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Bitterness in cucumber fruit and foliage is due to the presence of cucurbitacins. Several genes have been described that control the trait, with bi (bi-1) making fruit and foliage bitter free and Bt (Bt-1) making the fruit highly bitter. Previous studies have reported the inheritance and molecular markers linked to bi-1 or Bt-1, but we were interested in studying the inheritance of fruit bitterness in the progeny of 2 nonbitter fruit inbred lines. The objective was to determine the inheritance of cucumber fruit and foliage bitterness and to locate them on a current linkage map using a recombinant inbred lines (RILs) population derived by crossing 9110Gt and 9930. It was concluded from the inheritance analysis that there were 2 loci controlling fruit bitterness in the population. One locus was in the same position as the location previously identified for bi-1, and another locus was for bi-3. Using a simple sequence repeat (SSR) linkage map, 2 loci for fruit bitterness in this RILs population were mapped. The locus of bi-1 was located at the region between SSR0004 and SSR02309 within the genetic distance of 5.2 cM on chromosome 6. The locus of bi-3 was placed in the region of SSR00116-SSR05321 within the genetic distance of 6.3 cM on chromosome 5. The physical distances for the regions of bi-1 and bi-3 were 11,430.94 Kb with 160 predicted genes and 1528.23 Kb with 198 predicted genes, respectively. Among 160 predicted genes for bi-1, there is a terpene synthase gene named Csa008595, which was speculated as the candidate gene of bi-1.

The extreme resistance to Turnip mosaic virus observed in the Chinese cabbage (Brassica rapa) line, BP8407, is monogenic and recessive. Bulked segregant analysis was carried out to identify simple sequence repeat and Indel markers linked to this recessive resistance gene, termed recessive Turnip mosaic virus resistance 02 (retr02). Mapping of PCR-specific Indel markers on 239 individuals of a BP8407 × Ji Zao Chun F(2) population, located this resistance gene to a 0.9-cM interval between two Indel markers (BrID10694 and BrID101309) and in scaffold000060 or scaffold000104 on chromosome A04 of the B. rapa genome. Eleven eukaryotic initiation factor 4E (eIF4E) and 14 eukaryotic initiation factor 4G (eIF4G) genes are predicted in the B. rapa genome. A candidate gene, Bra035393 on scaffold000104, was predicted within the mapped resistance locus. The gene encodes the eIF(iso)4E protein. Bra035393 was sequenced in BP8407 and Ji Zao Chun. A polymorphism (A/G) was found in exon 3 between BP8407 and Ji Zao Chun. This gene was analysed in four resistant and three susceptible lines. A correlation was observed between the amino acid substitution (Gly/Asp) in the eIF(iso)4E protein and resistance/susceptibility. eIF(iso)4E has been shown previously to interact with the TuMV genome-linked protein, VPg.

Glucosinolates (GS) are a group of amino acid-derived secondary metabolites found throughout the Cruciferae family. Glucosinolates and their degradation products play important roles in pathogen and insect interactions, as well as in human health. In order to elucidate the glucosinolate biosynthetic pathway in Brassica rapa, we conducted comparative genomic analyses of Arabidopsis thaliana and B. rapa on a genome-wide level. We identified 102 putative genes in B. rapa as the orthologs of 52 GS genes in A. thaliana. All but one gene was successfully mapped on 10 chromosomes. Most GS genes exist in more than one copy in B. rapa. A high co-linearity in the glucosinolate biosynthetic pathway between A. thaliana and B. rapa was also established. The homologous GS genes in B. rapa and A. thaliana share 59–91% nucleotide sequence identity and 93% of the GS genes exhibit synteny between B. rapa and A. thaliana. Moreover, the structure and arrangement of the B. rapa GS (BrGS) genes correspond with the known evolutionary divergence of B. rapa, and may help explain the profiles and accumulation of GS in B. rapa.

The Brassicaceae family which includes Arabidopsis thaliana, is a natural priority for reaching beyond botanical models to more deeply sample angiosperm genomic and functional diversity. Here we report the draft genome sequence and its annoation of Brassica rapa, one of the two ancestral species of oilseed rape. We modeled 41,174 protein-coding genes in the B. rapa genome. B. rapa has experienced only the second genome triplication reported to date, with its close relationship to A. thaliana providing a useful outgroup for investigating many consequences of triplication for its structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one copy containing a greater proportion of genes expected to have been present in its ancestor (70 percent) than the remaining two (46 percent and 36 percent). Both a generally rapid evolutionary rate, and specific copy number amplifications of particular gene families, may contribute to the remarkable propensity of Brassica species for the development of new morphological variants. The B. rapa genome provides a new resource for comparative and evolutionary analysis of the Brassicaceae genomes and also a platform for genetic improvement of Brassica oil and vegetable crops.

Scab, caused by Cladosporium cucumerinum Ell. et Arthur, is a prevalent disease of cucumber (Cucumis sativus L.) worldwide. Scab can cause serious losses for cucumber production, especially in protected culture such as high tunnel production. Resistance to cucumber scab is dominant and is controlled by a single gene, Ccu. Breeding for resistant cultivars is the most efficient way to control the disease. Selection for resistance might be made easier if the gene were mapped to linked markers. Thus far, there are no tightly linked (genetic distance less than 1 cM) simple sequence repeat (SSR) markers for the Ccu gene, and no studies on mapping of the Ccu gene in cucumber using SSR markers. The objective of this study was to identify SSR markers for use in molecular breeding of scab resistance. In this study, we used a population of recombinant inbred lines (RILs). The population included 148 individuals derived from the cucumber inbred line 9110 Gt (Ccu Ccu) crossed with line 9930 (ccu ccu). The Ccu gene was mapped to linkage group 2, corresponding to chromosome 2 of cucumber. The flanking markers SSR03084 and SSR17631 were linked to the Ccu gene with distances of 0.7 and 1.6 cM, respectively. The veracity of SSR03084 and SSR17631 was tested using 59 diverse inbred lines and hybrids, and the accuracy rate for the two markers was 98.3%. In conclusion, two SSRs closely linked to scab resistance gene Ccu have been identified and can be used in a cucumber breeding program.

FLOWERING LOCUS C (FLC), encoding a MADS-domain transcription factor in Arabidopsis, is a repressor of flowering involved in the vernalization pathway. This provides a good reference for Brassica species. Genomes of Brassica species contain several FLC homologues and several of these colocalize with flowering-time QTL. Here the analysis of sequence variation of BrFLC1 in Brassica rapa and its association with the flowering-time phenotype is reported. The analysis revealed that a G--A polymorphism at the 5' splice site in intron 6 of BrFLC1 is associated with flowering phenotype. Three BrFLC1 alleles with alternative splicing patterns, including two with different parts of intron 6 retained and one with the entire exon 6 excluded from the transcript, were identified in addition to alleles with normal splicing. It was inferred that aberrant splicing of the pre-mRNA leads to loss-of-function of BrFLC1. A CAPS marker was developed for this locus to distinguish Pi6+1(G) and Pi6+1(A). The polymorphism detected with this marker was significantly associated with flowering time in a collection of 121 B. rapa accessions and in a segregating Chinese cabbage doubled-haploid population. These findings suggest that a naturally occurring splicing mutation in the BrFLC1 gene contributes greatly to flowering-time variation in B. rapa.

In Chinese cabbage (Brassica rapa L. ssp. pekinensis), the locus associated with orange inner leaves has been mapped. The mechanism responsible for carotenoid pigment synthesis in orange inner leaves of Chinese cabbage is still unclear, however, and limited molecular research has been conducted on the candidate gene. In this study, high-performance liquid chromatographic analysis indicated that orange leaf coloration in Chinese cabbage is due to accumulation of prolycopene and other carotenoid pigments. Mapping of simple sequence repeat and insertion/deletion markers from 269 individuals of an F2 population pinpointed the Bror locus within a 1.0-cM interval, with the physical distance of 65.555 kb, on B. rapa chromosome A09. Using B. rapa genome annotation information, the candidate gene BrCRTISO (Bra031539) was predicted to reside within the mapped Bror locus. Coding and promoter regions were sequenced in white- and orange-type homozygous lines. A 6-bp deletion and 53 single nucleotide polymorphisms (SNPs), corresponding to two glutamic acid deletions and 12 amino acid mutations, were identified in the coding sequence of the orange-type cultivar. The orange-type promoter was approximately 141 bp shorter than that of the white type, and many SNPs were located in the promoter region. Two functional markers were designed and found to cosegregate with the Bror locus in F2 individuals. Expression analysis demonstrated that BrCRTISO transcription levels were higher in white-type Chinese cabbage than in the orange-type cultivar. These results offer insights into the molecular mechanism of carotenoid biosynthesis and lay the foundation for molecular breeding of orange-type Chinese cabbage.

Brassica rapa is a crop species of economic importance. It is cultivated worldwide as oil and vegetable crops. It belongs to the genus Brassica, tribe Brassiceae of the family Brassicaceae. The genus Brassica includes many important crops. Among them, relationship of six species formed the model of U’s triangle, with three basic diploid species B. rapa (A genome, n = 10), Brassica oleracea (C genome, n = 9) and B. nigra (B genome, n = 8) gave rise to three amphidiploid species Brassica napus (AC genome, n = 19), B. juncea (AB genome, n = 18) and B. carinata (BC genome, n = 17). Brassica species are rich in diversities, which are sufficient resources for plenty of crop morphotypes. In this chapter, as the start of the book, we will introduce the origin, evolution history, diversified morphotypes, and features for breeding application of B. rapa, as well as its investigation progresses in disease resistances, quality improvements focusing on glucosinolate contents and creatings of new materials.

Recessive strain-specific resistance to a number of plant viruses in the Potyvirus genus has been found to be based on mutations in the eukaryotic translation initiation factor 4E (eIF4E) and its isoform, eIF(iso)4E. We identified three copies of eIF(iso)4E in a number of Brassica rapa lines. Here we report broad-spectrum resistance to the potyvirus Turnip mosaic virus (TuMV) due to a natural mechanism based on the mis-splicing of the eIF(iso)4E allele in some TuMV-resistant B. rapa var. pekinensis lines. Of the splice variants, the most common results in a stop codon in intron 1 and a much truncated, non-functional protein. The existence of multiple copies has enabled redundancy in the host plant's translational machinery, resulting in diversification and emergence of the resistance. Deployment of the resistance is complicated by the presence of multiple copies of the gene. Our data suggest that in the B. rapa subspecies trilocularis, TuMV appears to be able to use copies of eIF(iso)4E at two loci. Transformation of different copies of eIF(iso)4E from a resistant B. rapa line into an eIF(iso)4E knockout line of Arabidopsis thaliana proved misleading because it showed that, when expressed ectopically, TuMV could use multiple copies which was not the case in the resistant B. rapa line. The inability of TuMV to access multiple copies of eIF(iso)4E in B. rapa and the broad spectrum of the resistance suggest it may be durable.

Udgivelsesdato: 2009-Dec Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most important vegetables in China. Genetic dissection of leaf mineral accumulation and tolerance to Zn stress is important for the improvement of the nutritional quality of Chinese cabbage by breeding. A mapping population with 183 doubled haploid (DH) lines was used to study the genetics of mineral accumulation and the growth response to Zn. The genetic map was constructed based on 203 AFLPs, 58 SSRs, 22 SRAPs and four ESTPs. The concentration of 11 minerals was determined in leaves for 142 DH lines grown in an open field. In addition shoot dry biomass (SDB) under normal, deficient and excessive Zn nutritional conditions were investigated in hydroponics experiments. Ten QTLs, each explaining 11.1¿17.1% of the Na, Mg, P, Al, Fe, Mn, Zn and Sr concentration variance, were identified by multiple-QTL model (MQM) mapping. One common QTL was found affecting SDB under normal, deficient and excessive Zn nutritional conditions. An additional QTL was detected for SDB under Zn excess stress only. These results offer insights into the genetic basis of leaf mineral accumulation and plant growth under Zn stress conditions in Chinese cabbage

Brassica rapa L. is an important vegetable crop in eastern Asia. The objective of this study was to investigate the genetic variation in leaf Zn, Fe and Mn accumulation, Zn toxicity tolerance and Zn efficiency in B. rapa. In total 188 accessions were screened for their Zn-related characteristics in hydroponic culture. In experiment 1, mineral assays on 111 accessions grown under sufficient Zn supply (2 ¿M ZnSO4) revealed a variation range of 23.2-155.9 ¿g g¿1 dry weight (d. wt.) for Zn, 60.3-350.1 ¿g g¿1 d. wt. for Fe and 20.9-53.3 ¿g g¿1 d. wt. for the Mn concentration in shoot. The investigation of tolerance to excessive Zn (800 ¿M ZnSO4) on 158 accessions, by using visual toxicity symptom parameters (TSPs), identified different levels of tolerance in B. rapa. In experiment 2, a selected sub-set of accessions from experiment 1 was characterized in more detail for their mineral accumulation and tolerance to excessive Zn supply (100 ¿M and 300 ¿M ZnSO4). In this experiment Zn tolerance (ZT) determined by relative root or shoot dry biomass varied about 2-fold. The same six accessions were also examined for Zn efficiency, determined as relative growth under 0 ¿M ZnSO4 compared to 2 ¿M ZnSO4. Zn efficiency varied 1.8-fold based on shoot dry biomass and 2.6-fold variation based on root dry biomass. Zn accumulation was strongly correlated with Mn and Fe accumulation both under sufficient and deficient Zn supply. In conclusion, there is substantial variation for Zn accumulation, Zn toxicity tolerance and Zn efficiency in Brassica rapa L., which would allow selective breeding for these traits.

Amplified fragment length polymorphism (AFLP) markers were employed to assess the genetic diversity amongst two large collections of Brassica rapa accessions. Collection A consisted of 161 B. rapa accessions representing different morphotypes among the cultivated B. rapa, including traditional and modern cultivars and breeding materials from geographical locations from all over the world and two Brassica napus accessions. Collection B consisted of 96 accessions, representing mainly leafy vegetable types cultivated in China. On the basis of the AFLP data obtained, we constructed phenetic trees using MEGA 2.1: software. The level of polymorphism was very high, and it was evident that the amount of genetic variation present within the groups was often comparable to the variation between the different cultivar groups. Cluster analysis revealed groups, often with low bootstrap values, which coincided with cultivar groups. The most interesting information revealed by the phenetic trees was that different morphotypes are often more related to other morphotypes from the same region (East Asia vs. Europe) than to similar morphotypes from different regions, suggesting either an independent origin and or a long and separate domestication and breeding history in both regions.

Background Carotenoids are isoprenoid compounds synthesized by all photosynthetic organisms. Despite much research on carotenoid biosynthesis in the model plant Arabidopsis thaliana, there is a lack of information on the carotenoid pathway in Brassica rapa. To better understand its carotenoid biosynthetic pathway, we performed a systematic analysis of carotenoid biosynthetic genes at the genome level in B. rapa. Results We identified 67 carotenoid biosynthetic genes in B. rapa, which were orthologs of the 47 carotenoid genes in A. thaliana. A high level of synteny was observed for carotenoid biosynthetic genes between A. thaliana and B. rapa. Out of 47 carotenoid biosynthetic genes in A. thaliana, 46 were successfully mapped to the 10 B. rapa chromosomes, and most of the genes retained more than one copy in B. rapa. The gene expansion was caused by the whole-genome triplication (WGT) event experienced by Brassica species. An expression analysis of the carotenoid biosynthetic genes suggested that their expression levels differed in root, stem, leaf, flower, callus, and silique tissues. Additionally, the paralogs of each carotenoid biosynthetic gene, which were generated from the WGT in B. rapa, showed significantly different expression levels among tissues, suggesting differentiated functions for these multi-copy genes in the carotenoid pathway. Conclusions This first systematic study of carotenoid biosynthetic genes in B. rapa provides insights into the carotenoid metabolic mechanisms of Brassica crops. In addition, a better understanding of carotenoid biosynthetic genes in B. rapa will contribute to the development of conventional and transgenic B. rapa cultivars with enriched carotenoid levels in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1655-5) contains supplementary material, which is available to authorized users.