The reference genetic linkage map for the multinational Brassica rapa genome sequencing project

The regulation of meiotic crossover distribution: a coarse solution to a century-old mystery?

Meiotic crossovers, which are exchanges of genetic material between homologous chromosomes, are more evenly and distantly spaced along chromosomes than expected by chance. This is because the occurrence of one crossover reduces the likelihood of nearby crossover events - a conserved and intriguing phenomenon called crossover interference. Although crossover interference was first described over a century ago, the mechanism allowing coordination of the fate of potential crossover sites half a chromosome away remains elusive. In this review, we discuss the recently published evidence supporting a new model for crossover patterning, coined the coarsening model, and point out the missing pieces that are still needed to complete this fascinating puzzle.

Molecular Markers for Detecting Inflorescence Size of Brassica oleracea L. Crops and B. oleracea Complex Species (n = 9) Useful for Breeding of Broccoli (B. oleracea var. italica) and Cauliflower (B. oleracea var. botrytis)

The gene flow from Brassica oleracea L. wild relatives to B. oleracea vegetable crops have occurred and continue to occur ordinarily in several Mediterranean countries, such as Sicily, representing an important hot spot of diversity for some of them, such as broccoli, cauliflower and kale. For detecting and for exploiting the forgotten alleles lost during the domestication processes of the B. oleracea crops, attention has been pointed to the individuation of specific markers for individuating genotypes characterized by hypertrophic inflorescence traits by the marker assisted selection (MAS) during the first plant growing phases after the crosses between broccoli (B. oleracea var. italica)/cauliflower (B. oleracea var. botrytis) with B. oleracea wild relatives (n = 9), reducing the cultivation and evaluation costs. The desired traits often found in several B. oleracea wild relatives are mainly addressed to improve the plant resistance to biotic and abiotic stresses and to increase the organoleptic, nutritive and nutraceutical traits of the products. One of the targeted traits for broccoli and cauliflower breeding is represented by the inflorescences size as is documented by the domestication processes of these two crops. Based on the previous results achieved, the numerical matrix, obtained utilizing five simple sequence repeats (SSRs), was analyzed to assess the relationship among the main inflorescence characteristics and the allelic variation of the SSRs loci analyzed (BoABI1, BoAP1, BoPLD1, BoTHL1 and PBCGSSRBo39), both for the Brassica oleracea and B. oleracea wild relatives (n = 9) accessions set. The main inflorescence morphometric characteristics, such as weight, height, diameter, shape, inflorescence curvature angle and its stem diameter, were registered before the flower anthesis. We analyzed the correlations among the allelic variation of the SSRs primers utilized and the inflorescence morphometric characteristics to individuate genomic regions stimulating the hypertrophy of the reproductive organ. The relationships found explain the diversity among B. oleracea crops and the B. oleracea complex species (n = 9) for the inflorescence size and structure. The individuated markers allow important time reduction during the breeding programs after crossing wild species for transferring useful biotic and abiotic resistances and organoleptic and nutraceutical traits to the B. oleracea crops by MAS.

The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency

Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C₃ plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light-use efficiency at high irradiance as identified in a small number of exceptional C₃ species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light-use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light-saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light-use efficiency and enhancing photosynthetic rates in crop species.

Patterns of genetic structure and evidence of Egyptian Citrus rootstock based on informative SSR, LTR-IRAP and LTR-REMAP molecular markers

Background

Releasing the draft genome of sweet orange provides useful information on genetic structure and molecular marker association with heritable breeding traits in citrus species and their structures. Last decades, microsatellite and retrotransposons are well known as a significant diverse component of the structural evolution. They represented the most potent elements for assessing sustainable utilization of the complicated classification in citrus breeding. Our study was performed to verify the structure analysis and the parentage genetic diversity among the Egyptian citrus rootstocks and the related species.

Results

Here, the performance of 26 SSR and 14 LTR-IRAP in addition to 20 LTR-REMAP markers have been used to conduct the discriminating power and the status of the genetic structure analysis among twenty specimens of citrus genotypes. As a result, the three markers approach exhibited a remarkable variation among the tested genotypes. Overall, the three markers have different discrimination power; the co-dominant SSR markers can differentiate within the group level only in addition to the species level of sour orange, while the dominant markers LTR-IRAP had the ability to discriminate among the group level in addition to species level and the origin of acids. Similarly, LTR-REMAP is suitable for classifying the group level and species level for mandarins as well the origin of Egyptian acids; probably due to it is integration of SSR and LTR-IRAP techniques. Structure and PCoA results of LTR-REMAP marker in strong support for the group structure of citrus species have been divided into four sets: acids, grapefruit/pummelo, mandarin/orange, and sour orange.

Conclusion

Our findings of the genetic structure analysis support the monophyletic nature of the citrus species; are able to provide unambiguous identification and disposition of true species and related hybrids like lemon, lime, citron, sour orange, grapefruit, mandarin, sweet orange, pummelo, and fortunella; and resulted in their placement in individual or overlap groups. The outcomes of these results will offer helpful and potential information for breeding programs and conservation approaches as a key stage toward identifying the interspecific admixture and the inferred structure origins of Egyptian citrus rootstock and acid cultivars.

Genetic Analysis and Fine Mapping of a Spontaneously Mutated Male Sterility Gene in Brassica rapa ssp. chinensis

Male sterility has been widely used in hybrid seed production in Brassica, but not in B. rapa ssp. chinensis, and genetic models of male sterility for this subspecies are unclear. We discovered a spontaneous mutant in B. rapa ssp. chinensis A series of progeny tests indicated that male sterility in B. rapa ssp. chinensis follows a three-allele model with BrMsa , BrMsb , and BrMsc The male sterility locus has been mapped to chromosome A07 in BC1 and F2 populations through genotyping by sequencing. Fine mapping in a total of 1,590 F2 plants narrowed the male sterility gene BrMs to a 400 kb region, with two SNP markers only 0.3 cM from the gene. Comparative gene mapping shows that the Ms gene in B. rapa ssp. pekinensis is different from the BrMs gene of B. rapa ssp. chinensis, despite that both genes are located on chromosome A07. Interestingly, the DNA sequence orthologous to a male sterile gene in Brassica napus, BnRf, is within 400 kb of the BrMs locus. The BnRf orthologs of B. rapa ssp. chinensis were sequenced, and one KASP marker (BrMs_indel) was developed for genotyping based on a 14 bp indel at intron 4. Cosegregation of male sterility and BrMs_indel genotypes in the F2 population indicated that BnRf from B. napus and BrMs from B. rapa are likely to be orthologs. The BrMs_indel marker developed in this study will be useful in marker-assisted selection for the male sterility trait.

Construction of pseudomolecule sequences of Brassica rapa ssp. pekinensis inbred line CT001 and analysis of spontaneous mutations derived via sexual propagation

Chinese cabbage (Brassica rapa ssp. pekinensis) is a major crop that is widely cultivated, especially in Korea, Japan, and China. With the advent of next generation sequencing technology, the cost and time required for sequencing have decreased and the development of genome research accelerated. Genome sequencing of Chinese cabbage was completed in 2011 using the variety Chiifu-401-42, and since then the genome has been continuously updated. In the present study, we conducted whole-genome sequencing of Chinese cabbage inbred line CT001, a line widely used in traditional or molecular breeding, to improve the accuracy of genetic polymorphism analysis. The constructed CT001 pseudomolecule represented 85.4% (219.8 Mb) of the Chiifu reference genome, and a total of 38,567 gene models were annotated using RNA-Seq analysis. In addition, the spontaneous mutation rate of CT001 was estimated by resequencing DNA obtained from individual plants after sexual propagation for six generations to estimate the naturally occurring variations. The CT001 pseudomolecule constructed in this study will provide valuable resources for genomic studies on Chinese cabbage.

Molecular Mapping of a Recessive Powdery Mildew Resistance Gene in Wheat Cultivar Tian Xuan 45 Using Bulked Segregant Analysis with Polymorphic Single Nucleotide Polymorphism Relative Ratio Distribution

Powdery mildew is a destructive foliar disease of wheat worldwide. Wheat cultivar Tian Xuan 45 exhibits resistance to the highly virulent isolate HY5. Genetic analysis of the F₂ and F_2:3 populations of a cultivar Ming Xian 169/Tian Xuan 45 cross revealed that the resistance to HY5 was controlled by a single recessive gene, temporarily designated as PmTx45. A Manhattan plot with the relative frequency distribution of single nucleotide polymorphisms (SNPs) was used to rapidly narrow down the possible chromosomal regions of the associated genes. This microarray-based bulked segregant analysis (BSA) largely improved traditional analytical methods. PmTx45 was located in chromosomal bin 4BL5-0.86-1.00 and was flanked by SNP marker AX-110673642 and intron length polymorphism (ILP) marker ILP-4B01G269900 with genetic distances of 3.0 and 2.6 cM, respectively. Molecular detection in a panel of wheat cultivars using the markers linked to PmTx45 showed that the presence of PmTx45 in commercial wheat cultivars was rare. Resistance spectrum and chromosomal position analyses indicated that PmTx45 may be a novel recessive gene with moderate powdery mildew resistance. This new microarray-based BSA method is feasible and effective and has the potential application for mapping genes in wheat in marker-assisted breeding.

A comprehensive and precise set of intervarietal substitution lines to identify candidate genes and quantitative trait loci in oilseed rape (Brassica napus L.)

A set of intervarietal substitution lines were developed in rapeseed by recurrent backcrossing and marker-assisted selection and employed for mapping both qualitative and quantitative traits. Intervarietal substitution lines (ISLs) may be assembled into advanced secondary mapping populations that have remarkable potential for resolving trait loci and mapping candidate genes. To facilitate the identification of important genes in oilseed rape (canola, Brassica napus), we developed 89 ISLs using an elite cultivar 'Zhongyou 821' (ZY821) as the recipient and a re-synthesized line 'No.2127' as the donor. In the whole process of ISLs development, the target chromosome segments were selected based on the genotypes of 300 microsatellite markers evenly distributed across the genome. Eighty-nine ISLs fixed at BC₅F₄ were genotyped by sequencing using double digestion to survey the lengths of target substitution segments from the donor parent and the background segments from the recurrent parent. The total length of the substituted chromosome segments was 3030.27 Mb, representing 3.56 × of the Darmor-bzh reference genome sequence (version 4.1). Gene mapping was conducted for two qualitative traits, flower colour and seed-coat colour, and nine quantitative traits including yield- and quality-related traits, with 19 QTLs identified for the latter. Overlapping substitution segments were identified for flower colour and seed-coat colour loci, as well as for QTLs consistently detected in 2 or 3 years. These results demonstrate the value of these ISLs for locus resolution and subsequent cloning, targeted mutation or editing of genes controlling important traits in oilseed rape.

Brassicaceae Mustards: Traditional and Agronomic Uses in Australia and New Zealand

Commonly cultivated Brassicaceae mustards, namely garlic mustard (Alliaria petiolata), white mustard (Brassica alba), Ethiopian mustard (B. carinata), Asian mustard (B. juncea), oilseed rape (B. napus), black mustard (B. nigra), rapeseed (B. rapa), white ball mustard (Calepina irregularis), ball mustard (Neslia paniculata), treacle mustard (Erysimum repandum), hedge mustard (Sisymbrium officinale), Asian hedge mustard (S. orientale), smooth mustard (S. erysimoides) and canola are the major economically important oilseed crops in many countries. Mustards were naturalized to Australia and New Zealand and Australia is currently the second largest exporter of Brassicaceae oilseeds to meet the global demand for a healthy plant-derived oil, high in polyunsaturated fats. Apart from providing edible oil, various parts of these plants and many of their phytochemicals have been used traditionally for both agronomic as well as medicinal purposes, with evidence of their use by early Australian and New Zealand settlers and also the indigenous population. This review provides an overview of the current knowledge of traditional and agronomic uses of Brassicaceae oilseeds and mustards with a focus on their importance in Australia and New Zealand.

Genome-wide survey indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) calcium-dependent protein kinase genes

Calcium-dependent protein kinases (CDPKs) as crucial sensors of calcium concentration changes play important roles in responding to abiotic and biotic stresses. In this study, 55 BrrCDPK genes, which were phylogenetically clustered into four subfamilies, were identified. Chromosome locations indicated that the CDPK family in turnip expanded by segmental duplication and genome rearrangement. Moreover, gene expression profiles showed that different BrrCDPKs were expressed in specific tissues or stages. Transcript levels of BrrCDPKs indicated that they were involved in abiotic and biotic stresses and that paralogs exhibited functional divergence. Additionally, we identified 15 Rboh genes in turnip; the results of yeast two-hybrid analysis suggested that BrrRbohD1 interacted only with BrrCDPK10 and that BrrRbohD2 interacted with BrrCDPK4/7/9/10/17/22/23. Most of the genes play an important role in pst DC3000 defense by regulating the accumulation of H2O2 and stomatal closure. Our study may provide an important foundation for future functional analysis of BrrCDPKs and reveal further biological roles.

Integrated analysis of leaf morphological and color traits in different populations of Chinese cabbage (Brassica rapa ssp. pekinensis)

QTLs and candidate gene markers associated with leaf morphological and color traits were identified in two immortalized populations of Brassica rapa, which will provide genetic information for marker-assisted breeding. Brassica rapa is an important leafy vegetable consumed worldwide and morphology is a key character for its breeding. To enhance genetic control, quantitative trait loci (QTLs) for leaf color and plant architecture were identified using two immortalized populations with replications of 2 and 4 years. Overall, 158 and 80 QTLs associated with 23 and 14 traits were detected in the DH and RIL populations, respectively. Among them, 23 common robust-QTLs belonging to 12 traits were detected in common loci over the replications. Through comparative analysis, five crucifer genetic blocks corresponding to morphology trait (R, J&U, F and E) and color trait (F, E) were identified in three major linkage groups (A2, A3 and A7). These might be key conserved genomic regions involved with the respective traits. Through synteny analysis with Arabidopsis, 64 candidate genes involved in chlorophyll biosynthesis, cell proliferation and elongation were co-localized within QTL intervals. Among them, SCO3, ABI3, FLU, HCF153, HEMB1, CAB3 were mapped within QTLs for leaf color; and CYCD3;1, CYCB2;4, AN3, ULT1 and ANT were co-localized in QTL regions for leaf size. These robust QTLs and their candidate genes provide useful information for further research into leaf architecture with crop breeding.

A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey): evidence from QTL analysis

Brassica rapa show a wide range of morphological variations. In particular, the leaf morphologies of the Japanese traditional leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey) are distinctly different, even though they are closely related cultivars that are easy to cross. In addition to the differences in the gross morphology of leaves, some cultivars of Mibuna (Kyo-nishiki) have many trichomes on its leaves, whereas Mizuna (Kyo-mizore) does not. To identify the genes responsible for the different number of trichomes, we performed a quantitative trait loci (QTL) analysis of Mizuna and Mibuna. To construct linkage maps for these cultivars, we used RNA-seq data to develop cleaved amplified polymorphic sequence (CAPS) markers. We also performed a restriction site-associated DNA sequencing (RAD-seq) analysis to detect single-nucleotide polymorphisms (SNPs). Two QTL analyses were performed in different years, and both analyses indicated that the largest effect was found on LG A9. Expression analyses showed that a gene homologous to GLABRA1 (GL1), a transcription factor implicated in trichome development in Arabidopsis thaliana, and the sequences 3'-flanking (downstream) of BrGL1, differed considerably between Mizuna (Kyo-mizore) and Mibuna (Kyo-nishiki). These results indicate that BrGL1 on LG A9 is one of the candidate genes responsible for the difference in trichome number between Mizuna and Mibuna. Detecting genes that are responsible for morphological variations allows us to better understand the breeding history of Mizuna and Mibuna.

A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage

The aim of this work was to construct a high-resolution genetic map for the dissection of complex morphological and agronomic traits in Chinese cabbage (Brassica rapa L. syn. B. campestris). Chinese cabbage, an economically important vegetable, is a good model plant for studies on the evolution of morphologic variation. Herein, two high-generation inbred Chinese cabbage lines, 'Huangxiaoza' and 'Bqq094-11', were crossed. Then restriction-site-associated DNA sequencing (RAD-seq) was performed on the parents and 120 F₂ individuals. A genetic map containing 711 bins representing 3985 single nucleotide polymorphism (SNP) markers was constructed. By using WinQTL with composite interval mapping (CIM) and mixed-model based composite interval mapping (MCIM) analysis via QTLNetwork, quantitative trait loci (QTL) linked to 16 genetic traits related to plant size, color and leaf characteristics were mapped to 10 linkage groups. The high density genetic map and QTL identified for morphological and agronomic traits lay the groundwork for functional gene mapping, map-based cloning and marker-assisted selection (MAS) in Chinese cabbage.

Piriformospora indica promotes growth, seed yield and quality of Brassica napus L

In current scenario, crop productivity is being challenged by decreasing soil fertility. To cope up with this problem, different beneficial microbes are explored to increase the crop productivity with value additions. In this study, Brassica napus L., an important agricultural economic oilseed crop with rich source of nutritive qualities, was interacted with Piriformospora indica, a unique root colonizing fungus with wide host range and multifunctional aspects. The fungus-treated plants showed a significant increase in agronomic parameters with plant biomass, lodging-resistance, early bolting and flowering, oil yield and quality. Nutritional analysis revealed that plants treated by P. indica had reduced erucic acid and glucosinolates contents, and increased the accumulation of N, Ca, Mg, P, K, S, B, Fe and Zn elements. Low erucic acid and glucosinolates contents are important parameters for high quality oil, because oils high in erucic acid and glucosinolates are considered undesirable for human nutrition. Furthermore, the expression profiles of two encoding enzyme genes, Bn-FAE1 and BnECR, which are responsible for regulating erucic acid biosynthesis, were down-regulated at mid- and late- life stages during seeds development in colonized plants. These results demonstrated that P. indica played an important role in enhancing plant growth, rapeseed yield and quality improvement of B. napus.

Identification of loci associated with embryo yield in microspore culture of Brassica rapa by segregation distortion analysis

We identified three physical positions associated with embryo yield in microspore culture of Brassica rapa by segregation distortion analysis. We also confirmed their genetic effects on the embryo yield. Isolated microspore culture is well utilized for the production of haploid or doubled-haploid plants in Brassica crops. Brassica rapa cv. 'Ho Mei' is one of the most excellent cultivars in embryo yield of microspore culture. To identify the loci associated with microspore embryogenesis, segregation analysis of 154 DNA markers anchored to B. rapa chromosomes (A01-A10) was performed using a population of microspore-derived embryos obtained from an F1 hybrid between 'CR-Seiga', a low yield cultivar in microspore-derived embryos, and 'Ho Mei'. Three regions showing significant segregation distortion with increasing 'Ho Mei' alleles were detected on A05, A08 and A09, although these regions showed the expected Mendelian segregation ratio in an F2 population. The additive effect of alleles in these regions on embryo yield was confirmed in a BC3F1 population. One region on A08 containing Br071-5c had a higher effect than the other regions. Polymorphism of nucleotide sequences around the Br071-5c locus was investigated to find the gene possibly responsible for efficient embryogenesis from microspores.

An efficient approach to BAC based assembly of complex genomes

BACKGROUND

There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success.

RESULTS

We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes.

CONCLUSIONS

We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.

Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.)

Clubroot is a devastating disease caused by Plasmodiophora brassicae and results in severe losses of yield and quality in Brassica crops. Many clubroot resistance genes and markers are available in Brassica rapa but less is known in Brassica oleracea. Here, we applied the genotyping-by-sequencing (GBS) technique to construct a high-resolution genetic map and identify clubroot resistance (CR) genes. A total of 43,821 SNPs were identified using GBS data for two parental lines, one resistant and one susceptible lines to clubroot, and 18,187 of them showed >5× coverage in the GBS data. Among those, 4,103 were credibly genotyped for all 78 F₂ individual plants. These markers were clustered into nine linkage groups spanning 879.9 cM with an average interval of 1.15 cM. Quantitative trait loci (QTLs) survey based on three rounds of clubroot resistance tests using F_2:3 progenies revealed two and single major QTLs for Race 2 and Race 9 of P. brassicae, respectively. The QTLs show similar locations to the previously reported CR loci for Race 4 in B. oleracea but are in different positions from any of the CR loci found in B. rapa. We utilized two reference genome sequences in this study. The high-resolution genetic map developed herein allowed us to reposition 37 and 2 misanchored scaffolds in the 02–12 and TO1000DH genome sequences, respectively. Our data also support additional positioning of two unanchored 3.3 Mb scaffolds into the 02–12 genome sequence.

Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Simple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%), amplicons were successfully generated with high quality. Seventeen (89.5%) showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.

Integrative Analysis of mRNA and miRNA Expression Profiles of the Tuberous Root Development at Seedling Stages in Turnips

The tuberous root of Brassica rapa L. (turnip) is an important modified organ for nutrition storage. A better understanding of the molecular mechanisms involved in the process of tuberous root development is of great value in both economic and biological context. In this study, we analyzed the expression profiles of both mRNAs and miRNAs in tuberous roots at an early stage before cortex splitting (ES), cortex splitting stage (CSS), and secondary root thickening stage (RTS) in turnip based on high-throughput sequencing technology. A large number of differentially expressed genes (DEGs) and several differentially expressed miRNAs (DEMs) were identified. Based on the DEG analysis, we propose that metabolism is the dominant pathway in both tuberous root initiation and secondary thickening process. The plant hormone signal transduction pathway may play a predominant role in regulating tuberous root initiation, while the starch and sucrose metabolism may be more important for the secondary thickening process. These hypotheses were partially supported by sequential DEM analyses. Of all DEMs, miR156a, miR157a, and miR172a exhibited relatively high expression levels, and were differentially expressed in both tuberous root initiation and the secondary thickening process with the expression profiles negatively correlated with those of their target genes. Our results suggest that these miRNAs play important roles in tuberous root development in turnips.

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.

Comparative analysis of disease-linked single nucleotide polymorphic markers from Brassica rapa for their applicability to Brassica oleracea

Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH—developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP—based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS—derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species.

Molecular marker applications in plants

Individuals within a population of a sexually reproducing species will have some degree of heritable genomic variation caused by mutations, insertion/deletions (INDELS), inversions, duplications, and translocations. Such variation can be detected and screened using molecular, or genetic, markers. By definition, molecular markers are genetic loci that can be easily tracked and quantified in a population and may be associated with a particular gene or trait of interest. This chapter will review the current major applications of molecular markers in plants.

Molecular marker databases

The detection and analysis of genetic variation plays an important role in plant breeding and this role is increasing with the continued development of genome sequencing technologies. Molecular genetic markers are important tools to characterize genetic variation and assist with genomic breeding. Processing and storing the growing abundance of molecular marker data being produced requires the development of specific bioinformatics tools and advanced databases. Molecular marker databases range from species specific through to organism wide and often host a variety of additional related genetic, genomic, or phenotypic information. In this chapter, we will present some of the features of plant molecular genetic marker databases, highlight the various types of marker resources, and predict the potential future direction of crop marker databases.

Construction of chromosome segment substitution lines enables QTL mapping for flowering and morphological traits in Brassica rapa

Chromosome segment substitution lines (CSSLs) represent a powerful method for precise quantitative trait loci (QTL) detection of complex agronomical traits in plants. In this study, we used a marker-assisted backcrossing strategy to develop a population consisting of 63 CSSLs, derived from backcrossing of the F1 generated from a cross between two Brassica rapa subspecies: "Chiifu" (ssp. pekinensis), the Brassica "A" genome-represented line used as the donor, and "49caixin" (ssp. parachinensis), a non-heading cultivar used as the recipient. The 63 CSSLs covered 87.95% of the B. rapa genome. Among them, 39 lines carried a single segment; 15 lines, two segments; and nine lines, three or more segments of the donor parent chromosomes. To verify the potential advantage of these CSSL lines, we used them to locate QTL for six morphology-related traits. A total of 58 QTL were located on eight chromosomes for all six traits: 17 for flowering time, 14 each for bolting time and plant height, six for plant diameter, two for leaf width, and five for flowering stalk diameter. Co-localized QTL were mainly distributed on eight genomic regions in A01, A02, A05, A06, A08, A09, and A10, present in the corresponding CSSLs. Moreover, new chromosomal fragments that harbored QTL were identified using the findings of previous studies. The CSSL population constructed in our study paves the way for fine mapping and cloning of candidate genes involved in late bolting, flowering, and plant architecture-related traits in B. rapa. Furthermore, it has great potential for future marker-aided gene/QTL pyramiding of other interesting traits in B. rapa breeding.

Tetralocular ovary and high silique width in yellow sarson lines of Brassica rapa (subspecies trilocularis) are due to a mutation in Bra034340 gene, a homologue of CLAVATA3 in Arabidopsis

Genetic locus for tetralocular ovary (tet-o) in Brassica rapa was identified and it was shown that the number of locules and width of silique are associated. Brassica rapa is a highly polymorphic species containing many vegetables and oleiferous types. An interesting group of oleiferous types is the yellow sarson group (subspecies trilocularis) grown mostly in eastern India. This group contains lines that have bilocular ovaries, a defining trait of Brassicaceae, but also lines that have tetralocular ovaries. Yellow sarson lines commonly have high silique width which is further enhanced in the tetralocular types. We mapped the locus influencing tetralocular ovary in B. rapa using three mapping populations (F2, F6 and F7) derived from a cross between Chiifu (subspecies pekinensis, having bilocular ovary) and Tetralocular (having tetralocular ovary). QTL mapping of silique width was undertaken using the three mapping populations and a F2 population derived from a cross between Chiifu and YSPB-24 (a bilocular line belonging to yellow sarson group). Qualitative mapping of the trait governing locule number (tet-o) in B. rapa mapped the locus to linkage group A4. QTL mapping for silique width detected a major QTL on LG A4, co-mapping with the tet-o locus in bilocular/tetralocular cross. This QTL was not detected in the bilocular/bilocular cross. Saturation mapping of the tet-o region with SNP markers identified Bra034340, a homologue of CLAVATA3 of Arabidopsis thaliana, as the candidate gene for locule number. A C → T transition at position 176 of the coding sequence of Bra034340 revealed co-segregation with the tetralocular phenotype. The study of silique related traits is of interest both for understanding evolution under artificial selection and for breeding of cultivated Brassica species.

SNP markers-based map construction and genome-wide linkage analysis in Brassica napus

An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 individuals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non-SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous-Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag-Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.

Constructing a dense genetic linkage map and mapping QTL for the traits of flower development in Brassica carinata

An integrated dense genetic linkage map was constructed in a B. carinata population and used for comparative genome analysis and QTL identification for flowering time. An integrated dense linkage map of Brassica carinata (BBCC) was constructed in a doubled haploid population based on DArT-Seq(TM) markers. A total of 4,031 markers corresponding to 1,366 unique loci were mapped including 639 bins, covering a genetic distance of 2,048 cM. We identified 136 blocks and islands conserved in Brassicaceae, which showed a feature of hexaploidisation representing the suggested ancestral crucifer karyotype. The B and C genome of B. carinata shared 85 % of commonly conserved blocks with the B genome of B. nigra/B. juncea and 80 % of commonly conserved blocks with the C genome of B. napus, and shown frequent structural rearrangements such as insertions and inversions. Up to 24 quantitative trait loci (QTL) for flowering and budding time were identified in the DH population. Of these QTL, one consistent QTL (qFT.B4-2) for flowering time was identified in all of the environments in the J block of the B4 linkage group, where a group of genes for flowering time were aligned in A. thaliana. Another major QTL for flowering time under a winter-cropped environment was detected in the E block of C6, where the BnFT-C6 gene was previously localised in B. napus. This high-density map would be useful not only to reveal the genetic variation in the species with QTL analysis and genome sequencing, but also for other applications such as marker-assisted selection and genomic selection, for the African mustard improvement.

Comparative genomics of Brassicaceae crops

The family Brassicaceae is one of the major groups of the plant kingdom and comprises diverse species of great economic, agronomic and scientific importance, including the model plant Arabidopsis. The sequencing of the Arabidopsis genome has revolutionized our knowledge in the field of plant biology and provides a foundation in genomics and comparative biology. Genomic resources have been utilized in Brassica for diversity analyses, construction of genetic maps and identification of agronomic traits. In Brassicaceae, comparative sequence analysis across the species has been utilized to understand genome structure, evolution and the detection of conserved genomic segments. In this review, we focus on the progress made in genetic resource development, genome sequencing and comparative mapping in Brassica and related species. The utilization of genomic resources and next-generation sequencing approaches in improvement of Brassica crops is also discussed.

A combined linkage and regional association mapping validation and fine mapping of two major pleiotropic QTLs for seed weight and silique length in rapeseed (Brassica napus L.)

BACKGROUND

Seed weight (SW) and silique length (SL) are important determinants of the yield potential in rapeseed (Brassica napus L.). However, the genetic basis of both traits is poorly understood. The main objectives of this study were to dissect the genetic basis of SW and SL in rapeseed through the preliminary mapping of quantitative trait locus (QTL) by linkage analysis and fine mapping of the target major QTL by regional association analysis.

RESULTS

Preliminary linkage mapping identified thirteen and nine consensus QTLs for SW and SL, respectively. These QTLs explained 0.7-67.1% and 2.1-54.4% of the phenotypic variance for SW and SL, respectively. Of these QTLs, three pairs of SW and SL QTLs were co-localized and integrated into three unique QTLs. In addition, the significance level and genetic effect of the three co-localized QTLs for both SW and SL showed great variation before and after the conditional analysis. Moreover, the allelic effects of the three QTLs for SW were highly consistent with those for SL. Two of the three co-localized QTLs, uq.A09-1 (mean R(2) = 20.1% and 19.0% for SW and SL, respectively) and uq.A09-3 (mean R(2) = 13.5% and 13.2% for SW and SL, respectively), were detected in all four environments and showed the opposite additive-effect direction. These QTLs were validated and fine mapped (their confidence intervals were narrowed down from 5.3 cM to 1 cM for uq.A09-1 and 13.2 cM to 2.5 cM for uq.A09-3) by regional association analysis with a panel of 576 inbred lines, which has a relatively rapid linkage disequilibrium decay (0.3 Mb) in the target QTL region.

CONCLUSIONS

A few QTLs with major effects and several QTLs with moderate effects might contribute to the natural variation of SW and SL in rapeseed. The meta-, conditional and allelic effect analyses suggested that pleiotropy, rather than tight linkage, was the genetic basis of the three pairs of co-localized of SW and SL QTLs. Regional association analysis was an effective and highly efficient strategy for the direct fine mapping of target major QTL identified by preliminary linkage mapping.

Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map

Background

Expressed sequence tag (EST)-based markers are preferred because they reflect transcribed portions of the genome. We report the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers derived from transcriptome sequences in cabbage, and their utility for map construction.

Results

Transcriptome sequences were obtained from two cabbage parental lines, C1184 and C1234, which are susceptible and resistant to black rot disease, respectively, using the 454 platform. A total of 92,255 and 127,522 reads were generated and clustered into 34,688 and 40,947 unigenes, respectively. We identified 2,405 SSR motifs from the unigenes of the black rot-resistant parent C1234. Trinucleotide motifs were the most abundant (66.15%) among the repeat motifs. In addition, 1,167 SNPs were detected between the two parental lines. A total of 937 EST-based SSR and 97 SNP-based dCAPS markers were designed and used for detection of polymorphism between parents. Using an F₂ population, we built a genetic map comprising 265 loci, and consisting of 98 EST-based SSRs, 21 SNP-based dCAPS, 55 IBP markers derived from B. rapa genome sequence and 91 public SSRs, distributed on nine linkage groups spanning a total of 1,331.88 cM with an average distance of 5.03 cM between adjacent loci. The parental lines used in this study are elite breeding lines with little genetic diversity; therefore, the markers that mapped in our genetic map will have broad spectrum utility.

Conclusions

This genetic map provides additional genetic information to the existing B. oleracea map. Moreover, the new set of EST-based SSR and dCAPS markers developed herein is a valuable resource for genetic studies and will facilitate cabbage breeding. Additionally, this study demonstrates the usefulness of NGS transcriptomes for the development of genetic maps even with little genetic diversity in the mapping population.

Identification of novel QTLs for isolate-specific partial resistance to Plasmodiophora brassicae in Brassica rapa

Plasmodiophora brassicae, the causal agent of clubroot disease of the Brassica crops, is widespread in the world. Quantitative trait loci (QTLs) for partial resistance to 4 different isolates of P. brassicae (Pb2, Pb4, Pb7, and Pb10) were investigated using a BC₁F₁ population from a cross between two subspecies of Brassica rapa, i.e. Chinese cabbage inbred line C59-1 as a susceptible recurrent parent and turnip inbred line ECD04 as a resistant donor parent. The BC₁F₂ families were assessed for resistance under controlled conditions. A linkage map constructed with simple sequence repeats (SSR), unigene-derived microsatellite (UGMS) markers, and specific markers linked to published clubroot resistance (CR) genes of B. rapa was used to perform QTL mapping. A total of 6 QTLs residing in 5 CR QTL regions of the B. rapa chromosomes A01, A03, and A08 were identified to account for 12.2 to 35.2% of the phenotypic variance. Two QTL regions were found to be novel except for 3 QTLs in the respective regions of previously identified Crr1, Crr2, and Crr3. QTL mapping results indicated that 1 QTL region was common for partial resistance to the 2 isolates of Pb2 and Pb7, whereas the others were specific for each isolate. Additionally, synteny analysis between B. rapa and Arabidopsis thaliana revealed that all CR QTL regions were aligned to a single conserved crucifer blocks (U, F, and R) on 3 Arabidopsis chromosomes where 2 CR QTLs were detected in A. thaliana. These results suggest that some common ancestral genomic regions were involved in the evolution of CR genes in B. rapa.

Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species

Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.

Construction of a genetic linkage map and QTL analysis of erucic acid content and glucosinolate components in yellow mustard (Sinapis alba L.)

BACKGROUND

Yellow mustard (Sinapis alba L.) is an important condiment crop for the spice trade in the world. It has lagged behind oilseed Brassica species in molecular marker development and application. Intron length polymorphism (ILP) markers are highly polymorphic, co-dominant and cost-effective. The cross-species applicability of ILP markers from Brassica species and Arabidopsis makes them possible to be used for genetic linkage mapping and further QTL analysis of agronomic traits in yellow mustard.

RESULTS

A total of 250 ILP and 14 SSR markers were mapped on 12 linkage groups and designated as Sal01-12 in yellow mustard. The constructed map covered a total genetic length of 890.4 cM with an average marker interval of 3.3 cM. The QTL for erucic content co-localized with the fatty acid elongase 1 (FAE1) gene on Sal03. The self-(in)compatibility gene was assigned to Sal08. The 4-hydroxybenzyl, 3-indolylmethyl and 4-hydroxy-3-indolylmethyl glucosinolate contents were each controlled by one major QTL, all of which were located on Sal02. Two QTLs, accounting for the respective 20.4% and 19.2% of the total variation of 2-hydroxy-3-butenyl glucosinolate content, were identified and mapped to Sal02 and Sal11. Comparative synteny analysis revealed that yellow mustard was phylogenetically related to Arabidopsis thaliana and had undergone extensive chromosomal rearrangements during speciation.

CONCLUSION

The linkage map based on ILP and SSR markers was constructed and used for QTL analysis of seed quality traits in yellow mustard. The markers tightly linked with the genes for different glucosinolate components will be used for marker-assisted selection and map-based cloning. The ILP markers and linkage map provide useful molecular tools for yellow mustard breeding.

RNA-seq based SNPs in some agronomically important oleiferous lines of Brassica rapa and their use for genome-wide linkage mapping and specific-region fine mapping

Background

Brassica rapa (AA) contains very diverse forms which include oleiferous types and many vegetable types. Genome sequence of B. rapa line Chiifu (ssp. pekinensis), a leafy vegetable type, was published in 2011. Using this knowledge, it is important to develop genomic resources for the oleiferous types of B. rapa. This will allow more involved molecular mapping, in-depth study of molecular mechanisms underlying important agronomic traits and introgression of traits from B. rapa to major oilseed crops - B. juncea (AABB) and B. napus (AACC). The study explores the availability of SNPs in RNA-seq generated contigs of three oleiferous lines of B. rapa - Candle (ssp. oleifera, turnip rape), YSPB-24 and Tetra (ssp. trilocularis, Yellow sarson) and their use in genome-wide linkage mapping and specific-region fine mapping using a RIL population between Chiifu and Tetra.

Results

RNA-seq was carried out on the RNA isolated from young inflorescences containing unopened floral buds, floral axis and small leaves, using Illumina paired-end sequencing technology. Sequence assembly was carried out using the Velvet de-novo programme and the assembled contigs were organised against Chiifu gene models, available in the BRAD-CDS database. RNA-seq confirmed the presence of more than 17,000 single-copy gene models described in the BRAD database. The assembled contigs and the BRAD gene models were analyzed for the presence of SSRs and SNPs. While the number of SSRs was limited, more than 0.2 million SNPs were observed between Chiifu and the three oleiferous lines. Assays for SNPs were designed using KASPar technology and tested on a F₇-RIL population derived from a Chiifu x Tetra cross. The design of the SNP assays were based on three considerations - the 50 bp flanking region of the SNPs should be strictly similar, the SNP should have a read-depth of ≥7 and no exon/intron junction should be present within the 101 bp target region. Using these criteria, a total of 640 markers (580 for genome-wide mapping and 60 for specific-region mapping) marking as many genes were tested for mapping. Out of 640 markers that were tested, 594 markers could be mapped unambiguously which included 542 markers for genome-wide mapping and 42 markers for fine mapping of the tet-o locus that is involved with the trait tetralocular ovary in the line Tetra.

Conclusion

A large number of SNPs and PSVs are present in the transcriptome of B. rapa lines for genome-wide linkage mapping and specific-region fine mapping. Criteria used for SNP identification delivered markers, more than 93% of which could be successfully mapped to the F₇–RIL population of Chiifu x Tetra cross.

Generation and identification of Brassica alboglabra-Brassica campestris monosomic alien addition lines

Four monosomic alien addition lines (MAALs) for Brassica alboglabra-Brassica campestris were developed through digenomic triploid (ACC) backcrossing with the recurrent parent B. alboglabra (CC). The objectives of this study were to compare morphological traits, microsatellite markers (simple sequence repeats), chromosomal karyotypes, and meiotic behaviors. Based on the new chromosome nomenclature system established for Brassica, we preliminarily identified these MAALs as CC+A1, CC+A3, CC+A6, and CC+A7. Their alien chromosomes were transmittable through both female and male gametes at rates of 11.46%-26.53% and 4.88%-12.90%, respectively.

Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea

BACKGROUND

The Brassica B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacterial artificial chromosome (BAC) library of Brassica nigra was developed and screened with 17 genes from a 222 kb region of A. thaliana that had been well characterised in both the Brassica A and C genomes.

RESULTS

Fingerprinting of 483 apparently non-redundant clones defined physical contigs for the corresponding regions in B. nigra. The target region is duplicated in A. thaliana and six homologous contigs were found in B. nigra resulting from the whole genome triplication event shared by the Brassiceae tribe. BACs representative of each region were sequenced to elucidate the level of microscale rearrangements across the Brassica species divide.

CONCLUSIONS

Although the B genome species separated from the A/C lineage some 6 Mya, comparisons between the three paleopolyploid Brassica genomes revealed extensive conservation of gene content and sequence identity. The level of fractionation or gene loss varied across genomes and genomic regions; however, the greatest loss of genes was observed to be common to all three genomes. One large-scale chromosomal rearrangement differentiated the B genome suggesting such events could contribute to the lack of recombination observed between B genome species and those of the closely related A/C lineage.

Development of a core set of single-locus SSR markers for allotetraploid rapeseed (Brassica napus L.)

Brassica napus (AACC) is a recent allotetraploid species evolved through hybridization between two diploids, B. rapa (AA) and B. oleracea (CC). Due to extensive genome duplication and homoeology within and between the A and C genomes of B. napus, most SSR markers display multiple fragments or loci, which limit their application in genetics and breeding studies of this economically important crop. In this study, we collected 3,890 SSR markers from previous studies and also developed 5,968 SSR markers from genomic sequences of B. rapa, B. oleracea and B. napus. Of these, 2,701 markers that produced single amplicons were putative single-locus markers in the B. napus genome. Finally, a set of 230 high-quality single-locus SSR markers were established and assigned to the 19 linkage groups of B. napus using a segregating population with 154 DH individuals. A subset of 78 selected single-locus SSR markers was proved to be highly stable and could successfully discriminate each of the 45 inbred lines and hybrids. In addition, most of the 230 SSR markers showed the single-locus nature in at least one of the Brassica species of the U's triangle besides B. napus. These results indicated that this set of single-locus SSR markers has a wide range of coverage with excellent stability and would be useful for gene tagging, sequence scaffold assignment, comparative mapping, diversity analysis, variety identification and association mapping in Brassica species.

Genetic and physical mapping of flowering time loci in canola (Brassica napus L.)

We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation-responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related amplified polymorphism, sequence characterised amplified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6% of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis; VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.

Molecular characterization of the CRa gene conferring clubroot resistance in Brassica rapa

Clubroot disease is one of the major diseases affecting Brassicaceae crops, and a number of these crops grown commercially, such as Chinese cabbage (Brassica rapa L. ssp. pekinensis), are known to be highly susceptible to clubroot disease. To provide protection from this disease, plant breeders have introduced genes for resistance to clubroot from the European turnip into susceptible lines. The CRa gene confers specific resistance to the clubroot pathogen Plasmodiophora brassicae isolate M85. Fine mapping of the CRa locus using synteny to the Arabidopsis thaliana genome and partial genome sequences of B. rapa revealed a candidate gene encoding a TIR-NBS-LRR protein. Several structural differences in this candidate gene were found between susceptible and resistant lines, and CRa expression was observed only in the resistant line. Four mutant lines lacking clubroot resistance were obtained by the UV irradiation of pollen from a resistant line, and all of these mutant lines carried independent mutations in the candidate TIR-NBS-LRR gene. This genetic and molecular evidence strongly suggests that the identified gene is CRa. This is the first report on the molecular characterization of a clubroot Resistance gene in Brassicaceae and of the disease resistance gene in B. rapa.

Design of new genome- and gene-sourced primers and identification of QTL for seed oil content in a specially high-oil Brassica napus cultivar

Rapeseed (Brassica napus L.) is one of most important oilseed crops in the world. There are now various rapeseed cultivars in nature that differ in their seed oil content because they vary in oil-content alleles and there are high-oil alleles among the high-oil rapeseed cultivars. For these experiments, we generated doubled haploid (DH) lines derived from the cross between the specially high-oil cultivar zy036 whose seed oil content is approximately 50% and the specially low-oil cultivar 51070 whose seed oil content is approximately 36%. First, to address the deficiency in polymorphic markers, we designed 5944 pairs of newly developed genome-sourced primers and 443 pairs of newly developed primers related to oil-content genes to complement the 2244 pairs of publicly available primers. Second, we constructed a new DH genetic linkage map using 527 molecular markers, consisting of 181 publicly available markers, 298 newly developed genome-sourced markers and 48 newly developed markers related to oil-content genes. The map contained 19 linkage groups, covering a total length of 2,265.54 cM with an average distance between markers of 4.30 cM. Third, we identified quantitative trait loci (QTL) for seed oil content using field data collected at three sites over 3 years, and found a total of 12 QTL. Of the 12 QTL associated with seed oil content identified, 9 were high-oil QTL which derived from the specially high-oil cultivar zy036. Two high-oil QTL on chromosomes A2 and C9 co-localized in two out of three trials. By QTL mapping for seed oil content, we found four candidate genes for seed oil content related to four gene markers: GSNP39, GSSR161, GIFLP106 and GIFLP046. This information will be useful for cloning functional genes correlated with seed oil content in the future.

A genetic linkage map of Brassica carinata constructed with a doubled haploid population

Brassica carinata is an important oilseed crop with unique favourable traits that are desirable for other Brassica crops. However, given the limited research into genetic resources in B. carinata, knowledge of the genetic structure of this species is relatively poor. Nine homozygous, genetically distinct accessions of B. carinata were obtained via microspore culture, from which two divergent doubled haploid (DH) lines were used to develop a DH mapping population that consisted of 183 lines. The mapping population showed segregation of multiple traits of interest. A genetic map was constructed with PCR-based markers, and a total of 212 loci, which covered 1,703 cM, were assigned to eight linkage groups in the B genome and nine linkage groups in the C genome, which allowed comparison with genetic maps of other important Brassica species that contain the B/C genome(s). Loci for two Mendelian-inherited traits related to pigmentation (petal and anther tip colour) and one quantitative trait (seed coat colour) were identified using the linkage map. The significance of the mapping population in the context of genetic improvement of Brassica crops is discussed.

Genetic linkage map construction and QTL mapping of cadmium accumulation in radish (Raphanus sativus L.)

Cadmium (Cd) is a widespread soil pollutant and poses a significant threat to human health via the food chain. Large phenotypic variations in Cd concentration of radish roots and shoots have been observed. However, the genetic and molecular mechanisms of Cd accumulation in radish remain to be elucidated. In this study, a genetic linkage map was constructed using an F(2) mapping population derived from a cross between a high Cd-accumulating cultivar NAU-Dysx and a low Cd-accumulating cultivar NAU-Yh. The linkage map consisted of 523 SRAP, RAPD, SSR, ISSR, RAMP, and RGA markers and had a total length of 1,678.2 cM with a mean distance of 3.4 cM between two markers. All mapped markers distributed on nine linkage groups (LGs) having sizes between 134.7 and 236.8 cM. Four quantitative trait loci (QTLs) for root Cd accumulation were mapped on LGs 1, 4, 6, and 9, which accounted for 9.86 to 48.64 % of all phenotypic variance. Two QTLs associated with shoot Cd accumulation were detected on LG1 and 3, which accounted for 17.08 and 29.53 % of phenotypic variance, respectively. A major-effect QTL, qRCd9 (QTL for root Cd accumulation on LG9), was identified on LG 9 flanked by NAUrp011_754 and EM5me6_286 markers with a high LOD value of 23.6, which accounted for 48.64 % of the total phenotypic variance in Cd accumulation of F(2) lines. The results indicated that qRCd9 is a novel QTL responsible for controlling root Cd accumulation in radish, and the identification of specific molecular markers tightly linked to the major QTL could be further applied for marker-assisted selection (MAS) in low-Cd content radish breeding program.

Identification of a major QTL for silique length and seed weight in oilseed rape (Brassica napus L.)

Silique length (SL) and seed weight (SW) are two important yield-related traits controlled by quantitative trait loci (QTL) in oilseed rape (Brassica napus L.). The genetic bases underlying these two traits are largely unknown at present. In this study, we conducted QTL analyses for SL and SW using 186 recombinant inbred lines (RILs) derived from a cross between S1, an EMS mutant with extremely long siliques and large seeds, and S2, an inbred line with regular silique length and seed size. RILs were grown in Wuhan in the 2008/09 (SS09) and 2009/10 (SS10) growing seasons, and mean SL and SW for each line were investigated. Ten non-redundant QTL were identified for SL. Of these, a major QTL, cqSLA9, consistently explained as much as 53.4% of SL variation across environments. The others are minor QTL and individually explained less than 10% of the SL variation. Nine non-redundant QTL were identified for SW. Of which, one major QTL, cqSWA9, explained as much as 28.2% of the total SW variation in the SS09 and SS10 environments. In addition, three additive by additive interactions with small effects were detected for SL, and no interactions were detected for SW. Interestingly, the two major QTL, cqSLA9 for SL and cqSWA9 for SW colocalized in the same chromosomal region and were integrated into a unique QTL, uqA9. The S1 allele at this locus increases both SL and SW, suggesting that uqA9 has pleiotropic effects on both SL and SW. The existence and effect of uqA9 was confirmed in genetically different RILs derived from the cross between S1 and No2127, a resynthesized DH line having regular silique length and seed size. Individuals in one residual heterozygous line for cqSLA9 showed significant difference in silique length. The results in this study revealed that silique length in the S1 mutant is mainly controlled by the cqSLA9 locus, which will be suitable for fine mapping and marker-assisted selection in rapeseed breeding for high yield.

Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.)

Blackleg, caused by Leptosphaeria maculans, is one of the most important diseases of oilseed and vegetable crucifiers worldwide. The present study describes (1) the construction of a genetic linkage map, comprising 255 markers, based upon simple sequence repeats (SSR), sequence-related amplified polymorphism, sequence tagged sites, and EST-SSRs and (2) the localization of qualitative (race-specific) and quantitative (race non-specific) trait loci controlling blackleg resistance in a doubled-haploid population derived from the Australian canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum using the whole-genome average interval mapping approach. Marker regression analyses revealed that at least 14 genomic regions with LOD ≥ 2.0 were associated with qualitative and quantitative blackleg resistance, explaining 4.6-88.9 % of genotypic variation. A major qualitative locus, designated RlmSkipton (Rlm4), was mapped on chromosome A7, within 0.8 cM of the SSR marker Xbrms075. Alignment of the molecular markers underlying this QTL region with the genome sequence data of B. rapa L. suggests that RlmSkipton is located approximately 80 kb from the Xbrms075 locus. Molecular marker-RlmSkipton linkage was further validated in an F(2) population from Skipton/Ag-Spectrum. Our results show that SSR markers linked to consistent genomic regions are suitable for enrichment of favourable alleles for blackleg resistance in canola breeding programs.

Exploiting comparative mapping among Brassica species to accelerate the physical delimitation of a genic male-sterile locus (BnRf) in Brassica napus

The recessive genic male sterility (RGMS) line 9012AB has been used as an important pollination control system for rapeseed hybrid production in China. Here, we report our study on physical mapping of one male-sterile locus (BnRf) in 9012AB by exploiting the comparative genomics among Brassica species. The genetic maps around BnRf from previous reports were integrated and enriched with markers from the Brassica A7 chromosome. Subsequent collinearity analysis of these markers contributed to the identification of a novel ancestral karyotype block F that possibly encompasses BnRf. Fourteen insertion/deletion markers were further developed from this conserved block and genotyped in three large backcross populations, leading to the construction of high-resolution local genetic maps where the BnRf locus was restricted to a less than 0.1-cM region. Moreover, it was observed that the target region in Brassica napus shares a high collinearity relationship with a region from the Brassica rapa A7 chromosome. A BnRf-cosegregated marker (AT3G23870) was then used to screen a B. napus bacterial artificial chromosome (BAC) library. From the resulting 16 positive BAC clones, one (JBnB089D05) was identified to most possibly contain the BnRf (c) allele. With the assistance of the genome sequence from the Brassica rapa homolog, the 13.8-kb DNA fragment covering both closest flanking markers from the BAC clone was isolated. Gene annotation based on the comparison of microcollinear regions among Brassica napus, B. rapa and Arabidopsis showed that five potential open reading frames reside in this fragment. These results provide a foundation for the characterization of the BnRf locus and allow a better understanding of the chromosome evolution around BnRf.

Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species

An understanding of nature and extent of nucleotide sequence variation is required for programmes of discovery and characterization of single nucleotide polymorphisms (SNPs), which provide the most versatile class of molecular genetic marker. A majority of higher plant species are polyploids, and allopolyploidy, because of hybrid formation between closely related taxa, is very common. Mutational variation may arise both between allelic (homologous) sequences within individual subgenomes and between homoeologous sequences among subgenomes, in addition to paralogous variation between duplicated gene copies. Successful SNP validation in allopolyploids depends on differentiation of the sequence variation classes. A number of biological factors influence the feasibility of discrimination, including degree of gene family complexity, inbreeding or outbreeding reproductive habit, and the level of knowledge concerning progenitor diploid species. In addition, developments in high-throughput DNA sequencing and associated computational analysis provide general solutions for the genetic analysis of allopolyploids. These issues are explored in the context of experience from a range of allopolyploid species, representing grain (wheat and canola), forage (pasture legumes and grasses), and horticultural (strawberry) crop. Following SNP discovery, detection in routine genotyping applications also presents challenges for allopolyploids. Strategies based on either design of subgenome-specific SNP assays through homoeolocus-targeted polymerase chain reaction (PCR) amplification, or detection of incremental changes in nucleotide variant dosage, are described.

A new broccoli × broccoli immortal mapping population and framework genetic map: tools for breeders and complex trait analysis

A unique broccoli × broccoli doubled haploid (DH) population has been created from the F(1) of a cross between two DH broccoli lines derived from cultivars Green Duke and Marathon. We genotyped 154 individuals from this population with simple sequence repeat and amplified fragment length polymorphism markers to create a B. oleracea L. var. italica 'intra-crop' specific framework linkage map. The map is composed of nine linkage groups with a total length of 946.7 cM. Previous published B. oleracea maps have been constructed using diverse crosses between morphotypes of B. oleracea; this map therefore represents a useful breeding resource for the dissection of broccoli specific traits. Phenotype data have been collected from the population over five growing seasons; the framework linkage map has been used to locate quantitative trait loci for agronomically important broccoli traits including head weight (saleable yield), head diameter, stalk diameter, weight loss and relative weight loss during storage, as well as traits for broccoli leaf architecture. This population and associated linkage map will aid breeders to directly map agronomically important traits for the improvement of elite broccoli cultivars.