Construction of two BAC libraries from cucumber (Cucumis sativus L.) and identification of clones linked to yield component quantitative trait loci

Comparative analysis of miRNA and mRNA abundance in determinate cucumber by high-throughput sequencing

Determinate cucumber is a type of short vines, fewer nodes, and terminal flowers, it is suitable for high-density planting and available harvesting in field cultivation, whereas the indeterminate cucumber is preferred to cultivate in greenhouses. However, many biotic or abiotic stresses could lead indeterminate cucumber to be determinate in greenhouse cultivation, which may decrease yield and fruit quality. Therefore, it is urgent and essential to investigate the key factors forming determinate and terminal flowering in cucumber. In this study, two close background inbred lines were selected and conducted the miRNA and mRNA high throughput sequencing. Interestingly, ethylene-associated miRNAs and mRNAs were intensively obtained, indicating that the plant hormone ethylene is a key factor impacting determinate and terminal flowering in cucumber. The ethylene metabolites analysis showed that significant higher ethylene was observed in determinate line than that in the indeterminate line. The RT-qPCR validation of ethylene related miRNAs Cas-miR172, Cas-miR396, and Cas-miR414 and their target mRNAs showed a significant negative correlation. These data suggested that ethylene-associated miRNAs might affect determinate and terminal flower phenotypes by regulating their target genes expression. This study not only provides a potential molecular mechanism for determinate formation in cucumber but also establishes a method to demonstrate important physiological processes through the comprehensive association of miRNA and mRNA high-throughput sequencing.

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 cytogenetic mapping of Cucumis sativus and C. melo using highly repetitive DNA sequences

Chromosomes often serve as one of the most important molecular aspects of studying the evolution of species. Indeed, most of the crucial mutations that led to differentiation of species during the evolution have occurred at the chromosomal level. Furthermore, the analysis of pachytene chromosomes appears to be an invaluable tool for the study of evolution due to its effectiveness in chromosome identification and precise physical gene mapping. By applying fluorescence in situ hybridization of 45S rDNA and CsCent1 probes to cucumber pachytene chromosomes, here, we demonstrate that cucumber chromosomes 1 and 2 may have evolved from fusions of ancestral karyotype with chromosome number n = 12. This conclusion is further supported by the centromeric sequence similarity between cucumber and melon, which suggests that these sequences evolved from a common ancestor. It may be after or during speciation that these sequences were specifically amplified, after which they diverged and specific sequence variants were homogenized. Additionally, a structural change on the centromeric region of cucumber chromosome 4 was revealed by fiber-FISH using the mitochondrial-related repetitive sequences, BAC-E38 and CsCent1. These showed the former sequences being integrated into the latter in multiple regions. The data presented here are useful resources for comparative genomics and cytogenetics of Cucumis and, in particular, the ongoing genome sequencing project of cucumber.

Comparative analysis of marker-assisted and phenotypic selection for yield components in cucumber

Theoretical studies suggest that marker-assisted selection (MAS) has case-specific advantages over phenotypic selection (PHE) for selection of quantitative traits. However, few studies have been conducted that empirically compare these selection methods in the context of a plant breeding program. For direct comparison of the effectiveness of MAS and PHE, four cucumber (Cucumis sativus L.; 2n = 2x = 14) inbred lines were intermated and then maternal bulks were used to create four base populations for recurrent mass selection. Each of these populations then underwent three cycles of PHE (open-field evaluations), MAS (genotyping at 18 marker loci), and random mating without selection. Both MAS and PHE were practiced for yield indirectly by selecting for four yield-component traits that are quantitatively inherited with 2-6 quantitative trait loci per trait. These traits were multiple lateral branching, gynoecious sex expression (gynoecy), earliness, and fruit length to diameter ratio. Both MAS and PHE were useful for multi-trait improvement, but their effectiveness depended upon the traits and populations under selection. Both MAS and PHE provided improvements in all traits under selection in at least one population, except for earliness, which did not respond to MAS. The populations with maternal parents that were inferior for a trait responded favorably to both MAS and PHE, while those with maternal parents of superior trait values either did not change or decreased during selection. Generally, PHE was most effective for gynoecy, earliness, and fruit length to diameter ratio, while MAS was most effective for multiple lateral branching and provided the only increase in yield (fruit per plant).

Construction of a fosmid library of cucumber (Cucumis sativus) and comparative analyses of the eIF4E and eIF(iso)4E regions from cucumber and melon (Cucumis melo)

A fosmid library of cucumber was synthesized as an unrestricted resource for researchers and used for comparative sequence analyses to assess synteny between the cucumber and melon genomes, both members of the genus Cucumis and the two most economically important plants in the family Cucurbitaceae. End sequencing of random fosmids produced over 680 kilobases of cucumber genomic sequence, of which 25% was similar to ribosomal DNAs, 25% to satellite sequences, 20% to coding regions in other plants, 4% to transposable elements, 13% to mitochondrial and chloroplast sequences, and 13% showed no hits to the databases. The relatively high frequencies of ribosomal and satellite DNAs are consistent with previous analyses of cucumber DNA. Cucumber fosmids were selected and sequenced that carried eukaryotic initiation factors (eIF) 4E and iso(4E), genes associated with recessively inherited resistances to potyviruses in a number of plants. Indels near eIF4E and eIF(iso)4E mapped independently of the zym, a recessive locus conditioning resistance to Zucchini yellow mosaic virus, establishing that these candidate genes are not zym. Cucumber sequences were compared with melon BACs carrying eIF4E and eIF(iso)4E and revealed extensive sequence conservation and synteny between cucumber and melon across these two independent genomic regions. This high degree of microsynteny will aid in the cloning of orthologous genes from both species, as well as allow for genomic resources developed for one Cucumis species to be used for analyses in other species.

The construction and characteristics of a BAC library for Cucumis sativus L. 'B10'

Cloning using bacterial artificial chromosomes (BACs) can yield high quality genomic libraries, which are used for the physical mapping, identification and isolation of genes, and for gene sequencing. A BAC genomic library was constructed from high molecular weight DNA (HMW DNA) obtained from nuclei of the cucumber (Cucumis sativus L. cv. Borszczagowski; B10 line). The DNA was digested with the HindIII restriction enzyme and ligated into the pCC1BAC vector. The library consists of 34,560 BAC clones with an average insert size of 135 kb, and 12.7x genome coverage. Screening the library for chloroplast and mitochondrial DNA content indicated an exceptionally low 0.26% contamination with chloroplast DNA and 0.3% with mitochondrial DNA.

Construction and characterization of the first bacterial artificial chromosome library for the cotton species Gossypium barbadense L

As the second most widely cultivated cotton, Gossypium barbadense is well known for its superior fiber properties and its high levels of resistance to Fusarium and Verticillium wilts. To enhance our ability to exploit these properties in breeding programs, we constructed the first bacterial artificial chromosome (BAC) library for this species. The library contains 167 424 clones (49 920 BamHI and 117 504 HindIII clones), with an estimated average insert size of 130 kb. About 94.0% of the clones had inserts over 100 kb, and the empty clones accounted for less than 4.0%. Contamination of the library with chloroplast clones was very low (0.2%). Screening the library with locus-specific probes showed that BAC clones represent 6.5-fold genome equivalents. This high-quality library provides an additional asset with which to exploit genetic variation for cotton improvement.

Construction of a watermelon BAC library and identification of SSRs anchored to melon or Arabidopsis genomes

A bacterial artificial chromosome (BAC) library was constructed for watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus) with an average insert-size of 106 kb, providing 21 haploid genome equivalents. The library was used to identify BAC clones that are anchored to probes evenly distributed on the genomes of melon or Arabidopsis. Twenty eight probes (representing 66% of the tested probes) from melon and 30 probes (65%) from Arabidopsis identified positive BAC clones. Two methods were implemented to identify SSRs from the positively hybridizing BAC clones. First, analysis of BAC end sequences revealed 37 SSRs. For the second method, pooled DNA of BACs identified by the melon probes was used to develop a shotgun library. The library was then screened with synthetic SSR oligonucleotides by hybridization. Sequence analysis of positively hybridizing shotgun clones revealed 142 different SSRs. Thirty eight SSRs were characterized using three watermelon cultivars, five plant introduction (PI) accessions of C. lanatus var lanatus and four PIs of C. lanatus var citroides. Of these, 36 (95%) were found to be polymorphic with up to six alleles per marker. Polymorphism information content values for polymorphic markers varied between 0.22 and 0.79 with an average of 0.53. The methods described herein will be valuable for the construction of a watermelon linkage map with SSRs evenly distributed on its genome that is anchored to the genomes of melon and Arabidopsis.

Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins

Quinoa (Chenopodium quinoa Willd.) is adapted to the harsh environments of the Andean Altiplano region. Its seeds have a well-balanced amino acid composition and exceptionally high protein content with respect to human nutrition. Quinoa grain is a staple in the diet of some of the most impoverished people in the world. The plant is an allotetraploid displaying disomic inheritance (2n=4x=36) with a di-haploid genome of 967 Mbp (megabase pair), or 2C=2.01 pg. We constructed two quinoa BAC libraries using BamHI (26,880 clones) and EcoRI (48,000 clones) restriction endonucleases. Cloned inserts in the BamHI library average 113 kb (kilobase) with approximately 2% of the clones lacking inserts, whereas cloned inserts in the EcoRI library average 130 kb and approximately 1% lack inserts. Three plastid genes used as probes of high-density arrayed blots of 73,728 BACs identified approximately 2.8% of the clones as containing plastid DNA inserts. We estimate that the combined quinoa libraries represent at least 9.0 di-haploid nuclear genome equivalents. An average of 12.2 positive clones per probe were identified with 13 quinoa single-copy ESTs as probes of the high-density arrayed blots, suggesting that the estimate of 9.0x coverage of the genome is conservative. Utility of the BAC libraries for gene identification was demonstrated by probing the library with a partial sequence of the 11S globulin seed storage protein gene and identifying multiple positive clones. The presence of the 11S globulin gene in four of the clones was verified by direct comparison with quinoa genomic DNA on a Southern blot. Besides serving as a useful tool for gene identification, the quinoa BAC libraries will be an important resource for physical mapping of the quinoa genome.