Historical demographic profiles and genetic variation of the East African Butana and Kenana indigenous dairy zebu cattle

Butana and Kenana breeds from Sudan are part of the East African zebu Bos indicus type of cattle. Unlike other indigenous zebu cattle in Africa, they are unique due to their reputation for high milk production and are regarded as dairy cattle, the only ones of their kind on the African continent. In this study, we sequenced the complete mitochondrial DNA (mtDNA) D‐loop of 70 animals to understand the maternal genetic variation, demographic profiles and history of the two breeds in relation to the history of cattle pastoralism on the African continent. Only taurine mtDNA sequences were identified. We found very high mtDNA diversity but low level of maternal genetic structure within and between the two breeds. Bayesian coalescent‐based analysis revealed different historical and demographic profiles for the two breeds, with an earlier population expansion in the Butana vis a vis the Kenana. The maternal ancestral populations of the two breeds may have diverged prior to their introduction into the African continent, with first the arrival of the ancestral Butana population. We also reveal distinct demographic history between the two breeds with the Butana showing a decline in its effective population size (N_e) in the recent past ~590 years. Our results provide new insights on the early history of cattle pastoralism in Sudan indicative of a large ancient effective population size.     

REMARKABLE SELECTIVE CONSTRAINTS ON EXONIC DINUCLEOTIDE REPEATS

Long dinucleotide repeats found in exons present a substantial mutational hazard: mutations at these loci occur often and generate frameshifts. Here, we provide clear and compelling evidence that exonic dinucleotides experience strong selective constraint. In humans, only 18 exonic dinucleotides have repeat lengths greater than six, which contrasts sharply with the genome‐wide distribution of dinucleotides. We genotyped each of these dinucleotides in 200 humans from eight 1000 Genomes Project populations and found a near‐absence of polymorphism. More remarkably, divergence data demonstrate that repeat lengths have been conserved across the primate phylogeny in spite of what is likely considerable mutational pressure. Coalescent simulations show that even a very low mutation rate at these loci fails to explain the anomalous patterns of polymorphism and divergence. Our data support two related selective constraints on the evolution of exonic dinucleotides: a short‐term intolerance for any change to repeat length and a long‐term prevention of increases to repeat length. In general, our results implicate purifying selection as the force that eliminates new, deleterious mutants at exonic dinucleotides. We briefly discuss the evolution of the longest exonic dinucleotide in the human genome—a 10 x CA repeat in fibroblast growth factor receptor‐like 1 (FGFRL1)—that should possess a considerably greater mutation rate than any other exonic dinucleotide and therefore generate a large number of deleterious variants.     

Short-term variability of plant populations within a regularly disturbed habitat

The changing populations of weeds during 13 years of the Broadbalk continuous wheat experiment were analysed to investigate the extent of differences in shortterm variability of cover between species. The data were from two sections of the experiment where winter wheat was grown continuously under herbicide treatment for 13 and 6 years respectively. Logistic regressions were fitted to the data. Equisetum arvense showed significant long-term increases on both sections; long-term trends were also detected in the longer data run for Agrostis stolonifera, Cirsium arvensa, Poa trivialis, Ranunculus arvensis and Vicia sativa, and for Medicago lupulina on the shorter data run. Variation around long-term trends was low in the case of Equisetum, and, in the longer data run, for Cirsium and Tussilago farfara, and high for Poa spp. and Vicia. Cover values on the two sections were positively correlated for Alopecurus myosuroides, Equisetum, Poa annua and Tripleurospermum inodorum. There was a weak correlation between C-S-R strategy and short-term variability; the more competitive species displayed less variability than the ruderal species. Furthermore, species regenerating from persistent seed banks were more variable in the short term than those regenerating from short-lived seed or bud banks. This can be explained by differences in response to year-to-year variation in environmental conditions, those species with persistent seed banks being typically more sensitive to annual fluctuations in the environment than those without.     

Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry)

A method for estimating and comparing population genetic variation using random amplified polymorphic DNA (RAPD) profiling is presented. An analysis of molecular variance (AMOVA) is extended to accomodate phenotypic molecular data in diploid populations in Hardy-Weinberg equilibrium or with an assumed degree of selfing. We present a two step strategy: 1) Estimate RAPD site frequencies without preliminary assumptions on the unknown population structure, then perform significance testing for population substructuring. 2) If population structure is evident from the first step, use this data to calculate better estimates for RAPD site frequencies and sub-population variance components. A nonparametric test for the homogeneity of molecular variance (HOMOVA) is also presented. This test was designed to statistically test for differences in intrapopulational molecular variances (heteroscedasticity among populations). These theoretical developments are applied to a RAPD data set in Vaccinium macrocarpon (American cranberry) using small sample sizes, where a gradient of molecular diversity is found between central and marginal populations. The AMOVA and HOMOVA methods provide flexible population analysis tools when using data from RAPD or other DNA methods that provide many polymorphic markers with or without direct allelic data.     

A two-step dilution tris-egg yolk extender containing Equex STM significantly improves sperm cryopreservation in the African wild dog (Lycaon pictus)

Conservation management of endangered African wild dogs (AWD; Lycaon pictus) can benefit greatly from development of sperm freezing and artificial insemination. Previous freezing attempts yielded nearly 0% motile sperm within 2 h of thawing. In this study, two canine freezing protocols were tested: Protocol 1: a one-step dilution in TRIS-20% egg yolk containing 8% glycerol; and Protocol 2: a two-step dilution in TRIS-20% egg yolk containing a final extender concentration of 5% glycerol and 0.5% Equex STM, coupled with a TRIS-citrate-fructose thawing solution. Semen was collected by electroejaculation from n = 24 AWDs, of which eight ejaculates of sufficient quality (four good quality with initial sperm motility of 75.0 ± 4.4% and four poor quality; showing rapid decrease in sperm motility to 3.3 ± 3.3% prior to freezing) were frozen. For good quality samples, motility and sperm motility index persisted for up to 8 h for Protocol 2, and was higher between 2 and 6 h after thawing with a decrease from 4 h of incubation. Motility dropped to nearly 0% after 2 h incubation for Protocol 1. Viability was higher for Protocol 2 throughout the 8 h of incubation, with a decrease after 6 h, compared to 4 h for Protocol 1. Acrosome integrity was higher for Protocol 2 throughout post-thaw incubation, with a decrease after 2 h for both protocols. Protocols did not differ in normal sperm morphology or DNA integrity. Poor quality samples yielded similar results, except for acrosome integrity, which declined for Protocol 2. In conclusion, a two-step dilution in TRIS-egg yolk-glycerol extender containing Equex STM yields significantly improved post-thaw quality and longevity of AWD spermatozoa, making it suitable for sperm banking and artificial insemination initiatives.     

Characterization of cDNA clones for differentially expressed genes in embryos of dormant and nondormant Avena fatua L. caryopses

The molecular regulation of seed dormancy was investigated using differential display to visualize and isolate cDNAs representing differentially expressed genes during early imbibition of dormant and nondormant Avena fatua L. embryos. Of about 3000 cDNA bands examined, 5 cDNAs hybridized with mRNAs exhibiting dormancy-associated expression patterns during the first 48 h of imbibition, while many more nondormancy-associated cDNAs were observed. Dormancy-associated clone AFD1 hybridized with a 1.5 kb mRNA barely detectable in dry dormant and nondormant embryos that became more abundant in dormant embryos after 24 h of imbibition. Clone AFD2 hybridized with two mRNAs, a 1.3 kb message constitutively expressed in dormant and nondormant embryos and a 0.9 kb message present at higher levels in dormant embryos after 3 h of imbibition. Nondormancy-associated clones AFN1, AFN2 and AFN3 hybridized with 1.5 kb, 1.7 kb and 1.1 kb mRNAs, respectively, that were more abundant in nondormant embryos during imbibition. Expression patterns of some mRNAs in dormant embryos induced to germinate by GA₃ treatment were different than water controls, but were not identical to those observed in nondormant embryos. DNA sequence analysis revealed 76% sequence identity between clone AFN3 and a Citrus sinensis glutathione peroxidase-like cDNA, while significant sequence similarities with known genes were not found for other clones. Southern hybridization analyses showed that all clones represent low (1 to 4) copy number genes.     

Effects of Peanut Genotypes on Meloidogyne Species Interactions

A 3-year microplot study was conducted to characterize the interaction between Meloidogyne arenaria race 1 (MA1) and M. hapla (MH), as affected by the five peanut genotypes: Florigiant, NC 7, NC 6, NC Ac 18416, and NC Ac 18016. The interactive effects on infection (total parasitic forms per root unit) and reproduction potentials of each nematode species and crop damage were determined. As a single population, MA1 had greater infection capacity and caused more crop damage than did MH, but both species had similar reproduction potentials. In mixed infestations, MA1 was more competitive than MH, as reflected by incidence of infection. Infection and reproduction potentials, and crop-damage capabilities of the mixed populations were similar to those of MA1 alone. All peanut genotypes were susceptible to infection by both nematodes. NC 6 was less susceptible to damage by MA1 and the mixed populations than other genotypes. A nematode treatment x genotype interaction was detected for root infection and crop damage, but not for population density or reproduction. With high preplant nematode levels (Pi), the populations reached their peak by midseason, whereas those with low Pi peaked after midseason. Crop damage in the second and third years was correlated with Pi level.