A Tutorial on Coding Methods for DNA-based Molecular Communications and Storage

Exponential increase of data has motivated advances of data storage technologies. As a promising storage media, DeoxyriboNucleic Acid (DNA) storage provides a much higher data density and superior durability, compared with state-of-the-art media. In this paper, we provide a tutorial on DNA storage and its role in molecular communications. Firstly, we introduce fundamentals of DNA-based molecular communications and storage (MCS), discussing the basic process of performing DNA storage in MCS. Furthermore, we provide tutorials on how conventional coding schemes that are used in wireless communications can be applied to DNA-based MCS, along with numerical results. Finally, promising research directions on DNA-based data storage in molecular communications are introduced and discussed in this paper

Breeding success and survival in relation to major effect loci affecting the age at maturation in Teno river Atlantic salmon (Salmo salar)

There is an age at maturity related trade-off between breeding success and survival in Atlantic salmon, and sex specific patterns exist in the expression of this life-history trait. A recent study identified three candidate genes, vgll3, akap11 and six6, which had a major effect on this trait. Sex-dependent dominance was also observed in the gene vgll3 with the strongest association to sea-age (years in ocean prior to maturation). This was assumed to be an adaptation to sexual conflict resulting from different optimal age at maturity between the sexes. However, direct effects on fitness were not investigated previously. Therefore, the aim of this study was to fill some of these knowledge gaps by studying sea-age candidate gene related breeding success and survival. A dataset of 167 single nucleotide polymorphism (SNP) loci interspersed through the salmon genome including loci tightly linked with the sea-age candidate genes was gen-erated for Teno river Atlantic salmon by sequencing DNA from one adult cohort and a subsequent cohort of juveniles on four consecutive years. Breeding success was studied by observing the trans-generational change in the sea-age candidate gene genotype fre-quencies and vgll3 genotype related mate choice, and survival by observing the change of genotype frequencies in freshwater juveniles. A significant deviation was observed between adult and juvenile vgll3 and six6 geno-type frequencies. The homozygous vgll3 genotype promoting later maturation in both sexes was significantly higher in juveniles than in adults, presumably due to better breeding success of males with this genotype. Homozygous six6 genotype with oppos-ing effect was similarly enriched. No vgll3 related mate choice nor change in genotype frequencies among juveniles was observed. These results show that these two genes af-fect the breeding success and likely marine survival, but further studies are needed in order to assess the lifelong fitness effects of different genotypes

Utilizing a historical wheat collection to develop new tools for modern plant breeding

Doctor of PhilosophyGenetics Interdepartmental ProgramJesse PolandThe Green Revolution is credited with saving billions of lives by effectively harnessing new genetic resources and breeding strategies to create high-yielding varieties for countries lacking adequate food security. To keep the next billion people in a state of food security, plant breeders will need to rapidly incorporate novel approaches and technologies into their breeding programs. The work presented here describes new genomic and phenomic strategies and tools aimed at accelerating genetic gain in plant breeding. Plant breeders have long relied on regional testing networks to evaluate new breeding lines across many locations. These are an attractive resource for both retrospective and contemporary analysis due to the vast amount of data available. To characterize genetic progress of plant breeding programs in the Central Plains, entries from the Southern Regional Performance Nursery dating back to 1992 were evaluated in field trials. The trend for annual improvement was 1.1% yr⁻¹, matching similar reports for genetic gain. During the same time period, growth of on-farm yields stagnated. Genomic selection, a promising method to increase genetic gain, was tested using historical data from the SRPN. A temporal-based model showed that, on average, yield predictions outperformed a year-to-year phenotypic correlation. A program-based model found that the predictability of a breeding program was similar when using either data from a single program or from the entire regional collection. Modern DNA marker platforms either characterize a small number of loci or profile an entire genome. Spiked genotyping-by-sequencing (sGBS) was developed to address the need in breeding programs for both targeted loci and whole-genome selection. sGBS uses a low-cost, integrated approach that combines targeted amplicons with reduced representation genotyping-by-sequencing. This approach was validated using converted and newly-designed markers targeting known polymorphisms in the leaf rust resistance gene Lr34. Plant breeding programs generate vast quantities of data during evaluation and selection of superior genotypes. Many programs still rely on manual, error-prone methods to collect data. To make this process more robust, we have developed several open-source phenotyping apps with simple, intuitive interfaces. A contemporary Green Revolution will rely on integrating many of these innovative technologies into modern breeding programs

Developing the Four Parent Maize Population (FPM): Phenotypic and Genotypic Characterization

In order to gain a better understanding of the effects and amount of recombination that can be available to future plant breeding endeavors, a unique mapping population was created. A di-hybrid maize (Zea mays L.) cross was used in this study to create inter-crossed recombinant inbred lines (IRILs). The four parents include two with blue aleurone, one with high oleic acid, and a highly aflatoxin resistant publicly available inbred, Tx772. The 1291 line population consisted of six sub-populations with various levels of crossing and inter-crossing which afforded the opportunity to examine an array of mapping population designs for phenotypic diversity, as well as genetic mapping effectiveness. An especially important outcome of this study for future maize genetic studies was to determine whether it is more prudent to increase the size of mapping populations, to increase the number of parents, or to add additional cycles of intermating. The added increased effective recombination in several of the sub-populations produced greater diversity of phenotypes and an increase in quantitative trait locus/ loci (QTL) accuracy and resolution in some cases. Phenotypic variation and genetic mapping resolution were to a greater extent affected by population size. Significant variation was observed for days to anthesis and silk, plant and ear height, leaf rolling, as well as cob and kernel color. Questions and outcomes that this population addressed concerning practical plant breeding applications included the added difficulty that various mapping population designs create, and that a direct relationship between increased phenotypic and genotypic variation and additional parents or intermating cycles did not seem to exist. Instead, variation was specific for the population and target trait in question. From a molecular and genetic mapping standpoint, the 4way population without intermating detected the gene for cob color, while the only other two groups that detected it were the 4way3sib, as well as all 4way subpopulations combined; both which had the largest population sizes, excluding the entire population which contained bi-parental populations. Because only one of the four parents, B73Olc1, expressed red cob, this observation may prove useful for future studies where a target trait is under represented in available germplasm. This indicates that larger population sizes, more so than exotic population designs may lead to improved results. Due to the incorporation of diverse mating designs, this population is a unique resource for future research including additional phenotypic analysis, genetic map construction, QTL linkage mapping, and analysis of recombination rate

Ecological and population genomics of the wild yellow-necked mouse, Apodemus flavicollis

Species belonging to the genus Apodemus are one of the most common and broadly distributed small mammals in the Palearctic, making them ideal for studying ecological and evolutionary processes in natural systems. Although much research has focused on the ecology of Apodemus sp., relatively little is known about the evolutionary processes which govern their natural variation in the wild. This is, in part, due to the limitations of de novo genomic research in traditionally non-model organisms. However, recent advances in high-throughput library preparation techniques such as RADseq, have made non-model organisms more accessible for genome wide analyses. This thesis shows how a modified RADseq protocol (quaddRAD) can be used to conduct ecological and evolutionary genomics research in a large population of wild yellow-necked mice, Apodemus flavicollis, that is subject to highly seasonal conditions. I show how a high quality genomic dataset of 21,011 SNPs can be generated using quaddRAD, and discuss the rationale behind the methodology in detail. I then use the genotypes to construct a multi-generational pedigree, and describe the population’s demography, fitness and allele frequency dynamics over time. I find significant variation in the genetic contributions of mice to each generation, where by the end of the study, 53.6% of the sampled population was descended from a single individual. Contrary to the expected high levels of inbreeding and low genetic diversity in such a population, I find it is largely panmictic, which suggests a large degree of connectivity to nearby populations allowing genetic rescue through high levels of migration and gene flow. Finally, I show how heterothermic responses, which reduce an individuals energy budget by up to 65% under harsh conditions, are not only highly variable in the population, but also highly heritable. This suggests heterothermy could be subject to natural selection. I show that heterothermic responses form two distinct thermal strategies in the morphospace, which may be the result of different modes of selection acting on the population to maintain significant natural variation. This thesis shows the viability of quaddRAD for large scale genomics research in wild Apodemus sp., to cement their role as a model organism for ecological and evolutionary genomics research