Arundinaria gigantea, a North American bamboo that historically grew in vast canebrakes, is now considered a critical component of an endangered ecosystem. Expressing self-incompatibility, restoration efforts must ensure genetic diversity within canebrakes for viable seed production. DNA fingerprinting methods were developed using 20 simple sequence repeat (SSR) markers and two sequence-characterized amplified region (SCAR) markers. Among 18 markers able to amplify rivercane DNA via polymerase chain reaction (PCR), 10 were demonstrated to be polymorphic within rivercane. Markers could distinguish rivercane among and between canebrakes and could discern full-sibling seedlings. The mostly-infertile Mississippi canebrakes of rivercane were determined to contain 46% genetic diversity within canebrakes and an average of 1.436 effective alleles. In contrast, the fertile North Carolina canebrakes contained 99% genetic diversity within canebrakes and an average of 6.435 effective alleles. Therefore, theoretically, at least seven distinct genotypes were needed for a healthy, viable rivercane brake.

Intensive aquaculture of Atlantic cod is fast developing in both Northern Europe and Canada. The last six years have seen major improvements in the larval rearing protocols and husbandry techniques for this species. Although breeding programmes are currently being developed by both governmental and private institutions in the main cod producing countries (i.e. Norway, Iceland and Canada), most hatcheries still rely on the mass spawning of their own broodstock. Mass spawning tanks are complex systems where fish are left to spawn naturally and fertilised eggs are collected with the overflowing water, with little or no control over the matings of the animals. Few published studies in other commercial marine species (i.e. turbot and sole) have attempted to analyse the output from such systems using microsatellite markers and several parentage analysis software programs. A review of these publications exposed a lack of consistency in the methods used to analyse such complex datasets. This problem was addressed by carrying out a detailed comparison of two analytical principals (i.e. assignment by strict exclusion and assignment by probabilities) and four parentage software programmes (i.e. FAP, VITASSIGN, CERVUS and PAPA), using the DNA profiles, at 5 loci, from 300 cod fry issued from the mass spawning of a large hatchery cod broodstock tank (consisting of 99 fish). This study revealed large discrepancies in the allocation outcomes between exclusion-based and probability-based assignments caused by the important rate of typing errors present in the dataset. Out of the four softwares tested, FAP (Taggart, 2007) was the most appropriate to use for handling such a dataset. It combined the most conservative method of assignment with the most informative output for the results displayed. In an attempt to study the breeding dynamics in a cod commercial hatchery, parental contributions to five groups of 300 fry (from five single days of spawning and from two commercial mass spawning cod tanks) were analysed, based on the genotyping data from eight loci. The parentage results from the exclusion-based analyses revealed that, on a single day, at least 25 to 30% of the total breeding population contributed to fertilised eggs that resulted in viable offspring at 50 and 83 days post-hatch. Family representations were highly skewed - with the marked dominance of a few males - and effective breeding populations were consistently low (approx. 5% of the total breeding population). Parental contribution to a group of 960 codlings - produced following intensive commercial practices (i.e. including successive size gradings and mixing of batches) and belonging to a single graded group - was also analysed, based on the genotyping data from eleven loci. The effective breeding population size of the juvenile batch (c. 14% of the total broodstock population) was two to three times greater than the effective size observed on a single day of mass spawning. The per-generation rate of inbreeding was however relatively high, for this batch alone, at 2.5%. Based on these results, suggestions were made to manage hatchery cod broodstock populations and implement genetic selection. Early maturation of farmed cod in sea cages (at two or three years old) is a major concern for ongrowers. Understanding the mechanism(s) behind sex determination in cod would probably help the development of a method to control sexual maturation. In an attempt to elucidate sex determination in cod, a protocol to induce gynogenesis was developed. Gynogenetic fish were successfully produced by irradiating cod milt with UV and applying a cold shock (at -6oC) to newly fertilised eggs. However, due to poor survival during larval rearing, only one gynogenetic fish survived long enough to be sexed; not enough to conclude anything on the sex determination mechanism(s) in cod.

Made available in DSpace on 2016-12-08T16:24:11Z (GMT). No. of bitstreams: 1 PGCA11MA083.pdf: 3400558 bytes, checksum: fedbf896e2daef8109b07884eb122a44 (MD5) Previous issue date: 2011-03-03 / Brazilian Caipira chicken are hardy birds that, it is believed, show high genetic diversity. However, there is almost no scientific studies that prove the alleged high genetic variability of the Caipira chicken. Studies that investigate this issue are very important, because the scientific evidence of this polymorphism makes the maintenance and conservation of these animals essential. The gene polymorphism is fundamental to the perpetuation of the species, besides being a source of alleles for genetic improvement programs for livestock. The commercial birds, for example, have lost much of their genetic variability because they have been through strict selection processes. Even though these animals are highly productive, some features related to production still deserve the attention of breeders, such as disease resistance. Some brazilian (blue-egg Caipira) chicken. This coloration of the egg shell is characteristic of a South American breed of chickens that participated in the formation of the native caipira chicken. This study used fifteen microsatellite loci to assess the genetic variability of brazilian (blue egg caipira) chicken. The animals were from the city of Two Lajeados - RS. By PCR, the amplicons obtained using a primer labeled with fluorophores were genotyped in an automatic sequencer and the results analyzed using the statistical program ARLEQUIN. It was detected a total of 168 alleles with an average of 11.2 alleles per locus, 288 genotypes, HE = 0.76 and HO = 0.49. These results confirmed the suspicion of high genetic variability in brazilian (blue egg Caipira) chicken / Galinhas caipiras brasileiras são aves rústicas, que, acredita-se, apresentam elevada diversidade genética. Entretanto, quase não há trabalhos científicos que comprovem a suposta alta variabilidade genética das aves caipiras. Trabalhos que investiguem esta questão são muito importantes, pois a comprovação científica deste polimorfismo transforma a manutenção e conservação destes animais imprescindível. O polimorfismo gênico é fundamental para a perpetuação da espécie, além de ser fonte de alelos para programas de melhoramento genético de animais de produção. As aves comerciais, por exemplo, perderam muito de sua variabilidade gênica por terem passado por rigorosos processos de seleção. Mesmo que estes animais sejam altamente produtivos, algumas características relacionadas à produção ainda merecem atenção dos melhoristas, como é o caso da resistência a doenças. Algumas galinhas caipiras brasileiras colocam ovos azuis. Esta coloração da casca do ovo é característica de uma raça sul-americana de galinhas que participou da formação das aves caipiras nacionais. Este trabalho utilizou quinze loci de microssatélites para avaliar a variabilidade genética de galinhas caipiras brasileiras de ovos azuis. Os animais foram provenientes do município de Dois Lajeados RS. Através da técnica da PCR, os amplicons obtidos com a utilização de iniciadores marcados com fluoróforos foram genotipados em seqüenciador automático e os resultados obtidos analisados através do programa estatístico ARLEQUIN. Foi detectado um total de 168 alelos, com média de 11,2 alelos por locus, 288 genótipos, HE=0,76 e HO=0,49. Estes resultados comprovaram a suspeita de alta variabilidade genética presente em galinhas caipiras brasileiras de ovos azuis