Garlic, an economically important vegetable, spice, and medicinal crop, produces highly enlarged bulbs and unique organosulfur compounds. Here, we report a chromosome-level genome assembly for garlic, with a total size of approximately 16.24 Gb, as well as the annotation of 57 561 predicted protein-coding genes, making garlic the first Allium species with a sequenced genome. Analysis of this garlic genome assembly reveals a recent burst of transposable elements, explaining the substantial expansion of the garlic genome. We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans, and provided new insights into the biosynthesis of these two compounds. Furthermore, a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs. The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding.

Two phenolic compound parameters (total phenolic and flavonoid contents) and 5 antioxidant parameters (DPPH [2, 2-diphenyl-1-picrylhydrazyl] radical scavenging activity, HRSC (hydroxyl radical scavenging capacity), FRAP (ferric ion reducing antioxidant power), CUPRAC (cupric ion reducing antioxidant capacity), and MCA (metal chelating activity) were measured in bulbs and bolts of 43 garlic cultivars. The bulbs of cultivar ‘74-x’ had the highest phenolic content (total phenolic, flavonoids) and the strongest antioxidant capacity (DPPH, FRAP, and CUPRAC), followed by bulbs of cultivar ‘Hanzhong purple’; the bulbs of cultivar ‘Gailiang’ had the lowest phenolic content and antioxidant capacity (FRAP, CUPRAC, MCA). The bolts of ‘Hanzhong purple’ also had higher phenolic content. Principal components analysis (PCA) separated the cultivars into 3 groups according to phenolic and flavonoid contents and strength of antioxidant activity. The first group had higher HRSC, FRAP, and flavonoid content; the second group had higher total phenolic content and MCA; some cultivars in the third group had higher HRSC and FRAP. All 8 test garlic bulb extracts successfully prevented Human Vascular Endothelial Cell death and significantly prevented reactive-oxygen species (ROS) formation in oxidative stress model, in which cultivar ‘74-x’ had highest protection capability, following by cultivar ‘Hanzhong purple’, and the bulbs of cultivar ‘No. 105 from Korea’ had the lower protection capability against cell death and ROS formation. The protection capability in vivo of these garlic cultivars was consistent with their phenolic content and antioxidant capacity.

A single-nucleotide insertion resulted in a premature stop codon that is responsible for white immature fruit color in cucumber. Despite our previous progress in the mapping of the gene controlling white color in immature cucumber fruit and the identification of candidate genes, the specific gene that governs chlorophyll metabolism and its regulatory mechanism remains unknown. Here, we generated a mapping population consisting of 9497 F2 plants to delimit the controlling gene to an 8.2-kb physical interval that defines a sole candidate gene, APRR2. Sequencing the full-length DNA and cDNA of APRR2 allowed for identification of an allele, aprr2, encoding a truncated 101-amino acid protein due to a frameshift mutation and a premature stop codon. Gene structure prediction indicated that these 101 residues are located in a domain necessary for the function of the protein. The expression patterns of APRR2 were entirely consistent with the visual changes in green color intensity during fruit development. A microscopic observation of the fruit pericarp revealed fewer chloroplasts and a lower chloroplast chlorophyll storage capacity in Q24 (white) than in Q30 (green). A single-base insertion in the white color gene w, which leads to a premature stop codon, is hypothesized to have disabled the function of this gene in chlorophyll accumulation and chloroplast development. These findings contribute to basic research and the genetic improvement of fruit color.

Relay intercropping represents an alternative for sustainable production of vegetables, but the changes of internally antioxidant defense combined with the growth and yield are not clear. Field experiment was carried out to investigate the malondialdehyde (MDA) content and activity levels of superoxide dismutase (SOD), peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL) in eggplant (Solanum melongena L.) and plant height, stem diameter, maximal leaf area, and yield of eggplant grown under successive cropping in the year 2011 and 2012 to see if relay intercropping with garlic (Allium sativum L.) could benefit to eggplant growth and yield. Three experimental treatments with three repeats in each were carried out (completely randomized block design): eggplant monoculture (CK), eggplant relay intercropping with normal garlic (NG), and eggplant relay intercropping with green garlic (GG). In both years, the MDA content was significantly lower and SOD and POD activities were generally lower in NG and GG compared with CK in most sampling dates. PPO activity trends were generally opposite to those of POD. The general trend of PAL activity was similar to MDA. The plant height and stem of eggplant was lower, but the maximal leaf area was larger in NG and GG in 2011; in 2012 the plant growth was stronger in relay intercropping treatments. For eggplant yield in 2011, NG was 2.85% higher than CK; after the time for the green garlic pulled out was moved forward in 2012, the yield was increased by 6.26 and 7.80%, respectively, in NG and GG. The lower MDA content and enzyme activities in relay intercropping treatments showed that the eggplant suffered less damage from environment and continuous cropping obstacles, which promoted healthier plant. Thus from both the growth and physiological perspective, it was concluded that eggplant/garlic relay intercropping is a beneficial cultivation practice maintaining stronger plant growth and higher yield.

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A pot-based experiment was conducted to investigate nutrient concentrations in cucumber plants intercropped with various amounts of green garlic. In addition, the soil nutrient contents were studied over two consecutive growing seasons. The results revealed that the accumulation of biomass and the nutritional elements nitrogen (N), phosphorus (P), potassium (K), calcium (Ca) and manganese (Mn) in cucumber plants were significantly increased for intercropping treatments during the two growing seasons compared to monoculture. Conversely, magnesium (Mg) concentrations were decreased in the cucumber plants. Shoot iron (Fe) concentrations decreased whereas root Fe concentrations increased in the intercropping system. Shoot and root zinc (Zn) concentrations decreased during the fall of 2011 but increased during the spring of 2012. Soil organic matter and available N, P and K were significantly increased as the proportion of intercropped green garlic increasing. Medium levels of intercropping green garlic improved cucumber nutrient concentrations the most. The regression analysis showed that the concentrations of most elements were significantly related to the amounts of garlic bulbs, especially the microelements in the spring 2011. The available soil N and organic matter were linearly related to the amounts of garlic bulbs. The results indicate that the nutritional status of the soil and plants of continuously cropped cucumber could be improved by intercropping with green garlic.

QTL analysis revealed two interacting loci, FS1.2 and FS2.1, underlying round fruit shape in WI7239 cucumber; CsSUN , a homolog of tomato fruit shape gene SUN , was a candidate for FS1.2. Fruit size is an important quality and yield trait in cucumber, but its genetic basis remains poorly understood. Here we reported QTL mapping results on fruit size with segregating populations derived from the cross between WI7238 (long fruit) and WI7239 (round fruit) inbred cucumber lines. Phenotypic data of fruit length and diameter were collected at anthesis, immature and mature fruit stages in four environments. Ten major-effect QTL were detected for six traits; synthesis of information from these QTL supported two genes, FS1.2 and FS2.1, underlying fruit size variation in the examined populations. Under the two-gene model, deviation from expected segregation ratio in fruit length and diameter among segregating populations was observed, which could be explained mainly by the interactions between FS1.2 and FS2.1, and segregation distortion in the FS2.1 region. Genome-wide candidate gene search identified CsSUN, a homolog of the tomato fruit shape gene SUN, as the candidate for FS1.2. The round-fruited WI7239 had a 161-bp deletion in the first exon of CsSUN, and its expression in WI7239 was significantly lower than that in WI7238. A marker derived from this deletion was mapped at the peak location of FS1.2 in QTL analysis. Comparative analysis suggested the melon gene CmSUN-14, a homolog of CsSUN as a candidate of the fl2/fd2/fw2 QTL in melon. This study revealed the unique genetic architecture of round fruit shape in WI7239 cucumber. It also highlights the power of QTL analysis for traits with a simple genetic basis but their expression is complicated by other factors.

Soil sickness is a critical problem for eggplant (Solanum melongena L.) under continuous cropping that affects sustainable eggplant production. Relay intercropping is a significant technique on promoting soil quality, improving eco-environment, and raising output. Field experiments were conducted from September 2010 to November 2012 in northwest China to determine the effects of relay intercropping eggplant with garlic (Allium sativum L.) on soil enzyme activities, available nutrient contents, and pH value under a plastic tunnel. Three treatments were in triplicate using randomized block design: eggplant monoculture (CK), eggplant relay intercropping with normal garlic (NG) and eggplant relay intercropping with green garlic (GG). The major results are as follows: (1) the activities of soil invertase, urease, and alkaline phosphatase were generally enhanced in NG and GG treatments; (2) relay intercropping significantly increased the soil available nutrient contents, and they were mostly higher in GG than NG. On April 11, 2011, the eggplant/garlic co-growth stage, the available nitrogen content in GG was 76.30 mg·kg−1, significantly higher than 61.95 mg·kg−1 in NG. For available potassium on April 17, 2012, they were 398.48 and 387.97 mg·kg−1 in NG and GG, both were significantly higher than 314.84 mg·kg−1 in CK; (3) the soil pH showed a significantly higher level in NG treatment, but lower in GG treatment compared with CK. For the last samples in 2012, soil pH in NG and GG were 7.70 and 7.46, the highest and lowest one among them; (4) the alkaline phosphatase activity and pH displayed a similar decreasing trend with continuous cropping. These findings indicate that relay intercropping eggplant with garlic could be an ideal farming system to effectively improve soil nutrient content, increase soil fertility, and alleviate soil sickness to some extent. These findings are important in helping to develop sustainable eggplant production.