Beans ( Phaseolus spp.) - model food legumes

Globally, 800 million people are malnourished. Heavily subsidised farmers in rich countries produce sufficient surplus food to feed the hungry, but not at a price the poor can afford. Even donating the rich world's surplus to the poor would not solve the problem. Most poor people earn their living from agriculture, so a deluge of free food would destroy their livelihoods. Thus, the only answer to world hunger is to safeguard and improve the productivity of farmers in poor countries. Diets of subsistence level farmers in Africa and Latin America often contain sufficient carbohydrates (through cassava, corn/maize, rice, wheat, etc.), but are poor in proteins. Dietary proteins can take the form of scarce animal products (eggs, milk, meat, etc.), but are usually derived from legumes (plants of the bean and pea family). Legumes are vital in agriculture as they form associations with bacteria that 'sfix-nitrogen' from the air. Effectively this amounts to internal fertilisation and is the main reason that legumes are richer in proteins than all other plants. Thousands of legume species exist but more common beans (Phaseolus vulgaris L.) are eaten than any other. In some countries such as Mexico and Brazil, beans are the primary source of protein in human diets. As half the grain legumes consumed worldwide are common beans, they represent the species of choice for the study of grain legume nutrition. Unfortunately, the yields of common beans are low even by the standards of legumes, and the quality of their seed proteins is sub-optimal. Most probably this results from millennia of selection for stable rather than high yield, and as such, is a problem that can be redressed by modern genetic techniques. We have formed an international consortium called Phaseomics' to establish the necessary framework of knowledge and materials that will result in disease-resistant, stress-tolerant, high-quality protein and high-yielding beans. Phaseomics will be instrumental in improving living conditions in deprived regions of Africa and the Americas. It will contribute to social equity and sustainable development and enhance inter- and intra-cultural understanding, knowledge and relationships. A major goal of Phaseomics is to generate new common bean varieties that are not only suitable for but also desired by the local farmer and consumer communities. Therefore, the socio-economic dimension of improved bean production and the analysis of factors influencing the acceptance of novel varieties will be an integral part of the proposed research (see Figure 1). Here, we give an overview of the economic and nutritional importance of common beans as a food crop. Priorities and targets of current breeding programmes are outlined, along with ongoing efforts in genomics. Recommendations for an international coordinated effort to join knowledge, facilities and expertise in a variety of scientific undertakings that will contribute to the overall goal of better beans are given. To be rapid and effective, plant breeding programmes (i.e., those that involve crossing two different 'sparents') rely heavily on molecular 'smarkers'. These genetic landmarks are used to positio

Translational Genomics for Crop Breeding: Biotic Stress, Volume 1

Genomic Applications for Crop Breeding: Biotic Stress is the first of two volumes looking at the latest advances in genomic applications to crop breeding. This volume focuses on genomic-assisted advances for improving economically important crops against biotic stressors, such as viruses, fungi, nematodes, and bacteria. Looking at key advances in crops such as rice, barley, wheat, and potato amongst others, Genomic Applications for Crop Breeding: Biotic Stress will be an essential reference for crop scientists, geneticists, breeders, industry personnel and advanced students in the field

Plant Growth Promoting Actinobacteria : A New Avenue for Enhancing the Productivity and Soil Fertility of Grain Legumes

Global yields of legumes have been relatively stagnant for the last five decades, despite the adoption of conventional and molecular breeding approaches. The use of plant growth-promoting (PGP) bacteria for improving agricultural production, soil and plant health has become one of the most attractive strategies for developing sustainable agriculture. Actinomycetes are bacteria that play an important role in PGP and plant protection, produce secondary metabolites of commercial interest, and their use is well documented in wheat, rice, beans, chickpeas and peas. In order to promote legumes, the general assembly of the UN recently declared 2016 the “International Year of Pulses.” In view of this development, this book illustrates how PGP actinomycetes can improve grain yield and soil fertility, improve control of insect pests and phytopathogens, and enhance host-plant resistance. It also addresses special topics of current interest, e.g. the role of PGP actinomycetes in the biofortification of legume seeds and bioremediation of heavy metals

Plant Virus Emergence

This compilation of articles elaborates on plant virus diseases that are among the most recent epidemiological concerns. The chapters explore several paradigms in plant virus epidemiology, outbreaks, epidemics, and pandemics paralleling zoonotic viruses and that can be consequential to global food security. There is evidence that the local, regional, national, and global trade of agricultural products has aided the global dispersal of plant virus diseases. Expanding farmlands into pristine natural areas has created opportunities for viruses in native landscapes to invade crops, while the movement of food and food products disseminates viruses, creating epidemics or pandemics. Moreover, plant virus outbreaks not only directly impact food supply, but also incidentally affect human health

Variabilidad poblacional en encina (quercus ilex subsp. Ballota (Desf.) Samp.): morfometría, espectroscopía de infrarrojo cercano y proteómica

La encina (Quercus ilex subsp. ballota [Desf.] Samp.) es una especie dominante en los sistemas silvopastorales mediterráneos, de entre los cuales forma parte la dehesa. Este sistema de explotación es el más característico y tradicional de los recursos naturales de la Península Ibérica donde los usos agrícola, ganadero y forestal se integran de una forma muy compleja. En España, las poblaciones de encinas cubren una superficie aproximada de 2 039 563 de ha. La importancia económica de esta especie se estima en más de 120 millones de euros en cuanto a la producción de bellota, ya que es un componente alimenticio muy importante de la dieta del cerdo ibérico. Actualmente la encina tiene un gran interés en los programas de conservación forestal, debido a que los encinares están sufriendo un continuo deterioro y desaparición como consecuencia de prácticas agrícolas desproporcionadas y por factores bióticos (enfermedades) y abióticos (estrés por sequía). Por tanto, el declive de los valores naturales de la dehesa puede ser una situación dramática en un futuro. Debido a estas razones, se está desarrollando una línea de investigación enfocada a estudiar, por un lado, la variabilidad genética intra e inter poblacional y, por otro lado, la identificación de rodales e individuos selectos con respuesta diferencial a estreses bióticos y abióticos en la encina, con el fin de identificar marcadores moleculares adecuados de calidad, productividad y tolerancias a estreses que afectan a dicha especie. Siguiendo con esta línea de estudio, en el presente trabajo de investigación se abordaron los siguientes objetivos: El estudio de la variabilidad poblacional de la encina basada en la morfometría y composición química de la bellota. El estudio de la variabilidad poblacional de la encina a través del análisis del perfil proteico de las bellotas. El estudio del proteoma del polen de encina. En esta tesis hemos realizado un estudio de la variabilidad poblacional de la encina basada en la morfometría y composición química de bellota, a partir de 13 poblaciones de la región de Andalucía. La morfometría de la bellota mostró diferencias significativas entre las poblaciones analizadas, presentando los valores más elevados en peso, longitud y diámetro aquellas localizadas en el norte (TJA, GSE, CTH, CHU, APS, y PCO), mientras que las poblaciones del sur (RMA, SAA, CCO, BCA, y SCA) presentaron los valores más bajos. La composición química de la bellota se analizó mediante la técnica de espectroscopía de infrarrojo cercano (NIRS) y también reveló diferencias significativas entre las poblaciones. El análisis de agrupamientos teniendo en cuenta los datos morfométricos y de composición química mostró dos agrupamientos de poblaciones bien diferenciados correspondientes a las poblaciones localizadas en el norte y aquellas localizadas en el sur de la región. Así, las poblaciones del norte (CTH, TJA, SCA, CHU, PCO, GSE, y APS) tuvieron una tendencia a presentar valores mas altos en peso (5,4 g vs. 3,2 g); longitud (37,2 mm vs. 28,7 mm); diámetro (16,1 mm vs. 13,7 mm); cenizas (1,8% vs. 1,5%); proteínas (4,8% vs. 4,3%); grasas (12,5% vs. 9,9%); y ácido oleico (66,9 vs. 66,4%). Por el contrario, las poblaciones del sur (SSA, VJA, CCO, BCA, RG, and RMA) mostraron una tendencia a presentar valores más bajos en azúcares (10,2% vs. 11,2%); contenido calórico (20 076,7 kJ/kg vs. 20 149,2 kJ/kg); y en los ácidos grasos palmítico (16,1% vs. 16,3%) y linoleico (13,0% vs. 13,1%). El siguiente objetivo fue el estudio de la variabilidad poblacional en la encina, mediante un análisis proteómico basado en electroforesis en gel (1-DE y 2-DE) de las proteínas de la bellota. Este estudio se llevo a cabo en diez de las trece poblaciones analizadas a través de datos morfométricos y bromatológicos. Las proteínas de bellota fueron extraídas usando el protocolo de precipitación basado en TCA-acetona. Las proteínas se separaron mediante SDS-PAGE y 2-DE, las bandas o manchas proteicas fueron cuantificadas, y sujetas a un análisis estadístico (ANOVA, SOM y de agrupamientos). Las bandas o manchas proteicas variables entre las poblaciones fueron identificadas a través de MALDI-TOF/TOF y nLC-MS/MS. El rendimiento de las proteínas varió entre las poblaciones de 2,9 a 5,9 mg/g de peso seco. Un total de 23 bandas fueron separadas por SDS-PAGE en un rango de Mr de 3-35 kDa, 8 de las cuales mostraron diferencias cualitativas y 12 diferencias cuantitativas entre las diferentes poblaciones analizadas. El análisis de los datos permitió agrupar a las poblaciones de acuerdo a las condiciones geográficas (norte y sur) y climáticas (xéricas, mésicas e intermedias). Las cuatro poblaciones geográficamente más alejadas y con los perfiles de proteína 1-DE más diferentes fueron analizadas mediante 2-DE, obteniéndose 56 manchas proteicas significativamente variables, las cuales fueron propuestas como marcadores moleculares de variabilidad entre las distintas poblaciones. Las proteínas identificadas fueron clasificadas en dos categorías principales: proteínas de almacenamiento y de respuesta a defensa/estrés. Igualmente hemos estudiado el proteoma del polen de encina, con el objetivo de estudiar la variabilidad poblacional en la región de Andalucía. En este estudio se realizó el análisis proteómico del polen de cuatro poblaciones, mediante dos aproximaciones metodológicas: técnicas basadas en gel (1-DE y 2-DE en combinación de MALDITOF/ TOF) y el análisis masivo de proteínas (nLC-LTQ Orbitrap MS). La comparación del análisis de los perfiles proteicos de las cuatro poblaciones reveló diferencias cualitativas y cuantitativas (18 bandas y 16 manchas proteicas), las cuales podrían ser también posibles marcadores moleculares de variabilidad en polen, junto con las proteínas variables en el análisis proteómico de la bellota. El análisis multivariante de los datos normalizados, ya sea de las bandas o de las manchas proteicas, claramente mostró diferentes agrupamientos entre las poblaciones estudiadas, y los resultados fueron relacionados con la localización de las poblaciones. Un total de 100 manchas proteicas, de las 402 observadas en geles 2-DE, fueron identificadas por MALDI-TOF/TOF. De forma complementaria, se realizó un análisis masivo de proteínas usando nLC-LTQ Orbitrap MS. La mayoría de las proteínas identificadas estuvieron relacionadas con el metabolismo y la respuesta a defensa/estrés. Dicho análisis permitió también la identificación de proteínas relacionadas con la división y pared celular, transporte y traducción complementando a las proteínas identificadas por MALDI-TOF/TOF.Holm oak (Quercus ilex subsp. ballota [Desf.] Samp.) is the dominant tree species in natural forest ecosystems over large areas of the Western Mediterranean Basin. In Spain, it is widely used for conservation and forestry practices, covering an approximate surface of 2,039,563 ha, with estimated values of over 120 million of Euros in fruit acorn production per year. The Holm oak acorns are a major component in the feeding systems of many Mediterranean wild and livestock species. Moreover, it is also the basic feed ingredient for domestically bred high quality meat pigs. Nowadays, forest restoration and reforestation are high priority objectives, and Holm oak is acquiring more interest for Mediterranean forestry. However, in the “dehesas” of Mediterranean areas of Western and Southwestern Spain, where grasslands reach between 70 and 90% cover, tree regeneration is very low because of an inappropriate livestock management, together with a high acorn predation by a variety of vertebrate herbivores (i.e., cattle, deer, wild boar, mice and rabbits), water limitations, and effect of the decline syndrome. Those factors are considered the major limitations for the seedling establishment, and subsequent growth of tree stands, and plant distribution Holm oak ecosystems. Criteria for tree selection for restoration programs are frequently the production of big and abundant acorns per individual tree. However, in order to create systems which are able to self-regenerate, it is important to take into account the seedling traits related to abiotic (drought) and biotic (pest and diseases) tolerance. Our group is carrying out a functional genomics approach - transcriptomics and proteomics- to characterize variability among Holm oak populations and its response to biotic and abiotic stresses. Within this general project, the objectives pursued in this PhD thesis were: Study of Holm oak population variability based on the morphometry and chemical composition of the acorn. Study of variability in Holm oak through the acorn protein profile analysis. Study of Holm oak pollen by proteomic analysis. We have studied in this PhD thesis the natural variability in Holm oak by analyzing acorn morphometry and chemical composition in 13 populations from the Andalusia region (southern Spain). The acorn morphometry showed statistic significant differences between the populations with a higher acorn weight, length, and diameter in the Northern provenances (TJA, GSE, CTH, CHU, APS, and PCO), while the Southern provenances (RMA, SAA, CCO, BCA, and SCA) showed the lower value that even decreased with the altitude. The acorn chemical composition was analyzed by near-infrared spectrometry (NIRS), and also showed statistic significant differences between populations. Morphometry and chemical composition data were subjected to cluster analysis, and two major clusters were detected. The cluster analysis showed that Northern populations (CTH, TJA, SCA, CHU, PCO, GSE, and APS) showed a tendency to present values higher in acorn weight (5.4 g vs. 3.2 g); acorn length (37.2 mm vs. 28.7 mm); acorn diameter (16.1 mm vs. 13.7 mm); ash (1.8% vs. 1.5%); protein (4.8% vs. 4.3%); fat (12.5% vs. 9.9%); and oleic acid (66.9 vs. 66.4%). On the contrary, Southern populations (SSA, VJA, CCO, BCA, RG, and RMA) showed a tendency to present values lowest in sugar (10.2% vs. 11.2%); energy (20,076.7 kJ/kg vs. 20,149.2 kJ/kg); palmitic (16.1% vs. 16.3%) and linoleic acids (13.0% vs. 13.1%). We have also studied the variability in Holm oak, using electrophoresis-based proteomic analysis of acorns. Ten populations distributed throughout the Andalusia region have been surveyed. Acorns were sampled from individual trees and proteins extracted from seed flour by using the TCA-acetone precipitation protocol. Extracts were subjected to SDS-PAGE and 2-DE for protein separation, gel images captured, spot or bands quantified, and subjected to statistical analysis (ANOVA, SOM and clustering). Variable bands or spots among populations were subjected to nLC-MS/MS and MALDI-TOF/TOF respectively for identification. The protein yield of the used protocol varied among populations, and it was in the 2.9-5.9 mg/g dry weight range. A total of 23 bands was resolved by SDS-PAGE in the 3-35 kDa Mr range, with 8 and 12, out of the total, showing respectively qualitative and quantitative statistically significant differences among populations. Data allowed grouping populations, with groups being correlated according to geographical location and climate conditions, to northern and southern, as well as the discrimination of both mesic and xeric groups. Acorn flour extracts from the most distant populations were analyzed by 2-DE, and 56 differential spots were proposed as markers of variability. Identified proteins were classified into two principal categories; storage and stress/defense protein. Additionally, we studied the Holm oak pollen proteome, together with an evaluation of the potentiality that a proteomic approach may have in the provenance variability assessment. Proteins were extracted from pollen of four Holm oak provenances, and they were analyzed by gel-based (1- and 2-DE in combination with MALDI-TOF/TOF) and gelfree (nLC-LTQ Orbitrap MS) approaches. A comparison of 1- and 2-DE protein profiles of the four provenances revealed significant differences, both qualitative and quantitative, in abundance (18 bands and 16 spots, respectively). Multivariate statistical analysis carried out on bands and spots clearly showed distinct associations between provenances, which highlight their geographical origins. A total of 100 spots selected from the 402 spots observed on 2-DE gels were identified by MALDI-TOF/TOF. Moreover, a complementary gel-free shotgun approach was performed by nLC-LTQ Orbitrap MS. The identified proteins were classified according to biological processes, and most proteins in both approaches were related to metabolism and defense/stress processes. The nLC-LTQ Orbitrap MS analysis allowed us the identification of proteins belonging to the cell wall and division, transport and translation categories

Plant Signaling Molecule: Role and Regulation under Stressful Environments

Plant Signaling Molecule: Role and Regulation under Stressful Environments explores tolerance mechanisms mediated by signaling molecules in plants for achieving sustainability under changing environmental conditions. Including a wide range of potential molecules, from primary to secondary metabolites, the book presents the status and future prospects of the role and regulation of signaling molecules at physiological, biochemical, molecular and structural level under abiotic stress tolerance. This book is designed to enhance the mechanistic understanding of signaling molecules and will be an important resource for plant biologists in developing stress tolerant crops to achieve sustainability under changing environmental conditions