New Insights into the TIFY Gene Family of Brassica napus and Its Involvement in the Regulation of Shoot Branching.

As plant-specific transcription factors, the TIFY family genes are involved in the responses to a series of biotic and abiotic stresses and the regulation of the development of multiple organs. To explore the potential roles of the TIFY gene family in shoot branching, which can shape plant architecture and finally determine seed yield, we conducted comprehensive genome-wide analyses of the TIFY gene family in Brassica napus. Here, HMMER search and BLASTp were used to identify the TIFY members. A total of 70 TIFY members were identified and divided into four subfamilies based on the conserved domains and motifs. These TIFY genes were distributed across 19 chromosomes. The predicted subcellular localizations revealed that most TIFY proteins were located in the nucleus. The tissue expression profile analyses indicated that TIFY genes were highly expressed in the stem, flower bud, and silique at the transcriptional level. High-proportioned activation of the dormant axillary buds on stems determined the branch numbers of rapeseed plants. Here, transcriptome analyses were conducted on axillary buds in four sequential developing stages, that is, dormant, temporarily dormant, being activated, and elongating (already activated). Surprisingly, the transcription of the majority of TIFY genes (65 of the 70) significantly decreased on the activation of buds. GO enrichment analysis and hormone treatments indicated that the transcription of TIFY family genes can be strongly induced by jasmonic acid, implying that the TIFY family genes may be involved in the regulation of jasmonic acid-mediated branch development. These results shed light on the roles of TIFY family genes in plant architecture.

Comparison of the cytoplastic genomes by resequencing: insights into the genetic diversity and the phylogeny of the agriculturally important genus Brassica.

BACKGROUND: The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of B. napus and certain detailed interspecific relationships within Brassica genus remains undetermined and somewhere confused. In the current high-throughput sequencing era, a systemic comparative genomic study based on a large population is necessary and would be crucial to resolve these questions. RESULTS: The chloroplast DNA and mitochondrial DNA were synchronously resequenced in a selected set of Brassica materials, which contain 72 accessions and maximally integrated the known Brassica species. The Brassica genomewide cpDNA and mtDNA variations have been identified. Detailed phylogenetic relationships inside and around Brassica genus have been delineated by the cpDNA- and mtDNA- variation derived phylogenies. Different from B. juncea and B. carinata, the natural B. napus contains three major cytoplasmic haplotypes: the cam-type which directly inherited from B. rapa, polima-type which is close to cam-type as a sister, and the mysterious but predominant nap-type. Certain sparse C-genome wild species might have primarily contributed the nap-type cytoplasm and the corresponding C subgenome to B. napus, implied by their con-clustering in both phylogenies. The strictly concurrent inheritance of mtDNA and cpDNA were dramatically disturbed in the B. napus cytoplasmic male sterile lines (e.g., mori and nsa). The genera Raphanus, Sinapis, Eruca, Moricandia show a strong parallel evolutional relationships with Brassica. CONCLUSIONS: The overall variation data and elaborated phylogenetic relationships provide further insights into genetic understanding of Brassica, which can substantially facilitate the development of novel Brassica germplasms.

High-throughput multiplex cpDNA resequencing clarifies the genetic diversity and genetic relationships among Brassica napus, Brassica rapa and Brassica oleracea.

Brassica napus (rapeseed) is a recent allotetraploid plant and the second most important oilseed crop worldwide. The origin of B. napus and the genetic relationships with its diploid ancestor species remain largely unresolved. Here, chloroplast DNA (cpDNA) from 488 B. napus accessions of global origin, 139 B. rapa accessions and 49 B. oleracea accessions were populationally resequenced using Illumina Solexa sequencing technologies. The intraspecific cpDNA variants and their allelic frequencies were called genomewide and further validated via EcoTILLING analyses of the rpo region. The cpDNA of the current global B. napus population comprises more than 400 variants (SNPs and short InDels) and maintains one predominant haplotype (Bncp1). Whole-genome resequencing of the cpDNA of Bncp1 haplotype eliminated its direct inheritance from any accession of the B. rapa or B. oleracea species. The distribution of the polymorphism information content (PIC) values for each variant demonstrated that B. napus has much lower cpDNA diversity than B. rapa; however, a vast majority of the wild and cultivated B. oleracea specimens appeared to share one same distinct cpDNA haplotype, in contrast to its wild C-genome relatives. This finding suggests that the cpDNA of the three Brassica species is well differentiated. The predominant B. napus cpDNA haplotype may have originated from uninvestigated relatives or from interactions between cpDNA mutations and natural/artificial selection during speciation and evolution. These exhaustive data on variation in cpDNA would provide fundamental data for research on cpDNA and chloroplasts.

Characterization of FAE1 in the zero erucic acid germplasm of Brassica rapa L.

The modification of erucic acid content in seeds is one of the major goals for quality breeding in oil-yielding Brassica species. However, few low erucic acid (LEA) resources are available, and novel LEA genetic resources are being sought. Fatty acid elongase 1 (FAE1) is the key gene that controls erucic acid synthesis. However, the mechanism for erucic acid synthesis in B. rapa lacks systematic study. Here, we isolated zero erucic acid lines from 1981 Chinese landraces of B. rapa and found that the formation of LEA is not attributable to variations in FAE1 coding sequences, as reported for B. napus, but may be attributable to the decrease in FAE1 expression. Moreover, the FAE1 promoter sequences of LEA and high erucic acid materials shared 95% similarity. Twenty-eight bases deletions (containing a 24-base AT-rich region) were identified approximately 1300 bp upstream from the FAE1 start codon in the LEA accessions. The genotype with the deletions co-segregated with the LEA trait in the segregating population. This study isolated an LEA B. rapa resource that can be exploited in Brassica cultivation. The promoter variations might modify the expression level of FAE1, and the results shed light on novel regulation mechanisms for erucic acid synthesis.

Genome-wide investigation of genetic changes during modern breeding of Brassica napus.

KEY MESSAGE: Considerable genome variation had been incorporated within rapeseed breeding programs over past decades. In past decades, there have been substantial changes in phenotypic properties of rapeseed as a result of extensive breeding effort. Uncovering the underlying patterns of allelic variation in the context of genome organisation would provide knowledge to guide future genetic improvement. We assessed genome-wide genetic changes, including population structure, genetic relatedness, the extent of linkage disequilibrium, nucleotide diversity and genetic differentiation based on F ST outlier detection, for a panel of 472 Brassica napus inbred accessions using a 60 k Brassica Infinium® SNP array. We found genetic diversity varied in different sub-groups. Moreover, the genetic diversity increased from 1950 to 1980 and then remained at a similar level in China and Europe. We also found ~6-10 % genomic regions revealed high F ST values. Some QTLs previously associated with important agronomic traits overlapped with these regions. Overall, the B. napus C genome was found to have more high F ST signals than the A genome, and we concluded that the C genome may contribute more valuable alleles to generate elite traits. The results of this study indicate that considerable genome variation had been incorporated within rapeseed breeding programs over past decades. These results also contribute to understanding the impact of rapeseed improvement on available genome variation and the potential for dissecting complex agronomic traits.

Comparison of the heat stress induced variations in DNA methylation between heat-tolerant and heat-sensitive rapeseed seedlings.

DNA methylation is responsive to various biotic and abiotic stresses. Heat stress is a serious threat to crop growth and development worldwide. Heat stress results in an array of morphological, physiological and biochemical changes in plants. The relationship between DNA methylation and heat stress in crops is relatively unknown. We investigated the differences in methylation levels and changes in the cytosine methylation patterns in seedlings of two rapeseed genotypes (heat-sensitive and heat-tolerant) under heat stress. Our results revealed that the methylation levels were different between a heat-tolerant genotype and a heat-sensitive one under control conditions. Under heat treatment, methylation increased more in the heat-sensitive genotype than in the heat-tolerant genotype. More DNA demethylation events occurred in the heat-tolerant genotype, while more DNA methylation occurred in the heat-sensitive genotype. A large and diverse set of genes were affected by heat stress via cytosine methylation changes, suggesting that these genes likely play important roles in the response and adaption to heat stress in Brassica napus L. This study indicated that the changes in DNA methylation differed between heat-tolerant and heat-sensitive genotypes of B. napus in response to heat stress, which further illuminates the molecular mechanisms of the adaption to heat stress in B. napus.

Assessing and broadening genetic diversity of a rapeseed germplasm collection.

Assessing the level of genetic diversity within a germplasm collection contributes to evaluating the potential for its utilization as a gene pool to improve the performance of cultivars. In this study, 45 high-quality simple sequence repeat (SSR) markers were screened and used to estimate the genetic base of a world-wide collection of 248 rapeseed (Brassica napus) inbred lines. For the whole collection, the genetic diversity of A genome was higher than that of C genome. The genetic diversity of C genome for the semi-winter type was the lowest among the different germplasm types. Because B. oleracea is usually used to broaden the genetic diversity of C genome in rapeseed, we evaluated the potential of 25 wild B. oleracea lines. More allelic variations and a higher genetic diversity were observed in B. oleracea than in rapeseed. One B. oleracea line and one oilseed B. rapa line were used to generate a resynthesized Brassica napus line, which was then crossed with six semi-winter rapeseed cultivars to produce 7 F1 hybrids. Not only the allele introgression but also mutations were observed in the hybrids, resulting in significant improvement of the genetic base.

PRDA1, a novel chloroplast nucleoid protein, is required for early chloroplast development and is involved in the regulation of plastid gene expression in Arabidopsis.

Chloroplast development requires accurate spatio-temporal expression of plastid genes. The regulation of plastid genes mediated by plastid-encoded RNA polymerase (PEP) is rather complex, and its related mechanism remains largely unclear. Here, we report the identification of a novel protein that is essential for plant development, PEP-Related Development Arrested 1 (PRDA1). Knock-out of PRDA1 in Arabidopsis (prda1 mutant) caused a seedling-lethal, albino phenotype and arrested the development of leaf chloroplasts. Localization analysis showed that PRDA1 was specifically targeted to chloroplasts and co-localized with chloroplast nucleoids, revealing that PRDA1 is a chloroplast nucleoid-associated protein. Gene expression analyses revealed that the PEP-dependent plastid transcript levels were greatly reduced in prda1. PRDA1 was co-expressed with most of the PEP-associated proteins. Protein interaction assays showed that PRDA1 clearly interacts with MRL7 and FSD2, both of which have been verified as essential for PEP-related chloroplast development. Reactive oxygen species scavenging through dimethylthiourea markedly alleviated the cotyledon-albino phenotypes of PRDA1 and MRL7 RNA interference seedlings. These results demonstrate that PRDA1 is required for early chloroplast development and involved in the regulation of plastid gene expression.

Automatic counting of rapeseed inflorescences using deep learning method and UAV RGB imagery.

Flowering is a crucial developing stage for rapeseed (Brassica napus L.) plants. Flowers develop on the main and branch inflorescences of rapeseed plants and then grow into siliques. The seed yield of rapeseed heavily depends on the total flower numbers per area throughout the whole flowering period. The number of rapeseed inflorescences can reflect the richness of rapeseed flowers and provide useful information for yield prediction. To count rapeseed inflorescences automatically, we transferred the counting problem to a detection task. Then, we developed a low-cost approach for counting rapeseed inflorescences using YOLOv5 with the Convolutional Block Attention Module (CBAM) based on unmanned aerial vehicle (UAV) Red-Green-Blue (RGB) imagery. Moreover, we constructed a Rapeseed Inflorescence Benchmark (RIB) to verify the effectiveness of our model. The RIB dataset captured by DJI Phantom 4 Pro V2.0, including 165 plot images and 60,000 manual labels, is to be released. Experimental results showed that indicators R2 for counting and the mean Average Precision (mAP) for location were over 0.96 and 92%, respectively. Compared with Faster R-CNN, YOLOv4, CenterNet, and TasselNetV2+, the proposed method achieved state-of-the-art counting performance on RIB and had advantages in location accuracy. The counting results revealed a quantitative dynamic change in the number of rapeseed inflorescences in the time dimension. Furthermore, a significant positive correlation between the actual crop yield and the automatically obtained rapeseed inflorescence total number on a field plot level was identified. Thus, a set of UAV- assisted methods for better determination of the flower richness was developed, which can greatly support the breeding of high-yield rapeseed varieties.

Automatic rape flower cluster counting method based on low-cost labelling and UAV-RGB images.

BACKGROUND: The flowering period is a critical time for the growth of rape plants. Counting rape flower clusters can help farmers to predict the yield information of the corresponding rape fields. However, counting in-field is a time-consuming and labor-intensive task. To address this, we explored a deep learning counting method based on unmanned aircraft vehicle (UAV). The proposed method developed the in-field counting of rape flower clusters as a density estimation problem. It is different from the object detection method of counting the bounding boxes. The crucial step of the density map estimation using deep learning is to train a deep neural network that maps from an input image to the corresponding annotated density map. RESULTS: We explored a rape flower cluster counting network series: RapeNet and RapeNet+. A rectangular box labeling-based rape flower clusters dataset (RFRB) and a centroid labeling-based rape flower clusters dataset (RFCP) were used for network model training. To verify the performance of RapeNet series, the paper compares the counting result with the real values of manual annotation. The average accuracy (Acc), relative root mean square error (rrMSE) and [Formula: see text] of the metrics are up to 0.9062, 12.03 and 0.9635 on the dataset RFRB, and 0.9538, 5.61 and 0.9826 on the dataset RFCP, respectively. The resolution has little influence for the proposed model. In addition, the visualization results have some interpretability. CONCLUSIONS: Extensive experimental results demonstrate that the RapeNet series outperforms other state-of-the-art counting approaches. The proposed method provides an important technical support for the crop counting statistics of rape flower clusters in field.

Automatic freezing-tolerant rapeseed material recognition using UAV images and deep learning.

BACKGROUND: Freezing injury is a devastating yet common damage that occurs to winter rapeseed during the overwintering period which directly reduces the yield and causes heavy economic loss. Thus, it is an important and urgent task for crop breeders to find the freezing-tolerant rapeseed materials in the process of breeding. Existing large-scale freezing-tolerant rapeseed material recognition methods mainly rely on the field investigation conducted by the agricultural experts using some professional equipments. These methods are time-consuming, inefficient and laborious. In addition, the accuracy of these traditional methods depends heavily on the knowledge and experience of the experts. METHODS: To solve these problems of existing methods, we propose a low-cost freezing-tolerant rapeseed material recognition approach using deep learning and unmanned aerial vehicle (UAV) images captured by a consumer UAV. We formulate the problem of freezing-tolerant material recognition as a binary classification problem, which can be solved well using deep learning. The proposed method can automatically and efficiently recognize the freezing-tolerant rapeseed materials from a large number of crop candidates. To train the deep learning network, we first manually construct the real dataset using the UAV images of rapeseed materials captured by the DJI Phantom 4 Pro V2.0. Then, five classic deep learning networks (AlexNet, VGGNet16, ResNet18, ResNet50 and GoogLeNet) are selected to perform the freezing-tolerant rapeseed material recognition. RESULT AND CONCLUSION: The accuracy of the five deep learning networks used in our work is all over 92%. Especially, ResNet50 provides the best accuracy (93.33[Formula: see text]) in this task. In addition, we also compare deep learning networks with traditional machine learning methods. The comparison results show that the deep learning-based methods significantly outperform the traditional machine learning-based methods in our task. The experimental results show that it is feasible to recognize the freezing-tolerant rapeseed using UAV images and deep learning.

Two novel proteins, MRL7 and its paralog MRL7-L, have essential but functionally distinct roles in chloroplast development and are involved in plastid gene expression regulation in Arabidopsis.

Chloroplast development requires the coordinated action of various proteins, many of which remain to be identified. Here, we report two novel genes, Mesophyll-cell RNAi Library line 7 (MRL7) and MRL7-Like (MRL7-L), that are involved in this process. An Arabidopsis knock-down transgenic plant (MRL7-RNAi) with delayed-greening phenotype was isolated from an RNA interference (RNAi) transformant library. Cotyledons and young leaves of MRL7-RNAi were pale in seedlings and gradually greened as the plant matured, while a knock-out in the MRL7 gene was seedling lethal. The MRL7 protein was shown to co-localize with a marker protein for nucleoids in chloroplasts, indicative of a role for the protein in chloroplast nucleic acid metabolism. Accordingly, chloroplast development was arrested upon loss of MRL7 function and the expression of plastid-encoded genes transcribed by plastid-encoded RNA polymerase (PEP) was significantly reduced in MRL7 knock-down and knock-out plants. A paralog of MRL7 (MRL7-L) was identified in the Arabidopsis genome. Both MRL7 and MRL7-L are only found in land plants and encode previously uncharacterized proteins without any known conserved domain. Like MRL7, knock-down of MRL7-L also resulted in a virescent phenotype, and a similar effect on plastid gene expression. However, the MRL7-L protein was localized to the chloroplast stroma. Taken together, our data indicate that the two paralogous proteins MRL7 and MRL7-L have essential but distinct roles during early chloroplast development and are involved in regulation of plastid gene expression.

Genome-wide analysis and expression profiles of glyoxalase gene families in Chinese cabbage (Brassica rapa L).

The glyoxalase pathway is composed of glyoxalase I (GLYI) and glyoxalase II (GLYII) and is responsible for the detoxification of a cytotoxic metabolite methylglyoxal (MG) into the nontoxic S-D-lactoylglutathione. The two glyoxalase enzymes play a crucial role in stress tolerance in various plant species. Recently, the GLY gene families have well been analyzed in Arabidopsis, rice and soybean, however, little is known about them in Chinese cabbage (Brassica rapa). Here, 16 BrGLYI and 15 BrGLYII genes were identified in the B. rapa genome, and the BrGLYI and BrGLYII proteins were both clustered into five subfamilies. The classifications, chromosomal distributions, gene duplications, exon-intron structures, localizations, conserved motifs and promoter cis-elements were also predicted and analyzed. In addition, the expression pattern of these genes in different tissues and their response to biotic and abiotic stresses were analyzed using publicly available data and a quantitative real-time PCR analysis (RT-qPCR). The results indicated that the expression profiles of BrGLY genes varied among different tissues. Notably, a number of BrGLY genes showed responses to biotic and abiotic stress treatments, including Plasmodiophora brassicae infection and various heavy metal stresses. Taken together, this study identifies BrGLYI and BrGLYII gene families in B. rapa and offers insight into their roles in plant development and stress resistance, especially in heavy metal stress tolerance and pathogen resistance.

Global DNA methylation variations after short-term heat shock treatment in cultured microspores of Brassica napus cv. Topas.

Heat stress can induce the cultured microspores into embryogenesis. In this study, whole genome bisulphite sequencing was employed to study global DNA methylation variations after short-term heat shock (STHS) treatments in cultured microspores of Brassica napus cv. Topas. Our results indicated that treatment on cultured Topas microspores at 32 °C for 6 h triggered DNA hypomethylation, particularly in the CG and CHG contexts. And the total number of T32 (Topas 32 °C for 6 h) vs. T0 (Topas 0 h) differentially methylated region-related genes (DRGs) was approximately two-fold higher than that of T18 (Topas 18 °C for 6 h) vs. T0 DRGs, which suggested that 32 °C might be a more intense external stimulus than 18 °C resulting in more changes in the DNA methylation status of cultured microspores. Additionally, 32 °C treatment for 6 h led to increased CHG differential methylations of transposons (DMTs), which were mainly constituted by overlaps between the hypomethylated differentially methylated regions (hypo-DMRs) and transposon elements (TEs). Further analysis demonstrated that the DRGs and their paralogs exhibited differential methylated/demethylated patterns. To summarize, the present study is the first methylome analysis of cultured microspores in response to STHS and may provide valuable information on the roles of DNA methylation in heat response.

Association Mapping of Flowering Time QTLs and Insight into Their Contributions to Rapeseed Growth Habits.

Plants have developed sophisticated systems to adapt to local conditions during evolution, domestication and natural or artificial selection. The selective pressures of these different growing conditions have caused significant genomic divergence within species. The flowering time trait is the most crucial factor because it helps plants to maintain sustainable development. Controlling flowering at appropriate times can also prevent plants from suffering from adverse growth conditions, such as drought, winter hardness, and disease. Hence, discovering the genome-wide genetic mechanisms that influence flowering time variations and understanding their contributions to adaptation should be a central goal of plant genetics and genomics. A global core collection panel with 448 inbred rapeseed lines was first planted in four independent environments, and their flowering time traits were evaluated. We then performed a genome-wide association mapping of flowering times with a 60 K SNP array for this core collection. With quality control and filtration, 20,342 SNP markers were ultimately used for further analyses. In total, 312 SNPs showed marker-trait associations in all four environments, and they were based on a threshold p-value of 4.06 × 10(-4); the 40 QTLs showed significant association with flowering time variations. To explore flowering time QTLs and genes related to growth habits in rapeseed, selection signals related to divergent habits were screened at the genome-wide level and 117 genomic regions were found. Comparing locations of flowering time QTLs and genes with these selection regions revealed that 20 flowering time QTLs and 224 flowering time genes overlapped with 24 and 81 selected regions, respectively. Based on this study, a number of marker-trait associations and candidate genes for flowering time variations in rapeseed were revealed. Moreover, we also showed that both flowering time QTLs and genes play important roles in rapeseed growth habits. These results will be applied to rapeseed breeding programs, and they will aid in our understanding of the relation between flowering time variations and growth habits in plants.

A genome-wide association study of plant height and primary branch number in rapeseed (Brassica napus).

Crop plant architecture plays a highly important role in its agronomic performance. Plant height (PH) and primary branch number (PB) are two major factors that affect the plant architecture of rapeseed (Brassica napus). Previous studies have shown that these two traits are controlled by multiple quantitative trait loci (QTL); however, QTLs have not been delimited to regions less than 10cM. Genome-wide association study (GWAS) is a highly efficient approach for identifying genetic loci controlling traits at relatively high resolution. In this study, variations in PH and PB of a panel of 472 rapeseed accessions that had previously been analyzed by a 60k SNP array were investigated for three consecutive years and studied by GWAS. Eight QTLs on chromosome A03, A05, A07 and C07 were identified for PH, and five QTLs on A01, A03, A07 and C07 were identified for PB. Although most QTLs have been detected in previous studies based on linkage analyses, the two QTLs of PH on A05 and the QTL of PB on C07 were novel. In the genomic regions close to the GWAS peaks, orthologs of the genes involved in flower development, phytohormone biosynthesis, metabolism and signaling in Arabidopsis were identified.

Identification and Characterization of a Glyoxalase I Gene in a Rapeseed Cultivar with Seed Thermotolerance.

Glyoxalase I (GLYI) is a ubiquitous enzyme in all organisms that catalyzes the conversion of the potent cytotoxin methylglyoxal to S-D-lactoylglutathione. Although many reports suggest the importance of GLYI in the plant response to stress, its function in seeds requires further study. Here, we identified a heat-induced GLYI from Brassica napus seeds, BnGLYI, using a comparative proteomics approach. Two-dimensional gel analyses revealed that BnGLYI protein expression upon heat treatment was significantly elevated in thermotolerant seeds but was diminished in heat-sensitive seeds. The BnGLYI-2 and BnGLYI-3 genes from the heat-sensitive and thermotolerant cultivars, respectively, were characterized, and analyzed. Only two amino acid residue variations were found between the amino acid sequences of the two genes. Moreover, overexpressing BnGLYI-3 in yeast cells enhanced tolerance to heat and cold stress and significantly increased GLYI activity compared to overexpressing BnGLYI-2. In addition, BnGLYI-3 transformants showed enhanced superoxide dismutase activities under heat and cold treatment, whereas these activities were diminished for BnGLYI-2 transformants. Taken together, these results indicate that overexpression of the BnGLYI-3 gene imparts thermotolerance and cold tolerance in yeast and that the variations in BnGLYI-3 may play an important role in the responses to temperature stresses.

Genome-wide survey and expression analysis of the putative non-specific lipid transfer proteins in Brassica rapa L.

BACKGROUND: Plant non-specific lipid transfer proteins (nsLtps) are small, basic proteins encoded by multigene families and have reported functions in many physiological processes such as mediating phospholipid transfer, defense reactions against phytopathogens, the adaptation of plants to various environmental conditions, and sexual reproduction. To date, no genome-wide overview of the Brassica rapa nsLtp (BrnsLtp) gene family has been performed. Therefore, as the first step and as a helpful strategy to elucidate the functions of BrnsLtps, a genome-wide study for this gene family is necessary. METHODOLOGY/PRINCIPAL FINDING: In this study, a total of 63 putative BrnsLtp genes were identified through a comprehensive in silico analysis of the whole genome of B. rapa. Based on the sequence similarities, these BrnsLtps was grouped into nine types (I, II, III, IV, V, VI, VIII, IX, and XI). There is no type VII nsLtps in B. rapa, and a new type, XI nsLtps, was identified in B. rapa. Furthermore, nine type II AtLtps have no homologous genes in B. rapa. Gene duplication analysis demonstrated that the conserved collinear block of each BrnsLtp is highly identical to those in Arabidopsis and that both segmental duplications and tandem duplications seem to play equal roles in the diversification of this gene family. Expression analysis indicated that 29 out of the 63 BrnsLtps showed specific expression patterns. After careful comparison and analysis, we hypothesize that some of the type I BrnsLtps may function like Arabidopsis pathogenesis-related-14 (PR-14) proteins to protect the plant from phytopathogen attack. Eleven BrnsLtps with inflorescence-specific expression may play important roles in sexual reproduction. Additionally, BrnsLtpI.3 may have functions similar to Arabidopsis LTP1. CONCLUSIONS/SIGNIFICANCE: The genome-wide identification, bioinformatic analysis and expression analysis of BrnsLtp genes should facilitate research of this gene family and polyploidy evolution and provide new insight towards elucidating their biological functions in plants.

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.