Enfoques genómicos y transcriptómicos hacia la selección de plantas

Omics era has opened a new window to biology. Genomics and transcriptomics are two well-known fields by which plant selection and breeding are studied more easily and accurately. They provide useful information about the genes, transcripts, their functions those are the principal data for other subsequent approaches. Reference genomes of various plants are available and facilitate genome-based studies. The complex of genomic, transcriptomic data and the findings from variant methods like QTLs (quantitative trait loci), SNPs (single nucleotide polymorphism), CNVs (copy number variant), resequencing, GBS (genome-by-sequencing) are extremely important for plant selection in terms of price and time. The new workflows are routinely using different approaches and mixing them based on the genomic/transcriptomic information in their subsequent steps and are validated during the whole process toward screening genotypes possessing agronomically important desired trait. SNP-Seq presented hereinafter is a new approach for analyzing plants toward selection and screening by SNP sequencing in various genotypes simultaneously. It can accelerate the cycle of plant selection from genotypes to phenotypes in a reverse engineering way.La era Omica ha abierto una nueva ventana a la biología. La genómica y la transcriptómica son dos campos conocidos, con los cuales, la selección y el mejoramiento de plantas se estudian con mayor facilidad y precisión. Proporcionan información útil sobre los genes, las transcripciones, sus funciones y sirven como datos primordiales para otros enfoques posteriores. Los genomas de referencia de varias plantas han sido secuenciados, y están disponibles, facilitando así el acceso a información ómica indispensable para llevar a cabo estudios basados ​​en estos mismos genomas. El total de datos genómicos, transcriptómicos y los hallazgos de métodos variantes que van desde QTL (rasgo cuantitativo), PSN (polimorfismo de un solo nucleótido), NCV (número de copias variante), GBS (genoma por secuencia) son extremadamente importantes para la selección y el mejoramiento de plantas en términos de precio y tiempo. Los nuevos flujos de trabajo utilizan diferentes enfoques basados ​​en la información genómica / transcriptómica en pasos posteriores mezclándolos y se validan durante todo el proceso para seleccionar genotipos que posean un rasgo deseado agronómicamente importante. SNP-Seq, que se presenta en este artículo, es un nuevo enfoque para analizar las plantas hacia la selección y la detección mediante secuenciación de SNP en varios genotipos simultáneamente. Este proceso puede acelerar el ciclo de selección de plantas desde los genotipos a los fenotipos en una forma de ingeniería inversa. &nbsp

Volatile organic compounds: plant natural defense mechanisms against herbivorous arthropods and an opportunity for plant breeding of cotton

Plants’ natural defense mechanisms against herbivorous arthropods include the emission of volatile organic compounds (VOC). Nowadays field observations about plant-insect interactions are better understood thanks to the increasingly scientific investigations over recent decades. There are now more precise data about molecules, action modes and physiological and genetic bases of these plant defense mechanisms. VOC present an important potential for crop protection and pesticide use reduction. In the present review, we focus on the latest research advances about plant protection provided by VOC, considering experimental methods of volatile analysis and the involved genes toward genetic improvement of natural defense in the future varieties, particularly for Upland cotton Gossypium hirsutum

Volatile organic compounds: Plant natural defense mechanisms against herbivorous arthropods and an opportunity for plant breeding of cotton

Plants' natural defense mechanisms against herbivorous arthropods include the emission of volatile organic compounds (VOC). Nowadays field observations about plant-insect interactions are better understood thanks to the increasingly scientific investigations over recent decades. There are now more precise data about molecules, action modes and physiological and genetic bases of these plant defense mechanisms. VOC present an important potential for crop protection and pesticide use reduction. In the present review, we focus on the latest research advances about plant protection provided by VOC, considering experimental methods of volatile analysis and the involved genes toward genetic improvement of natural defense in the future varieties, particularly for Upland cotton Gossypium hirsutum

Optimization of pH Levels in Soils Intended for Oil Palm (Elaeis Guineensis Jacq.) Cultivation Through the use of Solid and Flocculent Amendments

La investigación se realizó en dos tipos de finca (orgánica y convencional) y tuvo como objetivo determinar la eficiencia de enmiendas floables y sólidas en corrección de pH en el cultivo de palma aceitera. Para ello se emplearon tres tipos de enmiendas, dos floables y una sólida. Los lotes fueron divididos en parcelas de 9x27 m que ocuparon 8 plantas cada uno, con cuatro tratamientos y cuatro repeticiones. Se empleó un diseño de parcelas divididas (DPD) en un diseño completamente al azar (DCA). Los resultados fueron sometidos a la prueba de Tukey al 95% de probabilidad. El mejor tratamiento para mejorar el pH de un suelo cultivado de palma aceitera fue la enmienda floable 2 (T2) además de tener el menor costo. El tratamiento enmienda sólida (T3) presentó el valor más alto de disponibilidad de nitrógeno, en el suelo con 29,50 ppm de disponibilidad a los 60 días de aplicada la enmienda. En cuanto al fósforo, la enmienda floable 2 (T2) presentó el valor más alto con 34 ppm de disponibilidad a los 120 días de aplicada la enmienda. Mientras que, para potasio (K) la enmienda sólida (T3) presentó el valor más alto con 0,74 ppm.The research was carried out on two types of farms (organic and conventional) and its objective was to determine the efficiency of flocculent and solid amendments in pH correction in oil palm cultivation. Three types of amendments were used, two flocculent and one solid. The plots were divided into 9x27 m plots of 8 plants each, with four treatments and four replications. A split-plot design (DPD) was used in a completely randomized design (DCA). The results were subjected to Tukey's test at 95% probability. The best treatment for improving the pH of an oil palm cultivated soil was flocculent amendment 2 (T2), in addition to having the lowest cost. The solid amendment treatment (T3) presented the highest value of nitrogen availability in the soil, with 29.50 ppm availability 60 days after application of the amendment. As for phosphorus, the flocculent amendment 2 (T2) had the highest value with 34 ppm of availability 120 days after application of the amendment. For potassium (K), the solid amendment (T3) presented the highest value with 0.74 ppm

Being oneself through time: bases of self-continuity across 55 cultures

Self-continuity – the sense that one’s past, present, and future are meaningfully connected – is considered a defining feature of personal identity. However, bases of self-continuity may depend on cultural beliefs about personhood. In multilevel analyses of data from 7287 adults from 55 cultural groups in 33 nations, we tested a new tripartite theoretical model of bases of self-continuity. As expected, perceptions of stability, sense of narrative, and associative links to one’s past each contributed to predicting the extent to which people derived a sense of self-continuity from different aspects of their identities. Ways of constructing self-continuity were moderated by cultural and individual differences in mutable (vs. immutable) personhood beliefs – the belief that human attributes are malleable. Individuals with lower mutability beliefs based self-continuity more on stability; members of cultures where mutability beliefs were higher based self-continuity more on narrative. Bases of self-continuity were also moderated by cultural variation in contextualized (vs. decontextualized) personhood beliefs, indicating a link to cultural individualism-collectivism. Our results illustrate the cultural flexibility of the motive for self-continuity

Individual and culture-level components of survey response styles: a multi-level analysis using cultural models of selfhood

Variations in acquiescence and extremity pose substantial threats to the validity of cross-cultural research that relies on survey methods. Individual and cultural correlates of response styles when using two contrasting types of response mode were investigated, drawing on data from 55 cultural groups across 33 nations. Using seven dimensions of self-other relatedness that have often been confounded within the broader distinction between independence and interdependence, our analysis yields more specific understandings of both individual- and culture-level variations in response style. When using a Likert scale response format, acquiescence is strongest among individuals seeing themselves as similar to others, and where cultural models of selfhood favour harmony, similarity with others and receptiveness to influence. However, when using Schwartz’s (2007) portrait-comparison response procedure, acquiescence is strongest among individuals seeing themselves as self-reliant but also connected to others, and where cultural models of selfhood favour self-reliance and self-consistency. Extreme responding varies less between the two types of response modes, and is most prevalent among individuals seeing themselves as self-reliant, and in cultures favouring self-reliance. Since both types of response mode elicit distinctive styles of response, it remains important to estimate and control for style effects to ensure valid comparisons

Beyond the ‘East-West’ dichotomy: global variation in cultural models of selfhood

Markus and Kitayama’s (1991) theory of independent and interdependent self-construals had a major influence on social, personality, and developmental psychology by highlighting the role of culture in psychological processes. However, research has relied excessively on contrasts between North American and East Asian samples, and commonly used self-report measures of independence and interdependence frequently fail to show predicted cultural differences. We revisited the conceptualization and measurement of independent and interdependent self-construals in 2 large-scale multinational surveys, using improved methods for cross-cultural research. We developed (Study 1: N = 2924 students in 16 nations) and validated across cultures (Study 2: N = 7279 adults from 55 cultural groups in 33 nations) a new 7-dimensional model of self-reported ways of being independent or interdependent. Patterns of global variation support some of Markus and Kitayama’s predictions, but a simple contrast between independence and interdependence does not adequately capture the diverse models of selfhood that prevail in different world regions. Cultural groups emphasize different ways of being both independent and interdependent, depending on individualism-collectivism, national socioeconomic development, and religious heritage. Our 7-dimensional model will allow future researchers to test more accurately the implications of cultural models of selfhood for psychological processes in diverse ecocultural contexts

Etude génétique des réactions de défense induites par l'écimage chez les cotonniers/Gossypium hirsutum/ L., combinant : bioinformatique, capture de COV et expression génique

Gossypium hirsutum, le coton Upland, représente plus de 95% de la fibre de coton produite annuellement dans le monde et est cultivé dans environ 40 pays. La protection des champs de coton contre l’attaque des arthropodes herbivores nécessite des quantités importantes d’insecticides de synthèse, environ 18% de la consommation mondiale en 2000, bien que cela ait beaucoup diminué grâce au coton Bt et aux programmes d’éradication de certains ravageurs. Les composés organiques volatils (COV) naturellement émis par les plantes cultivées peuvent réduire les attaques d'insectes, les COV ayant une influence sur le comportement des arthropodes herbivores et des arthropodes auxiliaires. La recherche scientifique sur les COV des plantes a beaucoup augmenté depuis deux ou trois décennies. La stimulation des émissions de COV dans les champs de coton est désormais recommandée par les entomologistes du Cirad en tant que composante de la stratégie de protection. L’écimage (topping en anglais), c'est-à-dire couper la tête des cotonniers au cours de la floraison, stimule l'émission de COV de défense, une protection écologique qui limite les risques pour la santé dus aux insecticides synthétiques, pour les agriculteurs et les personnes des environs. L'objectif de la thèse était d'améliorer nos connaissances sur les bases génétiques des émissions de COV après l’écimage. La combinaison de plusieurs disciplines telles que la bio-informatique, l'écologie chimique et la génétique moléculaire nous a permis de: 1) analyser les séquences génomiques des gènes des voies de biosynthèse des COVs terpènes et terpénoïdes et des facteurs de transcription (TF) liés à la réponse au stress, à l'aide des bases de données publiées sur les génomes de trois espèces de coton, G. raimondii, G. arboreum (cotons diploïdes) et G. hirsutum (coton tétraploïde), 2) étudier les émissions de COV par les feuilles de coton des plants de G. hirsutum en réponse à l’écimage, en capturant ces molécules en serre et en caractérisant leurs profils cinétiques par chromatographie en phase gazeuse-spectrométrie de masse (GC-MS), incluant des mesures quantitatives, et 3) étudier les modifications de l'expression ARN des plants de coton G. hirsutum après l’écimage, pour 44 gènes impliqués dans la biosynthèse des COV, et également par une comparaison du transcriptome complet au moyen d'une analyse RNA-seq. Les résultats des trois domaines scientifiques, bio-informatique, analyse chimique et expression des gènes, ont pu être liés dans notre thèse de recherche: par ex., deux des gènes initialement identifiés par la bio-informatique, correspondant à deux enzymes, TPS50 (EC: 4.2.3.106 - (E ) bêta-ocimène synthase) et TPS16 (EC: 4.2.3.111 - alpha-terpinéol synthase), ont montré une augmentation de leur expression après l’écimage, et l'analyse GC-MS montre une modification correspondante des profils d'émission de COV. Ces mêmes composés avaient déjà été caractérisés dans d'autres plantes en réponse aux dégâts d’arthropodes. Ce travail de thèse constitue une première exploration des bases génétiques des émissions défensives de COV par les cotonniers cultivés G. hirsutum. La variabilité des comportements d’expression génique observés entre les trois génotypes étudiés de coton Upland africain G. hirsutum, permet de supposer qu’une diversité génétique est présente pour les émissions défensives de COV, ce qui pourrait permettre d’améliorer et d’adapter ces mécanismes de défense naturels et leur réponse à l’écimage, dans la perspective d'une protection naturelle plus efficace des champs de coton.Gossypium hirsutum, the Upland cotton, represents more than 95% of the cotton fiber annually produced worldwide and is grown in about 40 countries. The protection of cotton fields against the attack of herbivorous arthropods needs important quantities of synthetic insecticides, around 18% of the world consumption for the year 2000, although this decreased very much thanks to Bt cotton and eradication programs for some pests. Volatile organic compounds (VOCs) naturally emitted by crop plants can reduce insect attacks through the influence of VOCs on the behaviors of herbivorous arthropods and auxiliary arthropods. Scientific research about plant VOCs has been increasing much since two or three decades. The stimulation of VOCs emissions by cultivated cotton plants is now recommended by entomologists of CIRAD as a component of the cotton fields protection strategy. “Topping", that is, cutting the head of the cotton plants during the useful floriferous period, stimulates the emission of defense VOCs. It is an environmentally friendly method and it limits health hazards due to the use of synthetic insecticides for the farmers and the surrounding human populations. The objective of the thesis was to improve our knowledge about the genetic bases of VOCs emissions after topping. The combination of several disciplines such as bioinformatics, chemical ecology and molecular genetics allowed us to: 1) analyze the genomic sequences of VOCs genes of the terpene and terpenoid biosynthesis pathways and transcription factors (TF) related to stress response, using the published genome databases of three cotton species, G. raimondii, G. arboreum (both diploid cottons) and G. hirsutum (tetraploid cotton), 2) study the VOCs emissions by cotton leaves of G. hirsutum plants in response to topping, by capturing these molecules in greenhouse and then characterizing their kinetic profiles by means of gas-chromatography mass-spectrometry (GC-MS), with quantitative measurements, and, 3) study the modifications of the RNA expression of G. hirsutum cotton plants after topping, for genes involved in VOCs biosynthesis through quantitative PCR measurements on 44 targeted genes and also by means of a whole-transcriptome comparison through an RNA-seq analysis. The results from the three different fields, bioinformatics, chemical analysis and gene expression, could be interrelated in our research thesis: e.g., two of the genes initially identified by bioinformatics, corresponding to two enzymes, TPS50 (EC: 4.2.3.106 - (E) -beta-ocimene synthase) and TPS16 (EC: 4.2.3.111 - alpha-terpineol synthase), were shown to increase their expression after topping, while the GC-MS analysis showed an modification of the corresponding VOCs in emission profiles. These compounds have been already characterized in other organisms in response to wounds produced by herbivorous insects. This thesis work is a first exploration of the genetic bases of defensive VOCs emission by G. hirsutum cultivated cottons. The variability of genic expression behaviors observed amongst the three genotypes of African Upland cotton G. hirsutum that were studied permits to hypothesize that a genetic diversity is present for defensive VOCs emissions, that could permit to improve and adapt by breeding these natural defense mechanisms and the response to topping, in perspective of a more efficient natural protection of cotton fields