Chapter 9. Genome-informed discovery of genes and framework of functional genes in wheat

awais rasheed Rudi Appels (2024, [Capítulo de libro])

Wheat Genomics KASP Markers Gene Discovery Functional Markers Gene Networks CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA WHEAT GENOMICS SINGLE NUCLEOTIDE POLYMORPHISMS FUNCTIONAL GENOMICS

Variation of the ferulic acid concentration and kernel weight in CIMMYT bread wheat germplasm and selection of lines for functional food production

Wenfei Tian Maria Itria Ibba Govindan Velu Shuanghe Cao Zhonghu He (2024, [Artículo])

CIMMYT Germplasm CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA GERMPLASM FERULIC ACID FUNCTIONAL FOODS PHYTOCHEMICALS YIELD POTENTIAL WHEAT FOOD PRODUCTION

Nitrogen fertilizer application alters the root endophyte bacterial microbiome in maize plants, but not in the stem or rhizosphere soil

Alejandra Miranda Carrazco Yendi Navarro-Noya Bram Govaerts Nele Verhulst Luc Dendooven (2022, [Artículo])

Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the “diversity arrays technology sequencing,” while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled.

Bacterial Community Structure DArT-Seq Bacterial Community Functionality Genes Involved in N Cycling CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA AGRICULTURAL PRACTICES MAIZE RHIZOSPHERE STEMS NITROGEN FERTILIZERS

CARACTERIZACIÓN Y DISTRIBUCIÓN DE GERMOPLASMA SILVESTRE DE Jatropha curcas L. (EUPHORBIACEAE) EN EL NOROESTE DE MÉXICO

CHARACTERIZATION AND DISTRIBUTION OF WILD GERMPLASM Jatropha curcas L. (EUPHORBIACEAE) IN THE NORTHWEST OF MEXICO

NIDIA ARAIZA LIZARDE MIGUEL ANGEL ANGULO ESCALANTE TEODORO REYNOSO GRANADOS MARIA MAGDALENA ORTEGA NIEBLAS Lilia Alcaráz Meléndez Pedro Cruz Hernández (2016, [Artículo])

"Se estudiaron tres poblaciones silvestres de Jatropha curcas L. en la región sur y centro de Sinaloa en los sitios de Estación Dimas, La Campana y El Quelite. Los objetivos fueron caracterizar morfológicamente las plantas y semillas, evaluar la relación de las variables morfológicas con los factores ambientales y analizar el potencial de distribución de las especies en Sinaloa considerando los factores ambientales registrados en los sitios de estudio. En cada sitio de estudio se realizó el conteo del número de individuos/m2 y se midió la altura, el diámetro de copa, el diámetro basal y el número de ramas. De cada sitio se obtuvo también el número de semillas por kilogramo, color, peso, longitud y ancho de la semilla. La altura de las plantas estuvo en un intervalo de 2.25 a 4.59 m, el diámetro de la copa fue de 2.24 a 4.48 m, el diámetro basal de 18.75-24.81 cm y el número de ramificaciones de 2 a 4. No se observaron diferencias significativas entre las características morfológicas de las plantas de Estación Dimas y el Quelite pero sí con respecto a La Campana. En ambos sitios se observó que la altura de las plantas fue favorecida cuando la temperatura y velocidad del viento fueron menores, y cuando la precipitación y humedad relativa fueron mayores. Las dimensiones de las semillas fueron, ancho 7.41 a 7.9 mm y longitud de 15.1 a 15.9 mm. La humedad de las semillas fue de 3.57 a 4.21%, y el color de las semillas fue de 60.80 a 65.64°Hue. La mayor densidad de individuos se encontró en Estación Dimas (21 ind/ha), pero la utilización del campo con fines agrícolas que se encuentra cercana a este ecotipo amenaza al desarrollo de la vegetación silvestre de este sitio. Por lo que el germoplasma de las poblaciones en estudio puede ser útil para elaboración de planes y manejos de conservación de la especie, además constituye una alternativa para el establecimiento de cultivos en el estado con especies propias de la región y, posiblemente, para otras regiones del país. Por otro lado, se observó que la especie tiene un alto potencial de distribución en el estado de Sinaloa principalmente en los municipios de Sinaloa de Leyva, Guasave, Guamúchil, Culiacán, Elota, San Ignacio, Mazatlán, Villa Unión, Concordia y Escuinapa."

"Three wild populations of Jatropha curcas in the central and southern parts of Sinaloa were studied; Estación Dimas, La Campana, and El Quelite. The objectives were to characterize plants and seeds morphologically to assess the relationship between morphologica traits and environmental factors and the potential distribution of the species considering environmental factors from the study sites. All individuals/m2 and number of branches were counted, and height, diameter of cup, and basal diameter were measured. The number of seeds per kilogram was obtained, as well as color, weight, and seed length and width. Plant height ranged from 2.25 to 4.59 m; the crown diameter from 2.24 to 4.48 m; basal diameter from 18.75 to 24.81 cm; and branch number 2 to 4. No significant differences were found in morphological characteristics between plants from Estación Dimas and El Quelite but those from La Campana were significantly smaller. Plant height was favored in sites with lower temperature, altitude, and wind speed, and with higher precipitation and relative humidity. Seed length ranged from 7.41 to 7.9 mm and seed width from 15.1 to 15.9 mm. Seed moisture ranged from 3.57 to 4.21%. The seed color ranged from 60.80 to 65.54° Hue. The highest tree density was found in Estación Dimas (21 ind/ha), but agricultural practices threatens the vegetation in this site. The species has a high potential for distribution in the southern and central parts of the state. Germplasm from the studied populations may be useful for plans and management for species conservation; they also constitute an alternative to the establishment of crops in the state of Sinaloa with typical species of the region and possibly other regions of the country. Moreover, it was observed that the species has a high potential for distribution in the state mainly in the municipalities of Sinaloa de Leyva, Guasave, Guamuchil, Culiacan, Elota, San Ignacio, Mazatlan, Villa Union, Concordia, and Escuinapa."

densidad, distribución, semilla density, distribution, seed BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) SEMILLAS SEMILLAS

La Funcionalidad Física Arrecifal, indicador de la diversidad funcional en ensamblajes de peces de arrecifes en el Parque Nacional Islas Marietas, Nayarit, México

Reef Physical Functionality, indicator of functional diversity on reef fishes assemblages from Islas Marietas National Park, Nayarit, Mexico

Luis Mario Montalvo Jaramillo (2023, [Tesis de maestría])

La ecología funcional se basa en el uso de rasgos funcionales; características de las especies (morfológicas, fisiológicas, comportamiento) medidas a nivel individual que influencian el rendimiento de una especie, siendo de gran utilidad para determinar cambios dentro del ecosistema. El presente trabajo busca evaluar la funcionalidad física como indicador de disponibilidad de hábitat de peces y su relación con la diversidad funcional. La funcionalidad física del arrecife se evaluó mediante el IFA integrando datos de cobertura coralina, complejidad estructural y tasa de calcificación. La estructura de los ensamblajes de peces se analizó mediante el cálculo de índices de diversidad funcional (riqueza, equitatividad y divergencia) con base en cuatro rasgos funcionales (tamaño corporal, movilidad, tipo de agregación y dieta). La relación entre la diversidad funcional del ensamblaje y el IFA se evaluó mediante un análisis de regresión lineal. El IFA fue influenciado de manera positiva por la presencia Pocilloporidos al generar un mayor aporte a la funcionalidad física (FF) y consecuentemente, una mayor provisión de hábitat. Por el contrario, el IFA disminuyó con la presencia de Porites panamensis debido a su baja tasa de calcificación.La diversidad funcional de los ensamblajes no presentó variaciones temporales, atribuible a una baja variabilidad entre los sitios debido a una alta cercanía, baja variacion batimétrica y alta conectividad. La relación entre el IFA y la riqueza funcional de los ensamblajes se atribuye a que sitios con mayor funcionalidad física otorgan disponibilidad de hábitat y refugio contra la depredación a especies crípticas, de talla pequeña y juveniles; ya que, especies de este tipo se asocian a hoyos similares a su tamaño corporal y la supervivencia de las mismas aumenta en sustratos más complejos.

Functional diversity it’s based on functional traits; characteristics of species (morphological, physiological, behavior) measured at individual level that impact their performance and have great utility to determine changes within the ecosystem. This work aims to evaluate physical functionality as indicator of fish habitat availability and its relationship with functional diversity. The physical functionality of the reef was evaluated using the RFI, integrating data on coral cover, structural complexity, and calcification rate. The structure of the fish assemblages was analyzed by calculating functional diversity index (richness, evenness, and divergence) based on four functional traits (body size, mobility, type of aggregation and diet). The relationship between functional diversity and RFI was evaluated using linear regression analysis. The RFI was influenced on positive way for the presence of Pocilloporids due to the great contribution to physical functionality (PF) creating more habitat availability. For the other hand, the RFI was influenced on negative way for the presence of Porites panamensis due their low calcification rate. The functional diversity of the assemblages did not present temporal variations, attributable to a low variability between the sites due high proximity, low bathymetric variation and high connectivity. The relationship between RFI and the functional richness of the assemblages is attributed to fact that sites with greater physical functionality provide more availability of habitat and refuge against predation to cryptic, small and juvenile species; species of this type are associate with holes similar to their body size and their survival increases in more complex substrates.

Pacífico Méxicano, Índice de Función Arrecifal, Diversidad Funcional, Arrecife Reef, Functional Diversity, Reef Functional Index, Mexican Pacific BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA OTRAS ESPECIALIDADES DE LA BIOLOGÍA OTRAS OTRAS

The cerato-mandibular ligament: a key functional trait for grazing in damselfishes (Pomacentridae)

Damien Olivier Bruno Frederich MILTON ALEJANDRO SPANOPOULOS ZARCO Eduardo Francisco Balart Páez Eric Parmentier (2014, [Artículo])

"The success of a taxonomic group can be promoted by a key character that allows the group to interact with its environment in a different way and to potentially occupy new niches. The Pomacentridae possess a synapomorphic trait, the cerato-mandibular (c-md) ligament, which joins the hyoid bar to the inner part of the lower jaw. It has previously been shown that this ligament is a key trait in communication in damselfishes because it enables them to slam the oral jaws shut causing teeth collision and sound production. This specific behavior of mouth closing could, however, also be used for other tasks, such as feeding. Many territorial damselfishes are referred to as farmers, due to their ability to manage algal crops on which they feed. This study hypothesizes that the c-md ligament provides an advantage for grazing filamentous algae, and should thus be considered a key trait for farming behavior."

Biomechanics, Evolution, Farming, Functional morphology BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) ZOOLOGÍA MARINA ZOOLOGÍA MARINA

Funcionalidad física de los arrecifes de coral en el Pacífico mexicano (Bahía de Los Ángeles, Bahía de La Paz, Bahía de Banderas y Bahías de Huatulco

Physical functionality of coral reefs in the mexican Pacific (Bahía de Los Ángeles, Bahía de La Paz, Bahía de Banderas y Bahías de Huatulco)

CLAUDIA REBECA NAVARRETE TORICES (2023, [Tesis de maestría])

Los corales son la base en la estructura y funcionamiento de los arrecifes. Sin embargo, en las últimas décadas, estos ecosistemas han sufrido un deterioro debido a presiones naturales, antrópicas y factores de gran escala como el cambio climático. En general, la cobertura de corales ha disminuido y aunque en algunos casos se ha observado su recuperación, la caracterización de la funcionalidad de la estructura física de los sistemas ha sido escasamente explorada. El presente trabajo evalúa la funcionalidad física de los arrecifes de coral en cuatro áreas a lo largo del Pacífico mexicano, empleando el Índice Funcional Arrecifal (IFA). El IFA considera la tasa de calcificación, la complejidad estructural y la abundancia de las especies de coral de en cada sitio; los valores que el índice puede adquirir varían de cero a uno, son valores cercanos a cero refieren a un arrecife con baja funcionalidad, mientras que los valores cercanos a uno indican un arrecife con alta funcionalidad. La cobertura coralina promedio de las cuatro áreas fue 35.62 ± 15.01%, siendo Bahías de Huatulco (BH) quien presentó la mayor cobertura coralina con 55.61 ± 21.94 %, mientras que Bahía de Los Ángeles (BLA) tuvo la menor cobertura coralina (17.16 ± 0.08 %). El IFA promedio de las áreas fue de 0.54 ± 0.12, y con base en el indicador, BH tuvo una mayor funcionalidad con un IFA de 0.68 ± 0.09, mientras que BLA tuvo una menor funcionalidad (0.34 ± 0.08). Los corales del género Pocillopora fueron los que mayor IFA aportaron en la mayoría de los sitios excepto en BLA que es representada por Porites panamensis. El coral con mayor coeficiente funcional (CF) fue Pocillopora grandis con 0.81, perteneciente a Bahía de Banderas (BB) y por ende fue el coral que mayor contribuyó al IFA en el área. El valor del IFA de 0.68 a lo largo del Pacífico mexicano, nos indica que tiene una alta complejidad estructural, debido a la forma de los corales Pocillopora que son clave para la permanencia de los arrecifes del área.

Corals are the basis for the structure and functioning of reefs. However, in recent decades, these ecosystems have suffered deterioration due to natural and anthropogenic pressures and large-scale factors such as climate change. In general, coral cover has decreased and although in some cases their recovery has been observed, the characterization of the functionality of the physical structure of the systems has been barely explored. This study evaluates the physical functionality of coral reefs in four areas along the Mexican Pacific, using the Reef Functional Index (IFA). The IFA considers the calcification rate, structural complexity, and abundance of coral species at each site; The values that the index can acquire vary from zero to one, values close to zero refer to a reef with low functionality, while values close to one indicate a reef with high functionality. The average coral cover of the four areas was 35.62 ± 15.01%, with Bahías de Huatulco (BH) having the highest coral cover with 55.61 ± 21.94%, while Bahía de Los Ángeles (BLA) had the lowest coral cover (17.16 ± 0.08%). The average IFA of the areas was 0.54 ± 0.12, and based on the indicator, BH had higher functionality with an IFA of 0.68 ± 0.09, while BLA had lower functionality (0.34 ± 0.08). Corals of the genus Pocillopora were the ones that contributed the highest IFA in most of the sites except in BLA, which is represented by Porites panamensis. The coral with the highest functional coefficient (CF) was Pocillopora grandis with 0.81, belonging to Bahía de Banderas (BB) and therefore was the coral that contributed the greatest to the IFA in the area. The IFA value of 0.68 along the Mexican Pacific indicates that it has a high structural complexity, due to the shape of the Pocillopora corals that are key to the permanence of the reefs in the area.

Corales, Pocillopora, Índice de función arrecifal, Pacífico mexicano Corals, Pocillopora, mexican Pacific, Reef Functional Index BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA OTRAS ESPECIALIDADES DE LA BIOLOGÍA OTRAS OTRAS

Indicadores de estrés y desempeño biológico de juveniles de lobina rayada (Morone saxatilis) en agua marina: efecto de la densidad de cultivo y color del tanque

Stress indicators and biological performance of striped bass (Morone saxatilis) juvenile in seawater: effect stock density and tank color

DENISE ENCARNACION MAYORAL NORIEGA (2023, [Tesis de maestría])

Existen factores ambientales de naturaleza física, química o biológica que afectan directamente la alimentación de los peces. Por ejemplo, las altas densidades de cultivo pueden generar estrés en los organismos, resultando en la merma del consumo de alimento y por ende su crecimiento. Sin embargo, algunas especies toleran altas densidades formando un grupo o cardumen que les confiere un mejor desempeño. Otro factor que afecta el comportamiento de algunas especies es la coloración de los tanques de cultivo; demostrando la necesidad de utilizar tanques con un entorno físico adecuado para la especie a cultivar. Actualmente, M. saxatilis se produce en tanques en laboratorio y se engorda en jaulas marinas en Baja California; así que existe un gran interés por mejorar su crecimiento y eficiencia alimenticia. Por ello, el objetivo de esta investigación fue evaluar tres densidades de cultivo (alta: 6.2 kg·m-3, media: 3.1 kg·m-3 y baja: 1.5 kg·m-3) y dos colores de tanque (azul celeste y negro) en el crecimiento, supervivencia, utilización del alimento, índices corporales y concentración de cortisol y glucosa de juveniles de lobina rayada en agua marina para su mantenimiento en laboratorio durante nueve semanas. Los resultados demostraron que los organismos obtuvieron el mayor crecimiento en peso en la densidad media, indistintamente del color del tanque. Asimismo, la densidad afectó significativamente los índices hepatosomático y liposomático, ya que disminuyeron conforme aumentó la densidad. El color del tanque influyó de manera importante en el consumo de alimento (azules: 37.4 ± 1.9 g·pez-1; negros: 35.9 ± 2.0 g·pez-1). La interacción de los factores afectó la TCE, TCA y TEP. Las concentraciones de cortisol (81.8 ± 22.5 ng·ml-1) y glucosa (83.2 ± 11.4 mg·100 ml-1) fueron similares en todos los tratamientos y relativamente bajas para la especie. En conclusión, se logró elucidar bajo qué condiciones de cultivo en laboratorio los organismos lograron superar los factores de estrés sin comprometer su crecimiento y supervivencia, reflejándose en un mejor desempeño biológico. Se recomienda utilizar tanques azules o negros con densidades iniciales de 4.2 kg·m-3 o 233 peces·m-3 para el cultivo de juveniles de M. saxatilis en agua salada bajo condiciones de laboratorio.

Environmental factors of a physical, chemical or biological nature such as high stocking densities can directly affect fish feeding and generate stress in organisms, resulting in a decrease in food intake and therefore growth. However, some species tolerate high densities, forming a group or shoal resulting in better overall performance. Another factor that influences the behavior of some species is the color of the culture tank; warranting the need to use tanks with a physical environment suitable for the species to be cultivated. Currently, striped bass are produced in tank-based hatcheries to be socked in sea cages for growout in Baja California. Thus, there is interest in improving their growth rate and feed efficiency under laboratory conditions. Therefore, the objective of this research was to evaluate the effect of three stocking densities (high: 6.2 kg m-3, medium: 3.1 kg m-3 and low: 1.5 kg m-3) and two tank colors (light blue and black) on the biological performance (growth, survival, food utilization), somatic indices and fish stress using the concentration of cortisol and glucose in blood serum as response variables of juvenile striped bass cultured in seawater for nine weeks. The results showed that the organisms had greater growth in terms of final weight when they were cultured at the medium stocking density, regardless of tank color. Likewise, density had a significant effect on hepatosomatic and liposomatic indices, with a tendency to decrease as density increased. The color of the tank significantly influenced the food consumption (blues: 37.4 ± 1.9 g·fish-1; blacks: 35.9 ± 2.0 g·fish-1). The interaction of the factors influenced TCE, TCA and TEP. The concentrations of cortisol (81.8 ± 22.5 ng·ml-1) and glucose (83.2 ± 11.4 mg·100 ml-1) were similar in all treatments indicating low fish stress. In conclusion, it was possible to elucidate under which laboratory culture conditions the organisms were able to overcome the stress factors without compromising their growth and survival; reflected in better biological performance. A stocking density of 4.2 kg m-3 o 233 fish·m-3 for M. saxatilis juvenile reared in saltwater under laboratory culture conditions is recommended.

lobina rayada, densidad cultivo, color tanque, estrés, crecimiento striped bass, stocking density, tank color, stress, growth CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS PECES Y FAUNA SILVESTRE PISCICULTURA PISCICULTURA

Climate change and the northern elephant seal (Mirounga angustirostris) population in Baja California, Mexico

M. Concepción García-Aguilar (2018, [Artículo])

The Earth0s climate is warming, especially in the mid- and high latitudes of the Northern Hemisphere. The northern elephant seal (Mirounga angustirostris) breeds and haul-outs on islands and the mainland of Baja California, Mexico, and California, U.S.A. At the beginning of the 21st century, numbers of elephant seals in California are increasing, but the status of Baja California populations is unknown, and some data suggest they may be decreasing. We hypothesize that the elephant seal population of Baja California is experiencing a decline because the animals are not migrating as far south due to warming sea and air temperatures. Here we assessed population trends of the Baja California population, and climate change in the region. The numbers of northern elephant seals in Baja California colonies have been decreasing since the 1990s, and both the surface waters off Baja California and the local air temperatures have warmed during the last three decades. We propose that declining population sizes may be attributable to decreased migration towards the southern portions of the range in response to the observed temperature increases. Further research is needed to confirm our hypothesis; however, if true, it would imply that elephant seal colonies of Baja California and California are not demographically isolated which would pose challenges to environmental and management policies between Mexico and the United States. © 2018 García-Aguilar et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

air temperature, article, Baja California, climate change, human, Mirounga angustirostris, nonhuman, population size, warming, animal, ecosystem, environmental protection, Mexico, Phocidae, population density, population migration, temperature, Anima CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Maintenance of Coastal Surface Blooms by Surface Temperature Stratification and Wind Drift

MARY CARMEN RUIZ DE LA TORRE (2013, [Artículo])

Algae blooms are an increasingly recurrent phenomenon of potentially socio-economic impact in coastal waters globally and in the coastal upwelling region off northern Baja California, Mexico. In coastal upwelling areas the diurnal wind pattern is directed towards the coast during the day. We regularly found positive Near Surface Temperature Stratification (NSTS), the resulting density stratification is expected to reduce the frictional coupling of the surface layer from deeper waters and allow for its more efficient wind transport. We propose that the net transport of the top layer of approximately 2.7 kilometers per day towards the coast helps maintain surface blooms of slow growing dinoflagellate such as Lingulodinium polyedrum. We measured: near surface stratification with a free-rising CTD profiler, trajectories of drifter buoys with attached thermographs, wind speed and direction, velocity profiles via an Acoustic Doppler Current Profiler, Chlorophyll and cell concentration from water samples and vertical migration using sediment traps. The ADCP and drifter data agree and show noticeable current shear within the first meters of the surface where temperature stratification and high cell densities of L. polyedrum were found during the day. Drifters with 1m depth drogue moved towards the shore, whereas drifters at 3 and 5 m depth showed trajectories parallel or away from shore. A small part of the surface population migrated down to the sea floor during night thus reducing horizontal dispersion. The persistent transport of the surface bloom population towards shore should help maintain the bloom in favorable environmental conditions with high nutrients, but also increasing the potential socioeconomic impact of the blooms. The coast wise transport is not limited to blooms but includes all dissolved and particulate constituents in surface waters. © 2013 Ruiz-de la Torre et al.

chlorophyll, algal bloom, article, cell count, cell density, coastal waters, controlled study, dinoflagellate, Lingulodinium polyedrum, meteorological phenomena, Mexico, near surface temperature stratification, nonhuman, nutrient concentration, popul CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA