Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus

Background

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation. Identification of large numbers of SNPs is helpful for genetic diversity analysis, map-based cloning, genome-wide association analyses and marker-assisted breeding. Recently, identifying genome-wide SNPs in allopolyploid Brassica napus (rapeseed, canola) by resequencing many accessions has become feasible, due to the availability of reference genomes of Brassica rapa (2n = AA) and Brassica oleracea (2n = CC), which are the progenitor species of B. napus (2n = AACC). Although many SNPs in B. napus have been released, the objective in the present study was to produce a larger, more informative set of SNPs for large-scale and efficient genotypic screening. Hence, short-read genome sequencing was conducted on ten elite B. napus accessions for SNP discovery. A subset of these SNPs was randomly selected for sequence validation and for genotyping efficiency testing using the Illumina GoldenGate assay.

Results

A total of 892,536 bi-allelic SNPs were discovered throughout the B. napus genome. A total of 36,458 putative amino acid variants were located in 13,552 protein-coding genes, which were predicted to have enriched binding and catalytic activity as a result. Using the GoldenGate genotyping platform, 94 of 96 SNPs sampled could effectively distinguish genotypes of 130 lines from two mapping populations, with an average call rate of 92%.

Conclusions

Despite the polyploid nature of B. napus, nearly 900,000 simple SNPs were identified by whole genome resequencing. These SNPs were predicted to be effective in high-throughput genotyping assays (51% polymorphic SNPs, 92% average call rate using the GoldenGate assay, leading to an estimated >450 000 useful SNPs). Hence, the development of a much larger genotyping array of informative SNPs is feasible. SNPs identified in this study to cause non-synonymous amino acid substitutions can also be utilized to directly identify causal genes in association studies.     

A triallelic genetic male sterility locus in Brassica napus: an integrative strategy for its physical mapping and possible local chromosome evolution around it

Background and Aims

Spontaneous male sterility is an advantageous trait for both constructing efficient pollination control systems and for understanding the developmental process of the male reproductive unit in many crops. A triallelic genetic male-sterile locus (BnMs5) has been identified in Brassica napus; however, its complicated genome structure has greatly hampered the isolation of this locus. The aim of this study was to physically map BnMs5 through an integrated map-based cloning strategy and analyse the local chromosomal evolution around BnMs5.

Methods

A large F₂ population was used to integrate the existing genetic maps around BnMs5. A map-based cloning strategy in combination with comparative mapping among B. napus, Arabidopsis, Brassica rapa and Brassica oleracea was employed to facilitate the identification of a target bacterial artificial chromosome (BAC) clone covering the BnMs5 locus. The genomic sequences from the Brassica species were analysed to reveal the regional chromosomal evolution around BnMs5.

Key Results

BnMs5 was finally delimited to a 0·3-cM genetic fragment from an integrated local genetic map, and was anchored on the B. napus A8 chromosome. Screening of a B. napus BAC clone library and identification of the positive clones validated that JBnB034L06 was the target BAC clone. The closest flanking markers restrict BnMs5 to a 21-kb region on JBnB034L06 containing six predicted functional genes. Good collinearity relationship around BnMs5 between several Brassica species was observed, while violent chromosomal evolutionary events including insertions/deletions, duplications and single nucleotide mutations were also found to have extensively occurred during their divergence.

Conclusions

This work represents major progress towards the molecular cloning of BnMs5, as well as presenting a powerful, integrative method to mapping loci in plants with complex genomic architecture, such as the amphidiploid B. napus.     

Host Suitability of Rapeseed for Heterodera schachtii

Because rapeseed, especially canola, has the potential to be grown in rotation with sugarbeet in the north-central region of the United States, this study was initiated to assess its susceptibility to infection by Heterodera schachtii and to develop a screening method for Brassica germplasm. Existing methodology was adapted for growing Brassica juncea, B. napus, B. rapa, Brassica hybrids, and sugarbeet, Beta vulgaris, in H. schachtii-infested soil to count the females that developed on the roots. Cysts on sugarbeet contained a mean of 130 eggs compared with 240 for B. napus, lowest for the Brassica. Viability of eggs produced was assessed in soil planted with Brassica and sugarbeet and infested with with 0, 100, 1,000, 3,000, and 5,000 eggs to count resulting females and cysts. Number of females (y) was related linearly to infestation rate (x) by the regression equations y = 2.82 + 0.07(x) for the Brassica lines (R² = 0.79; P < 0.001) and y = 0.43 + 0.04(x) for sugarbeet (R² = 0.69; P < 0.007). These data indicated the potential for H. schachtii population increase if the two crops are used in rotation. All of the 111 germplasm lines tested were susceptible. The methodology developed during this research would benefit attempts to develop rapeseed cultivars resistant to H. schachtii.     

Identification and characterization of improved nitrogen efficiency in interspecific hybridized new-type Brassica napus

Background and Aims

Oilseed rape (Brassica napus) is an important oil crop worldwide. The aim of this study was to identify the variation in nitrogen (N) efficiency of new-type B. napus (genome A^rA^rC^cC^c) genotypes, and to characterize some critical physiological and molecular mechanisms in response to N limitation.

Methods

Two genotypes with contrasting N efficiency (D4-15 and D1-1) were identified from 150 new-type B. napus lines, and hydroponic and pot experiments were conducted. Root morphology, plant biomass, N uptake parameters and seed yield of D4-15 and D1-1 were investigated. Two traditional B. napus (genome AⁿAⁿCⁿCⁿ) genotypes, QY10 and NY7, were also cultivated. Introgression of exotic genomic components in D4-15 and D1-1 was evaluated with molecular markers.

Key Results

Large genetic variation existed among traits contributing to the N efficiency of new-type B. napus. Under low N levels at the seedling stage, the N-efficient new-type D4-15 showed higher values than the N-inefficient D1-1 line and the traditional B. napus QY10 and NY7 genotypes with respect to several traits, including root and shoot biomass, root morphology, N accumulation, N utilization efficiency (NutE), N uptake efficiency (NupE), activities of nitrate reductase (NR) and glutamine synthetase (GS), and expression levels of N transporter genes and genes that are involved in N assimilation. Higher yield was produced by the N-efficient D4-15 line compared with the N-inefficient D1-1 at maturity. More exotic genome components were introgressed into the genome of D4-15 (64·97 %) compared with D1-1 (32·23 %).

Conclusions

The N-efficient new-type B. napus identified in this research had higher N efficiency (and tolerance to low-N stress) than traditional B. napus cultivars, and thus could have important potential for use in breeding N-efficient B. napus cultivars in the field.     

Genome-Wide Association Study Dissects the Genetic Architecture of Seed Weight and Seed Quality in Rapeseed (Brassica napus L.)

Association mapping can quickly and efficiently dissect complex agronomic traits. Rapeseed is one of the most economically important polyploid oil crops, although its genome sequence is not yet published. In this study, a recently developed 60K Brassica Infinium^® SNP array was used to analyse an association panel with 472 accessions. The single-nucleotide polymorphisms (SNPs) of the array were in silico mapped using ‘pseudomolecules’ representative of the genome of rapeseed to establish their hypothetical order and to perform association mapping of seed weight and seed quality. As a result, two significant associations on A8 and C3 of Brassica napus were detected for erucic acid content, and the peak SNPs were found to be only 233 and 128 kb away from the key genes BnaA.FAE1 and BnaC.FAE1. BnaA.FAE1 was also identified to be significantly associated with the oil content. Orthologues of Arabidopsis thaliana HAG1 were identified close to four clusters of SNPs associated with glucosinolate content on A9, C2, C7 and C9. For seed weight, we detected two association signals on A7 and A9, which were consistent with previous studies of quantitative trait loci mapping. The results indicate that our association mapping approach is suitable for fine mapping of the complex traits in rapeseed.     

EST-based in silico identification and in vitro test of antimicrobial peptides in Brassica napus

Background

Brassica napus is the third leading source of vegetable oil in the world after soybean and oil palm. The accumulation of gene sequences, especially expressed sequence tags (ESTs) from plant cDNA libraries, has provided a rich resource for genes discovery including potential antimicrobial peptides (AMPs). In this study, we used ESTs including those generated from B. napus cDNA libraries of seeds, pathogen-challenged leaves and deposited in the public databases, as a model, to perform in silico identification and consequently in vitro confirmation of putative AMP activities through a highly efficient system of recombinant AMP prokaryotic expression.

Results

In total, 35,788 were generated from cDNA libraries of pathogen-challenged leaves and 187,272 ESTs from seeds of B. napus, and the 644,998 ESTs of B. napus were downloaded from the EST database of PlantGDB. They formed 201,200 unigenes. First, all the known AMPs from the AMP databank (APD2 database) were individually queried against all the unigenes using the BLASTX program. A total of 972 unigenes that matched the 27 known AMP sequences in APD2 database were extracted and annotated using Blast2GO program. Among these unigenes, 237 unigenes from B. napus pathogen-challenged leaves had the highest ratio (1.15 %) in this unigene dataset, which is 13 times that of the unigene datasets of B. napus seeds (0.09 %) and 2.3 times that of the public EST dataset. About 87 % of each EST library was lipid-transfer protein (LTP) (32 % of total unigenes), defensin, histone, endochitinase, and gibberellin-regulated proteins. The most abundant unigenes in the leaf library were endochitinase and defensin, and LTP and histone in the pub EST library. After masking of the repeat sequence, 606 peptides that were orthologous matched to different AMP families were found. The phylogeny and conserved structural motifs of seven AMPs families were also analysed. To investigate the antimicrobial activities of the predicted peptides, 31 potential AMP genes belonging to different AMP families were selected to test their antimicrobial activities after bioinformatics identification. The AMP genes were all optimized according to Escherichia coli codon usage and synthetized through one-step polymerase chain reaction method. The results showed that 28 recombinant AMPs displayed expected antimicrobial activities against E. coli and Micrococcus luteus and Sclerotinia sclerotiorum strains.

Conclusion

The study not only significantly expanded the number of known/predicted peptides, but also contributed to long-term plant genetic improvement for increased resistance to diverse pathogens of B.napus. These results proved that the high-throughput method developed that combined an in silico procedure with a recombinant AMP prokaryotic expression system is considerably efficient for identification of new AMPs from genome or EST sequence databases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1849-x) contains supplementary material, which is available to authorized users.     

Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.)

Flowering time adaptation is a major breeding goal in the allopolyploid species Brassica napus. To investigate the genetic architecture of flowering time, a genome-wide association study (GWAS) of flowering time was conducted with a diversity panel comprising 523 B. napus cultivars and inbred lines grown in eight different environments. Genotyping was performed with a Brassica 60K Illumina Infinium SNP array. A total of 41 single-nucleotide polymorphisms (SNPs) distributed on 14 chromosomes were found to be associated with flowering time, and 12 SNPs located in the confidence intervals of quantitative trait loci (QTL) identified in previous researches based on linkage analyses. Twenty-five candidate genes were orthologous to Arabidopsis thaliana flowering genes. To further our understanding of the genetic factors influencing flowering time in different environments, GWAS was performed on two derived traits, environment sensitivity and temperature sensitivity. The most significant SNPs were found near Bn-scaff_16362_1-p380982, just 13 kb away from BnaC09g41990D, which is orthologous to A. thaliana CONSTANS (CO), an important gene in the photoperiod flowering pathway. These results provide new insights into the genetic control of flowering time in B. napus and indicate that GWAS is an effective method by which to reveal natural variations of complex traits in B. napus.     

A survey of quantitative real-time polymerase chain reaction internal reference genes for expression studies in Brassica napus

Eight reference genes of Brassica napus were evaluated using quantitative real-time polymerase chain reaction (qRT-PCR) data, focusing on vegetative tissues and developing embryos. Analyses of expression stability indicated that UP1, UBC9, UBC21, and TIP41 were the top four choices as stably expressed reference genes for vegetative tissues, whereas ACT7, UBC21, TIP41, and PP2A were the top four choices for maturing embryos. In addition, radiolabeling of overall messenger RNA (mRNA) of maturing embryos indicated that the expression patterns of the top four ranked reference genes reflected the overall mRNA content changes in maturing embryos.     

Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts

Background

In addition to human and animal diseases, bacteria of the genus Burkholderia can cause plant diseases. The representative species of rice-pathogenic Burkholderia are Burkholderia glumae, B. gladioli, and B. plantarii, which primarily cause grain rot, sheath rot, and seedling blight, respectively, resulting in severe reductions in rice production. Though Burkholderia rice pathogens cause problems in rice-growing countries, comprehensive studies of these rice-pathogenic species aiming to control Burkholderia-mediated diseases are only in the early stages.

Results

We first sequenced the complete genome of B. plantarii ATCC 43733^T. Second, we conducted comparative analysis of the newly sequenced B. plantarii ATCC 43733^T genome with eleven complete or draft genomes of B. glumae and B. gladioli strains. Furthermore, we compared the genome of three rice Burkholderia pathogens with those of other Burkholderia species such as those found in environmental habitats and those known as animal/human pathogens. These B. glumae, B. gladioli, and B. plantarii strains have unique genes involved in toxoflavin or tropolone toxin production and the clustered regularly interspaced short palindromic repeats (CRISPR)-mediated bacterial immune system. Although the genome of B. plantarii ATCC 43733^T has many common features with those of B. glumae and B. gladioli, this B. plantarii strain has several unique features, including quorum sensing and CRISPR/CRISPR-associated protein (Cas) systems.

Conclusions

The complete genome sequence of B. plantarii ATCC 43733^T and publicly available genomes of B. glumae BGR1 and B. gladioli BSR3 enabled comprehensive comparative genome analyses among three rice-pathogenic Burkholderia species responsible for tissue rotting and seedling blight. Our results suggest that B. glumae has evolved rapidly, or has undergone rapid genome rearrangements or deletions, in response to the hosts. It also, clarifies the unique features of rice pathogenic Burkholderia species relative to other animal and human Burkholderia species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1558-5) contains supplementary material, which is available to authorized users.     

Quantitative trait loci for seed yield and yield-related traits, and their responses to reduced phosphorus supply in Brassica napus

Background and Aims

One of the key targets of breeding programmes in rapeseed (Brassica napus) is to develop high-yield varieties. However, the lack of available phosphorus (P) in soils seriously limits rapeseed production. The aim of this study was to dissect the genetic control of seed yield and yield-related traits in B. napus grown with contrasting P supplies.

Methods

Two-year field trials were conducted at one site with normal and low P treatments using a population of 124 recombinant inbred lines derived from a cross between ‘B104-2’ and ‘Eyou Changjia’. Seed yield, seed weight, seed number, pod number, plant height, branch number and P efficiency coefficient (PEC) were investigated. Quantitative trait locus (QTL) analysis was performed by composite interval mapping.

Key Results

The phenotypic values of most of the tested traits were reduced under the low P conditions. In total, 74 putative QTLs were identified, contributing 7·3–25·4 % of the phenotypic variation. Of these QTLs, 16 (21·6 %) were detected in two seasons and in the mean value of two seasons, and eight QTLs for two traits were conserved across P levels. Low-P-specific QTLs were clustered on chromosomes A1, A6 and A8. By comparative mapping between Arabidopsis and B. napus, 161 orthologues of 146 genes involved in Arabidopsis P homeostasis and/or yield-related trait control were associated with 45 QTLs corresponding to 23 chromosomal regions. Four gene-based markers developed from genes involved in Arabidopsis P homeostasis were mapped to QTL intervals.

Conclusions

Different genetic determinants were involved in controlling seed yield and yield-related traits in B. napus under normal and low P conditions. The QTLs detected under reduced P supply may provide useful information for improving the seed yield of B. napus in soils with low P availability in marker-assisted selection.     

Suppression of Root-knot Nematode Populations with Selected Rapeseed Cultivars as Green Manure

Meloidogyne chitwoodi races 1 and 2 and M. hapla reproduced on 12 cultivars of Brassica napus and two cultivars of B. campestris. The mean reproductive factors (Rf), Rf = Pf at 55 days ÷ 5,000, for the three nematodes were 8.3, 2.2, and 14.3, respectively. All three nematodes reproduced more efficiently (P < 0.05) on B. campestris than on B. napus. Amending M. chitwoodi-infested soil in plastic bags with chopped shoots of Jupiter rapeseed reduced the nematode population more (P < 0.05) than amendment with wheat shoots. Incorporating Jupiter shoots to soil heavily infested with M. chitwoodi in microplots reduced the nematode population more (P < 0.05) than fallow or corn shoot treatments. The greatest reduction in nematode population density was attained by cropping rapeseed for 2 months and incorporating it into the soil as a green manure.     

Effects of Rapeseed and Vetch as Green Manure Crops and Fallow on Nematodes and Soil-borne Pathogens

In a rapeseed-squash cropping system, Meloidogyne incognita race 1 and M. javanica did not enter, feed, or reproduce in roots of seven rapeseed cultivars. Both nematode species reproduced at low levels on roots of the third crop of rapeseed. Reproduction of M. incognita and M. javanica was high on squash following rapeseed, hairy vetch, and fallow. The application of fenamiphos suppressed (P = 0.05) root-gall indices on squash following rapeseed, hairy vetch, and fallow; and on Dwarf Essex and Cascade rapeseed, but not Bridger and Humus rapeseed in 1987. The incorporation of 30-61 mt/ha green biomass of rapeseed into the soil 6 months after planting did not affect the population densities of Criconemella ornata, M. incognita, M. javanica, Pythium spp., Rhizoctonia solani AG-4; nor did it consistently increase yield of squash. Hairy vetch supported larger numbers of M. incognita and M. javanica than rapeseed cultivars or fallow. Meloidogyne incognita and M. javanica survived in fallow plots in the absence of a host from October to May each year at a level sufficient to warrant the use of a nematicide to manage nematodes on the following susceptible crop.     

Intercropping Cover Crops with Pineapple for the Management of Rotylenchulus reniformis

Effect of cover crops intercropped with pineapple (Ananas comosus) on Rotylenchulus reniformis population densities and activity of nematode-trapping fungi (NTF) were evaluated in two cycles of cover crop and pineapple. Sunn hemp (Crotalaria juncea), rapeseed (Brassica napus), African marigold (Tagetes erecta), or weeds were intercropped with pineapples. Beds planted with sunn hemp or rapeseed had lower population densities of R. reniformis than African marigold, weeds, or pineapple plots during cover crop growth, and the subsequent pineapple-growing periods. Rapeseed was a good host to Meloidogyne javanica and resulted in high population densities of M. javanica in the subsequent pineapple crop. Fireweed (Erigeron canadensis) occurred commonly and was a good host to R. reniformis. Bacterivorous nematode population densities increased (P ≤ 0.05) most in sunn hemp, especially early after planting. Nematode-trapping fungi required a long period to develop measurable population densities. Population densities of NTF were higher in cover crops than weeds or pineapples during the first crop cycle (P < 0.05). Although pineapple produced heavier fruits following sunn hemp than in the other treatments (P < 0.05), commercial yields were not different among rapeseed, weed, and sunn hemp treatments.     

Identification of MicroRNAs in Helicoverpa armigera and Spodoptera litura Based on Deep Sequencing and Homology Analysis

The current identification of microRNAs (miRNAs) in insects is largely dependent on genome sequences. However, the lack of available genome sequences inhibits the identification of miRNAs in various insect species. In this study, we used a miRNA database of the silkworm Bombyx mori as a reference to identify miRNAs in Helicoverpa armigera and Spodoptera litura using deep sequencing and homology analysis. Because all three species belong to the Lepidoptera, the experiment produced reliable results. Our study identified 97 and 91 conserved miRNAs in H. armigera and S. litura, respectively. Using the genome of B. mori and BAC sequences of H. armigera as references, 1 novel miRNA and 8 novel miRNA candidates were identified in H. armigera, and 4 novel miRNA candidates were identified in S. litura. An evolutionary analysis revealed that most of the identified miRNAs were insect-specific, and more than 20 miRNAs were Lepidoptera-specific. The investigation of the expression patterns of miR-2a, miR-34, miR-2796-3p and miR-11 revealed their potential roles in insect development. miRNA target prediction revealed that conserved miRNA target sites exist in various genes in the 3 species. Conserved miRNA target sites for the Hsp90 gene among the 3 species were validated in the mammalian 293T cell line using a dual-luciferase reporter assay. Our study provides a new approach with which to identify miRNAs in insects lacking genome information and contributes to the functional analysis of insect miRNAs.     

Spontaneous hybridization between a male-sterile oilseed rape and two weeds

Spontaneous interspecific hybrids were produced under natural conditions (pollination by wind and bees) between a male-sterile cybrid Brassica napus (AACC, 2n = 38) and two weeds Brassica adpressa (AdAd, 2n = 14) and Raphanus raphanistrum (RrRr, 2n = 18). After characterization by chromosome counts and isozyme analyses, we observed 512 and 3 734 inter-specific seeds per m² for the B. napus-B. adpressa and B. napus-R. raphanistrum trials respectively. Most of the hybrids studied had the expected triploid structure (ACX). In order to quantify the frequency of allosyndesis between the genomes involved in the hybrids, their meiotic behavior was compared to a haploid of B. napus (AC). For the B. napus-B. adpressa hybrids, we concluded that probably no allosyndesis occurred between the two parental genomes, and that genetic factors regulating homoeologous chromosome pairing were carried by the B. adpressa genome. For the B. napus-R. raphanistrum hybrids, high chromosome pairing and the presence of multivalents (in 9.16% of the pollen mother cells) indicate that recombination is possible between chromosomes of different genomes. Pollen fertility of the hybrids ranged from 0 to 30%. Blackleg inoculation tests were performed on the three parental species and on the interspecific hybrids. BC₁ production with the weeds and with rapeseed was attempted. Results are discussed in regard to the risk assessment of transgenic rapeseed cultivation, F₁ hybrid rapeseed variety production, and rapeseed improvement.     

甘蓝型油菜抗茎倒材料的筛选与候选基因挖掘

该研究采用茎秆抗折力指标评价了200份甘蓝型油菜种质资源抗茎倒伏能力,据此筛选出极端抗茎倒材料和不抗茎倒材料各1份,随后测定了2份材料成熟期茎秆的理化组分含量,并对2份极端抗茎倒差异材料蕾苔期、盛花期茎秆进行转录组测序分析,为甘蓝型油菜抗茎倒伏的遗传改良奠定基础。结果表明:(1)200份甘蓝型油菜种质资源的茎秆抗折力和茎粗均为正态分布,均属于数量遗传性状,并依据茎秆抗折力和农艺性状筛选出生育期相近,株型相似,茎秆粗度差异不显著,但茎秆抗折力差异显著的极端不抗茎倒材料GY172和抗茎倒材料GY199。(2)GY199的韧皮部比GY172更加致密,而GY172成熟期茎秆中的半纤维素、木质素、中性洗涤纤维及总可溶性糖含量均显著高于GY199,而其纤维素含量极显著低于GY199,即成熟期茎秆纤维素含量与这2个材料的茎秆抗折力呈正相关。(3)蕾苔期、盛花期茎秆转录组测序发现,碳代谢、碳固定、磷酸戊糖途径、氨基酸的生物合成、糖酵解/糖异生等途径的14个基因(BnaA10G0056100ZS、BnaC08G0455100ZS、BnaA08G0262400ZS、BnaC08G0239700ZS、BnaA07G0362300ZS、BnaC02G0081300ZS、BnaC04G0273000ZS等)以及纤维素合成相关的9个基因(BnaA05G0152200ZS、BnaA01G0411100ZS、BnaA03G0018900ZS、BnaA03G0037800ZS等)在抗茎倒材料GY199中显著上调表达,这些基因可能参与调控了茎秆强度性状,可作为油菜抗茎倒候选基因。