Relevant bibliographies by topics / Population genetics

Academic literature on the topic 'Population genetics'

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Published: 4 June 2021
Last updated: 29 July 2024

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Journal articles on the topic "Population genetics"

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Laporte, Valérie, and Brian Charlesworth. "Effective Population Size and Population Subdivision in Demographically Structured Populations." Genetics 162, no. 1 (September 1, 2002): 501–19. http://dx.doi.org/10.1093/genetics/162.1.501.

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AbstractA fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age. This provides a general expression for the probability that a pair of alleles sampled from the population coalesce in the previous time interval. The effective population size is defined as the reciprocal of twice the product of generation time and the coalescence probability. Biologically explicit formulas for effective population size with discrete generations and separate sexes are derived for a variety of different modes of inheritance. The method is also applied to a nuclear gene in a population of partially self-fertilizing hermaphrodites. The effects of population subdivision on a demographically structured population are analyzed, using a matrix of net rates of movement of genes between different local populations. This involves weighting the migration probabilities of individuals of a given age/sex class by the contribution of this class to the leading left eigenvector of the matrix describing the movements of genes between age/sex classes. The effects of sex-specific migration and nonrandom distributions of offspring number on levels of genetic variability and among-population differentiation are described for different modes of inheritance in an island model. Data on DNA sequence variability in human and plant populations are discussed in the light of the results.
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Morin-Chassé, Alexandre. "Behavioral Genetics, Population Genetics, and Genetic Essentialism." Science & Education 29, no. 6 (November 4, 2020): 1595–619. http://dx.doi.org/10.1007/s11191-020-00166-y.

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Siegel, PB, and EA Dunnington. "Genetic selection strategies–population genetics." Poultry Science 76, no. 8 (August 1997): 1062–65. http://dx.doi.org/10.1093/ps/76.8.1062.

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Viney, M. E. "Nematode population genetics." Journal of Helminthology 72, no. 4 (December 1998): 281–83. http://dx.doi.org/10.1017/s0022149x00016606.

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Population genetics seeks to understand the genetic relationships within and between populations of a species and the processes that generate these patterns. Little is known about the population genetics of parasitic nematodes. This is a notable gap in our knowledge since understanding the population genetic patterns and processes of parasitic nematodes has profound implications for our ability to fully understand this important group of pathogens. For example, it is only possible to begin to understand how a parasite population will respond to an imposed selection pressure (such as an anthelmintic drug, a vaccine, or resistant hosts) when the population genetic structure and patterns of gene flow of that population is known. Equally, the epidemiology of many nematode parasites is well known empirically and theoretically, yet this epidemiological information is of limited use without a good understanding of the genetic structure of those populations (Anderson & May, 1992).
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Степанов, В. А. "Population Genomics of Russian populations." Nauchno-prakticheskii zhurnal «Medicinskaia genetika», no. 7(216) (July 30, 2020): 6–7. http://dx.doi.org/10.25557/2073-7998.2020.07.6-7.

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Популяционная геномика человека является мощным современным подходом в популяционной генетике, базирующемся на технологиях геномного секвенирования, биоинформатики и анализа больших данных. Геномный анализ генетической вариабельности в популяциях является фундаментальной основой генетики болезней и разработки путей их диагностики, терапии и профилактики. В работе представлены собственные данные о геномном анализе генетического разнообразия населения России. Показано, что генофонд современных народов России формировался на протяжении многих тысяч лет в ходе совокупного влияния миграций, изоляции расстоянием, эффектов основателя и естественного отбора. Сформировавшиеся в ходе микроэволюции геномные паттерны современных популяций в существенной мере определяют композицию генетических факторов как частых хронических, так и редких моногенных заболеваний. Human population genomics is a powerful modern approach in population genetics based on technologies of genomic sequencing, bioinformatics, and big data analysis. Genomic analysis of genetic variability in populations is a fundamental basis for the genetics of diseases and the development of ways for their diagnosis, therapy and prevention. The work presents the own data on the genomic analysis of the genetic diversity of the Russian populations. It is shown that the gene pool of modern populations of Russia was formed over many thousands of years by the combined effects of migrations, isolation by distance, founder effects and natural selection. The genomic patterns of modern populations formed during microevolution substantially determine the composition of genetic factors of both frequent chronic and rare monogenic diseases.
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Bedge, Kiran, and Pratima Salunkhe. "Population Genetics : A Review." International Journal of Scientific Research in Science and Technology 11, no. 2 (April 20, 2024): 746–48. http://dx.doi.org/10.32628/ijsrst24112109.

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Genetics is the study of genes and genetic variations alongwith the hereditary characteristics of an organism. Genetics is a central pillar of biology. It overlaps with other areas, such as: Agriculture, Medicine, Biotechnology. Genetics involves studying: Gene structure and function Gene variation and changes How genes affect health, appearance, and personality. Population genetics studies genetic variation within and among populations, based on the Hardy-Weinberg law, which remains constant in large populations with random mating and minimal mutation, selection, and migration.
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Nagylaki, T. "The inbreeding effective population number in dioecious populations." Genetics 139, no. 1 (January 1, 1995): 473–85. http://dx.doi.org/10.1093/genetics/139.1.473.

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Abstract The inbreeding effective population number in a dioecious population with discrete, nonoverlapping generations is investigated for both autosomal and X-linked loci. The recursion relations for the probabilities of genic identity, and the effective population numbers are analyzed and compared in two cases: (i) the offspring identified by sex in the calculation of the probability of common parentage and (ii) the offspring not so identified. Case i gives the correct evolution of the probabilities of identity, but case ii has been more widely studied and applied. A general symmetric framework that reduces the number of parameters is developed and used to examine a wide variety of models of panmixia and monogamy. Cases i and ii agree in many, but not all, models.
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Nagylaki, T. "The Inbreeding Effective Population Number in Dioecious Populations." Genetics 139, no. 3 (March 1, 1995): 1463d. http://dx.doi.org/10.1093/genetics/139.3.1463c.

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Russo, Eugene. "Population Genetics." Nature 413, no. 6855 (October 2001): 4–5. http://dx.doi.org/10.1038/35097203.

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Cavalli-Sforza, L. L. "Population genetics." Trends in Genetics 2 (January 1986): 220. http://dx.doi.org/10.1016/0168-9525(86)90234-9.

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Dissertations / Theses on the topic "Population genetics"

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Lundy, Ian J. "Theoretical population genetics of spatially structured populations /." Title page, contents and summary only, 1997. http://web4.library.adelaide.edu.au/theses/09PH/09phl962.pdf.

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Herbots, Hilde Maria Jozefa Dominiek. "Stochastic models in population genetics : genealogy and genetic differentiation in structured populations." Thesis, Queen Mary, University of London, 1994. http://qmro.qmul.ac.uk/xmlui/handle/123456789/1482.

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The theory of probability and stochastic processes is applied to a current issue in population genetics, namely that of genealogy and genetic differentiation in subdivided populations. It is proved that under a reasonable model for reproduction and migration, the ancestral process of a sample from a subdivided population converges weakly, as the subpopulation sizes tend to infinity, to a continuous-time Markov chain called the "structured coalescent". The moment-generating function, the mean and the cond moment of the time since the most recent common ancestor (called the "coalescence time") of a pair of genes are calculated explicitly for a range of models of population structure. The value of Wright's coefficient FST, which serves as a measure of the subpopulation differentiation and which can be related to the coalescence times of pairs of genes sampled within or among subpopulations, is calculated explicitly for various models of population structure. It is shown that the dependence of FST on the mutation rate may be more marked than is generally believed, particularly when gene flow is restricted to an essentially one-dimensional habitat with a large number of subpopulations. Several more general results about genealogy and subpopulation differentiation are proved. Simple relationships are found between moments of within and between population coalescence times. Weighting each subpopulation by its relative size, the asymptotic behaviour of FST at large mutation rates is independent of the details of population structure. Two sets of symmetry conditions on the population structure are found for which the mean coalescence time of a pair of genes from a single subpopulation is independent of the migration rate and equal to that of two individuals from a panmictic population of the same total size. Under graph-theoretic conditions on the population structure, there is a uniform relationship between the FST value of a pair of neighbouring subpopulations, in the limit of zero mutation rate, and the migration rate
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Zenger, Kyall Richard. "Genetic linkage maps and population genetics of macropods." Phd thesis, Australia : Macquarie University, 2002. http://hdl.handle.net/1959.14/47604.

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"November 2001".
Thesis (PhD)--Macquarie University, Division of Environmental and Life Sciences, Department of Biological Sciences, 2002.
Bibliography: leaves 136-157.
General introduction -- Molecular markers for comparative and quantitative studies in macropods -- Genetic linkage map construction in the tammar wallaby (M. eugenii) -- Intraspecific variation, sex-biased dispersal and phylogeography of the eastern grey kangaroo (M. giganteus) -- General discussion.
The analysis of DNA using molecular techniques is an important tool for studies of evolutionary relationships, population genetics and genome organisation. The use of molecular markers within marsupials is primarily limited by their availability and success of amplification. Within this study, 77 macropodid type II microsatellite loci and two type I genetic markers were characterised within M. eugenii to evaluate polymorphic levels and cross-species amplification artifacts. Results indicated that 65 microsatellite loci amplified a single locus in M. eugenii with 44 exhibiting high levels of variability. The success of crossspecies amplification of microsatellite loci was inversely proportional to the evolutionary distance between the macropod species. It is revealed that the majority of species within the Macropodidae are capable of using many of the available heterologous microsatellites. When comparing the degree of variability between source-species and M. eugenii, most were significantly higher within source species (P < 0.05). These differences were most likely caused by ascertainment bias in microsatellite selection for both length and purity. -- The production of a marsupial genetic linkage map is perhaps one of the most important objectives in marsupial research. This study used a total of 353 informative meioses and 64 genetic markers to construct a framework genetic linkage map for M. eugenii. Nearly all markers (93.7%) formed a significant linkage (LOD > 3.0) with at least one other marker. More than 70% (828 cM) of the genome had been mapped when compared with chiasmata data. Nine linkage groups were identified, with all but one (LG7; X-linked) allocated to the autosomes. Theses groups ranged in size from 15.7 cM to 176.5 cM, and have an average distance of 16.2 cM between adjacent markers. Of the autosomal linkage groups, LG2 and LG3 were assigned to chromosome 1 and LG4 localised to chromosome 3 based on physical localisation of genes. Significant sex-specific distortions towards reduced female recombination rates were revealed in 22% of comparisons. Positive interference was observed within all the linkage groups analysed. When comparing the X-chromosome data to closely related species it is apparent that it is conserved both in synteny and gene order. -- The investigation of population dynamics of eastern grey kangaroos has been limited to a few ecological studies. The present investigation provides analysis of mtDNA and microsatellite data to infer both historical and contemporary patterns of population structuring and dispersal. The average level of genetic variation across sample locations was exceedingly high (h = 0.95, HE = 0.82), and is one of the highest observed for marsupials. Contrary to ecological studies, both genic and genotypic analyses reveal weak genetic structure of populations where high levels of dispersal may be inferred up to 230 km. The movement of individuals was predominantly male-biased (average N,m = 22.61, average N p = 2.73). However, neither sex showed significant isolation by distance. On a continental scale, there was strong genetic differentiation and phylogeographic distinction between southern (TAS, VIC and NSW) and northern (QLD) Australian populations, indicating a current and / or historical restriction of geneflow. In addition, it is evident that northern populations are historically more recent, and were derived from a small number of southern eastern grey kangaroo founders. Phylogenetic comparisons between M. g. giganteus and M. g. tasmaniensis, indicated that the current taxonomic status of these subspecies should be revised as there was a lack of genetic differentiation between the populations sampled.
Mode of access: World Wide Web.
xv, 182 leaves ill
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Martien, Karen Kay Fear. "Conservation of spatially structured populations : lessons from population genetics /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2000. http://wwwlib.umi.com/cr/ucsd/fullcit?p9979969.

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Montemuiño, Sosa Carlos. "Parallelizing Population Genetics Applications." Doctoral thesis, Universitat Autònoma de Barcelona, 2021. http://hdl.handle.net/10803/673278.

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Amb la creixent disponibilitat de dades a escala de l'genoma per a la investigació genètica, els genetistes de poblacions moleculars han de treballar amb models més complexos, el que no pot fer-se en un temps determinat utilitzant el mètode coalescent estàndard. Aquest escenari va dur a el desenvolupament de diverses aplicacions alternatives de simulació numèrica. Tot i l'accés cada vegada més gran a les agrupacions de computació d'alt rendiment (HPC) a l'acadèmia, no s'està aprofitant en el camp de la genètica de poblacions. L'establiment de paral·lels entre les aplicacions existents és difícil d'aconseguir pels desenvolupadors sense una comprensió completa de la HPC, i les noves aplicacions només aprofiten les capacitats de multiprocessament d'una sola computadora. En aquesta tesi es proposa una metodologia per establir un paral·lelisme entre les aplicacions coalescents i utilitzar eficaçment tota la potència de processament disponible d'un grup d'HPC. La metodologia introdueix una estratègia per reduir les comunicacions intra-node en el paradigma de pas de missatges. Aquesta solució permet obtenir una millor escalabilitat per a les aplicacions coalescents que requereixen la generació de milions de rèpliques. Com a resultat, els genetistes de poblacions poden utilitzar les eines coalescents estàndard per executar l'anàlisi de Computació Bayesiana Aproximada (ABC) sense dependre d'aplicacions menys precises. Hem avaluat la nostra estratègia establint un paral·lelisme amb l'aplicació coalescent estàndard de facto i executant experiments a escala de l'genoma en un conglomerat HPC real. Afinant diferents aspectes de la nostra metodologia, hem obtingut importants guanys de rendiment, donant lloc a una velocitat de 4x per sobre de la nostra paral·lelització inicial, que representava una velocitat de 50x per sobre de l'aplicació coalescent de referència.
Con la creciente disponibilidad de datos a escala del genoma para la investigación genética, los genetistas de poblaciones moleculares tienen que trabajar con modelos más complejos, lo que no puede hacerse en un tiempo determinado utilizando el método coalescente estándar. Este escenario llevó al desarrollo de varias aplicaciones alternativas de simulación numérica. A pesar del acceso cada vez mayor a las agrupaciones de computación de alto rendimiento (HPC) en la academia, no se está aprovechando en el campo de la genética de poblaciones. El establecimiento de paralelos entre las aplicaciones existentes es difícil de lograr por los desarrolladores sin una comprensión completa de la HPC, y las nuevas aplicaciones sólo aprovechan las capacidades de multiprocesamiento de una sola computadora. En esta tesis se propone una metodología para establecer un paralelismo entre las aplicaciones coalescentes y utilizar eficazmente toda la potencia de procesamiento disponible de un grupo de HPC. La metodología introduce una estrategia para reducir las comunicaciones intra-nodo en el paradigma de paso de mensajes. Esta solución permite obtener una mejor escalabilidad para las aplicaciones coalescentes que requieren la generación de millones de réplicas. Como resultado, los genetistas de poblaciones pueden utilizar las herramientas coalescentes estándar para ejecutar el análisis de Computación Bayesiana Aproximada (ABC) sin depender de aplicaciones menos precisas. Hemos evaluado nuestra estrategia estableciendo un paralelismo con la aplicación coalescente estándar de facto y ejecutando experimentos a escala del genoma en un conglomerado HPC real. Afinando diferentes aspectos de nuestra metodología, hemos obtenido importantes ganancias de rendimiento, cuadruplicando el speedup de nuestra paralelización inicial, la cual representaba una mejora de 50x sobre la aplicación coalescente de referencia.
With the increasing availability of genome-scale data for genetic research, molecular population geneticists need to work with more complex models, which cannot be done in a time-fashion using the standard coalescent methods. This scenario led to the development of several alternative numerical simulation applications. Despite the ever-increasing access to High Performance Computing (HPC) clusters in the academy, it is not being leveraged in the field of population genetics. Parallelizing existing applications is hard to achieve by developers without a comprehensive understanding of the HPC, and new applications only take advantage of multiprocessing capabilities from a single computer. This thesis proposes a technique to parallelize coalescent applications and effectively use all the available processing power from an HPC cluster. We use a strategy to reduce the intra- node communications in the message-passing paradigm. This solution allows for getting better scalability for coalescent applications that require generating millions of replicas. As a result, population geneticists can use the standard coalescent tools for running Approximate Bayesian Computation (ABC) analysis without relying on less accurate applications. We have evaluated our strategy parallelizing the de facto standard coalescent application and run experiments at genome-scale in a real HPC cluster. We have obtained significant performance gains in tuning different aspects of our approach, leading to a 4x speedup over our initial parallelization, which accounted for a 50x speedup over the reference coalescent application.
Universitat Autònoma de Barcelona. Programa de Doctorat en Informàtica
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Mäki-Petäys, H. (Hannaleena). "Conservation and management of populations in a fragmented forest landscape:behavioural ecology meets population genetics." Doctoral thesis, University of Oulu, 2007. http://urn.fi/urn:isbn:9789514283482.

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Abstract The effects of habitat loss and fragmentation on the genetic structure and vulnerability of populations strongly depend on the behaviour of a particular species. In this thesis, I examined the effects of forest fragmentation on genetic population structure with the aim of identifying and evaluating the different genetic and behavioural factors important for species conservation and management on different geographical scales. The species studied were the mound building red wood ants Formica lugubris and F. aquilonia, and a lekking bird, the capercaillie, Tetrao urogallus. Habitat loss and fragmentation affected the genetic structure in both wood ants and capercaillie. In general, the effects were related to the time since fragmentation and to the level of habitat loss and isolation from the other existing populations. The loss of genetic diversity due to population fragmentation was less observable than the differences in population structure. The response to habitat fragmentation was further dependent on species characteristics such as dispersal and mating behaviour. Sociality affected the genetic vulnerability of wood ant populations by decreasing gene diversity, increasing inbreeding depression and restricting gene flow between subpopulations. The results on the capercaillie in turn suggested that lekking behaviour restricts dispersal of both sexes, thus elevating the occurrence of inbreeding between individuals. The present study provided important information on species conservation and management in terms of better understanding species' biology and behaviour, as well as increased knowledge concerning the genetic issues that should be taken into account when planning conservation actions. By examining the genetic structure of the species it was possible to clarify the conservation status including the effective population size, the question of origin, and the genetic vulnerability (genetic diversity, inbreeding and inbreeding depression) of the populations and/or species. Overall, the results emphasised the importance of preserving the effective population size and the connectivity of habitat patches when planning species specific management strategies. There were great differences in conservation needs among the species, which should be taken into account especially in local management actions.
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Grillenberger, Bernd K. "Biogeography, population genetics and mating systems of natural Nasonia populations." [S.l. : Groningen : s.n. ; University Library Groningen] [Host], 2009. http://irs.ub.rug.nl/ppn/317.

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Sjödin, Per. "Effects of Selection and Demography on DNA Polymorphism in Black Mustard (Brassica nigra)." Doctoral thesis, Uppsala universitet, Evolutionär funktionsgenomik, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6633.

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The evolution of three genes from the CONSTANS-LIKE gene family is studied in Brassica nigra. We use a combination of population genetic and phylogenetic techniques in order to assess the relative importance of selection and demography on the pattern of DNA variation. The analysis is complicated by the fact that they are recent duplicates of each other and hence there is a potential redundancy factor that has to be considered. The relationship between two of the genes, COa and COb, is however much closer than between any relationship to the third gene, COL1. The three genes are all suspected to play a part in the natural variation of flowering time of B. nigra. The thesis consists of four papers. The first paper is a technical paper concerning when and if the existence of an effective population size can be assumed. More specifically, the impact of population structure and a fluctuating (census) population size on the standard coalescent is studied. The second paper is a population genetic study of B. nigra using micro-satellites and RFLP. The resulting population genetic structure is argued to reflect the early spread of agriculture in Europe. In the third paper the general evolution of the three genes is studied. We find that not all aspects of the data could be accounted for by demography or redundancy effects, but that selection most likely played a part in the evolution of these genes. The fourth paper concerns the functional status of COb, whether it is a pseudogene or not. The most likely scenario is that COb recently became non-functional due to the fixation of a deleterious mutation during a recent bottleneck.
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Gagnon, Nicolas. "Mesure et analyse de l'effet fondateur dans les populations de Charlevoix et du Bas-Saint-Laurent." Thèse, Chicoutimi : Université du Québec à Chicoutimi, 1998. http://theses.uqac.ca.

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Røyrvik, Ellen C. "The peoples of Britain: population genetics, archaeology and linguistics : population genetics, archaeology and linguistics." Thesis, University of Oxford, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.669909.

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The history of peoples has always evoked a great deal of both academic and popular interest, and the peoples of Britain, with its island position and semi-mythic serial invasions, have evoked as much as any. As most of the period during which Britain has been inhabited by modern humans lies in prehistory, archaeology has long been the best method for elucidating the past. In recent years, however, genetics has come to complement the reconstruction of peoples' pasts, with its ability to trace lineal human biology instead of transferable human culture. The purpose of this thesis is to assess population genetics systems of Britain against the backdrop of archaeologically determined history, informed for later periods by linguistics, and attempt to ascertain any marked congruities or incongruities between this history and modern genetic data. The genetic datasets included in this work are the People of the British Isles Project collection, and some ancillary cohorts from surrounding countries. The genetic systems assessed include mitochondrial DNA, classical marker genes, lactase, pigmentation genes and some phenotypes, and finally a suite of candidate genes for determining normal facial variation. In a self-contained section, the principle of relating population genetic data to population histories is illustrated by a study focusing on Central Asia (a larger area), but using fewer genetic markers. The chosen markers systems overall reveal modest amounts of genetic differentiation among different groups in Britain, but consistently highlight Wales and Orkney especially as relatively distanced from the rest of Britain. This is in keeping with the historically quite isolated state of the former, and the comparatively recent heavy influx of Norse Vikings in the latter. Further details are observable from subsets of this study: all are discussed in the context of archaeological and linguistic evidence. These findings provide support and foundation for a forthcoming study from the People of the British Isles Project, using a genome-wide SNP approach rather than selected markers, which will likely increase the nuance of this initial picture and contribute further to answering specific questions regarding Britain's past.
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Books on the topic "Population genetics"

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Doolittle, Donald P. Population Genetics. Berlin, Heidelberg: Springer Berlin Heidelberg, 1987. http://dx.doi.org/10.1007/978-3-642-71734-5.

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W, Feldman Marcus, ed. Population genetics. Palo Alto, Calif: Blackwell Scientific Publications, 1986.

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D, Brown A. H., and International Symposium on Population Genetics and Germplasm Resources in Crop Improvement (1988 : University of California, Davis), eds. Plant population genetics, breeding, and genetic resources. Sunderland, Mass: Sinauer Associates, 1990.

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Gale, J. S. Theoretical population genetics. Boston: Unwin Hyman, 1990.

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Majumder, Partha P., ed. Human Population Genetics. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2970-5.

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Relethford, John H. Human Population Genetics. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118181652.

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Ewens, Warren J. Mathematical Population Genetics. New York, NY: Springer New York, 2004. http://dx.doi.org/10.1007/978-0-387-21822-9.

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Gale, J. S. Theoretical Population Genetics. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-009-0387-6.

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Relethford, John. Human population genetics. Hoboken, N.J: Wiley-Blackwell, 2012.

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Hodge, Russ. Human genetics: Race, population, and disease. New York, NY: Facts on File, 2010.

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Book chapters on the topic "Population genetics"

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Lipp, O., D. Souery, and J. Mendlewicz. "Population Genetics." In Contemporary Psychiatry, 47–61. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-59519-6_3.

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Vogel, Friedrich, and Arno G. Motulsky. "Population Genetics." In Human Genetics, 433–511. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-662-02489-8_7.

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Jost, Jürgen. "Population Genetics." In Mathematical Methods in Biology and Neurobiology, 199–215. London: Springer London, 2014. http://dx.doi.org/10.1007/978-1-4471-6353-4_6.

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Barnholtz-Sloan, Jill S., and Hemant K. Tiwari. "Population Genetics." In Bioinformatics for Systems Biology, 163–80. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-440-7_10.

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Hastings, Alan. "Population Genetics." In Population Biology, 41–80. New York, NY: Springer New York, 1997. http://dx.doi.org/10.1007/978-1-4757-2731-9_3.

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Castillo-Ramírez, Santiago, and Edward J. Feil. "Population Genetics." In The Prokaryotes, 255–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-30194-0_83.

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Wöhrmann, Klaus, and Volker Loeschcke. "Population Genetics." In Progress in Botany, 228–38. Berlin, Heidelberg: Springer Berlin Heidelberg, 1985. http://dx.doi.org/10.1007/978-3-642-45607-7_16.

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Wöhrmann, Klaus. "Population Genetics." In Progress in Botany, 251–61. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-642-75154-7_16.

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Kowles, Richard. "Population Genetics." In Solving Problems in Genetics, 219–58. New York, NY: Springer New York, 2001. http://dx.doi.org/10.1007/978-1-4613-0205-6_7.

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Tomiuk, Jürgen, and Klaus Wöhrmann. "Population Genetics." In Progress in Botany, 276–87. Berlin, Heidelberg: Springer Berlin Heidelberg, 1994. http://dx.doi.org/10.1007/978-3-642-78568-9_17.

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Conference papers on the topic "Population genetics"

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Higgs, Paul G. "Linking population genetics to phylogenetics." In Stochastic Models in Biological Sciences. Warsaw: Institute of Mathematics Polish Academy of Sciences, 2008. http://dx.doi.org/10.4064/bc80-0-8.

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Kamidi, C. M., R. W. Waineina, C. B. Wasike, D. K. Ngeno, and E. D. Ilatsia. "707. Genetic diversity and population structure of dairy goat populations in Kenya." In World Congress on Genetics Applied to Livestock Production. The Netherlands: Wageningen Academic Publishers, 2022. http://dx.doi.org/10.3920/978-90-8686-940-4_707.

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Rabani, Yuval, Yuri Rabinovich, and Alistair Sinclair. "A computational view of population genetics." In the twenty-seventh annual ACM symposium. New York, New York, USA: ACM Press, 1995. http://dx.doi.org/10.1145/225058.225088.

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Mitrofanova, Antonina, and Bud Mishra. "Population genetics of human copy number variations." In the 2008 ACM symposium. New York, New York, USA: ACM Press, 2008. http://dx.doi.org/10.1145/1363686.1363990.

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Smatti, Maria K., Yasser Al-Sarraj, Omar Albagha, and Hadi M. Yassine. "Host Genetic Variants Potentially Associated with SARS-Cov-2: A Multi-Population Analysis." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0298.

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Background: Clinical outcomes of Coronavirus Disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed enormous inter-individual and interpopulation differences, possibly due to host genetics differences. Earlier studies identified single nucleotide polymorphisms (SNPs) associated with SARS-CoV-1 in Eastern Asian (EAS) populations. In this report, we aimed at exploring the frequency of a set of genetic polymorphisms that could affect SARS-CoV-2 susceptibility or severity, including those that were previously associated with SARS-CoV-1. Methods: We extracted the list of SNPs that could potentially modulate SARS-CoV-2 from the genome wide association studies (GWAS) on SARS-CoV-1 and other viruses. We also collected the expression data of these SNPs from the expression quantitative trait loci (eQTLs) databases. Sequences from Qatar Genome Programme (QGP, n=6,054) and 1000Genome project were used to calculate and compare allelic frequencies (AF). Results: A total of 74 SNPs, located in 10 genes: ICAM3, IFN-γ, CCL2, CCL5, AHSG, MBL, Furin, TMPRSS2, IL4, and CD209 promoter, were identified. Analysis of Qatari genomes revealed significantly lower AF of risk variants linked to SARS-CoV-1 severity (CCL2, MBL, CCL5, AHSG, and IL4) compared to that of 1000Genome and/or the EAS population (up to 25-fold change). Conversely, SNPs in TMPRSS2, IFN-γ, ICAM3, and Furin were more common among Qataris (average 2-fold change). Inter-population analysis showed that the distribution of risk alleles among Europeans differs substantially from Africans and EASs. Remarkably, Africans seem to carry extremely lower frequencies of SARS-CoV-1 susceptibility alleles, reaching to 32-fold decrease compared to other populations. Conclusion: Multiple genetic variants, which could potentially modulate SARS-CoV-2 infection, are significantly variable between populations, with the lowest frequency observed among Africans. Our results highlight the importance of exploring population genetics to understand and predict COVID-19 outcomes. Indeed, further studies are needed to validate these findings as well as to identify new genetic determinants linked to SARS-CoV-2.
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"569. Using ‘population-specific haplotypes’ to select for resistance to SRS in an admixed population of coho salmon (Oncorhynchus kisutch)." In World Congress on Genetics Applied to Livestock Production. The Netherlands: Wageningen Academic Publishers, 2022. http://dx.doi.org/10.3920/978-90-8686-940-4_569.

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Alvarado-Arnez, Lucia, Isabelle Moraes, Andrea Silva, Fernanda Kehdy, Giordano Souza, Wagner Magalhães, Thiago Leal, Nathalia Araujo, Eduardo Santos, and Milton Moraes. "IL28B polymorphisms: population genetics and relevance in the context of Brazilian admixed populations." In III Seminário Anual Científico e Tecnológico de Bio-Manguinhos. Instituto de Tecnologia em Imunobiológicos, 2016. http://dx.doi.org/10.35259/isi.sact.2016_27532.

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"Polymorphism of the stem rust population on avirulence genes in Western Siberia." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-177.

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Sepulveda, Victor, Roberto Solar, Alonso Inostrosa-Psijas, Veronica Gil-Costa, and Mauricio Marin. "Towards rapid population genetics forward-in-time simulations." In 2017 Winter Simulation Conference (WSC). IEEE, 2017. http://dx.doi.org/10.1109/wsc.2017.8247993.

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Moritz, Robin. "The population genetics of acaricide resistance inVarroa destructor." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.111432.

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Reports on the topic "Population genetics"

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Velsko, S. Bacterial Population Genetics in a Forensic Context. Office of Scientific and Technical Information (OSTI), November 2009. http://dx.doi.org/10.2172/972405.

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Bogoliubov, A. G., and C. Loehle. A theoretical analysis of population genetics of plants on restored habitats. Office of Scientific and Technical Information (OSTI), July 1997. http://dx.doi.org/10.2172/505323.

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Bogoliubov, A. G., and C. Loehle. A theoretical analysis of population genetics of plants on restored habitats. Office of Scientific and Technical Information (OSTI), February 1995. http://dx.doi.org/10.2172/26698.

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Kohrn, Brendan. An Efficient Pipeline for Assaying Whole-Genome Plastid Variation for Population Genetics and Phylogeography. Portland State University Library, January 2000. http://dx.doi.org/10.15760/etd.5891.

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Fagerheim White, Ellen-Louisa, Mervi Honkatukia, Jaana Peippo, and Maria Kjetså. Equines in the Nordics – History, Status and Genetics. The Nordic Genetic Resource Center (NordGen), June 2024. http://dx.doi.org/10.53780/flkb7985.

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With roots as far as the Bronze age, equines have played an invaluable role in history, both with regards to agriculture and forestry, warfare, transportation and leisure, and therefore hold important cultural significance in the Nordics. The link between horses and the welfare benefits of their caregivers makes the species an important part of society as well. Since the agricultural and industrial revolution, the equine sector has been influenced by a range of challenges due to the dramatic change in the role of horses in society, especially for the Nordic native breeds. However, as society adapts and finds new ways to use and protect them, there is a hope for the future. Although there has been cooperation between the Nordic countries in the horse sector, a collective report of the status of all the Nordic countries has been missing. This report marks a start for this type of effort by considering both commercial and native breeds. Further, it comprises the horse sector in the Nordics, with a special focus on the native horse breeds and the possibilities they carry for environmental sustainability, their socio-economic importance, their genetics as well as their risk status. The report further evaluates the Domestic Animal Diversity Information System (DAD-IS) maintained and developed by FAO as a tool for gathering information about the development and current status of the native breeds. The goal of this report is to identify knowledge gaps and areas of improvement for the Nordic equine sector and the collected data of the native horse breeds. One of the biggest challenges has been to find validated information sources for the population numbers of the breeds in each country – there are varying estimates for both commercial and native breeds. The numbers have significant impact for the determination of managing strategies of the populations. Reports for each of the countries (Denmark, Finland, the Faroe Islands, Iceland, Norway and Sweden) are presented, and depict the current role of horses, breeding, population development and economic values of the equine sector are listed in each of the country-reports. The information in the country reports were derived from a questionnaire and by using DAD-IS.
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Brannon, Ernest L. Columbia River White Sturgeon Genetics and Early Life History: Population Segregation and Juvenile Feeding Behavior, 1987 Final Report. Office of Scientific and Technical Information (OSTI), June 1988. http://dx.doi.org/10.2172/6783328.

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Blum, Abraham, Henry T. Nguyen, and N. Y. Klueva. The Genetics of Heat Shock Proteins in Wheat in Relation to Heat Tolerance and Yield. United States Department of Agriculture, August 1993. http://dx.doi.org/10.32747/1993.7568105.bard.

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Fifty six diverse spring wheat cultivars were evaluated for genetic variation and heritability for thermotolerance in terms of cell-membrane stability (CMS) and triphenyl tetrazolium chloride (TTC) reduction. The most divergent cultivars for thermotolerance (Danbata-tolerant and Nacozari-susceptible) were crossed to develop an F8 random onbred line (RIL) population. This population was evaluated for co-segragation in CMS, yield under heat stress and HSP accumulation. Further studies of thermotolerance in relations to HSP and the expression of heterosis for growth under heat stress were performed with F1 hybrids of wheat and their parental cultivars. CMS in 95 RILs ranged from 76.5% to 22.4% with 71.5% and 31.3% in Danbata and Nacozari, respectively. The population segregated with a normal distribution across the full range of the parental values. Yield and biomass under non-stress conditions during the normal winter season at Bet Dagan dit not differ between the two parental cultivar, but the range of segregation for these traits in 138 RILs was very high and distinctly transgressive with a CV of 35.3% and 42.4% among lines for biomass and yield, respectively. Mean biomass and yield of the population was reduced about twofold when grown under the hot summer conditions (irrigated) at Bet Dagan. Segregation for biomass and yield was decreased relative to the normal winter conditions with CV of 20.2% and 23.3% among lines for biomass and yield, respectively. However, contrary to non-stress conditions, the parental cultivars differed about twofold in biomass and yield under heat stress and the population segregated with normal distribution across the full range of this difference. CMS was highly and positively correlated across 79 RILs with biomass (r=0.62**) and yield (r=0.58**) under heat stress. No such correlation was obtained under the normal winter conditions. All RILs expressed a set of HSPs under heat shock (37oC for 2 h). No variation was detected among RILs in high molecular weight HSP isoforms and they were similar to the patterns of the parental cultivars. There was a surprisingly low variability in low molecular weight HSP isoforms. Only one low molecular weight and Nacozari-specific HSP isoform (belonging to HSP 16.9 family) appeared to segregate among all RILs, but it was not quantitatively correlated with any parameter of plant production under heat stress or with CMS in this population. It is concluded that this Danbata/Nacozari F8 RIL population co-segregated well for thermotolerance and yield under heat stress and that CMS could predict the relative productivity of lines under chronic heat stress. Regretfully this population did not express meaningful variability for HSP accumulation under heat shock and therefore no role could be seen for HSP in the heat tolerance of this population. In the study of seven F1 hybrids and their parent cultivars it was found that heterosis (superiority of the F1 over the best parent) for CMs was generally lower than that for growth under heat stress. Hybrids varied in the rate of heterosis for growth at normal (15o/25o) and at high (25o/35o) temperatures. In certain hybrids heterosis for growth significantly increased at high temperature as compared with normal temperature, suggesting temperature-dependent heterosis. Generally, under normal temperature, only limited qualitative variation was detected in the patterns of protein synthesis in four wheat hybrids and their parents. However, a singular protein (C47/5.88) was specifically expressed only in the most heterotic hybrid at normal temperature but not in its parent cultivars. Parental cultivars were significantly different in the sets of synthesized HSP at 37o. No qualitative changes in the patterns of protein expression under heat stress were correlated with heterosis. However, a quantitative increase in certain low molecular weight HSP (mainly H14/5.5 and H14.5.6, belonging to the HSP16.9 family) was positively associated with greater heterosis for growth at high temperature. None of these proteins were correlated with CMS across hybrids. These results support the concept of temperature-dependent heterosis for growth and a possible role for HSP 16.9 family in this respect. Finally, when all experiments are viewed together, it is encouraging to find that genetic variation in wheat yield under chronic heat stress is associated with and well predicted by CMS as an assay of thermotolerance. On the other hand the results for HSP are elusive. While very low genetic variation was expressed for HSP in the RIL population, a unique low molecular weight HSP (of the HSP 16.9 family) could be associated with temperature dependant heterosis for growth.
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Cahaner, Avigdor, Susan J. Lamont, E. Dan Heller, and Jossi Hillel. Molecular Genetic Dissection of Complex Immunocompetence Traits in Broilers. United States Department of Agriculture, August 2003. http://dx.doi.org/10.32747/2003.7586461.bard.

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Objectives: (1) Evaluate Immunocompetence-OTL-containing Chromosomal Regions (ICRs), marked by microsatellites or candidate genes, for magnitude of direct effect and for contribution to relationships among multiple immunocompetence, disease-resistance, and growth traits, in order to estimate epistatic and pleiotropic effects and to predict the potential breeding applications of such markers. (2) Evaluate the interaction of the ICRs with genetic backgrounds from multiple sources and of multiple levels of genetic variation, in order to predict the general applicability of molecular genetic markers across widely varied populations. Background: Diseases cause substantial economic losses to animal producers. Emerging pathogens, vaccine failures and intense management systems increase the impact of diseases on animal production. Moreover, zoonotic pathogens are a threat to human food safety when microbiological contamination of animal products occurs. Consumers are increasingly concerned about drug residues and antibiotic- resistant pathogens derived from animal products. The project used contemporary scientific technologies to investigate the genetics of chicken resistance to infectious disease. Genetic enhancement of the innate resistance of chicken populations provides a sustainable and ecologically sound approach to reduce microbial loads in agricultural populations. In turn, animals will be produced more efficiently with less need for drug treatment and will pose less of a potential food-safety hazard. Major achievements, conclusions and implications:. The PI and co-PIs had developed a refined research plan, aiming at the original but more focused objectives, that could be well-accomplished with the reduced awarded support. The successful conduct of that research over the past four years has yielded substantial new information about the genes and genetic markers that are associated with response to two important poultry pathogens, Salmonella enteritidis (SE) and Escherichia coli (EC), about variation of immunocompetence genes in poultry, about relationships of traits of immune response and production, and about interaction of genes with environment and with other genes and genetic background. The current BARD work has generated a base of knowledge and expertise regarding the genetic variation underlying the traits of immunocompetence and disease resistance. In addition, unique genetic resource populations of chickens have been established in the course of the current project, and they are essential for continued projects. The US laboratory has made considerable progress in studies of the genetics of resistance to SE. Microsatellite-marked chromosomal regions and several specific genes were linked to SE vaccine response or bacterial burden and the important phenomenon of gene interaction was identified in this system. In total, these studies demonstrate the role of genetics in SE response, the utility of the existing resource population, and the expertise of the research group in conducting such experiments. The Israeli laboratories had showed that the lines developed by selection for high or low level of antibody (Ab) response to EC differ similarly in Ab response to several other viral and bacterial pathogens, indicating the existence of a genetic control of general capacity of Ab response in young broilers. It was also found that the 10w-Ab line has developed, possibly via compensatory "natural" selection, higher cellular immune response. At the DNA levels, markers supposedly linked to immune response were identified, as well as SNP in the MHC, a candidate gene responsible for genetic differences in immunocompetence of chickens.
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Sherman, Amir, Rebecca Grumet, Ron Ophir, Nurit Katzir, and Yiqun Weng. Whole genome approach for genetic analysis in cucumber: Fruit size as a test case. United States Department of Agriculture, December 2013. http://dx.doi.org/10.32747/2013.7594399.bard.

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The Cucurbitaceae family includes a broad array of economically and nutritionally important crop species that are consumed as vegetables, staple starches and desserts. Fruit of these species, and types within species, exhibit extensive diversity as evidenced by variation in size, shape, color, flavor, and others. Fruit size and shape are critical quality determinants that delineate uses and market classes and are key traits under selection in breeding programs. However, the underlying genetic bases for variation in fruit size remain to be determined. A few species the Cucurbitaceae family were sequenced during the time of this project (cucumber was already sequenced when the project started watermelon and melon sequence became available during the project) but functional genomic tools are still missing. This research program had three major goals: 1. Develop whole genome cucumber and melon SNP arrays. 2. Develop and characterize cucumber populations segregating for fruit size. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. As suggested by the reviewers the work concentrated mostly in cucumber and not both in cucumber and melon. In order to develop a SNP (single nucleotide polymorphism) array for cucumber, available and newly generated sequence from two cucumber cultivars with extreme differences in shape and size, pickling GY14 and Chinese long 9930, were analyzed for variation (SNPs). A large set of high quality SNPs was discovered between the two parents of the RILs population (GY14 and 9930) and used to design a custom SNP array with 35000 SNPs using Agilent technology. The array was validated using 9930, Gy14 and F1 progeny of the two parents. Several mapping populations were developed for linkage mapping of quantitative trait loci (QTL) for fruit size These includes 145 F3 families and 150 recombinant inbred line (RILs F7 or F8 (Gy14 X 9930) and third population contained 450 F2 plants from a cross between Gy14 and a wild plant from India. The main population that was used in this study is the RILs population of Gy14 X 9930. Phenotypic and morphological analyses of 9930, Gy14, and their segregating F2 and RIL progeny indicated that several, likely independent, factors influence cucumber fruit size and shape, including factors that act both pre-anthesis and post-pollination. These include: amount, rate, duration, and plane of cell division pre- and post-anthesis and orientation of cell expansion. Analysis of F2 and RIL progeny indicated that factors influencing fruit length were largely determined pre-anthesis, while fruit diameter was more strongly influenced by environment and growth factors post-anthesis. These results suggest involvement of multiple genetically segregating factors expected to map independently onto the cucumber genome. Using the SNP array and the phenotypic data two major QTLs for fruit size of cucumber were mapped in very high accuracy (around 300 Kb) with large set of markers that should facilitate identification and cloning of major genes that contribute to fruit size in cucumber. In addition, a highly accurate haplotype map of all RILS was created to allow fine mapping of other traits segregating in this population. A detailed cucumber genetic map with 6000 markers was also established (currently the most detailed genetic map of cucumber). The integration of genetics physiology and genomic approaches in this project yielded new major infrastructure tools that can be used for understanding fruit size and many other traits of importance in cucumber. The SNP array and genetic population with an ultra-fine map can be used for future breeding efforts, high resolution mapping and cloning of traits of interest that segregate in this population. The genetic map that was developed can be used for other breeding efforts in other populations. The study of fruit development that was done during this project will be important in dissecting function of genes that that contribute to the fruit size QTLs. The SNP array can be used as tool for mapping different traits in cucumber. The development of the tools and knowledge will thus promote genetic improvement of cucumber and related cucurbits.
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Hovav, Ran, Peggy Ozias-Akins, and Scott A. Jackson. The genetics of pod-filling in peanut under water-limiting conditions. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597923.bard.

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Pod-filling, an important yield-determining stage is strongly influenced by water stress. This is particularly true for peanut (Arachishypogaea), wherein pods are developed underground and are directly affected by the water condition. Pod-filling in peanut has a significant genetic component as well, since genotypes are considerably varied in their pod-fill (PF) and seed-fill (SF) potential. The goals of this research were to: Examine the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Detect global changes in mRNA and metabolites levels that accompany PF and SF. Explore the response of the duplicate peanut pod transcriptome to drought stress. Study how entire duplicated PF regulatory processes are networked within a polyploid organism. Discover locus-specific SNP markers and map pod quality traits under different environments. The research included genotypes and segregating populations from Israel and US that are varied in PF, SF and their tolerance to water deficit. Initially, an extensive field trial was conducted to investigate the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Significant irrigation and genotypic effect was observed for the two main PF related traits, "seed ratio" and "dead-end ratio", demonstrating that reduction in irrigation directly influences the developing pods as a result of low water potential. Although the Irrigation × Genotype interaction was not statistically significant, one genotype (line 53) was found to be more sensitive to low irrigation treatments. Two RNAseq studies were simultaneously conducted in IL and the USA to characterize expression changes that accompany shell ("source") and seed ("sink") biogenesis in peanut. Both studies showed that SF and PF processes are very dynamic and undergo very rapid change in the accumulation of RNA, nutrients, and oil. Some genotypes differ in transcript accumulation rates, which can explain their difference in SF and PF potential; like cvHanoch that was found to be more enriched than line 53 in processes involving the generation of metabolites and energy at the beginning of seed development. Interestingly, an opposite situation was found in pericarp development, wherein rapid cell wall maturation processes were up-regulated in line 53. Although no significant effect was found for the irrigation level on seed transcriptome in general, and particularly on subgenomic assignment (that was found almost comparable to a 1:1 for A- and B- subgenomes), more specific homoeologous expression changes associated with particular biosynthesis pathways were found. For example, some significant A- and B- biases were observed in particular parts of the oil related gene expression network and several candidate genes with potential influence on oil content and SF were further examined. Substation achievement of the current program was the development and application of new SNP detection and mapping methods for peanut. Two major efforts on this direction were performed. In IL, a GBS approach was developed to map pod quality traits on Hanoch X 53 F2/F3 generations. Although the GBS approach was found to be less effective for our genetic system, it still succeeded to find significant mapping locations for several traits like testa color (linkage A10), number of seeds/pods (A5) and pod wart resistance (B7). In the USA, a SNP array was developed and applied for peanut, which is based on whole genome re-sequencing of 20 genotypes. This chip was used to map pod quality related traits in a Tifrunner x NC3033 RIL population. It was phenotyped for three years, including a new x-ray method to phenotype seed-fill and seed density. The total map size was 1229.7 cM with 1320 markers assigned. Based on this linkage map, 21 QTLs were identified for the traits 16/64 weight, kernel percentage, seed and pod weight, double pod and pod area. Collectively, this research serves as the first fundamental effort in peanut for understanding the PF and SF components, as a whole, and as influenced by the irrigation level. Results of the proposed study will also generate information and materials that will benefit peanut breeding by facilitating selection for reduced linkage drag during introgression of disease resistance traits into elite cultivars. BARD Report - Project4540 Page 2 of 10
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