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.

The occurrence of spot type net blotch (Pyrenophora teres f. maculata) and net type net blotch (P. teres f. teres) as well as the occurrence of net blotch mating types has been investigated in Lithuania, Latvia and Estonia. Genetic diversity of barley net blotch isolates from various locations in Lithuania was investigated using ISSR and AFLP markers. The net blotch resistance of 150 spring barley varieties was investigated under artificial and natural infection conditions in the field. / Panaudojant molekulinius žymeklius ištirta tinkliškosios dryžligės patogeno Pyrenophora teres populiacijos genetinė įvairovė, nustatyti P. teres formų ir lytinio dauginimosi tipų sutinkamumas Lietuvoje, Latvijoje ir Estijoje. Lietuvos sąlygomis įvertintas Vakarų Europos ekotipo 150 vasarinių miežių veislių ir linijų jaurumas tinkliškajai dryžligei esant skirtingai pradinei infekcijai.

Humans and horses weaved together wonderful stories of adventure and generosity. As a part of human history and civilization, Arabian horses ignite imagination throughout the world. Populations of this breed exist in many countries. Here I explored different populations of Arabians representing Middle Eastern and Western populations. The main two aims of this study were to provide the genetic diversity description of Arabians from different origins and to examine the traditional classification system of the breed. A third aim was to tackle the distribution pattern of the genetic variability within the genome to show whether there are differences in relative variability of different types of markers. First, I analyzed the genetic structure of 537Arabian horses from seven populations by using microsatellites. The results consistently showed higher levels of diversity within the Middle Eastern populations compared to the Western populations. All American-Arabians showed differentiation from Middle Eastern populations. Second, I sequenced the whole mtDNA D-loop of 251 Arabian horses. The whole D-loop sequence was more informative than using just the HVR1. Native populations from the Middle East, such as Syrian, represented a hot spot of genetic diversity. Most importantly, there was no evidence that the Arabian horse breed has clear subdivisions depending on the traditional maternal based strain classification system. Third, I tested the heterozygosity distribution pattern along the genome of 22 Peruvian Paso horses using 232 microsatellites and Single Nucleotide Polymorphisms (SNPs). The pattern of genetic diversity was completely different between these two markers where no correlation was found. Runs of homozygosity test of SNPs and associated microsatellites noticeably showed that all of associated microsatellites loci were homozygous in the matched case. The findings of this study will help in understanding the evolutionary history and developing breeding and conservation programs of horses. This study provided databases including parentage testing system and maternal lineages that will help to recover the Syrian Arabian population after the armed conflict started in Syria in 2011. The results here can be applied not only to horses, but also to other animal species with similar criteria.

No description available.

Biodiversity provides the raw material for evolution and adaptation of populations and species. In agricultural biodiversity, the within-population genetic diversity is of major importance. On one hand, it can provide a buffering effect against the year-to-year variation of climate or biotic pressures and on the other hand diversity serves as a resource for the population to respond to selective pressures due to specific local conditions, thus allowing for local adaptation, particularly in the case where a population is introduced into a new location. Due to its wide geographic distribution indicating a high adaptiveotential and its socio-economic importance, wheat was chosen as model crop in this study. Flowering time is a major adaptive trait which has allows wheat to grow over a wide range of ecological and climatic conditions. This PhD study was designed to gain insights about the influence of within population diversity on the short term response of populations to contrasting agro-climatic conditions by studying the genetic, epigenetic and phenotypic variation. But due to the lack of prior existence of epigenetic markers, this thesis study is divided of two parts: In the first part, European wheat populations coming from a set of seven farmer and one modern varieties, each of which was grown on seven farms (distributed across Europe) for three years, were used to study their short term response to contrasting agro-climatic conditions in Europe by analysing their phenotypic and genotypic variations. For the second part the effect of vernalization on the DNA methylation profile of theVRN-A1 gene in winter wheat was studied as a first step towards the development for the epigenetic marker in this gene.The results from the first part of the study revealed that conservation history of these farmer varieties strongly influenced the genetic diversity and fine genetic structure. Ex situ conserved farmer varieties showed low genetic diversity and simpler structure whereas in situ conserved farmer varieties and mixtures revealed higher level of genetic diversity and complex genetic structure. Genetic and phenotypic spatio-temporal differentiation depending upon the level of diversity and structural complexity of the farmer variety was observed. The traditional varieties tend to become more differentiated than the modern variety arguing in favour of use of these diverse traditional (farmer) varieties in organic and low input agriculture systems. Interestingly, a significant phenotypic differentiation for varieties with very low genetic diversity has also been observed in this study, which gives indication of a possible role of epigenetic variation in the process of evolution.From the second part of the study (effect of vernalization on the DNA methylation profile of the VRN-A1 gene), it was found that in addition to the detection of gene body methylation across the VRN-A1 gene, we identified a region within intron 1 that shows significant increase in DNA methylation in response to vernalization treatment that is positively correlated with the gene expression. Although the role of this shift in gene regulation is still unclear due to time limitations in the thesis and the small number of genotypes analysed, this study will provide a good material towards future identification of new epialleles and the development of epigenetic markers to study the epigenetic variability of these populations.This study at large provides useful knowledge on the understanding of farmers' varieties evolutionary response to be used in the development of different breeding and conservation approaches for organic agriculture, taking into consideration of the importance of within population diversity, to satisfactorily address the problems of organic agriculture.

No description available.

Gene flow and hybridization are pervasive in nature, and can lead to different evolutionary outcomes. They can either accelerate divergence and promote speciation or reverse differentiation. The process of divergence and speciation are strongly influenced by both neutral and selective forces. Disentangling the interplay between these processes in natural systems is important for understanding the general importance of interspecific gene flow in generating novel biodiversity in plants. This thesis first examines the importance of introgressive hybridization in the evolution of the genus Pinus as a whole, and then focusing on specific pine species, investigates the role of geographical, environmental and demographical factors in driving divergence and adaptation. By examining the distribution of cytoplasmic DNA variation across the wide biogeographic range of the genus Pinus, I revealed historical introgression and mtDNA capture events in several groups of different pine species. This finding suggests that introgressive hybridization was common during past species’ range contractions and expansions and thus has played an important role in the evolution of the genus. To understand the cause and process of hybrid speciation, I focused on the significant case of hybrid speciation in Pinus densata. I established the hybridization, colonization and differentiation processes that defined the origin of this species. I found P. densata originated via multiple hybridization events in the late Miocene. The direction and intensity of introgression with two parental species varied among geographic regions of this species. During the colonization on Tibetan Plateau from the ancestral hybrid zone, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. Divergence within P. densata started from the late Pliocene onwards, induced by regional topographic changes and Pleistocene glaciations. To address the role of neutral and selective forces on genetic divergence, I examined the association of ecological and geographical distance with genetic distance in Pinus yunnanensis populations. I found both neutral and selective forces have contributed to population structure and differentiation in P. yunnanensis, but their relative contributions varied across the complex landscape. Finally, I evaluated genetic diversity in the Vietnamese endemic Pinus krempfii. I found extremely low genetic diversity in this species, which is explained by a small ancestral population, short-term population expansion and recent population decline and habitat fragmentation. These findings highlight the role of hybridization in generating novel genetic diversity and the different mechanisms driving divergence and adaptation in the genus Pinus.

Nothofagus moorei is a long-lived, Gondwana relict cool temperate rainforest tree. Nothofagus-dominated rainforests were widespread across much of eastern Australia during the mid-Tertiary but today, N. moorei occurs only as a series of disjunct, isolated populations in south-east Queensland and northern New South Wales. Clonal regeneration via coppicing is reported to be a common feature of most N. moorei populations, while successful sexual regeneration is believed to be rare, occurring largely only in niches with high light levels and limited competition. While clonal propagation enables population persistence and individual longevity, it cannot generate novel genotypes. Isolated populations, potentially high levels of clonality, low-potential for successful sexual regeneration, long-lived individuals and predicted global warming effects make N. moorei vulnerable to local, if not total, population extinction. The current study aimed to assess the relative conservation status of extant N. moorei populations in order to develop appropriate conservation management strategies for long-term population persistence. Levels of genetic diversity and population structure were examined across the remaining natural distribution of N. moorei using nuclear amplified fragment length polymorphism (AFLP), microsatellite and chloroplast DNA markers. In total 607 individuals were sampled from 20 populations and 5 geographical regions: Lamington/Border Ranges, Ballow, Dorrigo/New England, Werrikimbe and Barrington. Genetic results were then analysed to assess conservation status of each population and geographical region. Microsatellite and AFLP data identified comparatively high levels of genetic diversity in all remnant populations sampled. The prevalence of coppicing in the northern Lamington/Border Ranges populations appears to have had little impact on relative levels of genetic diversity, heterozygosity or population structure. Population differentiation was limited, with the majority of genetic variation retained within populations, no regional structuring and high levels of admixture. Analysis of cpDNA variation showed that the three Dorrigo/New England populations were divergent from all other populations, suggesting an ancient divergence in N. moorei prior to Pleistocene glaciations. While levels of genetic diversity were essentially the same across all populations, Bayesian analysis of genetic structure did identify four populations with differing gene pool proportions which would be important to include in conservation efforts in addition to individuals from other populations. Similarly, individuals from four significantly differentiated groups identified using traditional F-statistics suggests individuals from each of these four groups should be included in future conservation plans. In order to maintain ancient chloroplast lineages, populations from the Dorrigo/New England region should also be assigned special conservation value. Populations of N. moorei appear to have retained significant levels of genetic diversity and show little population divergence in spite of marked reductions in the natural distribution since the Early Miocene. Sampling of these ancient trees however, suggests current levels of diversity in N. moorei actually reflect past diversity and differentiation, and that there have been insufficient generations since the historical contraction in distribution for genetic diversity to be adversely affected and regional differentiation to evolve. Long-term persistence of N. moorei is still threatened by future accelerated climate change and the limited preferred habitat that remains where N. moorei can expand its range. While the ability to regenerate clonally may enable long-term persistence of N. moorei, populations are still likely to continue to decline as climatic conditions will increasingly favour sub-tropical and warm temperate species across much of N. moorei's northern distribution. Southern populations of N. moorei, in contrast, could expand their ranges into eucalypt woodlands as predicted climate becomes warmer and wetter. However, this will ultimately be determined by the frequency of fires, with increased fire frequencies favouring the expansion of eucalypts and contraction and possible local population extinction of N. moorei dominated cool temperate rainforests.

Thesis (MScAgric)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: Research into markers for the detection of genetic diversity and cultivar identification has become an important component of the genetic improvement of crops. However, the incorporation of marker assisted selection (MAS) as a tool for the identification and characterization of breeding material has not been fully implemented in the breeding of spring triticale at Stellenbosch University’s Plant Breeding laboratory (SU-PBL). The present study served as a case study in order to achieve this. The first part of the study concerned the detection of genetic diversity in 101 newly sourced triticale cultivars, from a USDA germplasm bank, together with five local control cultivars, in order to identify possible crossing parents. Eight SSR markers, including five derived from rye and three from wheat, and five agronomic characteristics were used to assess diversity. In seedling screening the foreign cultivars showed resistance towards the stem rust isolate used, but were mostly susceptible to the leaf rust isolate. Out of the 8 SSR markers tested, 7 markers were polymorphic and revealed 140 alleles varying from 12 to 26 with an average of 17.5 alleles per locus. The observed polymorphic information content (PIC) value ranged from 0.39 to 0.88 with an average of 0.70, indicative of the good discriminatory ability of the SSR markers. The data revealed that the South African cultivars were genetically closely related to cultivars from the USA and Canada. The second part of the study focused on the introgression of a blue aleurone layer gene (Ba), carried by a wheat cultivar, ‘Cltr1202STR’, and purple pericarp genes (Pp1; Pp3) also carried by a wheat cultivar, ‘Amethyst’, into a triticale background. Unfortunately the introgression of the purple pericarp genes failed. Two lines containing the blue aleurone layer, 11T023 and 11T028, were however successfully created. Molecular typing of these lines with SSR markers were able to show that BC4F1 line 11T023 (Ba) B was genetically similar to the recurrent parent ‘Agbeacon’; and that the BC4F1 11T028 line (Ba) A was closest to the ‘US2007’ recurrent parent. The study illustrated that MAS was a reliable tool for detecting genetic diversity in newly sourced germplasm, and assisted in making a backcross breeding effort more effective. The data generated from MAS could therefore clearly assist in making the SU-PBL breeding program more effective by moving, better informed, decision making toward data based partly on the genotype, thereby minimizing the risks associated with purely phenotypic based decisions. / AFRIKAANSE OPSOMMING: Navorsing rondom die gebruik van merkers vir die bepaling van genetiese-diversiteit en kultivar identifikasie is ‘n toenemend belangriker komponent vir die genetiese verbetering van gewasse. Die inkorporering van merker-bemiddelde-seleksie (MBS) as gereedskap vir die identifikasie en karaktarisering van telingsmateriaal is nog nie ten volle geïmplimenteer in die lente korogtelingsprogram van die Stellenbosch Universiteit Planteteeltlaboratorium (SU-PTL). Die studie het gedien as gevallestudie ten einde dit te bereik. Die eerste gedeelte van die studie het gehandel oor die tipering van die genetiese diversiteit van ‘n 101 kultivars verkry vanaf ‘n USDA kiemplasmabank saam met 5 plaaslike kontroles. Dit was gedien ten einde moontlike kruisings-ouers te kon identifiseer. Agt SSR merkers, insluitend vyf afkomstig van rog en drie vanaf koring, asook vyf agronomiese kenmerke is aangewend om die materiaal se diversiteit te tipeer. Saailingtoetsing is ook gedoen en het aangetoon dat die meeste kultivars weerstandig was vir die stamroes-isolaat, maar nie die blaarroes-isolaat nie. Van die agt SSR merkers getoets het sewe getoon om polimorfies te wees en het ‘n 140 allele gegee wat gewissel het vanaf 12 tot 26 per lokus met ‘n gemiddeld van 17.5. Die waargenome polimorfiese inligtings inhoud (PII) waarde het gewissel vanaf 0.39 tot 0.88 met ‘n gemiddeld van 0.70. Die merkers kon dus suksesvol diskrimineer. Die data het aangetoon dat die Suid-Afrikaanse kultivars genetiese die naaste verwant was aan die kultivars afkomstig vanaf die VSA en Kanada. Die tweede gedeelte van die studie het gefokus op die introgressie van ‘n blou aleuron-laag geen (Ba), afkomstig vanaf die koringkultivar ‘Cltr1202STR’, en twee pers-perikarp gene (Pp1; Pp3), afkomstig vanaf die koringkultivar ‘Amethyst’, na ‘n korog agtergrond. Ongelukkig het die oordrag van die pers-perikarp gene gefaal. Twee lyne wat die blou aleuron- laag bevat, 11T023 en 11T028, is egter suksesvol geskep. Tipering van die lyne met die SSR merkers het aangetoon dat die BC4F1 lyn 11T023 (Ba) B genetiese baie na aan die herhalende ouers ‘Agbeacon’ is en dat die BC4F1 11T028 lyn (Ba) A nader is aan die herhalende ouer ‘US2007’. Die studie het dus geïllustreer dat MBS gebruik kan word as ‘n betroubare manier om genetiese diversiteit te bepaal en by te dra tot die sukses van ‘n terugkruisingsprogram. Die data wat dus voortspruit uit MBS kan dus help om die SU-PTL se telingsprogram te assisteer in die besluitnemingsproses tydens teling deur beter genotipe gebaseerde besluite te neem wat die riskio van fenotipe gebaseerde besluite kan help verminder.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: The decline of Haliotis midae (perlemoen) populations together with the ensuing collapse of commercial abalone fisheries in South Africa have shifted the responsibility to abalone farms to meet the demand for perlemoen. Attention has recently turned to the genetic enhancement of cultured abalone in order for the farms to remain competitive in the international aquaculture market. To develop a successful breeding programme it is imperative to draw on a good foundation of high levels of genetic diversity and to successfully maintain these levels in order to create an enhanced strain of cultured abalone. A Performance Recording Scheme (PRS) was established as the first breeding programme for Haliotis midae to utilise molecular tools. This programme was aimed at enhancing the growth rate of abalone in order to shorten the production times on farms. The current study made use of 12 species-specific microsatellite markers to assign parentage to a group of faster-growing PRS animals, as selected by the abalone farms, in order to select a diverse on-farm generation of broodstock. Additionally, the influence of standard selection practises on the genetic diversity of a population compared to genotypic selection was investigated. This data was also used to study the differentiation and levels of genetic diversities within and between cultured and wild populations. Selection based on genotypic traits successfully retained genetic diversity while some diversity was lost in phenotypically selected populations. These phenotypic populations differed significantly from each other and wild populations, while the genotypic populations were similar in genetic composition to each other and wild populations of the West coast. The broodstock populations used in the PRS spawning event were representative of the wild populations from where they were sourced, with no significant differentiation between the broodstock and West coast population. When these broodstock populations were compared to their corresponding offspring populations, only two populations displayed a significant loss in diversity; although all of the offspring populations showed significant differentiation with their corresponding broodstock populations. This was attributed to the differential contribution of broodstock and the effect of artificial selection. It was established that the cultured populations of the participating abalone farms should be used with caution in ranching and reseeding programmes. These populations differed significantly from both the East and West coast wild populations. This study concluded that it is possible to retain genetic diversity by selecting breeding animals based on genotypic traits. The loss of diversity in some cultured populations and significant differentiation from the wild populations indicate that animals are exposed to different selection pressures in the cultured environment. The results found in this study highlight the need for the effective management of hatchery practices and the genetic monitoring of the breeding animals. / AFRIKAANSE OPSOMMING: Die afname in Haliotis midae (perlemoen) populasies en die daaropvolgende ineenstorting van die kommersiële perlemoen bedryf in Suid-Afrika het die verantwoordelikheid om in die aanvraag na perlemoen te voorsien, na perlemoen plase verskuif. Die genetiese verbetering van verboude perlemoen geniet tans aandag in ‘n poging om kompeterend te bly in die internasionale mark. Dit is noodsaaklik vir die sukses van ‘n broeiprogram om gebruik te maak van ‘n goeie genetiese basis met hoë vlakke van genetiese diversiteit en die suksesvolle behoud van die vlakke om so ‘n verbeterde lyn te skep. ‘n Groeiprestasie aanteken stelsel [Performance Recording Scheme (PRS)] is gestig as die eerste broeiprogram vir Haliotis midae wat gebruik maak van molekulêre tegnieke. Die doel van hierdie program was om die groeitempo van verboude perlemoen te verbeter om produksie tye te verkort. Die huidige studie het gebruik gemaak van 12 spesie-spesifieke mikrosatelliet merkers om ouerskap toe te ken aan ‘n groep vinnig-groeiende PRS-diere, soos geselekteer deur die perlemoen plase, om ‘n diverse generasie gekultiveerde diere te selekteer wat as broeidiere kan dien. Die invloed van standaard seleksie metodes op die genetiese diversitiet van ‘n populasie in vergelyking met genotipiese seleksie is ook ondersoek. Die ouerskap data is ook gebruik om differensiasie en vlakke van genetiese diversiteit tussen verboude perlemoene en wilde populasies vas te stel. Seleksie gebasseer op genetiese eienskappe het daarin geslaag om genetiese diversiteit te behou, terwyl diversiteit verlore gegaan het in die fenotipies geselekteerde populasies. Hierdie fenotipiese populasies het ook beduidend met mekaar sowel as met die wilde populasies verskil, terwyl genotipiese populasies soortgelyk was in hul genetiese samestelling en nie van die wilde populasies van die Weskus verskil het nie. Die broeidiere wat in die PRS broeiprogram gebruik is, was verteenwoordigend van die wilde populasies vanwaar hulle oorspronlik gekom het, met geen beduidende differensiasie tussen die broeidiere en die Wes kus populasies nie. Met die vergelyking van die broeidiere en hul ooreenstemmende nageslag, het dit geblyk dat slegs twee populasies ‘n beduidende verlies aan genetiese diversiteit getoon het, alhoewel al die nageslag beduidende populasie differensiasie met hul ouers getoon het. Hierdie bevindinge is toegeskryf aan oneweredige bydraes van die broeidiere tydens gameetvrystelling en die invloed van kunsmatige seleksie. Hierdie studie het ook vasgestel dat die verboude perlemoen populasies met sorg gebruik moet word om wilde populasies te herstel, aangesien hierdie populasies beduidend verskil het van wilde populasies van beide die Oos en Wes-kus. Hierdie studie het gevind dat dit moontlik is om genetiese diversiteit te behou deur diere te selekteer op grond van genotipiese eienskappe. Die verlies van diversiteit in sommige van die verboude perlemoen populasies en die beduidende verskil met die wilde populasies dui daarop dat diere in die gekultiveerde omgewing blootgestel word aan verskillende tipes seleksiedruk. Hierdie bevindinge beklemtoon die belang vir effektiewe bestuur van broeiery praktyke en genetiese monitering van broeidiere.