A Functional Allele of CsFUL1 Regulates Fruit Length through Repressing CsSUP and Inhibiting Auxin Transport in Cucumber

FRUITFULL-like genes regulate flowering time and inflorescence architecture in tomato

The timing of flowering and the inflorescence architecture are critical for the reproductive success of tomato (Solanum lycopersicum), but the gene regulatory networks underlying these traits have not been fully explored. Here, we show that the tomato FRUITFULL-like (FUL-like) genes FUL2 and MADS-BOX PROTEIN 20 (MBP20) promote the vegetative-to-reproductive transition and repress inflorescence branching by inducing floral meristem (FM) maturation. FUL1 fulfils a less prominent role and appears to depend on FUL2 and MBP20 for its upregulation in the inflorescence- and floral meristems. MBP10, the fourth tomato FUL-like gene, has probably lost its function. The tomato FUL-like proteins cannot homodimerize in in vitro assays, but heterodimerize with various other MADS-domain proteins, potentially forming distinct complexes in the transition meristem and FM. Transcriptome analysis of the primary shoot meristems revealed various interesting downstream targets, including four repressors of cytokinin signaling that are upregulated during the floral transition in ful1 ful2 mbp10 mbp20 mutants. FUL2 and MBP20 can also bind in vitro to the upstream regions of these genes, thereby probably directly stimulating cell division in the meristem upon the transition to flowering. The control of inflorescence branching does not occur via the cytokinin oxidase/dehydrogenases (CKXs) but may be regulated by repression of transcription factors such as TOMATO MADS-box gene 3 (TM3) and APETALA 2b (AP2b).

CmFSI8/CmOFP13 encoding an OVATE family protein controls fruit shape in melon

Fruit shape is an important quality and yield trait in melon (Cucumis melo). Although some quantitative trait loci for fruit shape have been reported in in this species, the genes responsible and the underlying mechanisms remain poorly understood. Here, we identified and characterized a gene controlling fruit shape from two melon inbred lines, B8 with long-horn fruit and HP22 with flat-round fruit. Genetic analysis suggested that the shape was controlled by a single and incompletely dominant locus, which we designate as CmFSI8/CmOFP13. This gene was finely mapped to a 53.7-kb interval on chromosome 8 based on bulked-segregant analysis sequencing and map-based cloning strategies. CmFSI8/CmOFP13 encodes an OVATE family protein (OFP) and is orthologous to AtOFP1 and SlOFP20. The transcription level of CmFSI8/CmOFP13 in the ovary of HP22 was significantly higher than that in B8, and sequence analysis showed that a 12.5-kb genomic variation with a retrotransposon insertion identified in the promoter was responsible for elevating the expression, and this ultimately caused the differences in fruit shape. Ectopic overexpression of CmFSI8/CmOFP13 in Arabidopsis led to multiple phenotypic changes, including kidney-shaped leaves and shortened siliques. Taken together, our results demonstrate the involvement of an OFP in regulating fruit shape in melon, and our improved understanding of the molecular mechanisms will enable us to better manipulate fruit shape in breeding.

Genetic and Molecular Regulation Mechanisms in the Formation and Development of Vegetable Fruit Shape

Vegetable crops have a long history of cultivation worldwide and rich germplasm resources. With its continuous development and progress, molecular biology technology has been applied to various fields of vegetable crop research. Fruit is an important organ in vegetable crops, and fruit shape can affect the yield and commercialization of vegetables. In nature, fruits show differences in size and shape. Based on fruit shape diversity, the growth direction and coordination mechanism of fruits remain unclear. In this review, we discuss the latest research on fruit shape. In addition, we compare the current theories on the molecular mechanisms that regulate fruit growth, size, and shape in different vegetable families.

Cucurbitaceae genome evolution, gene function and molecular breeding

The Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationship, and functional genes associated with important agronomic traits (e.g., fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.

Pepper Fruit Elongation Is Controlled by Capsicum annuum Ovate Family Protein 20

Fruit shape is one of the most important quality traits of pepper (Capsicum spp.) and is used as a major attribute for the classification of fruit types. Wide natural variation in fruit shape exists among the major cultivated species Capsicum annuum, allowing the identification of several QTLs controlling the trait. However, to date, no genes underlying fruit shape QTLs have been conclusively identified, nor has their function been verified in pepper. We constructed a mapping population from a cross of round- and elongated-fruited C. annuum parents and identified a single major QTL on chromosome 10, termed fs10, explaining 68 and 70% of the phenotypic variation for fruit shape index and for distal fruit end angle, respectively. The QTL was mapped in several generations and was localized to a 5 Mbp region containing the ortholog of SlOFP20 that suppresses fruit elongation in tomato. Virus-induced gene silencing of the pepper ortholog CaOFP20 resulted in increased fruit elongation on two independent backgrounds. Furthermore, CaOFP20 exhibited differential expression in fs10 near-isogenic lines, as well as in an association panel of elongated- and round-fruited accessions. A 42-bp deletion in the upstream region of CaOFP20 was most strongly associated with fruit shape variation within the locus. Histological observations in ovaries and fruit pericarps indicated that fs10 exerts its effect on fruit elongation by controlling cell expansion and replication. Our results indicate that CaOFP20 functions as a suppressor of fruit elongation in C. annuum and is the most likely candidate gene underlying fs10.

Fine mapping and identification of the candidate gene BFS for fruit shape in wax gourd (Benincasa hispida)

Non-synonymous mutations in the BFS gene, which encodes the IQD protein, are responsible for the shape of wax gourd fruits. Fruit shape is an important agronomic trait in wax gourds. Therefore, in this study, we employed bulked segregant analysis (BSA) to identify a candidate gene for fruit shape in wax gourds within F₂ populations derived by crossing GX-71 (long cylindrical fruit, fruit shape index = 4.56) and MY-1 (round fruit, fruit shape index = 1.06) genotypes. According to BSA, the candidate gene is located in the 17.18 Mb region on chromosome 2. Meanwhile, kompetitive allele-specific PCR (KASP) markers were used to reduce it to a 19.6 Kb region. Only one gene was present within the corresponding region of the reference genome, namely Bch02G016830 (designated BFS). Subsequently, BFS was sequenced in six wax gourd varieties with different fruit shapes. Sequence analysis revealed two non-synonymous mutations in the round wax gourd and one non-synonymous mutation in the cylindrical wax gourd. Quantitative real‑time PCR (qRT-PCR) analysis further showed that the expression of BFS in round fruits was significantly higher than in long cylindrical fruits at the ovary formation stage. Therefore, BFS is a candidate gene for determination wax gourd shape. The predicted protein encoded by the BFS gene belongs to the IQ67-domain protein family, which have the structural characteristics of scaffold proteins and coordinate Ca²⁺ CaM signaling from the membrane to the nucleus. Ultimately, two derived cleaved amplified polymorphic sequence (dCAPS) markers were developed to facilitate marker-assisted selection for wax gourds breeding.

GmFULa improves soybean yield by enhancing carbon assimilation without altering flowering time or maturity

KEY MESSAGE

GmFULa improved soybean yield by enhancing carbon assimilation. Meanwhile, different from known yield-related genes, it did not alter flowering time or maturity. Soybean (Glycine max (L.) Merr.) is highly demanded by a continuously growing human population. However, increasing soybean yield is a major challenge. FRUITFULL (FUL), a MADS-box transcription factor, plays important roles in multiple developmental processes, especially fruit and pod development, which are crucial for soybean yield formation. However, the functions of its homologs in soybean are not clear. Here, through haplotype analysis, we found that one haplotype of the soybean homolog GmFULa (GmFULa-H02) is dominant in cultivated soybeans, suggesting that GmFULa-H02 was highly selected during domestication and varietal improvement of soybean. Interestingly, transgenic overexpression of GmFULa enhanced vegetative growth with more biomass accumulated and ultimately increased the yield but without affecting the plant height or changing the flowering time and maturity, indicating that it enhances the efficiency of dry matter accumulation. It also promoted the yield factors like branch number, pod number and 100-seed weight, which ultimately increased the yield. It increased the palisade tissue cell number and the chlorophyll content to promote photosynthesis and increase the soluble sugar content in leaves and fresh seeds. Furthermore, GmFULa were found to be sublocalized in the nucleus and positively regulate sucrose synthases (SUSs) and sucrose transporters (SUTs) by binding with the conserved CArG boxes in their promoters. Overall, these results showed GmFULa promotes the capacity of assimilation and the transport of the resultant assimilates to increase yield, and provided insights into the link between GmFULa and sucrose synthesis with transport-related molecular pathways that control seed yield.

GmFULc Is Induced by Short Days in Soybean and May Accelerate Flowering in Transgenic Arabidopsis thaliana

Flowering is an important developmental process from vegetative to reproductive growth in plant; thus, it is necessary to analyze the genes involved in the regulation of flowering time. The MADS-box transcription factor family exists widely in plants and plays an important role in the regulation of flowering time. However, the molecular mechanism of GmFULc involved in the regulation of plant flowering is not very clear. In this study, GmFULc protein had a typical MADS domain and it was a member of MADS-box transcription factor family. The expression analysis revealed that GmFULc was induced by short days (SD) and regulated by the circadian clock. Compared to wild type (WT), overexpression of GmFULc in transgenic Arabidopsis caused significantly earlier flowering time, while ful mutants flowered later, and overexpression of GmFULc rescued the late-flowering phenotype of ful mutants. ChIP-seq of GmFULc binding sites identified potential direct targets, including TOPLESS (TPL), and it inhibited the transcriptional activity of TPL. In addition, the transcription levels of FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and LEAFY (LFY) in the downstream of TPL were increased in GmFULc- overexpressionArabidopsis, suggesting that the early flowering phenotype was associated with up-regulation of these genes. Our results suggested that GmFULc inhibited the transcriptional activity of TPL and induced expression of FT, SOC1 and LFY to promote flowering.

Transcriptional control of local auxin distribution by the CsDFB1-CsPHB module regulates floral organogenesis in cucumber

Auxin is a key phytohormone influencing multiple aspects of plant development, including meristem maintenance, primordia initiation, floral organogenesis, and vascular differentiation. Local auxin biosynthesis and polar auxin transport are essential to establish and maintain auxin gradients that ensure proper plant development. Here, we demonstrate that CsDFB1, a member of the plant cystatin superfamily, which was previously implicated in defense responses, plays a critical role in regulating local auxin distribution and thus influences floral organogenesis in cucumber. Genetic and biochemical assays suggest that CsDFB1 affects local auxin distribution by acting as an attenuator that interacts with CsPHB and modulates CsPHB-mediated transcriptional control of CsYUC2 and CsPIN1. Our results shed light on the fine tuning of local auxin distribution in plants.

Plant cystatins are cysteine proteinase inhibitors that play key roles in defense responses. In this work, we describe an unexpected role for the cystatin-like protein DEFORMED FLORAL BUD1 (CsDFB1) as a transcriptional regulator of local auxin distribution in cucumber (Cucumis sativus L.). CsDFB1 was strongly expressed in the floral meristems, floral primordia, and vasculature. RNA interference (RNAi)-mediated silencing of CsDFB1 led to a significantly increased number of floral organs and vascular bundles, together with a pronounced accumulation of auxin. Conversely, accompanied by a decrease of auxin, overexpression of CsDFB1 resulted in a dramatic reduction in floral organ number and an obvious defect in vascular patterning, as well as organ fusion. CsDFB1 physically interacted with the cucumber ortholog of PHABULOSA (CsPHB), an HD-ZIP III transcription factor whose transcripts exhibit the same pattern as CsDFB1. Overexpression of CsPHB increased auxin accumulation in shoot tips and induced a floral phenotype similar to that of CsDFB1-RNAi lines. Furthermore, genetic and biochemical analyses revealed that CsDFB1 impairs CsPHB-mediated transcriptional regulation of the auxin biosynthetic gene YUCCA2 and the auxin efflux carrier PIN-FORMED1, and thus plays a pivotal role in auxin distribution. In summary, we propose that the CsDFB1-CsPHB module represents a regulatory pathway for local auxin distribution that governs floral organogenesis and vascular differentiation in cucumber.

Long-read genome assembly and genetic architecture of fruit shape in the bottle gourd

The bottle gourd (Lagenaria siceraria, Cucurbitaceae) is an important horticultural crop exhibiting tremendous diversity in fruit shape. The genetic architecture of fruit shape variation in this species remains unknown. We assembled a long-read-based, high-quality reference genome (ZAAS_Lsic_2.0) with a contig N50 value over 390-fold greater than the existing reference genomes. We then focused on dissection of fruit shape using a one-step geometric morphometrics-based functional mapping approach. We identified 11 quantitative trait loci (QTLs) responsible for fruit shape (fsQTLs), reconstructed their visible effects and revealed syntenic relationships of bottle gourd fsQTLs with 12 fsQTLs previously reported in cucumber, melon or watermelon. Homologs of several well-known and newly identified fruit shape genes, including SUN, OFP, AP2 and auxin transporters, were comapped with bottle gourd QTLs.

CsKTN1 for a katanin p60 subunit is associated with the regulation of fruit elongation in cucumber (Cucumis sativus L.)

We identified a short fruit3 (sf3) mutant in cucumber. Map-based cloning revealed that CsKTN1 gene encodes a katanin p60 subunit, which is associated with the regulation of fruit elongation. Fruit length is an important horticultural trait for both fruit yield and quality of cucumber (Cucumis sativus L.). Knowledge on the molecular regulation of fruit elongation in cucumber is very limited. In this study, we identified and characterized a cucumber short fruit3 (sf3) mutant. Histological examination indicated that the shorter fruit in the mutant was due to reduced cell numbers. Genetic analysis revealed that the phenotype of the sf3 mutant was controlled by a single gene with semi-dominant inheritance. By map-based cloning and Arabidopsis genetic transformation, we showed that Sf3 was a homolog of KTN1 (CsKTN1) encoding a katanin p60 subunit. A non-synonymous mutation in the fifth exon of CsKTN1 resulted in an amino acid substitution from Serine in the wild type to Phenylalanine in the sf3 mutant. CsKTN1 expressed in all tissues of both the wild type and the sf3 mutant. However, there was no significant difference in CsKTN1 expression levels between the wild type and the sf3 mutant. The hormone quantitation and RNA-seq analysis suggested that auxin and gibberellin contents are decreased in sf3 by changing the expression levels of genes related with auxin and gibberellin metabolism and signaling. This work helps understand the function of the katanin and the molecular mechanisms of fruit growth regulation in cucumber.

EjBZR1 represses fruit enlargement by binding to the EjCYP90 promoter in loquat

Loquat (Eriobotrya japonica) is a subtropical tree that bears fruit that ripens during late spring. Fruit size is one of the dominant factors inhibiting the large-scale production of this fruit crop. To date, little is known about fruit size regulation. In this study, we first discovered that cell size is more important to fruit size than cell number in loquat and that the expression of the EjBZR1 gene is negatively correlated with cell and fruit size. Virus-induced gene silencing (VIGS) of EjBZR1 led to larger cells and fruits in loquat, while its overexpression reduced cell and plant size in Arabidopsis. Moreover, both the suppression and overexpression of EjBZR1 inhibited the expression of brassinosteroid (BR) biosynthesis genes, especially that of EjCYP90A. Further experiments indicated that EjCYP90A, a cytochrome P450 gene, is a fruit growth activator, while EjBZR1 binds to the BRRE (CGTGTG) motif of the EjCYP90A promoter to repress its expression and fruit cell enlargement. Overall, our results demonstrate a possible pathway by which EjBZR1 directly targets EjCYP90A and thereby affects BR biosynthesis, which influences cell expansion and, consequently, fruit size. These findings help to elucidate the molecular functions of BZR1 in fruit growth and thus highlight a useful genetic improvement that can lead to increased crop yields by repressing gene expression.

A fruit ripening-associated transcription factor CsMADS5 positively regulates carotenoid biosynthesis in citrus

Carotenoids in citrus contribute to the quality of the fruit, but the mechanism of its transcriptional regulation is fairly unknown. Here, we characterized a citrus FRUITFULL sub-clade MADS gene, CsMADS5, that was ripening-inducible and acted as a nucleus-localized trans-activator. Transient overexpression of CsMADS5 in citrus induced fruit coloration and enhanced carotenoid concentrations. The expression of carotenogenic genes including phytoene synthase (PSY), phytoene desaturase (PDS), and lycopene β-cyclase 1 (LCYb1) was increased in the peels of fruits overexpressing CsMADS5. Similar results were observed from stable overexpression of CsMADS5 in tomato fruits and citrus calli, even though the effect of CsMADS5 on carotenoid metabolism in transgenic citrus calli was limited. Further biochemical analyses demonstrated that CsMADS5 activated the transcription of PSY, PDS, and LCYb1 by directly binding to their promoters. We concluded that CsMADS5 positively regulates carotenoid biosynthesis in fruits by directly activating the transcription of carotenogenic genes. Moreover, CsMADS5 physically interacted with a positive regulator CsMADS6, indicating that CsMADS5 may form an enhancer complex with CsMADS6 to synergistically promote carotenoid accumulation. These findings expand our understanding of the complex transcriptional regulatory hierarchy of carotenoid biosynthesis during fruit ripening.

A Positive Feedback Loop Mediated by CsERF31 Initiates Female Cucumber Flower Development: ETHYLENE RESPONSE FACTOR31 mediates a positive feedback loop that initiates female cucumber flower development

Sex determination is a crucially important developmental event that is pervasive throughout nature and enhances the adaptation of species. Among plants, cucumber (Cucumis sativus L.) can generate both unisexual and bisexual flowers, and the sex type is mainly controlled by several 1-aminocyclopropane-1-carboxylic acid (ACC) synthases. However, the regulatory mechanism of these synthases remains elusive. Here, we used gene expression analysis, protein-DNA interaction assays and transgenic plants to study the function of a gynoecium-specific gene, ETHYLENE RESPONSE FACTOR31 (CsERF31), in female flower differentiation. We found that in a predetermined female flower, ethylene signalling activates CsERF31 by CsEIN3, and then CsERF31 stimulates CsACS2, which triggers a positive feedback loop to ensure female rather than bisexual flower development. A similar interplay is functionally conserved in melon (Cucumis melo L.). Knockdown of CsERF31 by RNAi causes defective bisexual flowers to replace female flowers. Ectopic expression of CsERF31 suppresses stamen development and promotes pistil development in male flowers, demonstrating that CsERF31 functions as a sex switch. Taken together, our data confirm that CsERF31 represents the molecular link between female-male determination and female-bisexual determination, and provide mechanistic insight into how ethylene promotes female flowers, rather than bisexual flowers, in cucumber sex determination.

Roles of CsBRC1-like in leaf and lateral branch development in cucumber

TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) family genes, as plant-specific transcription factors, play vital roles in flower pattern, leaf development and plant architecture. Our recent study shows that the TCP gene BRANCHED1 (CsBRC1) specifically regulates shoot branching in cucumber. Here, we found CsBRC1 had a closely related paralogous gene CsBRC1-like. The synteny analysis revealed that these two genes originated from a segmental duplication. CsBRC1-like displayed different expression patterns in cucumber compared with CsBRC1, indicating that they may have functional differentiation. Ectopic expression of CsBRC1-like in Arabidopsis brc1-1 mutant resulted in reduced rosette branches and rosette leaves, whereas silencing CsBRC1-like in cucumber only led to a deformed true leaf of seedling rather than affecting the shoot branching. RNA-seq analysis of wild-type and CsBRC1-like-RNAi plants implicated that CsBRC1-like might regulate early leaf development through affecting the transcripts of auxin and cytokinin related genes in cucumber. Moreover, CsBRC1-like directly interacts with CsTCP10a and CsBRC1 in vivo. Our results demonstrated that CsBRC1-like has a specific role in regulating leaf development, and CsBRC1-like and CsBRC1 may have overlapping roles in shoot branching.

The Formation of Fruit Quality in Cucumis sativus L

Cucumber is one of the most widely grown vegetables in China and an indispensable fresh fruit in the diet. With the development of society, the demand of people for cucumber quality is higher and higher. Therefore, cultivating high-quality cucumber varieties is one of the main goals of cucumber breeding. With the rapid development of biotechnology such as molecular marker, cucumber quality control network is becoming clear. In this review, we describe the formation mechanism of cucumber fruit quality from three aspects: (1) the commercial quality of cucumber fruit, (2) nutritional quality formation, and (3) flavor quality of cucumber fruit. In addition, the determinants of cucumber fruit quality were summarized from two aspects of genetic regulation and cultivation methods in order to provide ideas for cucumber researchers and cultivators to improve fruit quality.

The VvSUPERMAN-like Gene Is Differentially Expressed between Bicarpellate and Tricarpellate Florets of Vitis vinifera L. Cv. 'Xiangfei' and Its Heterologous Expression Reduces Carpel Number in Tomato

Multicarpellate fruits are larger and produce more seeds than mono- or bicarpellate fruits, enhancing the reproductive capacity of the plant. To identify the phenotypic and molecular differences among florets of different carpel types, we studied carpel formation and fusion in the grapevine (Vitis vinifera) cultivar 'Xiangfei', which produces a high proportion of multicarpellate fruit. We also determined the function of VvSUPERMAN-like (VvSUP-like) and explored its relationship with VvWUS (VvWUSCHEL) and VvAG1 (VvAGAMOUS), which is related to the formation of carpel primordia. We showed that carpel formation and fusion were largely consistent between bicarpellate and tricarpellate ovaries, which both involve congenital fusion; rather, the differences between these ovary types arose from variation in carpel primordia number and location. Transgenic tomato (Solanum lycopersicum) plants expressing VvSUP-like produced significantly fewer carpels and other floral organs than the wild type. Moreover, transcriptome sequencing results indicate that VvSUP-like was more highly expressed in bicarpellate than in tricarpellate 'Xiangfei' florets. Luciferase reporter assays indicated that VvSUP-like inhibits the expression of VvAG1 and VvWUS by directly binding to their promoters, and VvWUS promotes VvAG1 expression by directly binding to its promoter. VvSUP-like inhibits the feedback signaling between VvWUS and VvAG1. Together, these results suggest that VvSUP-like negatively regulates the number of carpels that develop by inhibiting VvAG1 and VvWUS expression.

Localization shift of a sugar transporter contributes to phloem unloading in sweet watermelons

Unloading sugar from sink phloem by transporters is complex and much remains to be understood about this phenomenon in the watermelon fruit. Here, we report a novel vacuolar sugar transporter (ClVST1) identified through map-based cloning and association study, whose expression in fruit phloem is associated with accumulation of sucrose (Suc) in watermelon fruit. ClVST1⁹⁷ knockout lines show decreased sugar content and total biomass, whereas overexpression of ClVST1⁹⁷ increases Suc content. Population genomic and subcellular localization analyses strongly suggest a single-base change at the coding region of ClVST1⁹⁷ as a major molecular event during watermelon domestication, which results in the truncation of 45 amino acids and shifts the localization of ClVST1⁹⁷ to plasma membranes in sweet watermelons. Molecular, biochemical and phenotypic analyses indicate that ClVST1⁹⁷ is a novel sugar transporter for Suc and glucose efflux and unloading. Functional characterization of ClVST1 provides a novel strategy to increase sugar sink potency during watermelon domestication.

Arabidopsis Col/Ler and Ws/Ler hybrids and Hybrid Mimics produce seed yield heterosis through increased height, inflorescence branch and silique number

The seed yield increase of the hybrids and their derived Mimics compared to parents is associated with increased plant height and inflorescence branch number which are correlated with decreased expression of FT, SOC1 and FUL. In Arabidopsis, plant size has been extensively investigated, but few studies have been carried out on seed yield heterosis. In hybrids between Columbia (Col) and Landsberg erecta (Ler), and Wassilewskija (Ws) and Ler, there was significant seed yield heterosis. F6/F7 Hybrid Mimics derived from hybrids of each of the two systems had seed yield increases similar to that of the F1 hybrid (approximately 50-70% greater than the average of the parents). Increased seed yield of the Hybrid Mimics was accompanied by changes of plant architecture with increased plant height and increased inflorescence branch number relative to the parents. Three of the Hybrid Mimic lines derived from the Ws/Ler system had 20% increase in seed yield relative to the F1 hybrid. Genes which repress flowering were up-regulated and the expression levels of flowering -promoting genes including FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) and FRUITFULL (FUL) were negatively correlated with the increase in seed yield in both hybrids and F7 Mimics of both systems.

Localization of quantitative trait loci for cucumber fruit shape by a population of chromosome segment substitution lines

Cucumber fruit shape, a significant agronomic trait, is controlled by quantitative trait loci (QTLs). Feasibility of chromosome segment substitution lines (CSSLs) is well demonstrated to map QTLs, especially the minor-effect ones. To detect and identify QTLs with CSSLs can provide new insights into the underlying mechanisms regarding cucumber fruit shape. In the present study, 71 CSSLs were built from a population of backcross progeny (BC4F2) by using RNS7 (a round-fruit cucumber) as the recurrent parent and CNS21 (a long-stick-fruit cucumber) as the donor parent in order to globally detect QTLs for cucumber fruit shape. With the aid of 114 InDel markers covering the whole cucumber genome, 21 QTLs were detected for fruit shape-related traits including ovary length, ovary diameter, ovary shape index, immature fruit length, immature fruit diameter, immature fruit shape index, mature fruit length, mature fruit diameter and mature fruit shape index, and 4 QTLs for other traits including fruit ground and flesh color, and seed size were detected as well. Together our results provide important resources for the subsequent theoretical and applied researches on cucumber fruit shape and other traits.

Cucumber Fruit Size and Shape Variations Explored from the Aspects of Morphology, Histology, and Endogenous Hormones

Fruit size and shape are important qualities and yield traits in cucumber (Cucumis sativus L.), but the factors that influence fruit size and shape remain to be explored. In this study, we investigated the dynamic changes of fruit size and shape from the aspects of morphology, cellular levels and endogenous hormones for nine typical cucumber inbred lines. The results show that fruit length had a strong positive correlation to the cell number in the longitudinal section of fruit throughout the four stages of 0, 6, 12, and 30 DAA (days after anthesis). However, the significant negative correlations were found between fruit length and the fruit cell size at 12 and 30 DAA. Furthermore, fruit diameter was positively correlated to the cell number in the cross section at all the investigated fruit growth stages. The indole-3-acetic acid (IAA) content showed significant positive correlations to the fruit length at all fruit growth stages of −6, −3, 0, 3, 6, 9 and 12 DAA, but IAA content and fruit diameter showed significant negative correlations for all the stages except for at −6 DAA. The trans-zeatin riboside (tZR), zeatin (ZT), gibberellic acid (GA₃) and jasmonic acid (JA) content had a positive or negative correlation with fruit length or diameter only at certain stages. Neither fruit length nor diameter had significant correlations to abscisic acid (ABA) content. These results indicate that variations in fruit size and shape of different cucumber inbred lines mainly result from the differences in fruit cell number and endogenous IAA content. The present work is the first to propose cucumber fruit size and shape changes from the combined aspects of morphology, cellular levels, and endogenous hormones.

Recent progress on the molecular breeding of Cucumis sativus L. in China

Molecular breeding of Cucumis sativus L. is based on traditional breeding techniques and modern biological breeding in China. There are opportunities for further breeding improvement by molecular design breeding and the automation of phenotyping technology using untapped sources of genetic diversity. Cucumber (Cucumis sativus L.) is an important vegetable cultivated worldwide. It bears fruits of light fragrance, and crisp texture with high nutrition. China is the largest producer and consumer of cucumber, accounting for 70% of the world's total production. With increasing consumption demand, the production of Cucurbitaceae crops has been increasing yearly. Thus, new cultivars that can produce high-quality cucumber with high yield and easy cultivation are in need. Conventional genetic breeding has played an essential role in cucumber cultivar innovation over the past decades. However, its progress is slow due to the long breeding period, and difficulty in selecting stable genetic characters or genotypes, prompting researchers to apply molecular biotechnologies in cucumber breeding. Here, we first summarize the achievements of conventional cucumber breeding such as crossing and mutagenesis, and then focus on the current status of molecular breeding of cucumber in China, including the progress and achievements on cucumber genomics, molecular mechanism underlying important agronomic traits, and also on the creation of high-quality multi-resistant germplasm resources, new variety breeding and ecological breeding. Future development trends and prospects of cucumber molecular breeding in China are also discussed.

Genome-wide analysis of CsWOX transcription factor gene family in cucumber (Cucumis sativus L.)

WUSCHEL-related homeobox (WOX) transcription factors are plant-specific members that characterized by the presence of a homeodomain. It has been shown that WOX members regulate several aspects of plant development, but the biological functions of this CsWOX gene family remain largely unknown in cucumber (Cucumis sativus L.). In this study, we identified and characterized 11 putative CsWOX genes in cucumber, which are also divided into three major clades (e.g., the Ancient clade, the Intermediate clade and the WUS clade). Expression pattern analysis revealed tissue-specific expression patterns of CsWOX genes, including that CsWOX9 is mainly expressed in developing fruit and also has lower expression in tip and axillary bud, which was further confirmed by in situ hybridization assay. Moreover, overexpression of CsWOX9 in Arabidopsis led to increased branches and rosette leaves, and shorter siliques. Together, these results indicated that CsWOX members may regulate cucumber growth and development.

Gene regulatory network controlling carpel number variation in cucumber

The WUSCHEL-CLAVATA3 pathway genes play an essential role in shoot apical meristem maintenance and floral organ development, and under intense selection during crop domestication. The carpel number is an important fruit trait that affects fruit shape, size and internal quality in cucumber, but the molecular mechanism remains elusive. Here, we found that CsCLV3 expression was negatively correlated with carpel number in cucumber cultivars. CsCLV3-RNAi led to increased number of petals and carpels, whereas overexpression of CsWUS resulted in more sepals, petals and carpels, suggesting that CsCLV3 and CsWUS function as a negative and a positive regulator for carpel number variation, respectively. Biochemical analyses indicated that CsWUS directly bound to the promoter of CsCLV3 and activated its expression. Overexpression of CsFUL1^A , a FRUITFULL-like MADS-box gene, resulted in more petals and carpels. CsFUL1^A can directly bind to the CsWUS promoter to stimulate its expression. Furthermore, we found that auxin participated in carpel number variation in cucumber through interaction of CsARF14 with CsWUS. Therefore, we have identified a gene regulatory pathway involving CsCLV3, CsWUS, CsFUL1^A and CsARF14 in determining carpel number variation in an important vegetable crop - cucumber.

Glutamine application promotes nitrogen and biomass accumulation in the shoot of seedlings of the maize hybrid ZD958

Glutamine (Gln) is an efficient nitrogen source in promoting aboveground nitrogen and biomass accumulation in ZD958 (an elite maize hybrid with great potential for further genetic improvement) seedlings when conditioning a smaller but adequate root system. Amino acids account for a significant part of nitrogen (N) resources in the soil. However, how amino acid-N affects crop growth remains to be further investigated. Here, glutamine (Gln) application (80% NH₄NO₃ + 20% Gln; mixed N) enhanced shoot growth of the maize hybrid ZD958. N concentration in the shoot increased, which is associated with favorable increases in SPAD values, GS/GOGAT activities, and accumulation of glutamate, asparagine, total free amino acids and soluble proteins in the shoot under mixed N. On the other hand, root growth was reduced when exposed to Gln as indicated by the significantly lower dry weight, root/shoot ratio, and primary, seminal, crown, and total root lengths, as well as unfavorable physiological alterations. Up-regulation of expression of ZmAMT1.3, ZmNRT2.1, and ZmAAP2 in the root and that of ZmAMT1.1, ZmAMT1.3, and ZmLHT1 in the shoot preconditioned N over-accumulation in the shoot and facilitated shoot growth, presumably via enhancing N translocation to the shoot, when Gln was supplied. Together, Gln is an efficient N source in promoting aboveground N and biomass accumulation in ZD958 seedlings when conditioning a smaller but adequate root system. Notably, ZD958's parental lines Z58 and Chang7-2 displayed a wide range of variations in Gln responses, which may be partially attributed to single nucleotide polymorphisms (SNPs) in cis-elements and coding regions revealed in this study and much larger quantities of unidentified genetic variations between Z58 and Chang7-2. Extensive genetic divergence of these two elite inbred lines implied large potentials for further genetic improvement of ZD958 in relation to organic N use efficiency.

Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature

Cucumber, Cucumis sativus L. (2n = 2x = 14), is an important vegetable crop worldwide. It was the first specialty crop with a publicly available draft genome. Its relatively small, diploid genome, short life cycle, and self-compatible mating system offers advantages for genetic studies. In recent years, significant progress has been made in molecular mapping, and identification of genes and QTL responsible for key phenotypic traits, but a systematic review of the work is lacking. Here, we conducted an extensive literature review on mutants, genes and QTL that have been molecularly mapped or characterized in cucumber. We documented 81 simply inherited trait genes or major-effect QTL that have been cloned or fine mapped. For each gene, detailed information was compiled including chromosome locations, allelic variants and associated polymorphisms, predicted functions, and diagnostic markers that could be used for marker-assisted selection in cucumber breeding. We also documented 322 QTL for 42 quantitative traits, including 109 for disease resistances against seven pathogens. By alignment of these QTL on the latest version of cucumber draft genomes, consensus QTL across multiple studies were inferred, which provided insights into heritable correlations among different traits. Through collaborative efforts among public and private cucumber researchers, we identified 130 quantitative traits and developed a set of recommendations for QTL nomenclature in cucumber. This is the first attempt to systematically summarize, analyze and inventory cucumber mutants, cloned or mapped genes and QTL, which should be a useful resource for the cucurbit research community.

Comparative population genomics dissects the genetic basis of seven domestication traits in jujube

Jujube (Ziziphus jujuba Mill.) is an important perennial fruit tree with a range of interesting horticultural traits. It was domesticated from wild jujube (Ziziphus acidojujuba), but the genomic variation dynamics and genetic changes underlying its horticultural traits during domestication are poorly understood. Here, we report a comprehensive genome variation map based on the resequencing of 350 accessions, including wild, semi-wild and cultivated jujube plants, at a >15× depth. Using the combination of a genome-wide association study (GWAS) and selective sweep analysis, we identified several candidate genes potentially involved in regulating seven domestication traits in jujube. For fruit shape and kernel shape, we integrated the GWAS approach with transcriptome profiling data, expression analysis and the transgenic validation of a candidate gene to identify a causal gene, ZjFS3, which encodes an ethylene-responsive transcription factor. Similarly, we identified a candidate gene for bearing-shoot length and the number of leaves per bearing shoot and two candidate genes for the seed-setting rate using GWAS. In the selective sweep analysis, we also discovered several putative genes for the presence of prickles on bearing shoots and the postharvest shelf life of fleshy fruits. This study outlines the genetic basis of jujube domestication and evolution and provides a rich genomic resource for mining other horticulturally important genes in jujube.

Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective

The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.

CsBRC1 inhibits axillary bud outgrowth by directly repressing the auxin efflux carrier CsPIN3 in cucumber

Shoot branching is an important agronomic trait that directly determines plant architecture and affects crop productivity. To promote crop yield and quality, axillary branches need to be manually removed during cucumber production for fresh market and thus are undesirable. Auxin is well known as the primary signal imposing for apical dominance and acts as a repressor for lateral bud outgrowth indirectly. The TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) family gene BRANCHED1 (BRC1) has been shown to be the central integrator for multiple environmental and developmental factors that functions locally to inhibit shoot branching. However, the direct molecular link between auxin and BRC1 remains elusive. Here we find that cucumber BRANCHED1 (CsBRC1) is expressed in axillary buds and displays a higher expression level in cultivated cucumber than in its wild ancestor. Knockdown of CsBRC1 by RNAi leads to increased bud outgrowth and reduced auxin accumulation in buds. We further show that CsBRC1 directly binds to the auxin efflux carrier PIN-FORMED (CsPIN3) and negatively regulates its expression in vitro and in vivo. Elevated expression of CsPIN3 driven by the CsBRC1 promoter results in highly branched cucumber with decreased auxin levels in lateral buds. Therefore, our data suggest that CsBRC1 inhibits lateral bud outgrowth by direct suppression of CsPIN3 functioning and thus auxin accumulation in axillary buds in cucumber, providing a strategy to breed for cultivars with varying degrees of shoot branching grown in different cucumber production systems.