116 research outputs found
Genome Sequencing of Ancient Plant Remains: Findings, Uses and Potential Applications for the Study and Improvement of Modern Crops
The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). In the last 30 years, DNA extracted from the ancient remains of several plant species has been explored in small-scale studies, contributing to understand the adaptation, and migration patterns of important crops. More recently, NGS technologies applied on aDNA have opened up new avenues of research, allowing investigation of the domestication process on the whole-genome scale. Genomic approaches based on genome-wide and targeted sequencing have been shown to provide important information on crop evolution and on the history of agriculture. Huge amounts of next-generation sequencing (NGS) data offer various solutions to overcome problems related to the origin of the material, such as degradation, fragmentation of polynucleotides, and external contamination. Recent advances made in several crop domestication studies have boosted interest in this research area. Remains of any nature are potential candidates for aDNA recovery and almost all the analyses that can be made on fresh DNA can also be performed on aDNA. The analysis performed on aDNA can shed light on many phylogenetic questions concerning evolution, domestication, and improvement of plant species. It is a powerful instrument to reconstruct patterns of crop adaptation and migration. Information gathered can also be used in many fields of modern agriculture such as classical breeding, genome editing, pest management, and product promotion. Whilst unlocking the hidden genome of ancient crops offers great potential, the onus is now on the research community to use such information to gain new insight into agriculture
Tomato ionomic approach for food fortification and safety.
Food fortification is an issue of paramount of importance for people living both in developed
and in developing countries. Among substances listed as "nutriceuticals", essential minerals have
been recognised for their involvement in several healthy issues, involving all ages. In this frame,
food plants are playing a pivotal role since their capability to compartmentalise ions and proteinmetal
complexes in edible organs. Conversely, the accumulation of high metal levels in those
organs may lead to safety problems. In the recent years, thanks to the availability of new and
improved analytical apparatus in both ionic and genomic/transcrittomics areas, it is became feasible
to couple data coming from plant physiology and genetics. Ionomics is the discipline that studies
the cross-analysis of both data sets. Our group, in the frame of GenoPom project granted by MiUR,
is interested to study the ionomics of tomatoes cultivars derived by breeding programmes in which
wild relatives have been used to transfer several useful traits, such as resistance to biotic or abiotic
stresses, fruit composition and textiture, etc. The introgression of the wild genome into the
cultivated one produces new gene combinations. They might lead to the expression of some traits,
such as increased or reduced adsorption of some metals and their exclusion or loading into edible
organs, thus strongly involving the nutritional food value. Our final goal is to put together data
coming from ions homeostasis and gene expression analyses, thus obtaining an ionomic tomato
map related to ions absorption, translocation and accumulation in various plant organs, fruits
included. To follow our hypothesis, we are studying the ionome of Solanum lycopersicum cv. M82
along with 76 Introgression Lines (ILs) produced by interspecific crosses between this cultivar and
the wild species S. pennellii. These ILs are homozygous for small portions of the wild species
genome introgressed into the domesticated M82 one. They are used as a useful tool for mapping
QTL associated with many traits of interest. It is worthy to note that, until now, little information is
available on QTL for ions accumulation in tomato. Moreover, as our knowledge, effects of new
gene combinations in introgressed lines on ions uptake related to food safety have not been
extensively studied. In this presentation we show results coming from the ionome analysis, carried
out on S . lycopersicum M82 and several ILs. Plants were grown in pots in a greenhouse and
watered with deionised water Thirty day-old plants were left to grow for 15 days in the presence of
non-toxic concentration of Cd, Pb, As, Cr and Zn given combined. Leaves of all plants were then
harvested and stored at -80°C for ionome and gene expression analyses. Preliminary results of
ionome analysis of S. lycopersicum M82 and several ILs, carried out using an ICP-MS, showed that
traits correlated to toxic metals and micronutrients accumulation in apical leaves were significantly
modified in response to specific genetic backgrounds. Those results are perhaps due to the
introgression of traits linked to uptake, translocation and accumulation of useful and/or toxic metal
into plant apical leaves and to interactions of the wild type introgressed genomic regions with the
cultivated genome. Also, data are shown on the identification and isolation of Solanum gene
sequences related to ions uptake, translocation and accumulation, useful for further real-time gene
expression evaluation in both cultivated and ILs during the treatments with the above-mentioned
metals
A basic Helix-Loop-Helix (SlARANCIO), identified from a Solanum pennellii introgression line, affects carotenoid accumulation in tomato fruits
Abstract Carotenoid accumulation in tomato (Solanum lycopersicum) fruits is influenced by environmental stimuli and hormonal signals. However, information on the relative regulatory mechanisms are scanty since many molecular players of the carotenoid biosynthetic pathway are still unknown. Here, we reported a basic Helix-Loop-Helix transcription factor, named SlARANCIO (SlAR), whose silencing influences carotenoid accumulation in tomato fruits. The SlAR gene was found in the S. pennellii introgression line (IL) 12-4SL that holds the carotenoid QTL lyc12.1. We observed that the presence of the wild region in a cultivated genetic background led to a decrease in total carotenoid content of IL12-4SL fruits. To get insights into the function of SlAR, a quick reverse genetic approach was carried out. Virus-induced gene silencing of SlAR in S. lycopersicum M82 and MicroTom fruits reproduced the same phenotype observed in IL12-4SL, i.e. decreased content of lycopene and total carotenoids. Vice versa, the overexpression of SlAR in Nicotiana benthamiana leaves increased the content of total carotenoids and chlorophylls. Our results, combined with public transcriptomic data, highly suggest that SlAR acts indirectly on the carotenoid pathway and advances current knowledge on the molecular regulators controlling lyc12.1 and, potentially, precursors of carotenoid biosynthesis
SOLANUM LYCOPERSICUM X S. PENNELLII INTROGRESSION LINES WERE USEFUL TO CHARACTERISE THE IONOME OF TOMATO FRUIT
In the frame of "GenoPom" PON-MIUR project, we have
began a study of tomato ionome in order to identify the contribution of specific chromosome and
part of them on the ionome. For this purpose, we have analysed by ICP-MS plants of an
introgression line (IL) population derived from the cross between Solanum lycopersicum cv. M82
and S. pennellii (Eshed and Zamir, 1995) grown under controlled environmental conditions.we report results derived from tomato whole fruits ionome analysis of 30 IL,
covering all 12 tomato chromosomes, along with the recurrent parent cv. M82. Among several
detected elements, the following ones have firstly been analysed: Ca, Fe, Cu, Zn and Se. Each
element concentration data were referred to cv. M82
Ion uptake and YSL1 gene identification in tomato
Tomato breeder are using wild tomato relatives, even non-cross compatibles ones, in order to
obtain cultivars with highly commercial values bearing new traits. However, the introgression of a
wild genome into the cultivated one produces a new gene combinations that may lead to the
expression of undeliverable traits, perhaps not so easy to recognise; even more, phenotypic
variations may escape during the selection procedure when minor genes or non-abnormal
phenotypes are involved. In the frame of the “GenoPom” project funded by MIUR, we have
focused our interest on the alteration of heavy metals uptake from the soil and their loading into
edible organs in commercial lines coming from Solanum interspecific crosses. Our final aim is to
put together data coming from ion homeostasis and gene expression analyses, thus obtaining a
ionomic map of tomato. To pursue our goal, we have started to study the cv M82 of Solanum
lycopersicon, the wild relative Solanum pennelli and their introgression lines IL. Regarding the
experiments on ion homeostasis, S. lycopersicon M82 and the introgression line IL 6-4-2 were
grown in hydroponics under controlled environmental conditions. Twenty day-old plants were left
to grow for 10 days in the presence of non-toxic concentration of Cd (10 mM), Pb (3 mM), Zn (100
mM) given separately or combined. Control and treated roots and leaves were then harvested and
stored at -80°C for ionic and gene expression analyses. Ions analysis of Solanum lycopersicon M82
and IL 6-4-2 showed that traits correlated to ionic homeostasis is significantly modified in response
to all metals and to the genotype. The analysis of ions data, obtained by ICP-MS, give a pictures of
the different responses performed both to different stress and to combined stress, probably
correlated to the up-regulation and/or down regulation of metal uptake proteins. Performed
experiments demonstrate that the introgression of the wild genome into the cultivated one produces
a new phenotype, perhaps due to the expression of traits linked to uptake, translocation and
accumulation of useful and/or toxic metal into plant tissues and organs.
Regarding the functional genomics approach for gaining insight into gene networks involved
in mineral-ion accumulation in tomato plants, in literature has been reported that at least 25 major
family genes are involved for metal homeostasis in plants. Among them, the genes ysl, hma, mtp,
znt, zrt have been already studied at least in the plant species Arabidopsis thaliana, A. halleri and
Thlaspi caerulescens. So far, no such genes have been reported to be cloned in Solanum species.
We have focused our study on the genes YSL1, ZNT1 and MTP1 responsible for uptake,
translocation and accumulation of metal such as zinc, cadmium, and iron into plant compartment.
For all of them, consensous sequences from nucleotide multialignment have been obtained. Then,
each of those were blasted in a Solanum EST collection databank and an assembled UniGene
sequence was obtained.. Finally, we have designed primers and performed PCR analysis on S.
lycopersicon and S. pennelli genomic DNA. So far, we have cloned a putative ysl1 sequence from
tomato, that has shown that a very high percentage of identity (92%) with whole ysl1 gene of
Nicotiana tabacum; the in silico translated sequence of this sequence has shown a 89% of identity
with the same tobacco protein
Ionome variations in tomato Introgressed Lines (Solanum Pennellii x S. Lycopersicum cv. M82) following metal treatements shed new light on food health.
A tomato introgression line population that combines single chromosomal segments introgressed from the wild, green fruited species Solanum pennelli in the background of the domesticated tomato, S. lycopersicum cv. M82, was used in this study. Results shed light both on the metal accumulation of ILs
tomato plants and on theirs ionome modifications
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