Genetic Variation of Landraces of Common Bean Varying for Seed Coat Glossiness and Disease Resistance: Valuable Resources for Conservation and Breeding

In this chapter, we outline the significance of landraces of common bean (Phaseolus vulgaris L.) for unraveling novel morphological, biochemical and genetic variation that could be integrated to breeding programs, related to seed coat color and glossiness and disease resistance. Moreover, we emphasize how important the conservation of such genetic resources is in small-farming areas, the prevailing system for bean cultivation. A particular Brazilian landrace referred as Serro Azul by local farmers is highlighted to show new evidences of the genetic control of seed glossiness in common bean and how it implicates in the seed protection against diseases and insects. Moreover, new findings presented here give insights into a remarkable anthracnose resistance of one of the variants of Serro Azul, which also presents seed coat glossiness. The potential benefits for human health after consuming beans with glossy seed coat are also discussed. This is one among the various landraces that need better understanding for strengthening the knowledge of the genetic diversity of common bean. Such knowledge is important for conducting conservation actions and performing new crosses for providing genetic materials with desirable combinations for farmers, breeders and consumers

Landscape Genetics: From Classic Molecular Markers to Genomics

Landscape genetics combines population genetics and landscape ecology to understand processes that shape the distribution and organization of human, animal, or plant populations. This field of genetics emerged from the availability of several studies with classical molecular markers, such as isozymes, RAPD, AFLP, and microsatellites. Population genetic studies enabled the detection of population structure with those markers, but a more comprehensive analysis of natural populations was only possible with the development of statistical methods that combined both molecular data and environmental variables. Ultimately, the rapid development of sequencing technologies allowed studies at the genomic level, augmenting the resolution of association with environment factors. This chapter outlines basic concepts in landscape genetics, the main statistical methods used so far, and the perspectives of this field of knowledge into strategies for conservation of natural populations of plant and animal species. Moreover, we briefly describe the application of the field to understand historical human migration processes as well as how some diseases are spread throughout the world

Exploration of the Yield Potential of Mesoamerican Wild Common Beans From Contrasting Eco-Geographic Regions by Nested Recombinant Inbred Populations

Genetic analyses and utilization of wild genetic variation for crop improvement in common bean (Phaseolus vulgaris L.) have been hampered by yield evaluation difficulties, identification of advantageous variation, and linkage drag. The lack of adaptation to cultivation conditions and the existence of highly structured populations make association mapping of diversity panels not optimal. Joint linkage mapping of nested populations avoids the later constraint, while populations crossed with a common domesticated parent allow the evaluation of wild variation within a more adapted background. Three domesticated by wild backcrossed-inbred-line populations (BC1S4) were developed using three wild accessions representing the full range of rainfall of the Mesoamerican wild bean distribution crossed to the elite drought tolerant domesticated parent SEA 5. These populations were evaluated under field conditions in three environments, two fully irrigated trials in two seasons and a simulated terminal drought in the second season. The goal was to test if these populations responded differently to drought stress and contained progenies with higher yield than SEA 5, not only under drought but also under water-watered conditions. Results revealed that the two populations derived from wild parents of the lower rainfall regions produced lines with higher yield compared to the domesticated parent in the three environments, i.e., both in the drought-stressed environment and in the well-watered treatments. Several progeny lines produced yields, which on average over the three environments were 20% higher than the SEA 5 yield. Twenty QTLs for yield were identified in 13 unique regions on eight of the 11 chromosomes of common bean. Five of these regions showed at least one wild allele that increased yield over the domesticated parent. The variation explained by these QTLs ranged from 0.6 to 5.4% of the total variation and the additive effects ranged from 164 to 277 kg ha1, with evidence suggesting allelic series for some QTLs. Our results underscore the potential of wild variation, especially from droughtstressed regions, for bean crop improvement as well the identification of regions for efficient marker-assisted introgression

Functional Genomics of Biotic and Abiotic Stresses in Phaseolus vulgaris

Common bean is the most important legume for human consumption in the world, being a crop extremely diverse in cultivation methods, uses, range of environments in which it is adapted, morphological variety, among others. Besides its high demand and production, this crop is threatened by a series of biotic and abiotic adversities during its life cycle, which leads to losses in yield of up to 100%. In this chapter, we explored the main constraints that affect common bean and the ways this plant reaches tolerance or resistance to them, highlighting studies at the molecular level that enabled to understand the mechanisms by which common bean perceives, responds, and adapts to a stress condition. Special focus has been given to the most recent findings in the understanding of the mechanisms underlying drought tolerance and anthracnose resistance. Thereby, we reviewed some genetic and functional genomic studies concerning the genes and pathways involved in each case. Furthermore, we outline important genetic resources of Phaseolus vulgaris, as well as the technologies and methods used toward these findings

Photosynthetic light response curves in Eucalyptus benthamii and Eucalyptus dunnii clones

The photosynthetic light-response curve reflects the instantaneous response of the net photosynthetic rate to different gradients of photosynthetically active radiation. Genetic materials can respond differently to light and consequently alter productivity. Thus, this work aimed to compare clones of Eucalyptus benthamii and Eucalyptus dunnii by checking the CO2 assimilation rate due to the increase in photosynthetically active radiation. The evaluations were carried out in mini-stumps implanted in a clonal mini-garden system. The CO2 assimilation rate curves were determined with the aid of a portable photosynthesis meter. The curves of CO2 assimilation rate (A) in response to the increase in photosynthetically active radiation (PAR) were evaluated at values of 1500, 1000, 700, 450, 250, 120, 50 and 0 μmol m-2 s -1 for clones of E. benthamii and E. dunnii. The three Eucalyptus clones evaluated showed a similar behavior of the A/PAR curve, showing a high demand for photosynthetically active radiation. In general, the three clones were very similar in terms of CO2 assimilation rate due to the increase in photosynthetically active radiation

Diversidade genética de duas espécies de Eucalyptus usando marcadores ISSR

Here, we deployed a genetic diversity analysis using ISSR markers in two Eucalyptus species, as a fundamental step toward breeding strategies. The selected species were Eucalyptus urophylla and Eucalyptus microcorys, both with economic potential in forestry. The studied individuals belong to a species and the provenance test that was installed in 1974 and until now remains exempt from silvicultural treatments. Nine universal ISSR primers were used in the analyses. Intra and interspecific variation through the polymorphism percentage, polymorphism information content (PIC) and Euclidean distances among individuals were computed. The Euclidean distance among the individuals was used to perform a principal coordinate analysis (PCoA), as well as the permutation analysis of multivariate dispersion (PermDisp), followed by the Tukey’s test. A high percentage of polymorphic bands were detected, with 57.14% for Eucalyptus microcorys and 80.95% for Eucalyptus urophylla. PIC values were higher than 0.5 for four primers (UBC827, UBC835, UBC841, and UBC842). The genetic variability was significantly higher within the Eucalyptus urophylla population than in Eucalyptus microcorys, which may be associated with the greater ability of Eucalyptus urophylla to naturally hybridize, therefore, enabling the introduction of new alleles to their populations. Visando fornecer informações que sirvam de base para estudos de melhoramento genético de Eucalyptus foi realizada a análise da diversidade genética usando marcadores ISSR. As espécies estudadas foram Eucalyptus urophylla e Eucalyptus microcorys, ambas com potencial econômico florestal. Os indivíduos estudados pertencem a um teste de espécies e procedências instalado no ano de 1974 e permanecem isentos de tratos silviculturais. Para as análises foram utilizados nove primers ISSR universais. A partir dos resultados avaliou-se a existência de variação intra e interespecífica por meio da porcentagem de polimorfismo, conteúdo de informação polimórfica (PIC) e distância Euclidiana entre indivíduos. A fim de analisar a distância Euclidiana entre os indivíduos foram feitas a análise de coordenadas principais (PCoA) e análise permutacional de dispersão multivariada (PermDisp) seguida pelo teste de Tukey. Observouse elevada porcentagem de polimorfismo (57,14% para Eucalyptus microcorys e 80,95% para Eucalyptus urophylla). Considerando todos os grupos avaliados, os valores de PIC foram superiores a 0,5 para quatro primers (UBC827, UBC835, UBC841). A variabilidade interna foi significativamente maior na população de Eucalyptus urophylla em relação à Eucalyptus microcorys, o que pode estar associado à maior capacidade do Eucalyptus urophylla em hibridizar naturalmente

Diversidade genética de duas espécies de Eucalyptus usando marcadores ISSR

Here, we deployed a genetic diversity analysis using ISSR markers in two Eucalyptus species, as a fundamental step toward breeding strategies. The selected species were Eucalyptus urophylla and Eucalyptus microcorys, both with economic potential in forestry. The studied individuals belong to a species and the provenance test that was installed in 1974 and until now remains exempt from silvicultural treatments. Nine universal ISSR primers were used in the analyses. Intra and interspecific variation through the polymorphism percentage, polymorphism information content (PIC) and Euclidean distances among individuals were computed. The Euclidean distance among the individuals was used to perform a principal coordinate analysis (PCoA), as well as the permutation analysis of multivariate dispersion (PermDisp), followed by the Tukey’s test. A high percentage of polymorphic bands were detected, with 57.14% for Eucalyptus microcorys and 80.95% for Eucalyptus urophylla. PIC values were higher than 0.5 for four primers (UBC827, UBC835, UBC841, and UBC842). The genetic variability was significantly higher within the Eucalyptus urophylla population than in Eucalyptus microcorys, which may be associated with the greater ability of Eucalyptus urophylla to naturally hybridize, therefore, enabling the introduction of new alleles to their populations.Visando fornecer informações que sirvam de base para estudos de melhoramento genético de Eucalyptus foi realizada a análise da diversidade genética usando marcadores ISSR. As espécies estudadas foram Eucalyptus urophylla e Eucalyptus microcorys, ambas com potencial econômico florestal. Os indivíduos estudados pertencem a um teste de espécies e procedências instalado no ano de 1974 e permanecem isentos de tratos silviculturais. Para as análises foram utilizados nove primers ISSR universais. A partir dos resultados avaliou-se a existência de variação intra e interespecífica por meio da porcentagem de polimorfismo, conteúdo de informação polimórfica (PIC) e distância Euclidiana entre indivíduos. A fim de analisar a distância Euclidiana entre os indivíduos foram feitas a análise de coordenadas principais (PCoA) e análise permutacional de dispersão multivariada (PermDisp) seguida pelo teste de Tukey. Observouse elevada porcentagem de polimorfismo (57,14% para Eucalyptus microcorys e 80,95% para Eucalyptus urophylla). Considerando todos os grupos avaliados, os valores de PIC foram superiores a 0,5 para quatro primers (UBC827, UBC835, UBC841). A variabilidade interna foi significativamente maior na população de Eucalyptus urophylla em relação à Eucalyptus microcorys, o que pode estar associado à maior capacidade do Eucalyptus urophylla em hibridizar naturalmente

Evaluation of total protein, peroxidase, and nutrients measured by pXRF for the determination of tissue rejuvenation / reinvigoration of Eucalyptus microcorys

Ontogenetic aging of tissues and the gradual decrease of adventitious rooting are known challenges for the clonal propagation of woody species, hampering clonal forestry programs. This study examined possible signatures of tissue rejuvenation/reinvigoration in different propagated materials of Eucalyptus microcorys by analyzing the total protein profile, peroxidase activity, macro-and micronutrient contents, and adventitious rooting of mini cuttings. The analyses were performed on E. microcorys shoots which were successfully obtained by seminal and grafting propagation, micropropagation with epicormic shoots, and indirect organogenesis. Among four mature trees used in the propagation, tissues from the one with the best propagation results were investigated for signs of tissue rejuvenation and/or reinvigoration. Five individuals from each technique were randomly selected and transferred to a semi-hydroponic “channel” system. After four weeks in the seedbed, the total protein, peroxidase activity, nutrient content and rooting of the minicuttings were evaluated. SDS-PAGE enabled the differentiation of leaf samples obtained by grafting from the other propagation techniques, as revealed by two distinct bands. Materials obtained by micropropagation with epicormic shoots showed the highest peroxidase activity, while those obtained by seminal propagation and from the selected mature tree showed the lowest peroxidase activity. A portable X-ray fluorescence spectroscope (pXRF) identified adequate nutrient content in most of the nutrients tested in materials obtained by seminal and grafting propagation, and by indirect organogenesis. The analysis of adventitious rooting showed that the highest rooting percentage was observed in mini cuttings from seminal propagation (75%) followed by indirect organogenesis (35%). Based on principal component analysis, it was concluded that rooting of mini cuttings from both seminal propagation and indirect organogenesis organogenesis was associated with phosphorous, sulphur, and potassium contents, which suggests a higher level of tissue rejuvenation/reinvigoration in these propagated plants. Further studies are recommended to search for other methods that present similarities with the responses to adventitious rooting in forest species and thus optimize the rescue and propagation of plants with distinct ontogenetic stages