Transcriptome Analyses of Mosaic (MSC) Mitochondrial Mutants of Cucumber in a Highly Inbred Nuclear Background.

Cucumber (Cucumis sativus L.) has a large, paternally transmitted mitochondrial genome. Cucumber plants regenerated from cell cultures occasionally show paternally transmitted mosaic (MSC) phenotypes, characterized by slower growth, chlorotic patterns on the leaves and fruit, lower fertility, and rearrangements in their mitochondrial DNAs (mtDNAs). MSC lines 3, 12, and 16 originated from different cell cultures all established using the highly inbred, wild-type line B. These MSC lines possess different rearrangements and under-represented regions in their mtDNAs. We completed RNA-seq on normalized and non-normalized cDNA libraries from MSC3, MSC12, and MSC16 to study their nuclear gene-expression profiles relative to inbred B. Results from both libraries indicated that gene expression in MSC12 and MSC16 were more similar to each other than MSC3. Forty-one differentially expressed genes (DEGs) were upregulated and one downregulated in the MSC lines relative to B. Gene functional classifications revealed that more than half of these DEGs are associated with stress-response pathways. Consistent with this observation, we detected elevated levels of hydrogen peroxide throughout leaf tissue in all MSC lines compared to wild-type line B. These results demonstrate that independently produced MSC lines with different mitochondrial polymorphisms show unique and shared nuclear responses. This study revealed genes associated with stress response that could become selection targets to develop cucumber cultivars with increased stress tolerance, and further support of cucumber as a model plant to study nuclear-mitochondrial interactions

Cucumber: a model angiosperm for mitochondrial transformation

Abstract. Plants possess three major genomes, carried in the chloroplast, mitochondrion, and nucleus. The chloroplast genomes of higher plants tend to be of similar sizes and structure. In contrast both the nuclear and mitochondrial genomes show great size differences, even among closely related species. The largest plant mitochondrial genomes exist in the genus Cucumis at 1500 to 2300 kilobases, over 100 times the sizes of the yeast or human mitochondrial genomes. Biochemical and molecular analyses have established that the huge Cucumis mitochondrial genomes are due to extensive duplication of short repetitive DNA motifs. The organellar genomes of almost all organisms are maternally transmitted and few methods exist to manipulate these important genomes. Although chloroplast transformation has been achieved, no routine method exists to transform the mitochondrial genome of higher plants. A mitochondrial-transformation system for a higher plant would allow geneticists to use reverse genetics to study mitochondrial gene expression and to establish the efficacy of engineered mitochondrial genes for the genetic improvement of the mitochondrial genome. Cucumber possesses three unique attributes that make it a potential model system for mitochondrial transformation of a higher plant. Firstly, its mitochondria show paternal transmission. Secondly, microspores possess relatively few, huge mitochondria. Finally, there exists in cucumber unique mitochondrial mutations conditioning strongly mosaic (msc) phenotypes. The msc phenotypes appear after regeneration of plants from cell culture and sort with specific rearranged and deleted regions in the mitochondrial genome. These mitochondrial deletions may be a useful genetic tool to develop selectable markers for mitochondrial transformation of higher plants

The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions

Molecular Identification Of Trichoderma Strains Collected To Develop Plant Growth-Promoting And Biocontrol Agents

Trichoderma strains that are beneficial to both the growth and health of plants can be used as plant growth-promoting fungi (PGPF) or biological control agents (BCA) in agricultural and horticultural practices. In order to select PGPF or BCA strains, their biological properties and taxonomy must be carefully studied. In this study, 104 strains of Trichoderma collected at geographically different locations in Poland for selection as PGPF or BCA were identified by DNA barcoding, based on the sequences of internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and on the sequences of translation elongation factor 1 alpha (tef1), chitinase 18-5 (chi18-5), and RNA polymerase II subunit (rpb2) gene fragments. Most of the strains were classified as: T. atroviride (38%), T. harzianum (21%), T. lentiforme (9%), T. virens (9%), and T. simmonsii (6%). Single strains belonging to T. atrobrunneum, T. citrinoviride, T. crassum, T. gamsii, T. hamatum, T. spirale, T. tomentosum, and T. viridescens were identified. Three strains that are potentially pathogenic to cultivated mushrooms belonging to T. pleuroticola and T. aggressivum f. europaeum were also identified. Four strains: TRS4, TRS29, TRS33, and TRS73 were classified to Trichoderma spp. and molecular identification was inconclusive at the species level. Phylogeny analysis showed that three of these strains TRS4, TRS29, and TRS33 belong to Trichoderma species that is not yet taxonomically established and strain TRS73 belongs to the T. harzianum complex, however, the species could not be identified with certainty

Seed Lipid Composition of New Hybrids of Styrian Oil Pumpkin Grown in Poland

Styrian hull-less pumpkins are valued for their use in health-promoting foods such as oils and snacks. Although deriving from Styria, they are now cultivated globally. Seeds of Styrian oil pumpkins are rich in lipids and represent a high-value product. Thus, seed yield and quality are traits of economic importance. These seed characteristics depend mostly on the cultivated variety and plant growing conditions. This study aimed to assess the variation in hull-less seed lipids of new hybrids of Styrian oil pumpkin developed recently for cultivation in moderate/colder climate zones of the north-eastern part of Poland. The study showed that the newly-developed hybrids have a relatively high content of total lipids in seeds, with a substantially higher share of linoleic acid (up to 63%). However, sterols, tocopherols, and squalene content and composition were similar to pumpkin seed oils produced from plants cultivated in other, warmer regions. This study provides insights into the chemical composition of Styrian pumpkin oil produced from hybrids grown under the relatively severe climatic conditions of north-eastern Poland

Variability of selected quantitative traits in recombinant inbred lines of winter squash (Cucurbita maxima Duch.)

Przeprowadzono ocenę fenotypową populacji dyni olbrzymiej pod względem cech ilościowych takich jak: średnia masa owocu, liczba owoców na roślinę oraz plon handlowy. W eksperymencie wykorzystano populację mapującą składającą się ze 112 rekombinacyjnych linii wsobnych (RIL) pokolenia F6 dyni olbrzymiej uzyskanych z mieszańca dwóch linii wsobnych 802 × 801 o odmien¬nym pochodzeniu i skrajnie zróżnicowanych pod względem badanych cech. Doświadczenie polowe założono w układzie losowym w trzech powtórzeniach w 2013 i 2014 roku. Linie rodzicielskie wykazywały istotne statystycznie różnice w odniesieniu do wartości cech. Zakres zmienności cech w populacji mapującej przekraczał wartości cech dla linii rodzicielskich. Zakres zmienności dla średniej masy owocu wynosił od 0,6 kg do 9,0 kg, dla średniej liczby owoców na roślinie od 1,0 do 7,5 (2013) i od 1,0 do 11,5 (2014), dla plonu handlowego (kg/roślinę) 1,7–11,8 (2013) i 1,26–30,0 (2014). Odziedziczalność cech wynosiła 71% dla plon handlowego, 70% dla średniej masy owoców i 82% dla średniej liczby owoców na roślinę.The present study assessed the phenotypes of winter squash (Cucurbita maxima Duch.) population in terms of quantitative traits such as: average fruit weight, number of fruits per plant and marketable yield. Winter squash mapping population, developed by crossing two inbred lines of different origins and extremely diverse in terms of the studied traits, consisting of 112 recombinant inbred lines (RIL) F6 was used. The field experiments were established in a random arrangement with three replications in the years 2013 and 2014. Parental lines showed statistically significant differences in relation to the value of all the studied traits. Range of variability of all studied traits in the mapping population exceeded the values of parental lines. In case of average fruit weight the range of variation was 0.6–9.0 kg, for the average number of fruits per plant 1.0–7.5 (2013) and 1.0–11.5 (2014). In case of marketable yield, the variation range was 1.7–11.8 kg/plant (2013) and 1.26–30.0 kg/plant (2014). Heritability of the traits was: 71% for marketable yield, 70% for the average fruit weight and 82% for the average number of fruits per plant

Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines

Cucurbita maxima Duchesne squash and pumpkins are cultivated world-wide. Cucurbita maxima fruits are produced for fresh market and are valuable for food processing. Therefore, fruit characteristics and yield are the traits of high economic importance for breeders. To date, the genetic basis of fruit-associated traits in C. maxima have been poorly understood. In the present study, we evaluated fruit-associated traits and conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross of two inbred lines with different fruit morphotypes. Phenotypic data for nine fruit traits (earliness, weight, number per plant, yield per plant, length and diameter, shape index, flesh thickness, sucrose content and dry matter content) were collected for RILs in two open-field experiments. Pairwise analysis of the phenotypic data revealed correlations among the fruit and yield-associated traits. Using a previously developed genetic map, we identified 26 QTLs for eight traits. The QTLs were found in 10 locations on eight chromosomes of C. maxima. The QTLs were detected across experiments and explained up to 41.4% of the observed phenotypic variations. Major-effect QTLs for multiple fruit-associated traits were clustered on chromosome 4, suggesting that this genomic region has been under selection during diversification and/or domestication of C. maxima

The Evaluation and Conservation of Plant Genetic Resources Collected in Lithuania

The present work compiles the results of three-year expeditions organized between 2011 and 2013 aimed at plant crop collection in the area of Lithuania, an Eastern European country. Accessions of fruit trees, vegetables, cereals, forage, industrial, fibrous, medical, and spice crops as well as accompanying segetal plants were collected in 5 ethnographic regions of Lithuania. In total, 1010 samples of seeds, bulbs, and plant grafts were obtained. The majority of the collected samples belonged to the Cucurbitaceae, Fabaceae, Solanaceae, Alliaceae, and Rosaceae families. The accessions were described and deposited in the long-term storage in Lithuanian and Polish Gene Banks. Almost all collected cucumbers, pumpkins, squashes, and oat plants were morphologically characterized in field experiments. Cucurbita pepo accessions showed high morphological diversity, while limited diversity of cucumber accessions was observed. Oat plants were characterized by high morphological diversity and resistance to diseases present in some of the investigated accessions. Further characterization of collected apple trees and other accessions is underway. Obtaining germplasm in the area of Lithuania fulfills a gap in current plant crop collections. Collected material could be valuable for pre-breeding evaluation and further breeding programs as well as the study of genetic diversity