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Статті в журналах з теми "Introgression adaptative":
1
Di Pietro, Lorena, Mozhgan Boroumand, Wanda Lattanzi, Barbara Manconi, Martina Salvati, Tiziana Cabras, Alessandra Olianas, et al. "A Catalog of Coding Sequence Variations in Salivary Proteins’ Genes Occurring during Recent Human Evolution." International Journal of Molecular Sciences 24, no. 19 (October 9, 2023): 15010. http://dx.doi.org/10.3390/ijms241915010.
Анотація:
Saliva houses over 2000 proteins and peptides with poorly clarified functions, including proline-rich proteins, statherin, P-B peptides, histatins, cystatins, and amylases. Their genes are poorly conserved across related species, reflecting an evolutionary adaptation. We searched the nucleotide substitutions fixed in these salivary proteins’ gene loci in modern humans compared with ancient hominins. We mapped 3472 sequence variants/nucleotide substitutions in coding, noncoding, and 5′-3′ untranslated regions. Despite most of the detected variations being within noncoding regions, the frequency of coding variations was far higher than the general rate found throughout the genome. Among the various missense substitutions, specific substitutions detected in PRB1 and PRB2 genes were responsible for the introduction/abrogation of consensus sequences recognized by convertase enzymes that cleave the protein precursors. Overall, these changes that occurred during the recent human evolution might have generated novel functional features and/or different expression ratios among the various components of the salivary proteome. This may have influenced the homeostasis of the oral cavity environment, possibly conditioning the eating habits of modern humans. However, fixed nucleotide changes in modern humans represented only 7.3% of all the substitutions reported in this study, and no signs of evolutionary pressure or adaptative introgression from archaic hominins were found on the tested genes.
2
Mbah, David A., Chi Lawrence Tawah, and Magellan Guewo-Fokeng. "Genetic Modification of Animals: Potential benefits and concerns." Journal of the Cameroon Academy of Sciences 15, no. 3 (August 4, 2020): 163–74. http://dx.doi.org/10.4314/jcas.v15i3.2.
Анотація:
Genetic modification (GM), a process whereby gene and genotype frequencies are changed among individuals of each generation, is driven by natural and artificial forces. Natural forces include mutation, fitness and migration/introgression, while artificial forces include selection, crossbreeding and transgenesis/genetic engineering. Genetic modification, driven by natural forces, is essentially adaptive, while modification driven by artificial forces is controlled by human intervention aimed at meeting food, health and other needs. Conventional genetic modification, under sexual reproduction within species, produces both beneficial and negative effects. Modern genetic modification – interspecific exchange of genes using genetic engineering – has beneficial and negative effects as well, which are at varying degrees depending on the species involved. Control/management systems/mechanisms are developed and applied to enable societal benefits while minimizing/preventing negative effects of conventional and modern genetic modification. Targeted analysis of selected nutrients in animal products is made on a case-by-case basis to test substantial equivalence of any compositional changes resulting from genetic modification. Unique identifiers are established to track GM animals and their products in the food chain.
Modification génétique, processus par lequel les fréquences des gènes et des génotypes sont changes parmi les individus de chaque génération, est entraînée par des forces naturelles et artificielles. Les forces naturelles incluent la mutation, compétence de mère/père pour se reproduire/survivre et la migration / introgression. Les forces artificielles comprennent la sélection, le croisement et la transgénèse / génie génétique. La modification génétique entraînée par les forces naturelles est essentiellement adaptative, tandis que celle entraînée par les forces artificielles est contrôlée par une intervention humaine visant à répondre aux besoins alimentaires, sanitaires et autres. La modification génétique conventionnelle, lors de la reproduction sexuelle au sein des espèces, produit des effets à la fois bénéfiques et négatifs. Modification génétique moderne - échange interspécifique de gènes par génie génétique - a également des effets bénéfiques et négatifs mais à des degrés divers selon les espèces impliquées. Des systèmes / mécanismes de contrôle / gestion sont développés et appliqués pour permettre des avantages pour la société tout en minimisant / empêchant les effets négatifs des modifications génétiques conventionnelles et modernes. Une analyse ciblée de nutriments sélectionnés dans les produits d’origine animale est effectuée au cas par cas afin de tester l’équivalence substantielle de tout changement de composition résultant d’une modification génétique. Des identifiants uniques sont établis pour suivre les animaux GM et leurs produits dans la chaîne alimentaire.
3
Árnason, Einar, and Katrín Halldórsdóttir. "Codweb: Whole-genome sequencing uncovers extensive reticulations fueling adaptation among Atlantic, Arctic, and Pacific gadids." Science Advances 5, no. 3 (March 2019): eaat8788. http://dx.doi.org/10.1126/sciadv.aat8788.
Анотація:
Introgressive hybridization creates networks of genetic relationships across species. Among marine fish of the Gadidae family, Pacific cod and walleye pollock are separate invasions of an Atlantic cod ancestor into the Pacific. Cods are ecological success stories, and their ecologies allow them to support the largest fisheries of the world. The enigmatic walleye pollock differs morphologically, behaviorally, and ecologically from its relatives, representing a niche shift. Here, we apply whole-genome sequencing to Pacific, Arctic, and Atlantic gadids and reveal extensive introgression among them with the ABBA-BABA test and pseudolikelihood phylogenetic network analysis. We propose that walleye pollock resulted from extensive adaptive introgression or homoploid hybrid speciation. The path of evolution of these taxa is more web than a tree. Their ability to invade and expand into new habitats and become ecologically successful may depend on genes acquired through adaptive introgression or hybrid speciation.
4
Böheim, Denise, Felix Knauer, Milomir Stefanović, Richard Zink, Anna Kübber-Heiss, Annika Posautz, Christoph Beiglböck, et al. "Signals of Pig Ancestry in Wild Boar, Sus scrofa, from Eastern Austria: Current Hybridisation or Incomplete Gene Pool Differentiation and Historical Introgressions?" Diversity 15, no. 6 (June 19, 2023): 790. http://dx.doi.org/10.3390/d15060790.
Анотація:
In wild boar, Sus scrofa, from Europe, domestic pig-typical ancestry is traced at varying levels. We hypothesised wild boar with pig-typical gene pool characteristics, i.e., “introgression”, congregate more in peri-urban habitats, because of less shyness and better adaptation to anthropogenic stress. We used 16 microsatellites to study introgression levels of 375 wild boar from peri-urban Vienna, Austria, and rural regions in comparison to commercial slaughter pigs, Mangaliza, and Turopolje pigs. We also expected more introgression in locations of warmer climates and lower precipitation. Despite discrimination of wild boar and pigs with 99.73% and 97.87% probability, respectively, all wild boars exhibited pig-typical gene pool characteristics, mostly at a very low level. Recent hybridisation was suspected in only 0.53% of wild boar, corresponding to the current largely indoor pig breeding/rearing in the region, with no chance of natural gene exchange between pigs and wild boar. Rather, pig ancestry in wild boar stems from incomplete gene pool differentiation during domestication and/or historical introgressions, when free-ranging pig farming was common. Individual introgression levels were lower in wild boar from peri-urban habitats, possibly reflecting the largely historical absence of pig farms there. Moreover, a marginal precipitation effect, but no temperature effect on introgression was observed. The latter, however, needs to be explored further by a more comprehensive data set.
5
Arnold, Michael L., and Noland H. Martin. "Adaptation by introgression." Journal of Biology 8, no. 9 (2009): 82. http://dx.doi.org/10.1186/jbiol176.
6
Villanueva, Gloria, Elena Rosa-Martínez, Ahmet Şahin, Edgar García-Fortea, Mariola Plazas, Jaime Prohens, and Santiago Vilanova. "Evaluation of Advanced Backcrosses of Eggplant with Solanum elaeagnifolium Introgressions under Low N Conditions." Agronomy 11, no. 9 (September 3, 2021): 1770. http://dx.doi.org/10.3390/agronomy11091770.
Анотація:
Selection and breeding of eggplant (Solanum melongena) materials with good performance under low nitrogen (N) fertilization inputs is a major breeding objective to reduce environmental degradation, risks for human health, and production costs. Solanum elaeagnifolium, an eggplant wild relative, is a potential source of variation for introgression breeding in eggplant. We evaluated 24 plant, fruit, and composition traits in a set of genotyped advanced backcrosses (BC2 and BC3) of eggplant with S. elaeagnifolium introgressions under low N conditions. Significant differences were found between the two parents for most traits, and a wide phenotypic diversity was observed in the advanced backcrosses, with some individuals with a much higher yield, nitrogen use efficiency (NUE), and phenolics content than the S. melongena parent. In general, the lower the proportion of S. elaeagnifolium genome introgressed in the advanced backcrosses, the higher was the general phenotypic resemblance to S. melongena. Putative QTLs were detected for stem diameter (pd4), presence of prickles in stem (ps6), leaf (pl6) and fruit calyx (pc6), fruit width (fw7), chlorogenic acid content (cg5), total phenolic acid peaks area (ph6), chlorogenic acid peak area (ca1), and phenolic acids pattern (cp1). Our results reveal that introgression breeding of eggplant with S. elaeagnifolium has a great interest for eggplant breeding, particularly for adaptation to low N conditions. These materials can potentially contribute to the development of improved eggplant varieties for a more sustainable agriculture.
7
Gouy, Alexandre, and Laurent Excoffier. "Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens." Molecular Biology and Evolution 37, no. 5 (January 14, 2020): 1420–33. http://dx.doi.org/10.1093/molbev/msz306.
Анотація:
Abstract Anatomically modern humans carry many introgressed variants from other hominins in their genomes. Some of them affect their phenotype and can thus be negatively or positively selected. Several individual genes have been proposed to be the subject of adaptive introgression, but the possibility of polygenic adaptive introgression has not been extensively investigated yet. In this study, we analyze archaic introgression maps with refined functional enrichment methods to find signals of polygenic adaptation of introgressed variants. We first apply a method to detect sets of connected genes (subnetworks) within biological pathways that present higher-than-expected levels of archaic introgression. We then introduce and apply a new statistical test to distinguish between epistatic and independent selection in gene sets of present-day humans. We identify several known targets of adaptive introgression, and we show that they belong to larger networks of introgressed genes. After correction for genetic linkage, we find that signals of polygenic adaptation are mostly explained by independent and potentially sequential selection episodes. However, we also find some gene sets where introgressed variants present significant signals of epistatic selection. Our results confirm that archaic introgression has facilitated local adaptation, especially in immunity related and metabolic functions and highlight its involvement in a coordinated response to pathogens out of Africa.
8
Calfee, Erin, Daniel Gates, Anne Lorant, M. Taylor Perkins, Graham Coop, and Jeffrey Ross-Ibarra. "Selective sorting of ancestral introgression in maize and teosinte along an elevational cline." PLOS Genetics 17, no. 10 (October 11, 2021): e1009810. http://dx.doi.org/10.1371/journal.pgen.1009810.
Анотація:
While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays) and its wild teosinte relative, mexicana (Zea mays ssp. mexicana). Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low FST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations.
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Suarez-Gonzalez, Adriana, Christian Lexer, and Quentin C. B. Cronk. "Adaptive introgression: a plant perspective." Biology Letters 14, no. 3 (March 2018): 20170688. http://dx.doi.org/10.1098/rsbl.2017.0688.
Анотація:
Introgression is emerging as an important source of novel genetic variation, alongside standing variation and mutation. It is adaptive when such introgressed alleles are maintained by natural selection. Recently, there has been an explosion in the number of studies on adaptive introgression. In this review, we take a plant perspective centred on four lines of evidence: (i) introgression, (ii) selection, (iii) phenotype and (iv) fitness. While advances in genomics have contributed to our understanding of introgression and porous species boundaries (task 1), and the detection of signatures of selection in introgression (task 2), the investigation of adaptive introgression critically requires links to phenotypic variation and fitness (tasks 3 and 4). We also discuss the conservation implications of adaptive introgression in the face of climate change. Adaptive introgression is particularly important in rapidly changing environments, when standing genetic variation and mutation alone may only offer limited potential for adaptation. We conclude that clarifying the magnitude and fitness effects of introgression with improved statistical techniques, coupled with phenotypic evidence, has great potential for conservation and management efforts.
10
Falk, Duane E. "Generating and maintaining diversity at the elite level in crop breedingThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”." Genome 53, no. 11 (November 2010): 982–91. http://dx.doi.org/10.1139/g10-081.
Анотація:
Most breeding programs develop elite genotypes that are well adapted to the normal range of environmental conditions in the target production region. These elite lines have similar essential alleles for desirable end use characteristics, agronomics, disease resistance, and adaptation in the target region. The genetic makeup of these elite lines is complex. Intermating among the elite lines will often produce new variability through recombination with minimal risk of introducing new undesirable features, and is the source of most new cultivars. Eventually, this variation will be exhausted and new alleles must be introduced into the elite breeding population. Introducing desirable alleles from exotic germplasm may “pollute” the elite gene pool with undesirable alleles. Exotic germplasm may also disrupt essential allele combinations for adaptation, quality, and agronomic performance. New desirable alleles from exotic germplasm can be introgressed into an elite population in a systematic way through limited backcrossing with a minimal disturbance to the finely tuned elite background. Combining recurrent selection within elite germplasm with a systematic introgression from exotic germplasm in the recurrent introgressive population enrichment (RIPE) system has created an open-ended, continually improving, and sustainable elite population breeding system, which is simple, effective, and a regular source of new cultivars.
Дисертації з теми "Introgression adaptative":
1
Tellini, Nicolò. "Quantification du tri des lignées incomplètes et de l'introgression au cours de l'histoire évolutive de Saccharomyces cerevisiae." Electronic Thesis or Diss., Université Côte d'Azur, 2023. https://intranet-theses.unice.fr/2023COAZ6038.
Анотація:
L'étude de la distribution de la variation génétique au sein des populations et entre elles permet de mieux comprendre l'histoire évolutive d'une espèce. De plus, l'accès à de grands ensembles de données génomiques permet d'étudier les processus évolutifs qui façonnent la variation ségrégative de l'espèce. Dans ce travail, nous retraçons l'histoire évolutive de l'espèce Saccharomyces cerevisiae par la détection et la classification de polymorphismes partagés avec son espèce sœur Saccharomyces paradoxus. Nous identifions des polymorphismes partagés acquis par hybridation suivie d'introgression et des polymorphismes qui persistent à travers le processus de spéciation et de diversification résultant en des cas de triage incomplet des lignées (ILS).Nous définissons un ensemble de données de polymorphismes nucléotidiques simples diagnostiques bialléliques entre Saccharomyces cerevisiae et Saccharomyces paradoxus que nous utilisons comme marqueur diagnostique pour décrire la composition génomique de 1,673 S. cerevisiae, pour lesquels un séquençage à lecture courte du génome entier était publiquement disponible. Nous développons une méthode basée sur les marqueurs pour la détection et la classification des marqueurs de diagnostic organisés soit en 1) blocs de marqueurs S. paradoxus consécutifs, soit en 2) marqueurs S. paradoxus isolés à l'échelle du génome.Pour les blocs, nous décrivons les limites, et la distribution dans la collection S. cerevisiae et nous retraçons l'origine de S. paradoxus par comparaison de séquences avec des assemblages de génomes entiers télomère à télomère des principales populations de S. paradoxus. Pour un événement récurrent, nous avons effectué un test pour évaluer l'effet sur la condition physique de porter un haplotype S. paradoxus à un locus unique englobant une paire de gènes impliqués dans la dégradation de composés toxiques pour la levure. Nous avons démontré que l'haplotype S. paradoxus confère un avantage par rapport à l'haplotype S. cerevisiae dans des conditions environnementales caractéristiques de la niche habitée par la population S. cerevisiae.Pour les marqueurs isolés, nous appliquons une méthode classique de détection des signatures d'un tri lignager incomplet, qui peut expliquer l'excès de marqueurs S. paradoxus distribués à l'échelle du génome dans certaines populations de S. cerevisiae. Nous montrons des preuves convaincantes de la rétention d'allèles ancestraux dans une seule population sauvage de S. cerevisiae qui se trouve à la racine de l'espèce. Nous émettons l'hypothèse que la persistance d'une telle variation ancestrale est due à la possibilité réduite de croisement avec d'autres populations de S. cerevisiae dans la nature, en raison du nombre réduit de générations et des goulets d'étranglement moins spectaculaires qu'ont connu les autres lignées au cours de la dispersion et de la domestication. Dans l'ensemble, nous avons retracé l'histoire de la divergence et des contacts secondaires entre les populations de S. cerevisiae et de S. paradoxus et dévoilé un cas convaincant d'introgression interespèces avec un résultat fonctionnelThe study of the distribution of the genetic variation within and across populations provides insights into the evolutionary history of a species. Moreover, the access to large genomic datasets allows the investigation of the evolutionary processes that shape the species' segregating variation. In this work, we retrace the evolutionary history of the species Saccharomyces cerevisiae through the detection and classification of shared polymorphisms with its sister species Saccharomyces paradoxus. We identify shared polymorphisms acquired because hybridization followed by introgression and polymorphisms that persist across the process of speciation and diversification resulting in instances of incomplete lineage sorting (ILS). We define a dataset of biallelic diagnostic single nucleotide polymorphisms between Saccharomyces cerevisiae and Saccharomyces paradoxus that we use as diagnostic marker to describe the genomic composition of 1,673 S. cerevisiae, for which short-read whole-genome sequencing were publicly available. We develop a marker-based method for the detection and classification of diagnostic markers organized either in 1) blocks of consecutive S. paradoxus markers or in 2) genome-wide isolated S. paradoxus markers. For the blocks, we describe the boundaries, the distribution across the S. cerevisiae collection and we retrace the S. paradoxus origin by sequence comparison with telomere-to-telomere whole genome assemblies of the main S. paradoxus populations. For a recurrent event, we performed an assay to evaluate the fitness effect of carrying a S. paradoxus haplotype at a single locus encompassing a gene-pair involved in the degradation of toxic compounds for the yeast. We demonstrate that the S. paradoxus haplotype confers an advantage over the S. cerevisiae haplotype in environmental conditions that are characteristic of the niche that the S. cerevisiae population inhabits. For the isolated markers, we apply a classical method for detecting signatures of incomplete lineage sorting, which can explain the excess of genome-wide distributed S. paradoxus markers in certain populations of S. cerevisiae. We show convincing evidence of retention of ancestral alleles in a single wild S. cerevisiae population that stands at the root of the species. We speculate about the persistence of such ancestral variation because of reduced possibility of outcrossing with other S. cerevisiae populations into the wild due to fewer generations and less dramatic bottlenecks that were instead experienced by the other lineages during dispersal and domestication. Overall, we retraced histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveiled a compelling case of interspecies introgression with a functional outcome
2
Capblancq, Thibaut. "La spéciation hybride : réflexions générales et exploration d'un cas d'étude chez des papillons alpins du genre Coenonympha." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAV023/document.
Анотація:
L’hybridation interspécifique est un phénomène très étudié ces dernières années et les conséquences qui lui sont attribuées dans l’évolution des espèces sont diverses. Une littérature de plus en plus fournie met notamment en évidence le rôle que peut avoir l’hybridation sur l’émergence de nouveaux taxons. Mon travail de thèse s’attache à comprendre comment des croisements entre espèces peuvent impacter le processus de spéciation d’une nouvelle lignée évolutive et stimuler ainsi la diversification des organismes vivants.Une revue des différents cas d’espèces hybrides animales proposés dans la littérature a permis, dans la première partie de cette thèse, d’identifier les patrons associés de façon redondante au processus de spéciation hybride. Nous observons par exemple que, si l’apport premier de l’hybridation à la spéciation reste toujours la recombinaison de caractéristiques parentales divergentes, cela peut se traduire de manière différente lors de l’émergence de la lignée hybride. Cette synthèse a aussi été l’occasion de discuter des difficultés méthodologiques qui limitent une réelle estimation de la prévalence de ce phénomène dans l’évolution des espèces.Dans la seconde partie de ma thèse j’explore le processus de spéciation hybride chez un complexe d’espèces proches de papillons du genre Coenonympha. Je montre que, parmi les quatre lignées identifiées dans le complexe, deux sont issues de l’hybridation. Leurs caractéristiques génétiques, écologiques et morphologiques permettent de comprendre, en partie, comment leur phénotype recombinant a favorisé leur établissement en tant qu’espèces à part entière et leur isolement vis-à-vis de leurs espèces parentales.L’histoire évolutive de ces papillons est discutée en détail dans la dernière partie de mon travail de thèse. Les résultats obtenus pour ce cas particulier y sont confrontés aux autres exemples de spéciation hybride ainsi qu’aux attendus théoriques associés à ce phénomène. Les spécificités de ce système d’étude viennent ainsi enrichir les connaissances actuelles sur le processus de spéciation hybride et sur les impacts évolutifs de l’hybridationInterspecific hybridization is more and more studied these last years and its consequences on species evolution are diverse. The literature especially points out its potential impact on new species emergence and the number of hybrid speciation cases is increasing. My work aims at understanding how interspecific crosses can initiate the rise of a new hybrid lineage and stimulate the diversification of living organisms.Reviewing the examples of animals hybrid species described in the literature allows me, in the first part of this work, to identify the main patterns associated with the process of hybrid speciation. I observe in particular that, if the recombination of parental characteristics is always the main driver of hybrid speciation, it leads to various patterns in hybrid species establishment. I also discuss methodological issues concerning the identification of hybrid species, which limit our capacity to estimate the prevalence of such process in species evolution dynamic.In the second part of this work I investigate the process of hybrid speciation in a complex of closely related butterfly species of the genus Coenonympha. I show that among the four lineages composing the complex, two originated through hybridization events. Their genetic, ecological and morphological characteristics allow us to better understand how their recombinant phenotype led to their emergence and their isolation from parental species.The evolutionary history of these butterflies is discussed in detail in the last part of this work. The results obtained in this particular case are compared with other examples of hybrid species and with theoretical expectations from literature. This example adds its specificities to the current knowledges about hybrid speciation and evolutionary impacts of hybridization
3
Liu, Yongbo. "Conséquences écologiques et évolutives du flux de gènes entre Brassica napus transgénique et ses apparentés sauvages." Phd thesis, Université de Bourgogne, 2010. http://tel.archives-ouvertes.fr/tel-00584017.
Анотація:
Les conséquences des flux de gènes et de l'introgression entre les cultures transgéniques et leurs apparentés sauvages sont encore au cœur des débats associés à la commercialisation des plantes génétiquement modifiées. J'ai développé mon étude sur les conséquences écologiques et évolutives du flux de gènes entre le colza (Brassica napus) et ses apparentés, la moutarde brune sauvage (B. juncea) et la ravenelle (Raphanus raphanistrum), en réalisant une série d'expériences en serre, au jardin et au champ à Beijing et à Dijon. En premier, j'ai présenté une revue synthétique de la littérature publiée sur les flux de gènes et ses effets sur la fitness chez les Brassicées. En second, j'ai cherché à mettre en évidence le rôle de la taille des semences hybrides entre du colza transgénique Bt et la moutarde. La petite taille des semences a réduit les capacités de croissance et de reproduction, mais l'effet sur la fitness était variable en fonction des fonds génétiques ou spécifiques. Les rétrocroisements sur le colza étaient plus faciles et productifs que pour les autres types de descendants. La plupart de ces plantes avait une morphologie de colza. Liée à la résistance à l'herbicide, cette caractéristique pourrait permettre aux descendants de survivre dans les champs et de disséminer les transgènes aux repousses et aux autres colzas, ce qui serait peut être plus gênant que de voir l'introgression réelle dans le génome du parent sauvage. Troisièmement, j'ai simulé le phénomène d'herbivorie chez la moutarde pour étudier la compétition entre des plantes résistantes et des plantes sensibles indépendamment des problèmes de fitness des hybrides interspécifiques. Les plantes résistantes ont un avantage compétitif évident sous la pression d'herbivorie, et cet avantage est exacerbé sous des conditions difficiles telles que de faibles ressources du milieu et l'intensité de l'herbivorie. L'utilisation d'insectes pour attaquer des populations mixtes composées de rétrocroisements sensibles et Bt-résistants aux insectes a confirmé ce résultat et a montré que le transgène n'avait pas de coût en l'absence d'insectes. La productivité totale des populations a augmenté avec la proportion de plantes résistantes. Quatrièmement, des populations de ravenelles ont été échantillonnées dans quatre régions éloignées entre elles, dont une ayant une longue histoire de coexistence avec le colza et donc ayant plus de chance d'avoir été soumise à l'hybridation interspécifique avec le colza. J'ai interprété la divergence des traits et leur polymorphisme dans le cadre d'une hypothèse d'introgression stabilisée en opposition au simple hasard, bien que les différences avec les autres populations n'étaient pas assez marquées pour faire sortir ces populations du domaine de variation décrit pour les ravenelles. Ces études soulignent plusieurs facteurs qui peuvent accroître le risque des flux de transgènes et l'introgression entre les cultures génétiquement modifiées et leurs apparentés sauvages, et cela doit être pris en compte dans les procédures d'évaluation des risques de l'usage de ces plantes. A savoir : la morphologie cultivée qui rend confuse l'identification des introgressants dans le cadre de la bio-surveillance, les petites semences hybrides avec une dormance et une dispersion supérieures, et l'intensité de l'herbivorie et de la compétition qui exacerbe l'avantage adaptatif des plantes transgéniques résistantes aux insectes. Cependant, l'hypothèse de la formation de " super mauvaises herbes " ne semble pas justifiée.
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Zhou, Y. (Yongfeng). "Demographic history and climatic adaptation in ecological divergence between two closely related parapatric pine species." Doctoral thesis, Oulun yliopisto, 2014. http://urn.fi/urn:isbn:9789526206769.
Анотація:
Abstract Both demographic histories and natural selection complicate the speciation process. There is a need to jointly study the effects of natural selection on so called magic traits that can cause reproductive isolation such as climatic adaptation, and its interaction with neutral demographic histories. Closely related incipient coniferous species offer us a great system for this effort. I used genetic variation at one set of climate-related candidate genes and another set of reference loci and cytoplasmic genomic fragments of two closely related parapatric pine species: Pinus massoniana Lamb. and Pinus hwangshanensis Hisa. Population genetic analyses were used to measure genetic variation and detect signals of ancient and recent selection. Speciation parameters including migration rates and divergence times at candidate genes and reference loci were compared under the Isolation with migration model. Hierarchical Approximate Bayesian Computation (ABC) was used to define demographic and speciation models. Intra- and interspecific genetic variation at cytoplasmic and nuclear intronic sequences were compared between parapatric populations and allopatric populations to distinguish the effects of introgression and incomplete lineage sorting in generating shared genetic variation between the species. The results showed that ancient selection were shared by the lineages leading to the species while recent selection has been species-specific. Candidate genes had significant lower migration rates compared to reference loci. Recent differential climatic selection might counteract against gene flow at underlying genes, which therefore favors divergence between the two pines through ecological speciation. Shared mitotypes were randomly distributed across species’ ranges, which therefore supported the incomplete lineage sorting hypothesis, but the shared nuclear intronic variation distributed more frequently in parapatric populations than in allopatric populations, supported the introgression hypothesis. ABC and species’ distribution modeling also supported the secondary gene flow model. The three genomes had different rates of mutation and gene flow might mirror different phases of the speciation continuum. The results in this thesis are valuable for understanding evolution in general and for other applied purposes such as tree breeding and climate change adaptationTiivistelmä Luonnonvalinta ja populaatioiden historian demografia tekevät lajiutumisesta monimutkaisen tapahtumaketjun. Luonnonvalinnan ja demografisten tekijöiden vuorovaikutusta on paras tutkia samanaikaisesti, kun tarkastellaan lajiutumiseen vaikuttavia ominaisuuksia. Tällaisia ovat esimerkiksi ilmastoon sopeutumiseen liittyvät ominaisuudet. Lähisukuiset havupuulajit tarjoavat erinomaiset mahdollisuudet tähän työhön. Tutkin geneettistä muuntelua yhtäältä ilmastosopeutumiseen liittyvissä ns. ehdokasgeeneissä ja toisaalta neutraaleiksi oletetuissa verrokkigeeneissä sekä sytoplasman genomeissa kahdessa lähisukuisessa mäntylajissa Pinus massoniana Lamb. ja Pinus hwangshanensis Hisa, joiden populaatiot esiintyvät joskus erillään toisistaan (allopatrisesti), toisinaan vierekkäin (parapatrisesti). Mittasin muuntelun määrää ja etsin merkkejä valinnan vaikutuksesta. Vertasin erilaisia lajiutumismallien parametrejä verrokki- ja ehdokasgeeneissä. Käytin simulaatioita etsiäkseni parhaat demografiset ja lajiutumiseen liittyvät mallit. Vertasin kloroplastien ja mitokondrioiden genomien sekvenssien lajinsisäistä ja lajien välistä muuntelua allopatrisissa ja parapatrisissa populaatioissa tutkiakseni onko lajien yhteinen muuntelu seurausta siitä että lajien eriytymisestä on kulunut vain vähän aikaa vai siitä että sen jälkeen on tapahtunut geenivirtaa. Kauan sitten tapahtunut valinta on vaikuttanut samalla tavalla kumpaankin lajiin, osin koska tutkimus kohdistui myös niiden yhteiseen edeltäjälinjaan. Äskettäinen valinta taas oli suuremmassa määrin kummallekin lajille ominaista. Viime aikojen ilmastoon liittyvä valinta on voinut vähentää geenivirtaa ehdokasgeeneissä, mikä voisi edistää ekologista lajiutumista. Tuman DNA:n muuntelu jakautuminen tuki sitä mahdollisuutta että lajien yhteinen geneettinen muuntelu johtuu äskettäisestä geenivirrasta, ei vain siitä että lajiutuminen on niin varhaisessa vaiheessa. Mitokondrioiden geeneissä lajeilla yhtä paljon yhteistä muuntelua sekä allopatrisissa että parapatrisissa populaatioissa, mikä tukee sen sijaan eriytymisen jälkeistä epätäydellistä muuntelun erilaistumista. Eri genomit heijastavat lajiutumisprosessin eri vaiheita. Väitöskirjan tulokset ovat osaltaan tuottaneet uutta tietoa lajiutumisesta ja valinnasta. Lisäksi niillä on merkitystä ilmastomuutoksen vaikutusten ymmärtämisessä ja metsänjalostuksessa
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Schield, Drew R., Richard H. Adams, Daren C. Card, Blair W. Perry, Giulia M. Pasquesi, Tereza Jezkova, Daniel M. Portik, et al. "Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes." WILEY, 2017. http://hdl.handle.net/10150/624693.
Анотація:
Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater-than-expected overlap between genes linked to lineage-specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome-scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.
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Fraïsse, Christelle. "Génétique de l’adaptation et de la spéciation : théorie et analyse de données de séquençage haut-débit dans le complexe d’espèces Mytilus edulis." Thesis, Montpellier 2, 2014. http://www.theses.fr/2014MON20107/document.
Анотація:
Les génomes sont affectés par des régimes de sélection conflictuels. Ceci est particulièrement bien illustré par le concept de barrière semi-perméable au flux génique, issu de la littérature des zones hybrides. Certains gènes contribuent à empêcher le mélange entre lignées génétiques différenciées, soit parce qu'ils participent à l'adaptation aux conditions environnementales locales, soit parce qu'ils sont incompatibles avec les gènes d'autres lignées. D'autres parties du génome sont soit neutres, soit soumises à une sélection qui tend à homogénéiser les différentes lignées entre elles. Dans la première partie de cette thèse, des modèles d'évolution de l'isolement reproductif sont présentés pour expliquer les patrons d'isolements observés dans les expériences d'hybridation au laboratoire. Par modélisation classique d'incompatibilités génétiques de type Dobzhansky-Muller, il est montré que l'asymétrie et la complexité des incompatibilités sont imparfaitement expliquées par un filtre évolutif, c.a.d. une vitesse d'accumulation différente entre types d'incompatibilité. Une approche complémentaire de modélisation quantitative à l'aide d'une extension du modèle géométrique de Fisher a permis de préciser quelles conditions de divergence entre lignées isolées conduisaient à un effet fortement délétère des mutations dans les génotypes hybrides. L'importance relative du niveau d'épistasie moyen, de la distribution des effets des mutations et des modalités de l'adaptation de chaque lignée est discutée. La seconde partie de cette thèse profite des avancées techniques de la génomique pour étudier l'histoire de la spéciation et de l'adaptation dans un complexe d'espèces non-modèles, les moules du genre Mytilus. Une méthode statistique d'inférence de scénarios de spéciation est présentée. Les résultats montrent que les moules Européennes ont connu une histoire complexe de divergence stricte suivie d'une période de connectivité périodique. En accord avec le concept de barrière semi-perméable au flux génique, il est montré que les taux d'introgression sont hétérogènes le long du génome. Ensuite, des scans génomiques de la différenciation ont été menés entre paires de populations du complexe d'espèces. L'analyse de la variation génétique et des généalogies d'allèles sur une échelle chromosomique localisée a permis de reconstituer l'histoire évolutive de plus de 1000 régions du génome des moules. Cette analyse a révélé qu'une cause majeure, mais insoupçonnée, de la différenciation génétique intraspécifique est l'introgression différentielle d'allèles étrangers. Globalement, cette thèse montre non seulement le rôle majeur de la biogéographie de la spéciation, c.a.d. des patrons temporels et spatiaux du flux de gènes, dans notre compréhension de la biodiversité actuelle, mais aussi sa surprenante complexité et l'étendue de ses conséquences sur l'évolution des génomesGenomes are affected by conflicting selective regimes. This is particularly well illustrated by the concept of semi-permeable barriers to gene flow, as found in the hybrid zones literature. Some genes contribute to the prevention of mixing between differentiated genetic lineages, either because they are involved in adaptation to local environmental conditions, or because they are incompatible with alleles from other genetic lineages. Other parts of the genome are either neutral, or subjected to selection which tends to homogenize the genetic lineages. In the first part of this thesis, models of the evolution of reproductive isolation are presented to explain the isolation patterns observed in experimental hybridizing crosses between incipient species. Using standard models of Dobzhansky-Muller genetic incompatibilities, it is shown that the asymmetry and complexity of incompatibilities are not well explained by there being an “evolutionary sieve”, i.e. a different rate of accumulation between incompatibilities. A complementary approach to quantitative modeling (an extension of Fisher's Geometric Model) then clarifies which conditions of divergence between allopatric lines led to highly deleterious effects in hybrid genotypes. The relative importance of mean levels of fitness epistasis, the distribution of mutation sizes, and the way lineages adapt to new environmental conditions is discussed. The second part of this thesis takes advantage of technical advances in genomics to study the history of speciation and adaptation in a non-model species complex, Mytilus mussels. A statistical method of inferring speciation scenarios is presented. Results show that European mussels experienced a complex history of strict divergence followed by a period of periodic connectivity. In agreement with the concept of semi-permeable barriers to gene flow, it is shown that introgression rates are heterogeneous along the genome. Next, genome scans of differentiation were conducted between pairs of populations of the species complex. The analysis of genetic variation and allele genealogies on a small chromosomal scale allowed to reconstruct the evolutionary history of more than 1000 genomic regions. This analysis reveals that a major cause of intraspecific differentiation is the differential introgression of foreign alleles. Overall, this thesis shows not only that biogeography of speciation, i.e. the temporal and spatial patterns of gene flow, play a major role in our understanding of existing biodiversity, but also its amazing complexity and extent of its impact on genome evolution
7
Kost, Matthew. "Maize and Sunflower of North America: Conservation and Utilization of Genetic Diversity." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1408642177.
8
Rocha, Joana Maria Laranjeira. "Life in deserts: a genomic history of adaptation and introgression in North African foxes." Doctoral thesis, 2021. https://hdl.handle.net/10216/134849.
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Rocha, Joana Maria Laranjeira. "Life in deserts: a genomic history of adaptation and introgression in North African foxes." Tese, 2021. https://hdl.handle.net/10216/134849.
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Rossi, Maria Eugenia. "Adaptation to Mega-environments: Introgression of novel alleles for yield using Canadian x Chinese crosses in Soybean." Thesis, 2011. http://hdl.handle.net/10214/3184.
Анотація:
The main goal of soybean breeding is to increase yield with improved seed quality characters. The objectives of this thesis were: i) to identify yield quantitative trait loci (QTL) across different mega-environments (ME); ii) to evaluate the relationship between yield and yield components and the co-localization of QTL; iii) to analyze environmental factors that affect QTL expression and identify different ME. Two Canadian x Chinese soybean populations were tested across Canada, northern United States and China. Yield QTL were identified at one, two and three hypothetical ME. Most of them were co-localized with agronomic trait QTL. These results give strong evidence that Canada, northern United States and China are different ME. Novel alleles from plant introductions can favorably contribute directly or indirectly to seed yield and the use of QTL would facilitate their introgression into breeding populations in both North America and China.National Science and Engineering Research Council of Canada (NSERC) and the Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA)
Частини книг з теми "Introgression adaptative":
1
Sevanthi, Amitha Mithra V., Prashant Kale, Chandra Prakash, M. K. Ramkumar, Neera Yadav, V. Sureshkumar, Yugandhar Poli, et al. "National repository of EMS induced mutants of an upland rice cultivar Nagina 22: progress update on characterization and utilization." In Mutation breeding, genetic diversity and crop adaptation to climate change, 290–302. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0030.
Анотація:
Abstract The Indian initiative for creating mutant resources in rice has generated 87,000 mutants in the background of a popular drought- and heat-tolerant upland cultivar, Nagina 22 (N22), through EMS mutagenesis. So far, 541 macro-mutants from this resource have been identified, maintained in the mutant garden and characterized in detail based on 44 descriptors pertaining to distinctness, uniformity and stability (DUS) of rice and other agronomic parameters. The similarity index of the mutants was more than 0.6 for nearly 90% of the mutants with respect to DUS descriptors, further establishing the validity of the mutants. The available high-quality sequence resource of N22 has been improved by reducing the gaps by 0.02% in the coding sequence (CDS) region. This was made possible using the newly synthesized whole-genome data of N22 which helped to remove 9006 'Ns' and replace 12,746 existing nucleotides with the accurate ones. These sequence and morphological details have been updated in the mutant database 'EMSgardeN22'. Further, 1058 mutants have been identified for low-P tolerance, tolerance to sheath blight, blast, drought, heat, higher photosynthetic efficiency and agronomic and root traits from this resource. A novel herbicide-tolerant (imazethapyr) mutant earlier identified and characterized from this resource is now being used in introgressing the herbicide-tolerant trait in eight major rice varieties in India. Further, robust and simpler screening systems have been tested for studying low-P tolerance of the mutants. A grain-size mutant, heat-tolerant mutant, drought-tolerant mutant, stay-green mutant and low-P tolerant and water-use efficient high-root-volume mutants have been characterized at morphological and molecular levels. A brief account of all these mutants, the entire mutant resource and the elaborate trait-based screenings is presented in this chapter.
2
Melo, Martim, Luis M. P. Ceríaco, and Rayna C. Bell. "Biogeography and Evolution in the Oceanic Islands of the Gulf of Guinea." In Biodiversity of the Gulf of Guinea Oceanic Islands, 141–70. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-06153-0_6.
Анотація:
AbstractAs with most archipelagos, geography played a central role in the assembly and evolution of the endemic-rich biological communities of the Gulf of Guinea oceanic islands. The islands are located at moderate distances from the species-rich African continent that surrounds them to the east and north. This proximity facilitated colonization by many branches of the tree of life, but gene flow between the islands and continent was low enough that many lineages evolved in isolation once they reached the archipelago, resulting in many endemic species. Furthermore, several of the island taxa belong to groups typically considered to be “poor dispersers” across sea barriers, which strongly supports a role for natural rafts in seeding the islands. Oceanic currents, including the freshwater pathways that extend from large river drainages into the Gulf of Guinea during the rainy season, also support this hypothesis. The distances between the islands are equivalent to those between the islands and the continent such that inter-island dispersal events appear to be relatively rare and thus few taxa are shared between them. Still, the islands present multiple cases of secondary contact leading to hybridization and genetic introgression between closely related lineages—providing several models to study the role and consequences of gene flow in evolution. Most taxa for which molecular estimates of divergence time have been derived are much younger than the ages of the islands. This pattern is consistent with high species turnover, likely resulting from a combination of small island sizes, proximity to the African continent and a long history of intense volcanic activity. The Gulf of Guinea oceanic islands provide multiple examples of classical adaptations to island life (the “island syndrome”), including giants and dwarves, ornament and color loss, among others. In addition, emerging studies of birds are highlighting the importance of competition regimes in driving phenotypic change—with examples of both character release (low inter-specific competition) and character displacement (inter-specific competition upon secondary contact). Collectively, the Gulf of Guinea oceanic islands offer unique opportunities to study adaptation and speciation in a range of taxa and contexts.
3
Hill, Geoffrey E. "Compensatory coevolution." In Mitonuclear Ecology, 49–76. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198818250.003.0003.
Анотація:
In most eukaryotes, mitochondrial genes mutate at a higher rate than nuclear genes. In addition, mitochondrial genes are transmitted without recombination, so slightly deleterious mutations are predicted to perpetually accumulate in mt genes. Accumulation of deleterious mutations in mt genes can potentially lead to loss of mitonuclear coadaptation. There is growing evidence that variant nuclear genes evolve so as to compensate for mitochondrial mutations and restore mitochondrial function. This is compensatory coevolution and is the focus of this chapter. The chapter also explores the idea that the many nuclear-encoded subunits in eukaryotic electron transport system enzymes were recruited to regulate and control the core catalytic reactions undertaken by the core mitochondrial subunits. It will also consider the evidence that when mutational erosion occurs, corrupted mitochondrial genotypes can be rescued by introgression of entire mitochondrial genomes. Compensatory coevolution has important implications for speciation, sexual selection, and adaptation.
4
Chikezie Ogbu, Cosmas. "Utilization and Conservation of Landrace Chickens of Nigeria: Physical and Performance Characteristics, Issues and Concerns." In Landraces - Traditional Variety and Natural Breed. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.96580.
Анотація:
The Nigerian indigenous chickens (NICs) are a critical component of the global animal genetic resources. They are distributed in rural areas, kept by the majority of the rural poor. They constitute different strains, or ecotypes local to tribes, regions, or ecological zones and are valued for their disease resistance, adaptation, and yield of valuable products and income on marginal inputs making them a low risk species. They are hence a unique and vital genetic resource and gene pool for present and long-term genetic improvement and human need for food and sustenance. The NIC is however; threatened by extinction owing to neglect, negative selection, breed substitution, and genetic introgression. There is need to draw research and policy attention to the conservation of NICs in accord with the global effort for the conservation of indigenous chickens which is probably the most neglected among farm animal species. The present review therefore, focuses on the physical and performance characteristics, genetic diversity and improvement, utilization and conservation of NIC genetic resources.
5
"Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques." In Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques, edited by Marlis R. Douglas and Michael E. Douglas. American Fisheries Society, 2010. http://dx.doi.org/10.47886/9781934874141.ch8.
Анотація:
<em>Abstract</em>.—Our capabilities to address pertinent questions in stream fish ecology, such as population connectivity, biotic homogenization, species invasions, introgression, and effects of habitat alterations on population structure and demography, have been significantly expanded by the development of molecular genetic approaches. A broad spectrum of molecular markers can now be tailored to address specific questions while newer statistical approaches accommodate larger data sets and permit the test of alternative hypotheses. Furthermore, molecular approaches facilitate the evaluation of ecological processes across both spatial and temporal scales, which are often mutually exclusive parameters. Population expansions, declines, and movements can be examined from recent to deep history and scaled from local to continental drainages. The intrinsic properties of stream ecosystems also make them particularly amenable to molecular approaches. The hierarchical order reflected in streams is directly translatable into an expanding spatial scale, from restricted headwaters through entire basins. Additionally, stream habitats are generally linear, and consequently, fish populations are often distributed sequentially, with interactions constrained to neighboring populations. Finally, streams tend to develop vicariant barriers over time, thus isolating populations and promoting local adaptation, a process easily deciphered using molecular markers. The latter have also contributed to the resolution of conservation issues and guided appropriate adaptive management of stream fauna. Molecular approaches in stream fish ecology are far too diverse to be comprehensively reviewed herein. Instead, we illustrate their facility by emphasizing three case studies demonstrating their broad utility: (1) a range-wide analysis of mitochondrial DNA diversity in flannelmouth sucker <em>Catostomus latipinnis</em>, pointing to a population bottleneck likely induced by severe post-Pleistocene drought in the Colorado River basin; (2) single nucleotide polymorphism screening to evaluate hybridization and introgression among native flannelmouth sucker, bluehead sucker <em>C. discobolus </em>(also known as <em>Pantosteus discobolus</em>), and the introduced white sucker <em>C. commersonii </em>in the upper Colorado River basin; and (3) microsatellite DNA analysis to evaluate gene flow and contemporary relationships in the Grand Canyon among populations of an endangered cyprinid fish (the humpback chub <em>Gila cypha</em>). In an appendix, we outline several recent molecular approaches that have expanded our opportunities to study stream fish ecology. We review relevant literature by emphasizing new statistical approaches and potential pitfalls of marker selection and data, rather than by delving into abstruse technical details regarding protocol development.
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Mehandi, Suhel, Anita Yadav, Ramanuj Maurya, Sudhakar Prasad Mishra, Syed Mohd. Quatadah, Nagmi Praveen, and Namrata Dwivedi. "Current Scenario of Breeding Approaches in Rice." In Cereal Grains [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.98744.
Анотація:
Rice is the predominant crop in India and is the staple food in eastern and southern Indian populations. One of the oldest grown crops is rice. The initial discovery of cytoplasmic male sterile (CMS) three-line system made it possible to produce hybrids that significantly increase rice yields compared to its inbred counterparts. Further genetic and molecular studies help elucidate the mechanisms involved in CMS male sterility. Additional CMS types were also discovered with similar genetic control from wild sources by interspecific hybridization. In India more than 1200 varieties were released for cultivation suitable different ecosystems and out of them 128 varieties have been contributed from NRRI, Cuttack. A list of these varieties are furnished below with their duration, grain type, yield potential, reaction to major disease and insects grain quality and tolerance to different adverse situations. Recent advances in molecular approaches used in modern rice breeding include molecular marker technology and marker-assisted selection (MAS); molecular mapping of genes and QTLs and production of hybrids and alien introgression lines (AILs). Genomic selection (GS) has been projected as alternative to conventional MAS. GS has huge potential to enhance breeding efficiency by increasing gain per selection per unit time. Due to the adaptation of semi dwarf high yielding varieties, combined with intensive input management practices, the country witnessed an impressive rice production growth in the post-independent period. Rice production was increased four times, productivity three times while the area increase was only one and half times during this period. The projected rice requirement by 2025, in order to keep up with increasing population, is about 130 m.t. The challenge of growing rice production is made more difficult by declining trends in HYV’s yields, decreasing and degrading natural resources such as land and water and a severe labour shortage.
7
"Paddlefish: Ecological, Aquacultural, and Regulatory Challenges of Managing a Global Resource." In Paddlefish: Ecological, Aquacultural, and Regulatory Challenges of Managing a Global Resource, edited by Michael R. Schwemm, Allison M. Asher, Edward J. Heist, Thomas F. Turner, and Anthony A. Echelle. American Fisheries Society, 2019. http://dx.doi.org/10.47886/9781934874530.ch2.
Анотація:
<i>Abstract</i>.—Long-term sustainability of the Paddlefish <i>Polyodon spathula</i> will require effective consideration and application of genetic principles and tools by fisheries managers. Paddlefish migration patterns, harvest, and fish culture and stocking for mitigation collectively influence stock structure and genetic resources. Studies since the early 1980s have indicated that Paddlefish showed higher levels of genetic diversity and gene flow in open rivers, but that diversity and gene flow have typically been reduced within geographically isolated and impounded reaches, a result consistent with reduced migratory behavior, river fragmentation, and demographic bottlenecks. Concurrent hatchery propagation methods and broodstock selection probably also contributed to unintentional genetic changes in stocked Paddlefish populations (Gavins Point, South Dakota-Nebraska). We present case studies depicting how stocking has altered the genetic structure of populations and reduced within-population diversity. Documented genetic changes have resulted from 1) annual stocking and low natural reproduction leading to a low effective population size (Table Rock Lake, Missouri), 2) introgression by hatchery-reared broodstock from a distant source population (Gavins Point, South Dakota-Nebraska into Kaw Lake, Oklahoma), and 3) subsampling of genetic diversity in a stocked population (Oologah Lake, Verdigris River, Oklahoma) relative to the broodstock source (Grand Lake, Grand/Neosho River, Oklahoma). We present two other case studies of population genetics issues from Grand Lake, the first suggesting a population bottleneck due to impoundment by dam approximately 80 years ago, and the second detailing the potential genetic effects of episodic recruitment on genetic effective size. Paddlefish in some areas have fortunately retained genetic variation and avoided immediate concerns of inbreeding, due in part to life-history attributes and prudent management. Increased consideration of genetic structure both within states and across jurisdictional boundaries will additionally improve range-wide management decisions. These case studies offer several general conclusions useful to guide future management of Paddlefish populations in order to maintain evolutionary potential and local adaptation, important considerations for conservation and sustainable harvest in modified river systems.
Звіти організацій з теми "Introgression adaptative":
1
Dubcovsky, Jorge, and T. (Tzion) Fahima. Validation of candidate genes for a QTL responsible for water stress tolerance and their diversity in wheat. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2022. http://dx.doi.org/10.32747/2022.8134149.bard.
Анотація:
The main goals of this project as stated in the original proposal were to identify which of the candidate gene(s) identified in a 1.5 Mb region of wheat and rye chromosomes 1RS and 1BS were responsible for the differences in root architecture, reveal their natural variation and characterize the epistatic interactions that modulate their effect in different backgrounds. Background: Wheat is an essential crop for global food security and is well adapted to a wide variety of soils. However, the gene networks regulating different wheat root architectures remain poorly understood. Root depth and biomass distribution in the soil profile are critical traits for adaptation to water stress, and a good source for these traits is the introgression of the short arm of rye chromosome one (1RS) into common wheat. A recombinant 1RS chromosome with a small wheat 1BS introgressions and a duplicated 1RS segment (1RW) showed reduced drought tolerance and was used for the identification of the causal genes.
2
Abbo, Shahal, Hongbin Zhang, Clarice Coyne, Amir Sherman, Dan Shtienberg, and George J. Vandemark. Winter chickpea; towards a new winter pulse for the semiarid Pacific Northwest and wider adaptation in the Mediterranean basin. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7597909.bard.
Анотація:
Original objectives: [a] Screen an array of chickpea and wild annual Cicer germplasm for winter survival. [b] Genetic analysis of winter hardiness in domesticated x wild chickpea crosses. [c] Genetic analysis of vernalization response in domesticated x wild chickpea crosses. [d] Digital expression analysis of a core selection of breeding and germplasm lines of chickpea that differ in winter hardiness and vernalization. [e] Identification of the genes involved in the chickpea winter hardiness and vernalization and construction of gene network controlling these traits. [f] Assessing the phenotypic and genetic correlations between winter hardiness, vernalization response and Ascochyta blight response in chickpea. The complexity of the vernalization response and the inefficiency of our selection experiments (below) required quitting the work on ascochyta response in the framework of this project. Background to the subject: Since its introduction to the Palouse region of WA and Idaho, and the northern Great Plains, chickpea has been a spring rotation legume due to lack of winter hardiness. The short growing season of spring chickpea limits its grain yield and leaves relatively little stubble residue for combating soil erosion. In Israel, chilling temperatures limit pod setting in early springs and narrow the effective reproductive time window of the crop. Winter hardiness and vernalization response of chickpea alleles were lost due to a series of evolutionary bottlenecks; however, such alleles are prevalent in its wild progenitor’s genepool. Major conclusions, solutions, achievements: It appears that both vernalization response and winter hardiness are polygenic traits in the wild-domesticated chickpea genepool. The main conclusion from the fieldwork in Israel is that selection of domesticated winter hardy and vernalization responsive types should be conducted in late flowering and late maturity backgrounds to minimize interference by daylength and temperature response alleles (see our Plant Breeding paper on the subject). The main conclusion from the US winter-hardiness studies is that excellent lines have been identified for germplasm release and continued genetic study. Several of the lines have good seed size and growth habit that will be useful for introgressing winter-hardiness into current chickpea cultivars to develop releases for autumn sowing. We sequenced the transcriptomes and profiled the expression of genes in 87 samples. Differential expression analysis identified a total of 2,452 differentially expressed genes (DEGs) between vernalized plants and control plants, of which 287 were shared between two or more Cicer species studied. We cloned 498 genes controlling vernalization, named CVRN genes. Each of the CVRN genes contributes to flowering date advance (FDA) by 3.85% - 10.71%, but 413 (83%) other genes had negative effects on FDA, while only 83 (17%) had positive effects on FDA, when the plant is exposed to cold temperature. The cloned CVRN genes provide new toolkits and knowledge to develop chickpea cultivars that are suitable for autumn-sowing. Scientific & agricultural implications: Unlike the winter cereals (barley, wheat) or pea, in which a single allelic change may induce a switch from winter to spring habit, we were unable to find any evidence for such major gene action in chickpea. In agricultural terms this means that an alternative strategy must be employed in order to isolate late flowering – ascochyta resistant (winter types) domesticated forms to enable autumn sowing of chickpea in the US Great Plains. An environment was identified in U.S. (eastern Washington) where autumn-sown chickpea production is possible using the levels of winter-hardiness discovered once backcrossed into advanced cultivated material with acceptable agronomic traits. The cloned CVRN genes and identified gene networks significantly advance our understanding of molecular mechanisms underlying plant vernalization in general, and chickpea in particular, and provide a new toolkit for switching chickpea from a spring-sowing to autumn-sowing crop.
3
Sela, Hanan, Eduard Akhunov, and Brian J. Steffenson. Population genomics, linkage disequilibrium and association mapping of stripe rust resistance genes in wild emmer wheat, Triticum turgidum ssp. dicoccoides. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598170.bard.
Анотація:
The primary goals of this project were: (1) development of a genetically characterized association panel of wild emmer for high resolution analysis of the genetic basis of complex traits; (2) characterization and mapping of genes and QTL for seedling and adult plant resistance to stripe rust in wild emmer populations; (3) characterization of LD patterns along wild emmer chromosomes; (4) elucidation of the multi-locus genetic structure of wild emmer populations and its correlation with geo-climatic variables at the collection sites. Introduction In recent years, Stripe (yellow) rust (Yr) caused by Pucciniastriiformis f. sp. tritici(PST) has become a major threat to wheat crops in many parts of the world. New races have overcome most of the known resistances. It is essential, therefore, that the search for new genes will continue, followed by their mapping by molecular markers and introgression into the elite varieties by marker-assisted selection (MAS). The reservoir of genes for disease and pest resistance in wild emmer wheat (Triticumdicoccoides) is an important resource that must be made available to wheat breeders. The majority of resistance genes that were introgressed so far in cultivated wheat are resistance (R) genes. These genes, though confering near-immunity from the seedling stage, are often overcome by the pathogen in a short period after being deployed over vast production areas. On the other hand, adult-plant resistance (APR) is usually more durable since it is, in many cases, polygenic and confers partial resistance that may put less selective pressure on the pathogen. In this project, we have screened a collection of 480 wild emmer accessions originating from Israel for APR and seedling resistance to PST. Seedling resistance was tested against one Israeli and 3 North American PST isolates. APR was tested on accessions that did not have seedling resistance. The APR screen was conducted in two fields in Israel and in one field in the USA over 3 years for a total of 11 replicates. We have found about 20 accessions that have moderate stripe rust APR with infection type (IT<5), and about 20 additional accessions that have novel seedling resistance (IT<3). We have genotyped the collection using genotyping by sequencing (GBS) and the 90K SNP chip array. GBS yielded a total 341K SNP that were filtered to 150K informative SNP. The 90K assay resulted in 11K informative SNP. We have conducted a genome-wide association scan (GWAS) and found one significant locus on 6BL ( -log p >5). Two novel loci were found for seedling resistance. Further investigation of the 6BL locus and the effect of Yr36 showed that the 6BL locus and the Yr36 have additive effect and that the presence of favorable alleles of both loci results in reduction of 2 grades in the IT score. To identify alleles conferring adaption to extreme climatic conditions, we have associated the patterns of genomic variation in wild emmer with historic climate data from the accessions’ collection sites. The analysis of population stratification revealed four genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. The top three bioclimatic factors driving SNP distribution were temperature seasonality, precipitation seasonality, and isothermality. Association mapping approaches revealed 57 SNPs associated with these bio-climatic variables. Out of 21 unique genomic regions controlling heading date variation, 10 (~50%) overlapped with SNPs showing significant association with at least one of the three bioclimatic variables. This result suggests that a substantial part of the genomic variation associated with local adaptation in wild emmer is driven by selection acting on loci regulating flowering. Conclusions: Wild emmer can serve as a good source for novel APR and seedling R genes for stripe rust resistance. APR for stripe rust is a complex trait conferred by several loci that may have an additive effect. GWAS is feasible in the wild emmer population, however, its detection power is limited. A panel of wild emmer tagged with more than 150K SNP is available for further GWAS of important traits. The insights gained by the bioclimatic-gentic associations should be taken into consideration when planning conservation strategies.