Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array

Functional copy number variation of CsSHINE1 is associated with fruit skin netting intensity in cucumber, Cucumis sativus

Fruit skin netting in cucumber (Cucumis sativus) is associated with important fruit quality attributes. Two simply inherited genes H (Heavy netting) and Rs (Russet skin) control skin netting, but their molecular basis is unknown. Here, we reported map-based cloning and functional characterization of the candidate gene for the Rs locus that encodes CsSHINE1 (CsSHN1), an AP2 domain containing ethylene-responsive transcription factor protein. Comparative phenotypic analysis in near-isogenic lines revealed that fruit with netted skin had different epidermal structures from that with smooth skin including thicker cuticles, smaller, palisade-shaped epidermal and sub-epidermal cells with heavily suberized and lignified cell walls, higher peroxidase activities, which suggests multiple functions of CsSHN1 in regulating fruit skin netting and epidermal cell patterning. Among three representative cucumber inbred lines, three haplotypes at three polymorphic sites were identified inside CsSHN1: a functional copy in Gy14 (wild type) with light fruit skin netting, a copy number variant with two tandemly arrayed functional copies in WI7120 with heavy skin netting, and a loss-of-function copy in 9930 with smooth skin. The expression level of CsSHN1 in fruit exocarp of three lines was positively correlated with the skin netting intensity. Comparative analysis between cucumber and melon revealed conserved and divergent genetic mechanisms underlying fruit skin netting/reticulation that may reflect the different selection histories in the two crops. A discussion was made on genetic basis of fruit skin netting in the context of natural and artificial selections of fruit quality-related epidermal features during cucumber breeding.

Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies

High-throughput genotyping boosts genome-wide association studies (GWAS) in crop species, leading to the identification of single-nucleotide polymorphisms (SNPs) associated with economically important traits. Choosing a cost-effective genotyping method for crop GWAS requires careful examination of several aspects, namely, the purpose and the scale of the study, crop-specific genomic features, and technical and economic matters associated with each genotyping option. Once genotypic data have been obtained, quality control (QC) procedures must be applied to avoid bias and false signals in genotype–phenotype association tests. QC for human GWAS has been extensively reviewed; however, QC for crop GWAS may require different actions, depending on the GWAS population type. Here, we review most popular genotyping methods based on next-generation sequencing (NGS) and array hybridization, and report observations that should guide the investigator in the choice of the genotyping method for crop GWAS. We provide recommendations to perform QC in crop species, and deliver an overview of bioinformatics tools that can be used to accomplish all needed tasks. Overall, this work aims to provide guidelines to harmonize those procedures leading to SNP datasets ready for crop GWAS.

Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective

Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding,with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information onpopulation dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods.

QTL and Transcriptomic Analyses Implicate Cuticle Transcription Factor SHINE as a Source of Natural Variation for Epidermal Traits in Cucumber Fruit

The fruit surface is a unique tissue with multiple roles influencing fruit development, post-harvest storage and quality, and consumer acceptability. Serving as the first line of protection against herbivores, pathogens, and abiotic stress, the surface can vary markedly among species, cultivars within species, and developmental stage. In this study we explore developmental changes and natural variation of cucumber (Cucumis sativus L.) fruit surface properties using two cucumber lines which vary greatly for these traits and for which draft genomes and a single nucleotide polymorphism (SNP) array are available: Chinese fresh market type, Chinese Long '9930' (CL9930), and pickling type, 'Gy14'. Thin-section samples were prepared from the mid-region of fruit harvested at 0, 4, 8, 12, 16, 20, 24 and 30 days post pollination (dpp), stained with Sudan IV and evaluated for cuticle thickness, depth of wax intercalation between epidermal cells, epidermal cell size and shape, and number and size of lipid droplets. 'Gy14' is characterized by columnar shaped epidermal cells, a 2-3 fold thicker cuticular layer than CL9930, increased cuticular intercalations between cells and a larger number and larger sized lipid droplets. In both lines maximal deposition of cuticle and increase in epidermal size coincided with exponential fruit growth and was largely completed by approximately 16 dpp. Phenotyping and quantitative trait locus mapping (QTL) of fruit sampled from an F₇:F₈ Gy14 × CL9930 recombinant inbred line (RIL) population identified QTL regions on chromosomes 1, 4 and 5. Strong QTL for epidermal cell height, cuticle thickness, intercalation depth, and diameter of lipid droplets co-localized on chromosome 1. SSR markers on chromosome 1 were used to screen for recombinants in an extended RIL population to refine the QTL region. Further fine mapping by KASP assay combined with gene expression profiling suggested a small number of candidate genes. Tissue specificity, developmental analysis of expression, allelic diversity and gene function implicate the regulatory factor CsSHINE1/WIN1 as a source of natural variation for cucumber fruit epidermal traits.

QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population

Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized. The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line 'Coolgreen'. Phenotypic data on responses to natural DM and PM infection were collected in multi-year and multi-location replicated field trials. A high-density genetic map with 2780 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing and 55 microsatellite markers was developed, which revealed genomic regions with segregation distortion and mis-assemblies in the '9930' cucumber draft genome. QTL analysis identified 11 and 4 QTL for DM and PM resistances accounting for more than 73.5 and 63.0% total phenotypic variance, respectively. Among the 11 DM resistance QTL, dm5.1, dm5.2, and dm5.3 were major-effect contributing QTL, whereas dm1.1, dm2.1, and dm6.2 conferred susceptibility. Of the 4 QTL for PM resistance, pm5.1 was the major-effect QTL explaining 32.4% phenotypic variance and the minor-effect QTL pm6.1 contributed to disease susceptibility. Three PM QTL, pm2.1, pm5.1, and pm6.1, were co-localized with DM QTL dm2.1, dm5.2, and dm6.1, respectively, which was consistent with the observed linkage of PM and DM resistances in PI 197088. The genetic architecture of DM resistance in PI 197088 and another resistant line WI7120 (PI 330628) was compared, and the potential of using PI 197088 in cucumber breeding for downy and powdery mildew resistances is discussed.

Variation in cucumber (Cucumis sativus L.) fruit size and shape results from multiple components acting pre-anthesis and post-pollination

Morphological, QTL, and gene expression analyses indicate variation in cucumber fruit size and shape results from orientation, timing, and extent of cell division and expansion, and suggest candidate gene factors. Variation in cucumber (Cucumis sativus L.) fruit size and shape is highly quantitative, implicating interplay of multiple components. Recent studies have identified numerous fruit size and shape quantitative trait loci (QTL); however, underlying factors remain to be determined. We examined ovary and fruit development of two sequenced cucumber genotypes with extreme differences in fruit size and shape, Chinese Long '9930' (CL9930), and pickling type 'Gy14'. Differences were observed in several independent factors that can influence size and shape: ovule number, rate and period of cell division in longitudinal and cross section in ovaries and fruit, timing and rate of fruit expansion in length and diameter, and cell shape. Level and timing of expression of select fruit growth stage marker genes and candidate fruit size gene homologs associated with cucumber fruit size and shape QTL were examined from 5-day pre-anthesis to 20-day post-pollination. Our results indicate that variation in fruit size and shape results from differences in cell number and shape in longitudinal and cross section, driven in turn by differences in orientation, timing, and duration of cell division and expansion, both pre- and post-anthesis, and suggest candidate genes contributing to determination of cucumber fruit size and shape.

QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods

QTL mapping using NGS-assisted BSA was successfully applied to an F ₂ population for downy mildew resistance in cucumber. QTLs detected by NGS-assisted BSA were confirmed by conventional QTL analysis. Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive foliar diseases in cucumber. QTL mapping is a fundamental approach for understanding the genetic inheritance of DM resistance in cucumber. Recently, many studies have reported that a combination of bulked segregant analysis (BSA) and next-generation sequencing (NGS) can be a rapid and cost-effective way of mapping QTLs. In this study, we applied NGS-assisted BSA to QTL mapping of DM resistance in cucumber and confirmed the results by conventional QTL analysis. By sequencing two DNA pools each consisting of ten individuals showing high resistance and susceptibility to DM from a F₂ population, we identified single nucleotide polymorphisms (SNPs) between the two pools. We employed a statistical method for QTL mapping based on these SNPs. Five QTLs, dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1, were detected and dm2.2 showed the largest effect on DM resistance. Conventional QTL analysis using the F₂ confirmed dm2.2 (R ² = 10.8-24 %) and dm5.2 (R ² = 14-27.2 %) as major QTLs and dm4.1 (R ² = 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R ² = 28.2 %) was detected by the conventional QTL method using an F₃ population. This study demonstrated the effectiveness of NGS-assisted BSA for mapping QTLs conferring DM resistance in cucumber and revealed the unique genetic inheritance of DM resistance in this population through two distinct major QTLs on chromosome 2 that mainly harbor DM resistance.

QTL mapping for downy mildew resistance in cucumber inbred line WI7120 (PI 330628)

Host resistance in WI7120 cucumber to prevailing downy mildew pathogen field populations is conferred by two major-effect, one moderate-effect and two minor-effect QTL. Downy mildew (DM) caused by the obligate oomycete Pseudoperonospora cubensis is the most devastating fungal disease of cucumber worldwide. The molecular mechanism of DM resistance in cucumber is poorly understood, and use of marker-assisted breeding for DM resistance is not widely available. Here, we reported QTL mapping results for DM resistance with 243 F2:3 families from the cross between DM-resistant inbred line WI7120 (PI 330628) and susceptible '9930'. A linkage map was developed with 348 SSR and SNP markers. Phenotyping of DM inoculation responses were conducted in four field trails in 2 years at three locations. Four QTL, dm2.1, dm4.1, dm5.1, and dm6.1 were consistently and reliably detected across at least three of the four environments which together could explain 62-76 % phenotypic variations (R (2)). Among them, dm4.1 and dm5.1 were major-effect QTL (R (2) = 15-30 %) with only additive effects; dm2.1 (R (2) = 5-15 %) and dm6.1 (R (2) = 4-8 %) had moderate and minor effects, respectively. Epistatic effects were detected for dm2.1 and dm6.1 with both dm4.1 and dm5.1. One additional minor-effect QTL, dm6.2 (R (2) = 3-5 %) was only detectable with the chlorosis rating criterion. All alleles contributing to DM resistance were from WI7120. This study revealed two novel QTL for DM resistance and the unique genetic architecture of DM resistance in WI7120 conferring high level resistance to prevailing DM populations in multiple countries. The effects of disease rating scales, rating time and criteria, population size in phenotyping DM resistance on the power of QTL detection, and the use of DM resistance in WI7120 in cucumber breeding were discussed.

Integrated analysis in bi-parental and natural populations reveals CsCLAVATA3 (CsCLV3) underlying carpel number variations in cucumber

Carpel number variation in cucumber was controlled by a single gene, Cn . Linkage and association analysis revealed CsCLV3 as the candidate gene of the Cn locus. Carpel number (CN) is an important fruit quality trait of cucumber, but the genetic basis of CN variations is largely unknown. In the present study, segregating analysis in multiple bi-parental mapping populations (F2, F3, and RILs) derived from WI2757 (CN = 3) × True Lemon (CN = 5) suggested that CN is controlled by a simply inherited gene, Cn, with CN = 3 being incompletely dominant to CN = 5. Initial linkage mapping located Cn in a 1.9-Mb region of cucumber chromosome 1. Exploration of DNA sequence variations in this region with in silico bulked segregant analysis among eight re-sequenced lines allowed delimiting the Cn locus to a 16-kb region with five predicted genes including CsCLV3, a homolog of the Arabidopsis gene CLAVATA3. Fine genetic mapping in F2 and RIL populations and association analysis in natural populations confirmed CsCLV3 as the candidate gene for Cn, which was further evidenced from gene expression analysis and microscopic examination of floral meristem size in the two parent lines. This study highlights the importance of integrated use of linkage and association analysis as well as next-gen high-throughput sequencing in mapping and cloning genes that are difficult in accurate genotyping. The results provide new insights into the genetic control of CN variations in cucumber, which were discussed in the context of the well-characterized CLAVATA pathway for stem cell homeostasis and regulation of meristem sizes in plants. The associations of carpel number with fruit shape, size, and weight in cucumber and melon are also discussed.

QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes

QTL analysis in multi-development stages with different QTL models identified 12 consensus QTLs underlying fruit elongation and radial growth presenting a dynamic view of genetic control of cucumber fruit development. Fruit size is an important quality trait in cucumber (Cucumis sativus L.) of different market classes. However, the genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using F2, F2-derived F3 families and recombinant inbred lines (RILs) from a cross between two inbred lines Gy14 (North American picking cucumber) and 9930 (North China fresh market cucumber). Phenotypic data of fruit length and diameter were collected at three development stages (anthesis, immature and mature fruits) in six environments over 4 years. QTL analysis was performed with three QTL models including composite interval mapping (CIM), Bayesian interval mapping (BIM), and multiple QTL mapping (MQM). Twenty-nine consistent and distinct QTLs were detected for nine traits from multiple mapping populations and QTL models. Synthesis of information from available fruit size QTLs allowed establishment of 12 consensus QTLs underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Discussion was presented in the context of domestication and diversifying selection of fruit length and diameter, marker-assisted selection of fruit size, as well as identification of candidate genes for fruit size QTLs in cucumber.