scholarly journals Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

2021 ◽  
Vol 22 (18) ◽  
pp. 9713
Author(s):  
Fabio Palumbo ◽  
Alessandro Vannozzi ◽  
Gianni Barcaccia
Keyword(s):  
Molecular Data ◽  
Apium Graveolens ◽  
Rna Seq ◽  
Foeniculum Vulgare ◽  
Breeding Programs ◽  
Plastid Genomes ◽  
Economic Weight ◽  
New Varieties ◽  
Breeding Schemes ◽  
Nms Systems

The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.

Evaluation of antimicrobial potential of some spices from apiaceae sold in herbal shops

2019 ◽  
Author(s):  
Alev ONDER ◽  
Suna Sibel GURPINAR, Mujde ERYILMAZ ◽  
Bayram Kagan AKAY, Ahsen Sevde CINAR
Keyword(s):  
Antimicrobial Activity ◽  
Daucus Carota ◽  
Antimicrobial Effect ◽  
Coriandrum Sativum ◽  
Apium Graveolens ◽  
Dilution Method ◽  
Anethum Graveolens ◽  
Foeniculum Vulgare ◽  
Pimpinella Anisum ◽  
Hexane Extracts

Spices are a part of the plants used for many purposes as preservatives and as colorants in foods or as medicinal intention. Main aim of the present research was to estimate the potential antimicrobial activity of some spices from Apiaceae family such as Amni visnaga (Diş otu, Hıltan), Anethum graveolens (Dereotu), Apium graveolens (Kereviz), Coriandrum sativum (Kişniş), Cuminum cyminum (Kimyon), Daucus carota (Havuç), Foeniculum vulgare (Rezene), Petroselinum sativum (Maydanoz), Pimpinella anisum (Anason). Thus, the fruits of the plants are used in the experiments. The fruits have been extracted by n-hexane, and all extracts have been subjected to TLC (Thin Layer Chromatography). The n-hexane extracts were screened for their potential in vitro antibacterial activity against Staphylococcus aureus ATCC 29213, Enterococcus faecalis ATCC 29212, Escherichia coli ATCC 25922, Klebsiella pneumoniae ATCC 13883, Pseudomonas aeruginosa ATCC 27853 and antifungal activity against Candida albicans ATCC 10231 by microbroth dilution method. The hexane extracts of the fruits of Coriandrum sativum, Anethum graveolens, Daucus carota, and Pimpinella anisum did not show antimicrobial activity against tested microorganisms. Except these, the other extracts having MIC values of 2.5-5-10 mg/mL exhibited antimicrobial effect against some tested microorganisms. These results demonstrate that the extracts which have an antimicrobial effect can probably play a role as an antimicrobial agent owing to their nonpolar components which are accumulated to the n-hexane extracts.

scholarly journals Genetic variability and genome-wide association analysis of flavor and texture in cooked beans (Phaseolus vulgaris L.)

2021 ◽  
Author(s):  
Amber Bassett ◽  
Kelvin Kamfwa ◽  
Daniel Ambachew ◽  
Karen Cichy
Keyword(s):  
Genetic Variability ◽  
Seed Coat ◽  
Principal Component ◽  
Breeding Programs ◽  
Flavor Intensity ◽  
Genome Wide ◽  
White Bean ◽  
The Usa ◽  
New Varieties ◽  
End Use

Abstract Key message Cooked bean flavor and texture vary within and across 20 Andean seed types; SNPs are significantly associated with total flavor, beany, earthy, starchy, bitter, seed-coat perception, and cotyledon texture. Abstract Common dry beans are a nutritious food recognized as a staple globally, but their consumption is low in the USA. Improving bean flavor and texture through breeding has the potential to improve consumer acceptance and suitability for new end-use products. Little is known about genetic variability and inheritance of bean sensory characteristics. A total of 430 genotypes of the Andean Diversity Panel representing twenty seed types were grown in three locations, and cooked seeds were evaluated by a trained sensory panel for flavor and texture attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture. Extensive variation in sensory attributes was found across and within seed types. A set of genotypes was identified that exhibit extreme attribute intensities generally stable across all three environments. seed-coat perception and total flavor intensity had the highest broad-sense heritability (0.39 and 0.38, respectively), while earthy and vegetative intensities exhibited the lowest (0.14 and 0.15, respectively). Starchy and sweet flavors were positively correlated and highest in white bean genotypes according to principal component analysis. SNPs associated with total flavor intensity (six SNPs across three chromosomes), beany (five SNPs across four chromosomes), earthy (three SNPs across two chromosomes), starchy (one SNP), bitter (one SNP), seed-coat perception (three SNPs across two chromosomes), and cotyledon texture (two SNPs across two chromosomes) were detected. These findings lay a foundation for incorporating flavor and texture in breeding programs for the development of new varieties that entice growers, consumers, and product developers alike.

scholarly journals Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process

2021 ◽  
Vol 22 (13) ◽  
pp. 7029
Author(s):  
Cai-Yun Xiong ◽  
Qing-You Gong ◽  
Hu Pei ◽  
Chang-Jian Liao ◽  
Rui-Chun Yang ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Rna Seq ◽  
Short Branch ◽  
Transcriptional Dynamics ◽  
New Varieties ◽  
Elongation Process ◽  
Temporal Expression Pattern ◽  
Maize Ear

In maize, the ear shank is a short branch that connects the ear to the stalk. The length of the ear shank mainly affects the transportation of photosynthetic products to the ear, and also influences the dehydration of the grain by adjusting the tightness of the husks. However, the molecular mechanisms of maize shank elongation have rarely been described. It has been reported that the maize ear shank length is a quantitative trait, but its genetic basis is still unclear. In this study, RNA-seq was performed to explore the transcriptional dynamics and determine the key genes involved in maize shank elongation at four different developmental stages. A total of 8145 differentially expressed genes (DEGs) were identified, including 729 transcription factors (TFs). Some important genes which participate in shank elongation were detected via function annotation and temporal expression pattern analyses, including genes related to signal transduction hormones (auxin, brassinosteroids, gibberellin, etc.), xyloglucan and xyloglucan xyloglucosyl transferase, and transcription factor families. The results provide insights into the genetic architecture of maize ear shanks and developing new varieties with ideal ear shank lengths, enabling adjustments for mechanized harvesting in the future.

Captive management and the maintenance of genetic diversity in a vulnerable marsupial, the greater bilby

2015 ◽  
Vol 37 (2) ◽  
pp. 170 ◽  
Author(s):  
Emily J. Miller ◽  
Mark D. B. Eldridge ◽  
Keith Morris ◽  
Neil Thomas ◽  
Catherine A. Herbert
Keyword(s):  
Genetic Diversity ◽  
Captive Breeding ◽  
Natural Habitat ◽  
Species Conservation ◽  
Molecular Data ◽  
Breeding Programs ◽  
Captive Populations ◽  
Genetic Impact ◽  
Captive Breeding Programs

The endemic Australian greater bilby (Macrotis lagotis) is a vulnerable and iconic species. It has declined significantly due to habitat loss, as well as competition and predation from introduced species. Conservation measures include a National Recovery Plan that incorporates several captive breeding programs. Two of these programs were established within 12 months of one another (1997/98), with the same number and sex ratio of founding individuals, but executed different breeding strategies: (1) unmanipulated mating in semi–free range natural habitat versus (2) minimising mean kinship in large enclosures, with the supplementation of new individuals into both populations. This study evaluates the long-term genetic impact of these programs and examines the congruency between the pedigree studbook estimates of diversity and molecular data. Our data demonstrate that genetic diversity was maintained in both populations, with the supplementation of new individuals contributing to the gene pool. The studbook estimates of diversity and inbreeding are not consistent with the microsatellite data and should not solely be relied upon to evaluate the genetic health of captive populations. Our analyses suggest that captive breeding programs may not require costly and intensive management to effectively maintain long-term genetic diversity in a promiscuous species.

scholarly journals Breeding programs for smallholder sheep farming systems: I. Evaluation of alternative designs of breeding schemes

2014 ◽  
Vol 131 (5) ◽  
pp. 341-349 ◽  
Author(s):  
S. Gizaw ◽  
B. Rischkowsky ◽  
A. Valle-Zárate ◽  
A. Haile ◽  
J.A.M. van Arendonk ◽  
...  
Keyword(s):  
Farming Systems ◽  
Breeding Programs ◽  
Breeding Schemes ◽  
Alternative Designs

scholarly journals Gene Expression Does Not Support the Developmental Hourglass Model in Three Animals with Spiralian Development

2019 ◽  
Vol 36 (7) ◽  
pp. 1373-1383 ◽  
Author(s):  
Longjun Wu ◽  
Kailey E Ferger ◽  
J David Lambert
Keyword(s):  
Gene Expression ◽  
Large Fraction ◽  
Molecular Data ◽  
Development Stage ◽  
Data Sets ◽  
Rna Seq ◽  
Developmental Evolution ◽  
Phylotypic Stage ◽  
Hourglass Model ◽  
Almost All

Abstract It has been proposed that animals have a pattern of developmental evolution resembling an hourglass because the most conserved development stage—often called the phylotypic stage—is always in midembryonic development. Although the topic has been debated for decades, recent studies using molecular data such as RNA-seq gene expression data sets have largely supported the existence of periods of relative evolutionary conservation in middevelopment, consistent with the phylotypic stage and the hourglass concepts. However, so far this approach has only been applied to a limited number of taxa across the tree of life. Here, using established phylotranscriptomic approaches, we found a surprising reverse hourglass pattern in two molluscs and a polychaete annelid, representatives of the Spiralia, an understudied group that contains a large fraction of metazoan body plan diversity. These results suggest that spiralians have a divergent midembryonic stage, with more conserved early and late development, which is the inverse of the pattern seen in almost all other organisms where these phylotranscriptomic approaches have been reported. We discuss our findings in light of proposed reasons for the phylotypic stage and hourglass model in other systems.

Consistency of organoleptic and yield related traits of strawberry cultivars over time

2020 ◽  
Vol 10 (4) ◽  
pp. 623-636
Author(s):  
M.T. Ariza ◽  
L. Miranda ◽  
E. Martínez-Ferri ◽  
J.J. Medina ◽  
J.A. Gómez-Mora ◽  
...  
Keyword(s):  
Fragaria X Ananassa ◽  
Crop Season ◽  
Breeding Programs ◽  
Continuous Increase ◽  
Environment Temperature ◽  
New Varieties ◽  
Different Characteristics ◽  
Organoleptic Parameters ◽  
Over Time ◽  
Strawberry Cultivars

BACKGROUND: Strawberry (Fragaria x ananassa Duch.) is among the most widely consumed fruits in the world and its cultivation is increasing worldwide. This continuous increase in its cultivation acreage is concomitant with the development of new varieties by numerous breeding programs. Due to strawberry is a microclimatic crop, the behaviour of the cultivars could vary depending on many agronomical and environmental factors such as temperature or humidity. Thus, for some traits, data from a single crop season may not be enough to suspect the behaviour of a specific variety. OBJECTIVE: Generate information that allows knowing the consistency of different characteristics over time. METHODS: For four consecutive years, organoleptic and yield related traits were analysed in five strawberry cultivars. RESULTS: The overall result is a significant effect of genotype on all yield relates and organoleptic parameters studied. Our study also inferred an effect of environment, temperature and relative humidity, mainly on yield parameters. However, not all cultivars were similarly affected. CONCLUSIONS: With the information generated from this work, it will be possible to establish, based on the consistency of the cultivar trials over time, the suitability of using the results of a single season to predict the behaviour of a particular cultivar.

P2790Novel endomyocardial micro-biopsy device for higher precision and reduced complication risks

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
A Chireh ◽  
R Grankvist ◽  
M Sandell ◽  
A K Mukarram ◽  
N Jaff ◽  
...  
Keyword(s):  
Endomyocardial Biopsy ◽  
Diagnostic Yield ◽  
Molecular Data ◽  
Outer Diameter ◽  
The Novel ◽  
Rna Seq ◽  
Device Design ◽  
Biopsy Device ◽  
Different Parts

Abstract Introduction Endomyocardial biopsy (EMB) is the gold standard for diagnosis of several cardiac diseases, yet its use is limited by low diagnostic yield and significant complication risks. The size of the current devices allows only limited steering to different parts of the ventricle walls. In transplant monitoring, repeated biopsies with the current devices can cause scarring that makes it increasingly difficult to obtain adequate samples. We hypothesised that several of the shortcomings of EMB can be avoided with a smaller and more steerable device. Further, we hypothesised that the novel sampling procedure could be coupled to a low-input molecular analysis method, such as RNA-sequencing (RNA-seq), to provide molecular characterisation of the tissue without the need of large biopsy samples. Purpose To develop an EMB device with significantly smaller dimensions, for future use in diagnostics and research investigations. Specific aims were to test feasibility and safety of the procedure, as well as the quality of the generated molecular data. Methods 65 “micro biopsy” (micro-EMB) device prototypes were designed and evaluated in-house. The prototypes were evaluated either in an ex-vivo simulator or in acute non-survival pig experiments (n=23). Once the final device design was reached, an in vivo trial was set up using six naive Yorkshire farm pigs. Micro-EMB, conventional EMB, skeletal muscle and blood samples were collected for RNA-seq characterisation and comparison. In half of the animals (n=3), micro-EMB was the only intervention in order to prioritise safety evaluations. The animals were monitored for one week. Results The final device design has an outer diameter (OD) of 0.4 mm, compared to a conventional 11 mm device (in the opened position), Fig 1A. The device can be directed to different parts of the myocardium in both ventricles. In the in vivo evaluation in swine, 81% of the biopsy attempts (n=157) were successful. High quality RNA-seq data was generated from 91% of the sequenced heart micro-biopsy samples (n=32). The gene expression signatures of samples taken with the novel device were comparable with samples taken with a conventional device, Fig 1B. No major complications were detected either during periprocedural monitoring or during the follow-up. The tissue mark after micro-biopsy was markedly smaller than after conventional endomyocardial biopsy. A) Bioptome dimensions. B) RNA-seq data. Conclusions Our preliminary data suggest that the novel submillimeter biopsy device, coupled with RNA-seq, provides a feasible method to obtain molecular data from the myocardium. The method is less traumatic and has a higher flexibility compared to conventional methods, enabling safer and more specific sampling from different parts of the myocardium. In the long term, the procedure could open unprecedented diagnostic and research possibilities. Future studies should be directed to establish the capabilities of the novel method in a relevant disease model. Acknowledgement/Funding Family Erling Persson Foundation. The Söderberg foundations. KID (Karolinska Institutet). The 4D project. Stockholm county council. Astra Zeneca.

scholarly journals The Chemistry behind Tomato Quality

2018 ◽  
Vol 13 (9) ◽  
pp. 1934578X1801300
Author(s):  
Dario Paolo ◽  
Giulia Bianchi ◽  
Roberto Lo Scalzo ◽  
Carlo F. Morelli ◽  
Marco Rabuffetti ◽  
...  
Keyword(s):  
Nutritional Value ◽  
Detrimental Effect ◽  
Chemical Constituents ◽  
Fruit Size ◽  
Breeding Programs ◽  
Beneficial Effects ◽  
Fresh Vegetables ◽  
Nutritional Qualities ◽  
New Varieties

Tomato is one of the most widely consumed fresh vegetables in the industrialized world and an important source of healthy constituents of the human diet. Despite the unique flavor characteristics of tomatoes, which make them extremely valuable in cooking, and their recognized beneficial role in the diet, the quality of tomato was traditionally only considered in connection to external appearances. As it happened with other highly requested crops, breeding programs of tomato focused their efforts on developing new varieties with higher yields and stress resistance, with better uniformity in fruit size, brighter color and prolonged shelf life. The downside of these strategies was that organoleptic features and nutritional value were often neglected, with a detrimental effect on commercial tomatoes. Over the last years, there has been an increase in consumers’ demand for tasty and healthy products. This aspect, paired with novel and multidisciplinary approaches to tomato research, allowed both sensory and nutritional qualities to be reconsidered as valuable parameters in breeding. In this review we describe the main chemical constituents of tomato, focusing on the flavor compounds (both volatile and non-volatile compounds) and secondary metabolites. Particular attention is paid to their beneficial effects on human health and their relevance to the overall quality of tomato.

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