the taurine sire breeds were estimated from progeny from B dams. Relative to Tu = 100, the estimates were HS = 104, AX = 111 and Ch = 117. Crossbred progeny by B and Bo sires were generally significantly heavier at all ages than the corresponding straightbreds. However, Tu-sired progeny had similar birth weights too, but generally higher weaning and 18-month live weights than, the corresponding straightbreds. Relatively low birth weight and low heterosis for birth weight identify the Tu as a potentially useful sire breed when an increase in birth weight of crossbreds is undesirable.

Within each dam breed, no straightbred could match the growth rate of the best crossbred. At 18 months this advantage was proportionately 0·21, 0·09, 0·05 and 0·16 over that of the straightbred HS, AX, BX and B respectively. Live weight of every crossbred based on B dams exceeded that of the straightbred B, the most populous breed in northern Australia. Thus, increases in growth rates could be achieved by crossbreeding irrespective of the base breed. Live weights at 18 month for progeny of Bo, Tu and AX sires from B dams, all of which exceeded those of the straightbred B, suggest that the African breeds can be used to complement the B in crossbreeding programmes in northern Australia.

Evolutionary process of Bos taurus cattle in favourable versus unfavourable environments and its implications for genetic selection

The evolutionary processes that have enabled Bos taurus cattle to establish around the globe are at the core to the future success of livestock production. Our study focuses on the history of cattle domestication including the last 60 years of B. taurus breeding programmes in both favourable and unfavourable environments and its consequences on evolution and fitness of cattle. We discuss the emergence of 'production diseases' in temperate production systems and consider the evolutionary genetics of tropical adaptation in cattle and conclude that the Senepol, N'Dama, Adaptaur and Criollo breeds, among others with similar evolutionary trajectories, would possess genes capable of improving the productivity of cattle in challenging environments. Using our own experimental evidence from northern Australia, we review the evolution of the Adaptaur cattle breed which has become resistant to cattle tick. We emphasize that the knowledge of interactions between genotype, environment and management in the livestock systems will be required to generate genotypes for efficient livestock production that are both economically and environmentally sustainable. Livestock producers in the 21st century will have less reliance on infrastructure and veterinary products to alleviate environmental stress and more on the animal's ability to achieve fitness in a given production environment.

Genetics of steer daily and residual feed intake in two tropical beef genotypes, and relationships among intake, body composition, growth and other post-weaning measures

Genetic parameters for Brahman (BRAH) and Tropical Composite (TCOMP) cattle were estimated for steer production traits recorded at weaning (WEAN), 80 days post-weaning (POSTW), feedlot entry (ENTRY) and after ∼120 days feedlot finishing (EXIT). The TCOMP was 50% Bos indicus, African Sanga or other tropically adapted Bos taurus, and 50% non-tropically adapted Bos taurus. Data involved 2216 steers, comprising 1007 BRAH by 53 sires and 1209 TCOMP by 50 sires. Individual daily feed intake (DFI) and residual feed intake (RFI) were assessed on 680 BRAH and 783 TCOMP steers over an ~70-day feedlot test. Other traits were liveweight (LWT), average daily gain (ADG), ultrasonically scanned rump (SP8) fat depth, rib (SRIB) fat depth, M. longissimus area (SEMA) and intra-muscular fat % (SIMF), body condition score (CS), hip height (HH), flight time (FT) and serum insulin-like growth factor-I concentration (IGF-I). BRAH were significantly (P < 0.05) lighter at ENTRY and EXIT, and had lower DFI (10.8 v. 13.2 kg/day) and RFI (–0.30 v. 0.17 kg/day), greater SP8 (5.8 v. 5.1 mm) but similar SRIB at ENTRY, lower SRIB (8.2 v. 8.9 mm) but similar SP8 at EXIT, and greater HH than TCOMP. Heritabilities for DFI, RFI, LWT, ADG, scanned body composition, HH and IGF-I measures, across measurement times, were generally in the 20 to 60% range for both genotypes. Genetic variance for RFI was 0.19 (kg/day)2 in BRAH and 0.41 (kg/day)2 in TCOMP, suggesting a clear potential to genetically change RFI in both genotypes. Trait variances and genetic correlations often differed between the genotypes, supporting the use of genotype-specific parameters in genetic evaluation. The genotype differences may be associated with evolutionary changes that have occurred in B. indicus as a part of their adaptation to tropical environments. Measures with potential to be used as genetic indicators of DFI were LWT measures in BRAH and TCOMP, ADG at ENTRY in TCOMP, and SP8 and SIMF at ENTRY in BRAH. Measures with potential to be genetic indicators of RFI were HH and ADG at ENTRY in BRAH, and IGF-I in both genotypes. Taller and faster-growing BRAH steers at ENTRY had genetically lower RFI. IGF-I was negatively genetically correlated with RFI whether IGF-I was measured at POSTW, ENTRY or EXIT. SRIB fatness at EXIT was strongly positively genetically correlated with RFI in TCOMP but only lowly correlated in BRAH. Fatness at ENTRY was lowly and negatively genetically correlated with RFI. The results emphasise the need for a population-specific understanding of trait relationships and of trait differences between measurement times if genetic indicator traits are to be utilised in genetic evaluation of RFI.

Genetics of heifer performance in 'wet' and 'dry' seasons and their relationships with steer performance in two tropical beef genotypes

The genetics of heifer performance in tropical ‘wet’ and ‘dry’ seasons, and relationships with steer performance, were studied in Brahman (BRAH) and Tropical Composite (TCOMP) (50% Bos indicus, African Sanga or other tropically adapted Bos taurus; 50% non-tropically adapted Bos taurus) cattle of northern Australia. Data were from 2159 heifers (1027 BRAH, 1132 TCOMP), representing 54 BRAH and 51 TCOMP sires. Heifers were assessed after post-weaning ‘wet’ (ENDWET) and ‘dry’ (ENDDRY) seasons. Steers were assessed post-weaning, at feedlot entry, over a 70-day feed test, and after ∼120-day finishing. Measures studied in both heifers and steers were liveweight (LWT), scanned rump fat, rib fat and M. longissimus area (SEMA), body condition score (CS), hip height (HH), serum insulin-like growth factor-I concentration (IGF-I), and average daily gains (ADG). Additional steer measures were scanned intra-muscular fat %, flight time, and daily (DFI) and residual feed intake (RFI). Uni- and bivariate analyses were conducted for combined genotypes and for individual genotypes. Genotype means were predicted for a subset of data involving 34 BRAH and 26 TCOMP sires. A meta-analysis of genetic correlation estimates examined how these were related to the difference between measurement environments for specific traits. There were genotype differences at the level of means, variances and genetic correlations. BRAH heifers were significantly (P < 0.05) faster-growing in the ‘wet’ season, slower-growing in the ‘dry’ season, lighter at ENDDRY, and taller and fatter with greater CS and IGF-I at both ENDWET and ENDDRY. Heritabilities were generally in the 20 to 60% range for both genotypes. Phenotypic and genetic variances, and genetic correlations, were commonly lower for BRAH. Differences were often explained by the long period of tropical adaptation of B. indicus. Genetic correlations were high between corresponding measures at ENDWET and ENDDRY, positive between fat and muscle measures in TCOMP but negative in BRAH (mean of 13 estimates 0.50 and –0.19, respectively), and approximately zero between steer feedlot ADG and heifer ADG in BRAH. Numerous genetic correlations between heifers and steers differed substantially from unity, especially in BRAH, suggesting there may be scope to select differently in the sexes where that would aid the differing roles of heifers and steers in production. Genetic correlations declined as measurement environments became more different, the rates of decline (environment sensitivity) sometimes differing with genotype. Similar measures (LWT, HH and ADG; IGF-I at ENDWET in TCOMP) were genetically correlated with steer DFI in heifers as in steers. Heifer SEMA was genetically correlated with steer feedlot RFI in BRAH (0.75 ± 0.27 at ENDWET, 0.66 ± 0.24 at ENDDRY). Selection to reduce steer RFI would reduce SEMA in BRAH heifers but otherwise have only small effects on heifers before their first joining.

Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites

Hybridization between wild and domestic bovine species occurs worldwide either spontaneously or by organized crossing. We have analysed hybridization of banteng (Bos javanicus) and zebu (Bos indicus) in south-east Asian cattle using mitochondrial DNA (PCR-RFLP and sequencing), AFLP, satellite fragment length polymorphisms (SFLP or PCR-RFLP of satellite DNA) and microsatellite genotyping. The Indonesian Madura zebu breed is reputed to be of hybrid zebu-banteng origin, but this has never been documented and Bali cattle are considered to be a domesticated form of banteng. The banteng mitochondrial type was found in all animals sampled on the isle of Bali, Indonesia, but only in 35% of the animals from a Malaysian Bali-cattle population. The Madura animals also carried mitochondrial DNA of either zebu and banteng origin. In both populations, zebu introgression was confirmed by AFLP and SFLP. Microsatellite analysis of the Malaysian Bali population revealed for 12 out of 15 loci screened, Bali-cattle-specific alleles, several of which were also found in wild banteng animals. The tools we have described are suitable for the detection of species in introgression studies, which are essential for the genetic description of local breeds and the preservation of their economic and cultural value.

Geographic distribution and frequency of a taurine Bos taurus and an indicine Bos indicus Y specific allele amongst sub-saharan African cattle breeds

We report for the first time, and for the whole of sub-Saharan Africa, the geographical distribution and the frequency of an indicine and a taurine Y specific allele amongst African cattle breeds. A total of 984 males from 69 indigenous African populations from 22 countries were analysed at the microsatellite locus INRA 124. The taurine allele is probably the oldest one on the continent. However, the taurine and the indicine alleles were present in 291 males (30%), and 693 males (70%), respectively. More particularly, 96% of zebu males (n = 470), 50% of taurine males (n = 263), 29% of sanga males (crossbreed Bos taurus x Bos indicus, n = 263) and 95% of zebu x sanga crossbred males (n = 56) had the indicine allele. The Borgou, a breed classified as zebu x taurine cross showed only the zebu allele (n = 12). The indicine allele dominates today in the Abyssinian region, a large part of the Lake Victoria region and the sahelian belt of West Africa. All the sanga males (n = 64) but only one from the Abyssinian region had the indicine allele. The taurine allele is the commonest only among the sanga breeds of the southern African region and the trypanotolerant taurine breeds of West Africa. In West Africa and in the southern Africa regions, zones of introgression were detected with breeds showing both Y chromosome alleles. Our data also reveal a pattern of male zebu introgression in Mozambique and Zimbabwe, probably originating from the Mozambique coast. The sanga cattle from the Lake Victoria region and the Kuri cattle of Lake Chad, cattle populations surrounded by zebu breeds were, surprisingly, completely devoid of the indicine allele. Human migration, phenotypic preferences by the pastoralists, adaptation to specific habitats and to specific diseases are the main factors explaining the present-day distribution of the alleles in sub-Saharan Africa.

Satellite DNA polymorphisms and AFLP correlate with Bos indicus-taurus hybridization

We describe satellite DNA variation that detects hybridization of Bos indicus (zebu or indicine cattle) and Bos taurus (taurine cattle) in African cattle populations. On Southern blots hybridized to a satellite III probe, relative intensities of Hinfl fragments correlated with the taurine-zebu composition in hybrid animals as deduced from AFLP genotyping of the same animals and previous data on microsatellite allele frequencies. Similar results were obtained by PCR-RFLP analysis of a zebu-specific mutation in the repeat unit of satellite 1.711b. Analysis of individuals from 20 African cattle breeds indicate that the centromeric satellites of the sanga breeds are of the taurine type and that several East-African zebu breeds are hybrids between taurine and zebu. These satellite RFLP, or SFLP, markers provide a fast method to screen the genetic makeup of African cattle.