Segmental and Tandem Duplications Driving the Recent NBS-LRR Gene Expansion in the Asparagus Genome

Garden asparagus is an important horticultural plant worldwide. It is, however, susceptible to a variety of diseases, which can affect the potential yield, spear quality, and lifespan of production fields. Screening studies have identified resistant germplasm. The genetic resistance is usually complex, and the genes underlying that resistance are still unknown. Most often, disease resistance is determined by resistance genes (R). The most predominant R-genes contain nucleotide binding site and leucine-rich repeat (NBS-LRR) domains. Using bioinformatics and data mining approaches, we identified and characterized 68 NBS predicted proteins encoded by 49 different loci in the asparagus genome. The NBS-encoding genes were grouped into seven distinct classes based on their domain architecture. The NBS genes are unevenly distributed through the genome and nearly 50% of the genes are present in clusters. Chromosome 6 is significantly NBS-enriched and one single cluster hosts 10% of the genes. Phylogenetic analysis points to their diversification into three families during their evolution. Recent duplications are likely to have dominated the NBS expansion with both tandem genes and duplication events across multiple chromosomes. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. The total number of cis-regulatory elements as well as their relative positions within the NBS promoters suggests a complex transcriptional network regulating defense responses. Our study provides a strong groundwork for the isolation of candidate R-genes in garden asparagus

El Paleolítico Medio en el territorio valenciano y la variabilidad tecno-económica de la Cova del Bolomor

En el presente artículo se exponen las principales características de las industrias líticas del Paleolítico Medio en el territorio valenciano. Se hace especial hincapié en la variabilidad tecno-económica observada en la secuencia estratigráfica de la Cova del Bolomor. Con dicho análisis se pretende contribuir al establecimiento de los rasgos evolutivos de las industrias asociadas a los grupos de neandertales. En este sentido, el estudio pone de manifiesto que en estas sociedades se produjo, en los momentos finales, cierto progreso tecnológico, en un contexto arqueológico en el que es difícil precisar si hubo, o no, influencia externa o aculturación por parte de las poblaciones de cromañones en el territorio valenciano.En el present article s'exposen les principals característiques de les indústries lítiques del Paleolític Mitjà en el territori valencià. Es posa especial atenció a la variabilitat tecno-econòmica observada en la seqüència estratigràfica de la Cova del Bolomor. Amb aquesta anàlisi es pretén contribuir a l'establiment dels trets evolutius de les indústries associades als grups de neandertals. En aquest sentit, l'estudi posa de manifest que en aquestes societats es va produir, en els moments finals, un cert progrés tecnològic, en un context arqueològic en el qual és difícil precisar si va haver-hi, o no, influència externa o aculturació per part de les poblacions de cromanyons en el territori valencià.Dans l'article ci-dessous, s'exposent les principales caractéristiques des industries lithiques du Paléolithique Moyen dans le territoire valencien. On veut mettre en relief la variabilité techno-économique observée dans la séquence stratigraphique de la Cova del Bolomor. Avec cette analyse, on cherche à établir les traits évolutifs des industries associées aux groupes néandertaliens. Dans ce sens, l'étude met en relief que ces sociétés ont probablement connu, dans un dernier temps, un certain progrès technologique, dans un contexte archéologique où il est difficile de préciser s'il y a eu ou pas une influence externe ou une acculturation venue des populations cromagnones dans la région de Valence.In this paper main characteristics of the Middle Palaeolithic lithic industries from the territory of Valencia are presented. Particular attention is paid to the techno-economical variability of the archaeological record in Cova del Bolomor. This study aims to discuss the evolutionary features of Neanderthal industries; our analysis shows that there was some technological progress at the end of the Middle Palaeolithic, in an archaeological context in which it is uncertain whether or not there was external influence or acculturation from Cro-Magnon populations in the valencian territory

QTL Analysis of Morpho-Agronomic Traits in Garden Asparagus (Asparagus officinalis L.)

In order to understand the genetic control of quantitative agronomic traits in garden asparagus, we performed a quantitative trait loci (QTL) analysis. A population (n = 167) derived from a cross between a female and male plants was evaluated for morpho-agronomic traits over three years. Interval mapping (IM) and restricted multiple QTL mapping (rMQM) analysis was applied, and 18 QTLs were detected. QTLs were located in two linkage groups (LG): 5 in LG5 and 13 in LG6. The physical position of markers of both groups was mapped onto the reference genome through BLAST analysis. LG5 and LG6 match with chromosome 1 (sex-determining chromosome) and chromosome 5, respectively. Haplotypes of both chromosomes of the heterozygous parent and their progeny were obtained, and a bin map was developed. Bins were used to map the QTLs on the reference genome and to perform the association analysis with the morpho-agronomic traits. Two major and stable QTLs over the years (R2 > 10%) for number of stalk and earliness were mapped in the end of chromosome 1 into a bin that spans 3.25 Mb and includes the sex-determination locus. In chromosome 5, some QTLs were located in the center of chromosome for the year 2016. Branching is tightly regulated by both internal factors (such as plant hormones) and external factors (such as light conditions). QTLs for branching height and earliness were detected in a bin that spans 4.96 Mb. Functional annotation of genes within the two bins revealed candidate genes with potential roles in SA and light signaling and photomorphogenesis pathways that may be involved in branching and/or tillering. This is the first study providing the identification of genomic regions associated with yield-related morpho-agronomic traits in asparagus

An evaluation of management strategies for Atlantic tuna stocks

International agreements for the International Commission for the Conservation of Atlantic Tunas (ICCAT) convention area imply that Atlantic tuna stocks should be managed by strategies based on maximum sustainable yield (MSY); however, there is concern whether this will actually ensure sustainability with sufficiently high probability consistent with the principals of the precautionary approach. Therefore, the performance of MSY management strategies based on current assessment procedures was evaluated using a computer simulation framework. The framework includes the data collection, assessment, prediction, and management processes, as well as the implementation of management regulations. It therefore provides an integrated way to evaluate the relative importance of and the interactions between each component of the system with regard to the overall success of the management strategy. The study elucidates guidelines about assessment and management that are general enough to be applied to all tunas in the Atlantic Ocean. It does so by comparing different hypotheses about management and assessment for three stocks (North Atlantic albacore, Atlantic bigeye and East Atlantic skipjack), which are representative of the variety encountered (i.e. from data rich to poor and tropical to temperate waters) in ICCAT stocks. Management performance was especially sensitive to the carrying capacity of the stock. The type of proxy used for MSY was more important to the success of the procedure than the frequency of assessment or the number of indices used in the assessment. Whilst the procedure was successful at achieving the management objectives for albacore, it was only partially successful for bigeye and was too conservative for skipjack.No disponibl

Characterization and Analysis of Anthocyanin-Related Genes in Wild-Type Blueberry and the Pink-Fruited Mutant Cultivar ‘Pink Lemonade’: New Insights into Anthocyanin Biosynthesis

Blueberries are one of the richest sources of antioxidants, such as anthocyanins, among fruits and vegetables. Anthocyanin mutants, like the pink-fruited cultivar ‘Pink Lemonade’, are valuable resources for investigating anthocyanin biosynthesis in blueberries. In this study, we examined expression of flavonoid pathway genes during fruit development in wild-type, blue-fruited blueberries using quantitative real-time PCR. Expression was also compared between wild-type and the pink-fruited ‘Pink Lemonade’. This revealed significantly lower expression in ‘Pink Lemonade’ than in wild-type of nearly all the structural genes examined suggesting that a transcriptional regulator of the pathway was affected. Hence, we compared expression of three known regulatory genes and found that the gene encoding the transcription factor MYB1 was expressed at a significantly lower level in ‘Pink Lemonade’ than in the wild-type. To validate the capacity of this MYB1 to regulate the transcription of anthocyanin genes in blueberries, a transient expression assay was conducted. Results indicated MYB1 overexpression enhanced anthocyanin production. Comparative sequence analysis between wild-type and mutant MYB1 variants found differences in highly conserved features suggesting a mechanistic explanation for the mutant phenotype. Collectively, the results presented here contribute to a better understanding of mechanisms regulating anthocyanin biosynthesis in Vaccinium

RNA-seq combined with a bulked-segregant analysis identifies candidate genes for the waxy coating on blueberry fruit

The most significant difference between blueberries with a light blue fruit color and black fruit color is the visible layer of an epicuticular waxy coating. This layer functions in disease defense and prevention of water loss. In this study, we constructed a northern-adapted rabbiteye hybrid breeding population, ‘Nocturne’ x T 300, which segregated for fruit color (light blue versus black). We screened this population and selected plants of each extreme phenotype, waxy- coated plants with light blue colored fruit versus non-waxy plants with black colored fruit, then isolated RNA from fruit tissue of each bulk, respectively. We sequenced the transcriptome of each bulk using RNA-seq, which resulted in a total of 167,093,354 reads for both libraries combined. We de novo assembled this data set into 171,678 contigs and used the assembled transcriptome as a reference for differential expression analysis using EdgeR. A total of 515 differentially expressed genes were identified with at least a four-fold difference in expression, and efforts were made to functionally annotate them using publicly available databases. From these, one excellent candidate ‘waxy’ gene has emerged, which we are investigating further

Aldehyde Dehydrogenase 3 Is an Expanded Gene Family with Potential Adaptive Roles in Chickpea

Legumes play an important role in ensuring food security, improving nutrition and enhancing ecosystem resilience. Chickpea is a globally important grain legume adapted to semi-arid regions under rain-fed conditions. A growing body of research shows that aldehyde dehydrogenases (ALDHs) represent a gene class with promising potential for plant adaptation improvement. Aldehyde dehydrogenases constitute a superfamily of proteins with important functions as ‘aldehyde scavengers’ by detoxifying aldehydes molecules, and thus play important roles in stress responses. We performed a comprehensive study of the ALDH superfamily in the chickpea genome and identified 27 unique ALDH loci. Most chickpea ALDHs originated from duplication events and the ALDH3 gene family was noticeably expanded. Based on the physical locations of genes and sequence similarities, our results suggest that segmental duplication is a major driving force in the expansion of the ALDH family. Supported by expression data, the findings of this study offer new potential target genes for improving stress tolerance in chickpea that will be useful for breeding programs

Microarrays as a diagnostic tool in prenatal screening strategies: ethical reflection

Obstetric