The construction of a genetic linkage map of non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino)

SSR marker based analysis for identification and of genetic diversity of non-heading Chinese cabbage varieties

As a widely cultivated vegetable in China and Southeast Asia, the breeding of non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) is widespread; more than 400 varieties have been granted new plant variety rights (PVRs) in China. Distinctness is one of the key requirements for the granting of PVRs, and molecular markers are widely used as a robust supplementary method for similar variety selection in the distinctness test. Although many genome-wide molecular markers have been developed, they have not all been well used in variety identification and tests of distinctness of non-heading Chinese cabbage. In this study, by using 423 non-heading Chinese cabbage varieties collected from different regions of China, 287 simple sequence repeat (SSR) markers were screened for polymorphisms, and 23 core markers were finally selected. The polymorphic information content (PIC) values of the 23 SSR markers ranged from 0.555 to 0.911, with an average of 0.693, and the average number of alleles per marker was 13.65. Using these 23 SSR markers, 418 out of 423 varieties could be distinguished, with a discrimination rate of 99.994%. Field tests indicated that those undistinguished varieties were very similar and could be further distinguished by a few morphological characteristics. According to the clustering results, the 423 varieties could be divided into three groups: pak-choi, caitai, and tacai. The similarity coefficient between the SSR markers and morphological characteristics was moderate (0.53), and the efficiency of variety identification was significantly improved by using a combination of SSR markers and morphological characteristics.

Lipidomic study reveals the effect of morphological variation and other metabolite interactions on the lipid composition in various cultivars of Bok choy

Bok choy is an important Brassica vegetable which is also known for its wide range of cultivars that differ in their appearance, leaf color, size and shape. For the purpose to investigate the effect of these phenotypic differences on their lipid composition, seven morphotypes of NHCC (Suzhouqing, Aijaohuang, Wutacai, Yellowrose, Ziluolan, Xiangqingcai and Zicaitai) were selected for this study. For this reason, extensive metabolic approach was adopted which was mainly focused on lipidomics. The overall metabolic position of lipids was determined and the isolated lipid compounds were characterized on the basis of their lipid classes. Moreover, discriminative analysis was applied to monitor the distribution pattern of lipid in different cultivars. Aijiaohuang was the leading cultivar which contained highest lipid levels, whereas least proportion was found in Zicaitai. We proposed that leaf color might have an effect on the lipid composition such as purple cultivars were dominated in glycerophopholipids, light green in fatty acids and dark green were rich in glycerolipids. The level of metabolites differed greatly among different genotypes. Lipid-metabolite interactions revealed the positive correlation of lipids with flavonoid and hydroxycinnamoyl derivatives, whereas negative correlation was noticed in case of phenylamines. This is the first comprehensive study based on lipidomics in order to evaluate the substantial impact of various phenotypes on the metabolic composition of NHCC.

Genome-wide identification of SSR and SNP markers from the non-heading Chinese cabbage for comparative genomic analyses

BACKGROUND

Non-heading Chinese cabbage (NHCC), belonging to Brassica, is an important leaf vegetable in Asia. Although genetic analyses have been performed through conventional selection and breeding efforts, the domestication history of NHCC and the genetics underlying its morphological diversity remain unclear. Thus, the reliable molecular markers representative of the whole genome are required for molecular-assisted selection in NHCC.

RESULTS

A total of 20,836 simple sequence repeats (SSRs) were detected in NHCC, containing repeat types from mononucleotide to nonanucleotide. The average density was 62.93 SSRs/Mb. In gene regions, 5,435 SSRs were identified in 4,569 genes. A total of 5,008 primer pairs were designed, and 74 were randomly selected for validation. Among these, 60 (81.08%) were polymorphic in 18 Cruciferae. The number of polymorphic bands ranged from two to five, with an average of 2.70 for each primer. The average values of the polymorphism information content, observed heterozygosity, Hardy-Weinberg equilibrium, and Shannon's information index were 0.2970, 0.4136, 0.5706, and 0.5885, respectively. Four clusters were classified according to the unweighted pair-group method with arithmetic average cluster analysis of 18 genotypes. In addition, a total of 1,228,979 single nucleotide polymorphisms (SNPs) were identified in the NHCC through a comparison with the genome of Chinese cabbage, and the average SNP density in the whole genome was 4.33/Kb. The number of SNPs ranged from 341,939 to 591,586 in the 10 accessions, and the average heterozygous SNPs ratio was ~42.53%. All analyses showed these markers were high quality and reliable. Therefore, they could be used in the construction of a linkage map and for genetic diversity studies for NHCC in future.

CONCLUSIONS

This is the first systematic and comprehensive analysis and identification of SSRs in NHCC and 17 species. The development of a large number of SNP and SSR markers was successfully achieved for NHCC. These novel markers are valuable for constructing genetic linkage maps, comparative genome analysis, quantitative trait locus (QTL) mapping, genome-wide association studies, and marker-assisted selection in NHCC breeding system research.

Transmission ratio distortion of molecular markers in a doubled haploid population originated from a natural hybrid between Osmunda japonica and O. lancea

In ferns, intra-gametophytic selfing occurs as a mode of reproduction where two gametes from the same gametophyte form a completely homozygous sporophyte. Intra-gametophytic selfing is considered to be prevented by lethal or deleterious recessive genes in several diploid species. In order to investigate the modes and tempo of selection acting different developmental stages, doubled haploids obtained from intra-gametophytic selfing within isolated gametophytes of a putative F1 hybrid between Osmunda japonica and O. lancea were analyzed with EST_derived molecular markers, and the distribution pattern of transmission ratio distortion (TRD) along linkage map was clarified. As the results, the markers with skewness were clustered in two linkage groups. For the two highly distorted regions, gametophytes and F2 population were also examined. The markers skewed towards O. japonica on a linkage group (LG_2) showed skewness also in gametophytes, and the TRD was generated in the process of spore formation or growth of gametophytes. Also, selection appeared to be operating in the gametophytic stage. The markers on other linkage group (LG_11) showed highest skewness towards O. lancea in doubled haploids, and it was suggested that the segregation of LG_11 were influenced by zygotic lethality or genotypic evaluation and that some deleterious recessive genes exist in LG_11 and reduce the viability of homozygotes with O. japonica alleles. It is very likely that a region of LG_11were responsible for the low frequencies of intra-gametophytic selfing in O. japonica.

Genetic characterization and fine mapping of a yellow-seeded gene in Dahuang (a Brassica rapa landrace)

The development of yellow-seeded cultivars in Brassica rapa (B. rapa) would improve the quality and quantity of available oil. The identification and mapping of the seed coat color gene may aid in the development of yellow-seeded cultivars and facilitate introgression of the yellow-seeded gene into desirable Brassica napus (B. napus) lines through marker-assisted selection. In the current study, we investigated the inheritance of a yellow-seeded landrace in B. rapa, "Dahuang", originating from the Qinghai-Tibetan plateau. Genetic analysis revealed that the phenotype of the yellow-seeded trait in Dahuang is controlled by one recessive gene, termed Brsc1. Mapping of the Brsc1 gene was subsequently conducted in a BC(1) population comprised 456 individuals, derived from (Dahuang × 09A-126) × Dahuang. From a survey of 256 amplified fragment length polymorphism (AFLP) primer combinations, 10 tightly linked AFLP markers were obtained. The closest AFLP markers flanking Brsc1, Y10 and Y06, were 0.2 and 0.4 cM away, respectively. Subsequently, using simple sequence repeat (SSR) markers in the reference map, the Brsc1 gene was mapped on A09 in B. rapa. Blast analysis revealed that seven AFLP markers showed sequence homology to A09 of B. rapa, wherein six AFLP markers in our map were in the same order as those in A09 of B. rapa. The two closest markers, Y10 and Y06, delimited the Brsc1 gene within a 2.8 Mb interval. Furthermore, Y05 and Y06, the two closest AFLP markers on one side linked to Brsc1, were located in scaffold000059 on A09 of B. rapa, whereas the closet AFLP marker on the opposite side of Brsc1, Y10, was located in scaffold000081 on A09 of B. rapa. Molecular markers developed from these studies may facilitate marker-assisted selection (MAS) of yellow-seeded lines in B. rapa and B. napus and expedite the process of map-based cloning of Brsc1.