Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran

Background: Iran is an area of particular interest for investigating goat diversity. Archaeological remains indicate early goat domestication (about 10 000 years ago) in the Iranian Zagros Mountains as well as in the high Euphrates valley and southeastern Anatolia. In addition, mitochondrial DNA data of domestic goats and wild ancestors (C. aegagrusor bezoar) suggest a pre-domestication management of wild populations in southern Zagros and central Iranian Plateau. In this study genetic diversity was assessed in seven Iranian native goat breeds, namely Markhoz, Najdi, Taleshi, Khalkhali, Naini, native Abadeh and Turki-Ghashghaei. A total of 317 animals were characterized using 14 microsatellite loci. Two Pakistani goat populations, Pahari and Teddy, were genotyped for comparison.Results: Iranian goats possess a remarkable genetic diversity (average expected heterozygosity of 0.671 across loci, 10.7 alleles per locus) mainly accounted for by the within-breed component (G(ST) = 5.9%). Positive and highly significant F-IS values in the Naini, Turki-Ghashghaei, Abadeh and Markhoz breeds indicate some level of inbreeding in these populations. Multivariate analyses cluster Iranian goats into northern, central and western groups, with the western breeds relatively distinct from the others. Pakistani breeds show some relationship with Iranian populations, even if their position is not consistent across analyses. Gene flow was higher within regions (west, north, central) compared to between regions but particularly low between the western and the other two regions, probably due to the isolating topography of the Zagros mountain range. The Turki-Ghashghaei, Najdi and Abadeh breeds are reared in geographic areas where mtDNA provided evidence of early domestication. These breeds are highly variable, located on basal short branches in the neighbor-joining tree, close to the origin of the principal component analysis plot and, although highly admixed, they are quite distinct from those reared on the western side of the Zagros mountain range.Conclusions: These observations call for further investigation of the nuclear DNA diversity of these breeds within a much wider geographic context to confirm or re-discuss the current hypothesis (based on maternal lineage data) of an almost exclusive contribution of the eastern Anatolian bezoar to the domestic goat gene pool.

Reproductive and behavioral aspects of red-winged tinamous (Rhynchotus rufescens) in groups with different sex ratios

The aim of this research study was to evaluate the reproductive performance of tinamous submitted to five different male:female ratios. The study was carried out with 72 birds in a randomized experimental design with 4 replications. Tinamous were housed in cages, using the ratios of one (1:1), two (2:1), three (3:1) and four (4:1) females per male, and also one male was housed with three females individually (3R:1), in a rotational system. Reproductive records of the breeding season from September 2004 to March 2005 were used. The reproductive traits studied were: number of eggs laid, fertility, and percentage of eggs damaged and cracked by pecking. Nonparametric analyses of these traits were performed using Kruskal-Wallis test. Two replications of treatments 1:1 and 4:1, and one of treatment 2:1 were video-taped for three days, 12 hours/day. The videotapes were sampled according to the scan method to fit an ethogram. Birds were also watched for one hour per day to study dominance and agonistic behavior. None of the reproductive traits was affected by mating sex ratio (p<0.05). Female dominance could be related to displacement behavior (r=1.00), and male sitting in immobility plus sitting in activity behaviors were related to lower number of damaged eggs (r=-0.90). Social dominance was indirectly determined by displacement behavior in the study situation. A large number of damaged eggs occurred in all treatments, thereby not allowing a clear conclusion on the best male:female ratio.

African-Derived mitochondria in South American native cattle breeds (Bos taurus): Evidence of a new taurine mitochondrial lineage

This article reports the nucleotide diversity within the control region of 42 mitochondrial chromosomes belonging to five South American native cattle breeds (Bos taurus). Analysis of these data in conjunction with B. taurus and B. indicus sequences from Africa, Europe, the Near East, India, and Japan allowed the recognition of eight new mitochondrial haplotypes and their relative positions in a phylogenetic network. The structure of genetic variation among different hypothetical groupings was tested through the molecular variance decomposition, which was best explained by haplotype group components. Haplotypes surveyed were classified as European-related and African-related. Unexpectedly, two haplotypes within the African cluster were more divergent from the African consensus than the latter from the European consensus. A neighbor-joining tree shows the position of two haplotypes compared to European/African mitochondrial lineage splitting. This different and putatively ancestral mitochondrial lineage (AA) is supported by the calibration of sequence divergence based on the Bos-Bison separation. The European/African mitochondria divergence might be subsequent (67,100 years before present) to that between AA and Africans (84,700 years before present), also preceding domestication times. These genetic data could reflect the haplotype distribution of Iberian cattle five centuries ago.

Straw collecting behaviour by pacas (Agouti paca) in captivity

Agouti paca is both considered as a species vulnerable to extinction and recognised with the potential for domestication. In spite of this, its behaviour is poorly documented and captive breeding is mainly based on trial and error. The aim of the present research was to analyse whether different strategies of straw supply could affect the behaviour and welfare of pacas in captivity. The study was done with eight adult pacas grouped in four mated pairs, three of them with one offspring. Each group was housed separately in 10 m 2 pens and the straw collecting behaviour was recorded. The quantity of straw collected per day was measured to compare four different strategies for straw supply and nest removal, where: every day nest removal treatment (1R) = supplying 1 kg of straw every day (outside the burrow) and removing all straw from inside the burrow every day; every 3 days nest removal treatment (3R) = supplying 1 kg every day and removing after 3, 6, and 9 days; no nest removal treatment (9R) = supplying 1 kg every day and removing after 9 days; nest deprivation treatment (Dep) = supplying 1 kg every day except at days 3, 4, and 5 and removing after 3 and 9 days. Straw collecting was always performed after 17:30 h, with three behavioural acts being performed: mouthing, transporting, and depositing the straw into the artificial burrow. The straw collected per day mean of 1R was significantly higher than the means of other treatments. During the deprivation period of Dep, chips cut from the eucalyptus branches and a great quantity of fruits and manioc were found inside the burrows. The motivation to collect seemed to increase as a consequence of straw deprivation. By these we conclude that straw should be offered to pacas in captivity, giving them the opportunity to collect straw by themselves. Doing this we expect to promote an effective environmental enrichment for this species in captivity. (c) 2005 Elsevier B.V. All rights reserved.

Genetic relatedness among wild, domestic and Brazilian fighting roosters

Except for the meat- and egg-type strains used in commercial poultry farms in Brazil, there are no scientific reports about the origin of birds from the genus Gallus that have been introduced in this country with domestication or fighting purposes. Therefore, the aim of this study was to identify the position of the Brazilian Game Bird in the phylogenetic tree of the genus Gallus by nucleotide sequence analysis of the mitochondrial DNA D-loop region. The results indicate that fighting roosters comprise two different clusters within the species Gallus gallus domesticus. One of the clusters is related to the wild ancestors, while the other one is more related to the birds raised by the poultry industry. In conclusion, Brazilian fighting roosters have originated from the red jungle fowl (Gallus gallus) and belong to the subspecies Gallus gallus domesticus.

Avaliação do incremento em volume de madeira de Quassia amara L.- Simaroubaceae, em cultivo agroecológico no trópico úmido da Costa Rica

Quassia amara é arbusto de 3 a 6 metros de altura, tendo sido retirado indiscriminadamente das florestas para extrair do caule as quassinas usadas na indústria farmacêutica e como inseticida em agricultura orgânica. Não se tem muita informação técnica acerca do crescimento desta espécie para subsidiar estratégias de manejo sustentado. Este trabalho tem como objetivo avaliar o crescimento de Q. amara L. em cultivo agroecológico na Costa Rica. O trabalho consistiu em realizar avaliações do desenvolvimento de indivíduos de Q. amara em parcelas permanentes de medições, instaladas em meio às plantações desta espécie em consórcio com essências arbóreas. Foram efetuadas medições de diâmetro do caule a 10 cm do solo e altura total. Foi observado que em função das taxas de crescimento vegetal e incrementos médio e corrente anuais (IMA e ICA), mesmo após cinco anos de plantio, a madeira de Quassia amara para extração de quassinas não está pronta para colheita.

Pesquisas agronômicas das plantas medicinais da Mata Atlântica regulamentadas pela ANVISA

Com a divulgação da lista das espécies medicinais pela Agência Nacional de Vigilância Sanitária (ANVISA), de acordo com a Resolução RDC Nº10, de 09 de março de 2010, o uso dessas plantas passa a ter a chancela oficial do órgão governamental regulamentando seu uso e, em consequência disso, ter sua demanda bastante aumentada. A obtenção desses materiais adquire então grande importância, uma vez que haverá a necessidade de se produzir essas plantas. Com o objetivo de se avaliar a situação das pesquisas agronômicas com essas espécies, particularmente as de ocorrência na Mata Atlântica, foi feito um levantamento do número de publicações a partir dos nomes científicos, na base de dados eletrônica CAB Abstract, de 1990 a 2011. A pesquisa mostrou que o número de publicações por espécie varia de 2 a 1129, sendo que as espécies com maior número de artigos são aquelas já cultivadas como alimentícias. Das 66 espécies listadas, 36 são exóticas, 24 são da Mata Atlântica e 6 são nativas de outros biomas. Dentre as espécies da Mata Atlântica, foram excluídas as ruderais, frutíferas e arbóreas, devido à maioria dos trabalhos na área agronômica estarem relacionados ao manejo, controle ou produção de frutos e não ao seu cultivo sobre o ponto de vista medicinal. A única exceção foi a espécie medicinal arbórea Maytenus ilicifolia. Assim, foram selecionadas 16 espécies, as quais tiveram as publicações divididas em quatro áreas: Agronomia; Fitoquímica, Ensaios biológicos e Outros. Nesta pesquisa foi possível identificar que 32% dos artigos publicados são agronômicos, área que apresenta menos publicações do que a área de atividade biológica, que tem 40% das publicações, e a área de fitoquimica tem 20% das publicações. Estes resultados mostram que os pesquisadores estão atentos à importância das pesquisas agronômicas com plantas medicinais, mas que se faz necessário realizar trabalhos de domesticação das espécies selvagens e de fitotecnia com as espécies menos estudadas, para viabilizar o cultivo, a conservação dos recursos genéticos vegetais e do meio ambiente.

Mapping of quantitative trait loci controlling tick [Riphicephalus (Boophilus) microplus] resistance on bovine chromosomes 5, 7 and 14

Differences in domestication and selection processes have contributed to considerable phenotypic and genotypic differences between Bos taurus and Bos indicus cattle breeds. of particular interest in tropical and subtropical production environments are those genetic differences between subspecies that underlie the phenotypic extremes in tolerance and susceptibility to parasite infection. In general, B. taurus cattle are more susceptible to ectoparasites than B. indicus cattle in tropical environments, and much of this difference is under genetic control. To identify genomic regions involved in tick resistance, we developed a B. taurus x B. indicus F-2 experimental population to map quantitative trait loci (QTL) for resistance to the Riphicephalus (Boophilus) microplus tick. About 300 individuals were measured for parasite load in two seasons (rainy and dry) and genotyped for 23 microsatellite markers covering chromosomes 5, 7 and 14. We mapped a suggestive chromosome-wide QTL for tick load in the rainy season (P < 0.05) on chromosome 5. For the dry season, suggestive (P < 0.10) chromosome-wide QTL were mapped on chromosomes 7 and 14. The additive effect of the QTL on chromosome 14 corresponds to 3.18% of the total observed phenotypic variance. Our QTL-mapping study has identified different genomic regions controlling tick resistance; these QTL were dependent upon the season in which the ticks were counted, suggesting that the QTL in question may depend on environmental factors.

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

Losing identity: structural diversity of transposable elements belonging to different classes in the genome of Anopheles gambiae

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Relação entre tricomas foliares de genótipos de feijoeiro comum, Phaseolus vulgaris L. e resistência a Diabrotica speciosa Germar, 1824 (Coleoptera: Chrysomelidae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Collection of Fafia [Pfaffia glomerata (Spreng.) Pedersen] in northwestern state of Parana-Brazil

Interviews were conducted with fafia (Pfaffia glomerata (Spreng.) Pedersen) collectors from the municipal districts of Querencia do Norte and Porto Rico, where enterprises and buyers of this plant are concentrated. The results allowed us to conclude that both the adults and children make collection. Each adult collects from 50 to 150 kg of roots/day, depending on the collection area, for about 8 months/year. Collections mostly occur all over the year, but the activity becomes more intense from May to August. All families are not exclusively dedicated to fafia collection and also develop other rural activities. They have been collecting fafia for 2 to 13 years, indicating that an intensive exploitation has been present in the region for over a decade. During collection, no plant part is used for replanting the species. The roots are commercialised by regional buyers. The price of the roots varies from US $ 0.07 to US $ 0.13/kg and average gain is about US $ 2,055/family/year, representing a considerable profit for the collectors.

The contribution of transposable elements to Bos taurus gene structure

In an effort to identify the contribution of TEs to bovine genome evolution, the abundance, distribution and insertional orientation of TEs were examined in all bovine nuclear genes identified in sequence build 2.1 (released October 11, 2005). Exons, introns and promoter segments (3 kb upstream the transcription initiation sites) were screened with the RepeatMasker program. Most of the genes analyzed contained TE insertions, with an average of 18 insertions/gene. The majority of TE insertions identified were classified as retrotransposons and the remainder classified as DNA transposons. TEs were inserted into exons and promoter segments infrequently, while insertion into intron sequences was strikingly more abundant. The contribution of TEs to exon sequence is of great interest because TE insertions can directly influence the phenotype by altering protein sequences. We report six cases where the entire exon sequences of bovine genes are apparently derived from TEs and one of them, the insertion of Charlie into a bovine transcript similar to the zinc finger 452 gene is analyzed in detail. The great similarity of the TE-cassette sequence to the ZNF452 protein and phylogenetic relationship strongly suggests the occurrence of Charlie 10 DNA exaptation in the mammalian zinc finger 452 gene. (c) 2006 Published by Elsevier B.V.

Transposable elements in Coffea (Gentianales : Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants

Transposable elements are major components of plant genomes and they influence their evolution, acting as recombination hot spots, acquiring specific cell functions or becoming part of protein-coding regions. The latter is the subject of the present analysis. This study is a report on the annotation of transposable elements (TEs) in expressed sequences of Coffea arabica, Coffea canephora and Coffea racemosa, showing the occurrence of 383 ESTs and 142 unigenes with TE fragments in these three Coffea species. Based on selected unigenes, it was possible to suggest 26 putative proteins with TE-cassette insertions, demonstrating a likely contribution to protein variability. The genes for two of those proteins, the fertility restorer (FR) and the pyrophosphate-dependent phosphofructokinase (PPi-PFKs) genes, were selected for evaluating the impact of TE-cassettes on host gene evolution of other plant genomes (Arabidopsis thaliana, Oryza sativa and populus trichocarpa). This survey allowed identifying a FR gene in O. sativa harboring multiple insertions of LTR retrotransposons that originated new exons, which however does not necessarily mean a case of molecular domestication. A possible transduction event of a fragment of the PPi-PFK beta-subunit gene mediated by Helitron ATREPX1 in Arabidopsis thaliana was also highlighted.

On the Origin of Cattle: How Aurochs Became Cattle and Colonized the World

Since their domestication in the Neolithic, cattle have belonged to our cultural heritage. The reconstruction of their history is an active field of research 1 that contributes to our understanding of human history. Archeological data are now supplemented by analyses of modern and ancient samples of cattle with DNA markers of maternal, paternal, or autosomal inheritance. The most recent genetic data suggest that maternal lineages of taurine cattle originated in the Fertile Crescent with a possible contribution of South-European wild cattle populations, while zebu cattle originate from the Indus Valley. Subsequently, cattle accompanied human migrations, which led to the dispersal of domestic cattle of taurine, indicine, or mixed origin over Asia, Africa, Europe, and the New World. This has resulted in their adaptation to different environments and considerable variation in appearance and performance. More recently, rational management of breeding led to international movements of sires, which again changed the global patterns of genetic diversity.