Genetic and transcriptomic analyses of lignin- and lodging-related traits in Brassica napus

Targeted mutagenesis of flavonoid biosynthesis pathway genes reveals functional divergence in seed coat colour, oil content and fatty acid composition in Brassica napus L

Yellow-seed is widely accepted as a good-quality trait in Brassica crops. Previous studies have shown that the flavonoid biosynthesis pathway is essential for the development of seed colour, but its function in Brassica napus, an important oil crop, is poorly understood. To systematically explore the gene functions of the flavonoid biosynthesis pathway in rapeseed, several representative TRANSPARENT TESTA (TT) genes, including three structural genes (BnaTT7, BnaTT18, BnaTT10), two regulatory genes (BnaTT1, BnaTT2) and a transporter (BnaTT12), were selected for targeted mutation by CRISPR/Cas9 in the present study. Seed coat colour, lignin content, seed quality and yield-related traits were investigated in these Bnatt mutants together with Bnatt8 generated previously. These Bnatt mutants produced seeds with an elevated seed oil content and decreased pigment and lignin accumulation in the seed coat without any serious defects in the yield-related traits. In addition, the fatty acid (FA) composition was also altered to different degrees, i.e., decreased oleic acid and increased linoleic acid and α-linolenic acid, in all Bnatt mutants except Bnatt18. Furthermore, gene expression analysis revealed that most of BnaTT mutations resulted in the down-regulation of key genes related to flavonoid and lignin synthesis, and the up-regulation of key genes related to lipid synthesis and oil body formation, which may contribute to the phenotype. Collectively, our study generated valuable resources for breeding programs, and more importantly demonstrated the functional divergence and overlap of flavonoid biosynthesis pathway genes in seed coat colour, oil content and FA composition of rapeseed.

An integrated QTL mapping and transcriptome sequencing provides further molecular insights and candidate genes for stem strength in rapeseed (Brassica napus L.)

KEY MESSAGE

We detected the major QTL- qSR.A07, which regulated stem strength and was fine-mapped to 490 kb. BnaA07G0302800ZS and BnaA07G0305700ZS as the candidate functional genes were identified at qSR.A07 locus. The stem's mechanical properties reflect its ability to resist lodging. In rapeseed (Brassica napus L.), although stem lodging negatively affects yield and generates harvesting difficulties, the molecular regulation of stem strength remains elusive. Hence, this study aimed to unravel the main loci and molecular mechanisms governing rapeseed stem strength. A mapping population consisting of 267 RILs (recombinant inbred lines) was developed from the crossed between ZS11 (high stem strength) and 4D122 (low stem strength), and two mechanical properties of stems including stem breaking strength and stem rind penetrometer resistance were phenotyped in four different environments. Four pleiotropic QTLs that were stable in at least two environments were detected. qSR.A07, the major one, was fine-mapped to a 490 kb interval between markers SA7-2711 and SA7-2760 on chromosome 7. It displayed epistatic interaction with qRPR.A09-2. Comparative transcriptome sequencing and analysis unveiled methionine/S-adenosylmethionine cycle (Met/SAM cycle), cytoskeleton organization, sulfur metabolism and phenylpropanoid biosynthesis as the main pathways associated with high stem strength. Further, we identified two candidate genes, BnaA07G0302800ZS and BnaA07G0305700ZS, at qSR.A07 locus. Gene sequence alignment identified a number of InDels, SNPs and amino acid variants in sequences of these genes between ZS11 and 4D122. Finally, based on these genetic variants, we developed three SNP markers of these genes to facilitate future genetic selection and functional studies. These findings offer important genetic resources for the molecular-assisted breeding of novel rapeseed stem lodging-resistant varieties.

Genetic analyses and prediction for lodging‑related traits in a diverse Iranian hexaploid wheat collection

Lodging is one of the most important limiting environmental factors for achieving the maximum yield and quality of grains in cereals, including wheat. However, little is known about the genetic foundation underlying lodging resistance (LR) in wheat. In this study, 208 landraces and 90 cultivars were phenotyped in two cropping seasons (2018-2019 and 2019-2020) for 19 LR-related traits. A genome-wide association study (GWAS) and genomics prediction were carried out to dissect the genomic regions of LR. The number of significant marker pairs (MPs) was highest for genome B in both landraces (427,017) and cultivars (37,359). The strongest linkage disequilibrium (LD) between marker pairs was found on chromosome 4A (0.318). For stem lodging-related traits, 465, 497, and 478 marker-trait associations (MTAs) and 45 candidate genes were identified in year 1, year 2, and pooled. Gene ontology exhibited genomic region on Chr. 2B, 6B, and 7B control lodging. Most of these genes have key roles in defense response, calcium ion transmembrane transport, carbohydrate metabolic process, nitrogen compound metabolic process, and some genes harbor unknown functions that, all together may respond to lodging as a complex network. The module associated with starch and sucrose biosynthesis was highlighted. Regarding genomic prediction, the GBLUP model performed better than BRR and RRBLUP. This suggests that GBLUP would be a good tool for wheat genome selection. As a result of these findings, it has been possible to identify pivotal QTLs and genes that could be used to improve stem lodging resistance in Triticum aestivum L.

Integrating biochemical and anatomical characterizations with transcriptome analysis to dissect superior stem strength of ZS11 (Brassica napus)

Stem lodging resistance is a serious problem impairing crop yield and quality. ZS11 is an adaptable and stable yielding rapeseed variety with excellent resistance to lodging. However, the mechanism regulating lodging resistance in ZS11 remains unclear. Here, we observed that high stem mechanical strength is the main factor determining the superior lodging resistance of ZS11 through a comparative biology study. Compared with 4D122, ZS11 has higher rind penetrometer resistance (RPR) and stem breaking strength (SBS) at flowering and silique stages. Anatomical analysis shows that ZS11 exhibits thicker xylem layers and denser interfascicular fibrocytes. Analysis of cell wall components suggests that ZS11 possessed more lignin and cellulose during stem secondary development. By comparative transcriptome analysis, we reveal a relatively higher expression of genes required for S-adenosylmethionine (SAM) synthesis, and several key genes (4-COUMATATE-CoA LIGASE, CINNAMOYL-CoA REDUCTASE, CAFFEATE O-METHYLTRANSFERASE, PEROXIDASE) involved in lignin synthesis pathway in ZS11, which support an enhanced lignin biosynthesis ability in the ZS11 stem. Moreover, the difference in cellulose may relate to the significant enrichment of DEGs associated with microtubule-related process and cytoskeleton organization at the flowering stage. Protein interaction network analysis indicate that the preferential expression of several genes, such as LONESOME HIGHWAY (LHW), DNA BINDING WITH ONE FINGERS (DOFs), WUSCHEL HOMEOBOX RELATED 4 (WOX4), are related to vascular development and contribute to denser and thicker lignified cell layers in ZS11. Taken together, our results provide insights into the physiological and molecular regulatory basis for the formation of stem lodging resistance in ZS11, which will greatly promote the application of this superior trait in rapeseed breeding.

Genetic mapping of some key plant architecture traits in Brassica juncea using a doubled haploid population derived from a cross between two distinct lines: vegetable type Tumida and oleiferous Varuna

Genetic mapping of some key plant architectural traits in a vegetable type and an oleiferous B. juncea cross revealed QTL and candidate genes for breeding more productive ideotypes. Brassica juncea (AABB, 2n = 36), commonly called mustard, is an allopolyploid crop of recent origin but contains considerable morphological and genetic variation. An F₁-derived doubled haploid population developed from a cross between an Indian oleiferous line, Varuna, and a Chinese stem type vegetable mustard, Tumida showed significant variability for some key plant architectural traits-four stem strength-related traits, stem diameter (Dia), plant height (Plht), branch initiation height (Bih), number of primary branches (Pbr), and days to flowering (Df). Multi-environment QTL analysis identified twenty Stable QTL for the above-mentioned nine plant architectural traits. Though Tumida is ill-adapted to the Indian growing conditions, it was found to contribute favorable alleles in Stable QTL for five architectural traits-press force, Dia, Plht, Bih, and Pbr; these QTL could be used to breed superior ideotypes in the oleiferous mustard lines. A QTL cluster on LG A10 contained Stable QTL for seven architectural traits that included major QTL (phenotypic variance ≥ 10%) for Df and Pbr, with Tumida contributing the trait-enhancing alleles for both. Since early flowering is critical for the cultivation of mustard in the Indian subcontinent, this QTL cannot be used for the improvement of Pbr in the Indian gene pool lines. Conditional QTL analysis for Pbr, however, identified other QTL which could be used for the improvement of Pbr without affecting Df. The Stable QTL intervals were mapped on the genome assemblies of Tumida and Varuna for the identification of candidate genes.

Transcriptome analysis identifies differentially expressed genes involved in lignin biosynthesis in barley

Lignin is an essential metabolite for plant growth but negatively affects the quality of forage barley. Genetic modification of quality traits to improve the forage digestibility requires an understanding of the molecular mechanism of lignin biosynthesis. RNA-Seq was used to quantify transcripts differentially expressed among leaf, stem and spike tissues from two barley genotypes. A total of 13,172 differentially expressed genes (DEGs) were identified, of which much more up-regulated DEGs were detected from the contrasting groups of leaf vs spike (L-S) and stem vs spike (S-S), and down-regulated DEGs were dominant in the group of stem vs leaf (S-L). 47 DEGs were successfully annotated to the monolignol pathway and six of them were candidate genes regulating the lignin biosynthesis. The qRT-PCR assay verified the expression profiles of the six candidate genes. Among them, four genes might positively regulate the lignin biosynthesis during forage barley development in terms of the consistency of their expression levels and changes of lignin content among the tissues, while the other two genes may have the reverse effects. These findings provide target genes for further investigations on molecular regulatory mechanisms of lignin biosynthesis and genetic resources for improvement of forage quality in barley molecular breeding programme.

Shading decreases lodging resistance of wheat under different planting densities by altering lignin monomer composition of stems

To clarify the influences of shading stress and planting density on the lignin monomer composition of wheat stems and their relationship with lodging resistance, Lodging resistant variety Shannong 23 (SN23) and lodging sensitive variety Shannong 16 (SN16) were grown during 2018-2019 and 2019-2020 growing seasons. The planting densities were 150 × 10⁴ plants ha^-1 (D1), 225 × 10⁴ plants ha^-1 (D2) and 300 × 10⁴ plants ha^-1 (D3). At the jointing stage, an artificial shading shed was used to simulate shading stress. Then the effects of shading on stem morphological characteristics, lignin monomer composition and lodging resistance of wheat under different planting densities were studied. Results indicate that shading at the jointing stage increased the length of basal internodes and the plant height and moved the height of center of gravity (CG) upward. Moreover, the stem diameter and the wall thickness decreased by 0.10-0.53 mm and 0.18-0.40 mm, respectively. The stem filling degree was reduced accordingly. As indicated by the correlation analysis and the stepwise regression analysis, shading-induced lodging mainly resulted from changes in the stem morphological characteristics and lignin accumulation. The influential magnitude of these factors was ordered as follows: stem filling degree, wall thickness, lignin content, contents and proportions of monomers S and H, and length of the second internode. The expression abundance of TaPAL, TaCOMT, TaCCR, and TaCAD declined in response to shading stress and high planting density. As a result, the distribution ratios of photosynthetic carbon sources to lignin monomers S, G and H were changed. The lignin content of stems on the day 42 after the jointing stage decreased by 18.48%. The monomer S content decreased, while the content and proportion of monomer H increased, thus weakening the breaking strength of wheat stems.

Integration of transcriptome and metabolome analyses reveals key lodging-resistance-related genes and metabolic pathways in maize

Stalk lodging, or breakage of the stalk at or below the ear, is one of the vital factors causing substantial yield losses in maize (Zea mays. L). Lodging affects maize plants’ physiological and molecular processes, eventually impacting plant growth and productivity. Despite this known fact, few researchers have investigated the genetic architecture underlying lodging in maize. Herein, through integrated transcriptome, metabolome, and phenotypic analyses of stalks of three diverse hybrid cultivars (highly resistant JNK738, mildly resistant JNK728, and lowly resistant XY335) at the tasseling (10 days to silking, 10 DTS) stage, we identified key genes and metabolic pathways modulating lodging resistance in maize. Based on the RNA-Seq analysis, a total of 10093 differentially expressed genes (DEGs) were identified from the comparison of the three varieties in pairs. Additionally, key lodging resistance–related metabolic pathways were obtained by KEGG enrichment analysis, and the DEGs were found predominantly enriched in phenylpropanoid and secondary metabolites biosynthesis pathways in the L_vs._H and M_vs._H comparison groups. Moreover, K-means analysis clustered the DEGs into clear and distinct expression profiles for each cultivar, with several functional and regulatory genes involved in the cell wall assembly, lignin biosynthetic process and hormone metabolic process being identified in the special clusters related to lodging resistance. Subsequently, integrating metabolome and transcriptome analyses revealed nine key lignin-associated metabolites that showed different expression trends in the three hybrid cultivars, among which L-phenylalanine and p-coumaric acid were regarded as differentially changed metabolites (DCMs). These two DCMs belonged to phenylalanine metabolism and biosynthesis pathways and were also supported by the RNA-Seq data. Furthermore, plant hormone signal transduction pathway–related genes encoding auxin, abscisic acid, jasmonates, and salicylic acid were differentially expressed in the three comparisons of lodging resistance, indicating these DEGs were valuable potential targets for improving maize lodging resistance. Finally, comparative physiological and qRT-PCR analyses results supported our transcriptome-based findings. Our research not only provides a preliminary theoretical basis and experimental ideas for an in-depth study of the regulatory networks involved in maize lodging resistance regulation but also opens up new avenues for molecular maize stalk lodging resistance breeding.

The Transcriptome and Metabolome Reveal the Potential Mechanism of Lodging Resistance in Intergeneric Hybrids between Brassica napus and Capsella bursa-pastoris

Lodging is one of the main reasons for the reduction in seed yield and is the limitation of mechanized harvesting in B. napus. The dissection of the regulatory mechanism of lodging resistance is an important goal in B. napus. In this study, the lodging resistant B. napus line, YG689, derived from the hybridization between B. napus cv. Zhongyou 821 (ZY821) and Capsella bursa-pastoris, was used to dissect the regulation mechanism of hard stem formation by integrating anatomical structure, transcriptome and metabolome analyses. It was shown that the lignocellulose content of YG689 is higher than that of ZY821, and some differentially expressed genes (DEGs) involved in the lignocellulose synthesis pathway were revealed by transcriptome analyses. Meanwhile, GC–TOF–MS and UPLC–QTOF–MS identified 40, 54, and 31 differential metabolites in the bolting stage, first flower stage, and the final flower stage. The differential accumulation of these metabolites might be associated with the lignocellulose biosynthesis in B. napus. Finally, some important genes that regulate the metabolic pathway of lignocellulose biosynthesis, such as BnaA02g18920D, BnaA10g15590D, BnaC05g48040D, and NewGene_216 were identified in B. napus through the combination of transcriptomics and metabolomics data. The present results explored the potential regulatory mechanism of lignocellulose biosynthesis, which provided a new clue for the breeding of B. napus with lodging resistance in the future.

iTRAQ-based proteomic analysis of heteromorphic leaves reveals eco-adaptability of Populus euphratica Oliv

BACKGROUND

Heterophylly is regard as adaptation to different environments in plant, and Populus euphratica is an important heterophyllous woody plant. However, information on its molecular mechanism in eco-adaptability remains obscure.

RESULTS

In this research, proteins were identified by isobaric tags for relative and absolute quantitation (iTRAQ) technology in lanceolate, ovate, and dentate broad-ovate leaves from adult P. euphratica trees, respectively. Besides, chlorophyll content, net photosynthetic rate, stomatal conductance, transpiration rate and peroxidase activity in these heteromorphic leaves were investigated. A total number of 2,689 proteins were detected in the heteromorphic leaves, of which 56, 73, and 222 differential abundance proteins (DAPs) were determined in ovate/lanceolate, dentate broad-ovate/lanceolate, and dentate broad-ovate/ovate comparison groups. Bioinformatics analysis suggested these altered proteins related to photosynthesis, stress tolerance, respiration and primary metabolism accumulated in dentate broad-ovate and ovate leaves, which were consistent with the results of physiological parameters and Real-time Quantitative PCR experiments.

CONCLUSION

This research demonstrated the mechanism of the differential abundance proteins in providing an optimal strategy of resource utilization and survival for P. euphratica, that could offer clues for further investigations into eco-adaptability of heterophyllous woody plants.

Integration of GWAS and transcriptome analyses to identify SNPs and candidate genes for aluminum tolerance in rapeseed (Brassica napus L.)

BACKGROUND

The exchangeable aluminum (Al), released from the acid soils, is another addition to the environmental stress factors in the form of Al toxicity stress. Al stress affects the normal crop development and reduces the overall yield of rapeseed (Brassica napus L.). The response mechanism of plants to Al toxicity is complicated and difficult to understand with few QTL related studies in rapeseed under Al toxicity stress.

RESULT

Using 200,510 SNPs developed by SLAF-seq (specific-locus amplified fragment sequencing) technology, we carried out the genome-wide association analysis (GWAS) in a population of 254 inbred lines of B. napus with large genetic variation and Al-tolerance differences. There were 43 SNPs significantly associated with eight Al-tolerance traits in the seedling stage were detected on 14 chromosomes, and 777 candidate genes were screened at the flanking 100 kb region of these SNPs. Moreover, RNA-seq detected 8291 and 5341 DEGs (the differentially expressed gene) in the Al -tolerant line (ATL) and -sensitive line (ASL), respectively. Based on integration of GWAS and RNA-seq analysis, 64 candidate genes from GWAS analysis differentially expressed at least once in 6 h vs 0 h or 24 h vs 0 h conditions in ATL or ASL. Moreover, four out of sixty-four candidate genes (BnaA03g30320D, BnaA10g11500D, BnaC03g38360D and BnaC06g30030D) were differentially expressed in both 6 h and 24 h compared to 0 h (control) conditions in both lines. The proposed model based on the candidate genes excavated in this study highlighted that Al stress disturb the oxidation-redox balance, causing abnormal synthesis and repair of cell wall and ABA signal transduction, ultimately resulting in inhibition of root elongation.

CONCLUSIONS

The integration of GWAS and transcriptome analysis provide an effective strategy to explore the SNPs and candidate genes, which has a potential to develop molecular markers for breeding Al tolerant rapeseed varieties along with theoretical basis of molecular mechanisms for Al toxicity response of Brassica napus plants.

Evaluation of Cell Wall Chemistry of Della and Its Mutant Sweet Sorghum Stalks

The cell wall compositional (lignin and polysaccharides) variation of two sweet sorghum varieties, Della (D) and its variant REDforGREEN (RG), was evaluated at internodes (IN) and nodes (N) using high-performance liquid chromatography (HPLC), pyrolysis-gas chromatography-mass spectrometry (Py-GCMS), X-ray diffraction (XRD), and two-dimensional (2D) ¹H-¹³C nuclear magnetic resonance (NMR). The stalks were grown in 2018 (D1 and RG1) and 2019 (D2 and RG2) seasons. In RG1, Klason lignin reductions by 16-44 and 2-26% were detected in IN and N, respectively. The analyses also revealed that lignin from the sorghum stalks was enriched in guaiacyl units and the syringyl/guaiacyl ratio was increased in RG1 and RG2, respectively, by 96% and more than 2-fold at IN and 61 and 23% at N. The glucan content was reduced by 23-27% for RG1 and by 17-22% for RG2 at internodes. Structural variations due to changes in both cellulose- and hemicellulose-based sugars were detected. The nonacylated and γ-acylated β-O-4 linkages were the main interunit linkages detected in lignin. These results indicate compositional variation of stalks due to the RG variation, and the growing season could influence their mechanical and lodging behavior.

QTL Identification for Stem Fiber, Strength and Rot Resistance in a DH Population from an Alien Introgression of Brassica napus

Stem fiber, stem strength and stem-rot resistance are important agronomic traits in Brassica napus. To understand the molecular mechanism that controls the stem-related traits, we investigated the stem lignin (ADL), cellulose (Cel), hemicellulose (Hem) content, S/G monolignol ratio (SG), stem breaking force (BF), breaking strength (F) and Sclerotinia sclerotiorum resistance (SSR). Each trait was significantly positively or negatively correlated with more than three of the other six traits. QTL mapping for ADL, Cel, Hem, SG, BF, F and SSR were performed using a doubled haploid population derived from an intertribal B. napus introgression line 'Y689' crossed with B. napus cv. 'Westar'. A total of 67 additive QTL were identified and integrated into 55 consensus QTL by meta-analysis. Among the 55 consensus QTL, 23 (41.8%) QTL were co-located and were integrated into 11 unique QTL. The QTL by environment (Q × E) interactions were analyzed and 22 combined QTL were identified. In addition, candidate genes within the QTL intervals were proposed based on the known function of Arabidopsis orthologs. These results provided valuable information for improving lodging resistance, S. sclerotiorum resistance and mechanized harvesting of B. napus.

Knockout of the lignin pathway gene BnF5H decreases the S/G lignin compositional ratio and improves Sclerotinia sclerotiorum resistance in Brassica napus

Ferulate-5-hydroxylase is a key enzyme involved in the conversion of the guaiacyl monolignol to the syringyl monolignol in angiosperms. The monolignol ratio has been proposed to affect biomass recalcitrance and the resistance to plant disease. Stem rot caused by the fungus Sclerotinia sclerotiorum in Brassica napus causes severe losses in its production. To date, there is no information about the effect of the lignin monomer ratio on the resistance to S. sclerotiorum in B. napus. Four dominantly expressed ferulate-5-hydroxylase genes were concertedly knocked out by CRISPR/Cas9 in B. napus, and three mutant lines were generated. The S/G lignin compositional ratio was decreased compared to that of the wild type based on the results of Mӓule staining and 2D-NMR profiling in KO-7. The resistance to S. sclerotiorum in stems and leaves increased for the three f5h mutant lines compared with WT. Furthermore, we found that the stem strength of f5h mutant lines was significantly increased. Overall, we demonstrate for the first time that decreasing the S/G ratio by knocking out of the F5H gene improves S. sclerotiorum resistance in B. napus and increases stem strength.

High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits in Eucalyptus

Introduction

Eucalyptus urophylla, E. tereticornis and their hybrids are the most important commercial forest tree species in South China where they are grown for pulpwood and solid wood production. Construction of a fine-scale genetic linkage map and detecting quantitative trait loci (QTL) for economically important traits linked to these end-uses will facilitate identification of the main candidate genes and elucidate the regulatory mechanisms.

Method

A high-density consensus map (a total of 2754 SNPs with 1359.18 cM) was constructed using genotyping by sequencing (GBS) on clonal progenies of E. urophylla × tereticornis hybrids. QTL mapping of growth and wood property traits were conducted in three common garden experiments, resulting in a total of 108 QTLs. A total of 1052 candidate genes were screened by the efficient combination of QTL mapping and transcriptome analysis.

Results

Only ten QTLs were found to be stable across two environments, and only one (qSG10Stable mapped on chromosome 10, and associated with lignin syringyl-to-guaiacyl ratio) was stable across all three environments. Compared to other QTLs, qSG10Stable explained a very high level of phenotypic variation (18.4-23.6%), perhaps suggesting that QTLs with strong effects may be more stably inherited across multiple environments. Screened candidate genes were associated with some transcription factor families, such as TALE, which play an important role in the secondary growth of plant cell walls and the regulation of wood formation.

Discussion

While QTLs such as qSG10Stable, found to be stable across three sites, appear to be comparatively uncommon, their identification is likely to be a key to practical QTL-based breeding. Further research involving clonally-replicated populations, deployed across multiple target planting sites, will be required to further elucidate QTL-by-environment interactions.

Genome-wide identification and expression profiling of the COBRA-like genes reveal likely roles in stem strength in rapeseed (Brassica napus L.)

The COBRA-like (COBL) genes play key roles in cell anisotropic expansion and the orientation of microfibrils. Mutations in these genes cause the brittle stem and induce pathogen responsive phenotypes in Arabidopsis and several crop plants. In this study, an in silico genome-wide analysis was performed to identify the COBL family members in Brassica. We identified 44, 20 and 23 COBL genes in B. napus and its diploid progenitor species B. rapa and B. oleracea, respectively. All the predicted COBL genes were phylogenetically clustered into two groups: the AtCOB group and the AtCOBL7 group. The conserved chromosome locations of COBLs in Arabidopsis and Brassica, together with clustering, indicated that the expansion of the COBL gene family in B. napus was primarily attributable to whole-genome triplication. Among the BnaCOBLs, 22 contained all the conserved motifs and derived from 9 of 12 subgroups. RNA-seq analysis was used to determine the tissue preferential expression patterns of various subgroups. BnaCOBL9, BnaCOBL35 and BnaCOBL41 were highly expressed in stem with high-breaking resistance, which implies these AtCOB subgroup members may be involved in stem development and stem breaking resistance of rapeseed. Our results of this study may help to elucidate the molecular properties of the COBRA gene family and provide informative clues for high stem-breaking resistance studies.

Comparative transcriptomic analysis of seed coats with high and low lignin contents reveals lignin and flavonoid biosynthesis in Brassica napus

BACKGROUND

Brassica napus L. (2n = 38, AACC) is one of the most important oil crops and sources of protein for animal feed worldwide. Lignin is a large molecule aromatic polymer and a major cell wall component. However, lignin in the seed coat reduces the availability and restricts the development of rapeseed cake. Therefore, it is critical to reduce the lignin content of the seed coat. Here, high-lignin (H-lignin) and low-lignin (L-lignin) content recombinant inbred lines (RILs) were selected from an RIL population for analysis.

RESULTS

The cross-section results indicated that the seed coat of the H-lignin lines was thicker than that of the L-lignin lines, especially the palisade layer. The seed coats and embryos at 35, 40 and 46 days after flowering (DAF) were subjected to RNA sequencing (RNA-Seq), and the expression of the BnPAL and BnC4H gene families in the lignin pathway was significantly higher in the H-lignin seed coat than in the L-lignin seed coat. The Bn4CL gene family also showed this trend. In addition, among the genes related to plant hormone synthesis, BnaC02g01710D was upregulated and BnaA07g11700D and BnaC09g00190D were downregulated in H-lignin lines. Some transcription factors were upregulated, such as BnNAC080, BnNAC083, BnMYB9, BnMYB9-1, BnMYB60 and BnMYB60-1, while BnMYB91 was downregulated in H-lignin lines. Moreover, most genes of the flavonoid pathway, such as BnCHS and BnDFR, were strongly expressed in H-lignin seed coat.

CONCLUSIONS

In Our study, some key genes such as hormone synthesis genes, transcription factors and miRNAs related to lignin and flavonoid biosynthesis were identified. A regulatory model of B. napus seed coat lignin was proposed. These results provide new insight into lignin and flavonoid biosynthesis in B. napus.

Assessment of differences in morphological and physiological leaf lodging characteristics between two cultivars of Hippeastrum rutilum

BACKGROUND

Environmental lodging stress, which is a result of numerous factors, is characterized by uncertainty. However, several studies related to lodging in cereal crops have reported that lodging in the Hippeastrum rutilum environment is very rare. Hippeastrum rutilum is a garden flower with high ornamental value and abundant germplasm resources. Under past cultivation practices, it was found that the plant types of 'Red Lion', with red flowers, and 'Apple Blossom', with pink flowers, are quite different. The leaves of 'Red Lion' are upright, while the leaves of 'Apple Blossom' show lodging, which seriously affects its ornamental value. The aims of this study were to compare the differences between the two varieties with leaf lodging and upright leaves according to morphological and physiological attributes. In this study, karyotype analysis and phenotypic morphological and physiological characteristics were compared to explore the differences between the two plant types.

RESULTS

The karyotype analysis of the two cultivars showed that their chromosome types were both tetraploid plants. The results showed that the lignin content in the leaves of 'Red Lion' was high, the cross-sectional structure of the leaf vascular bundle was more stable, and the chlorophyll content was high. In addition, significantly less energy was transferred to the electron transport chain (ETR) during the photoreaction. Similarly, the results regarding the maximum photosynthetic rate (Fv/Fm), nonphotochemical quenching (NPQ) and effective quantum yield of photosystem II photochemistry (△F/Fm') all indicated that the photosynthetic capacity of "Red Lion" was greater than that of "Apple Blossom", which was affected by leaf lodging. The size of the leaves was significantly smaller, and the leaf sag angle, leaf width, and leaf tip angle presented significantly lower values in 'Red Lion' than in 'Apple Blossom', which exhibits leaf sag. The difference in these factors may be the reason for the different phenotypes of the two cultivars.

CONCLUSION

The results of this study proved that lodging affects the photosynthetic capacity of Hippeastrum rutilum and revealed some indexes that might be related to leaf lodging, laying a theoretical foundation for cultivating and improving new varieties.

Insights on SNP types, detection methods and their utilization in Brassica species: Recent progress and future perspectives

The genus Brassica, family Brassicaceae (Cruciferae), comprises many important species of oil crops, vegetables and medicinal plants including B. rapa, B. oleracea, B. nigra, B. napus, B. juncea, B. carinata. Genomic researches in Brassica species is constrained by polyploidization, mainly due to its complicated genomic structure. However, rapid development of methods for detecting single nucleotide polymorphisms (SNP), such as next generation sequencing and SNP microarray, has accelerated release of reference Brassica species genomes as well as discovery of large numbers and genome-wide SNPs, thus intensifying forward genetics in this genus. In this review, we summarize biological characteristics, classification and various methods for detecting SNPs, focusing on high-throughput techniques. Moreover, we describe the pivotal roles of SNPs in genetic diversity, linkage map construction and QTL mapping, comparative genomics, linkage disequilibrium and genome-wide association studies. These insights are expected to deepen our understanding and guide further advancements in Brassica species research.

TaEXPB7-B, a β-expansin gene involved in low-temperature stress and abscisic acid responses, promotes growth and cold resistance in Arabidopsis thaliana

Low temperature is one of the primary causes of economic loss in agricultural production, and in this regard, expansin proteins are known to play important roles in plant growth and responses to various abiotic stresses and plant hormones. In order to elucidate the roles of expansin genes in the response of Dongnongdongmai 2 (D2), a highly cold-resistant winter wheat variety, to low-temperature stress, we exposed plants to a temperature of 4℃ and analysed the transcriptome of tillering nodes. Expression levels of TaEXPB7-B were significantly increased in response to both low-temperature stress and abscisic acid (ABA) treatment. To further confirm these observations, we transformed Arabidopsis plants with the β-glucuronidase (GUS) gene driven by the TaEXPB7-B promoter. GUS staining results revealed that TaEXPB7-B showed similar responses to low-temperature and ABA treatments. Our transcriptome data indicated that the AREB/ABF transcription factor gene TaWABI5 was also induced by low temperature in D2. Yeast one-hybrid experiments demonstrated that TaWABI5 binds to an ABRE cis-element in the TaEXPB7-B promoter, and overexpression of TaWABI5 in wheat protoplasts enhanced the expression of endogenous TaEXPB7-B by 7.7-fold, implying that TaWABI5 plays important roles in regulating the expression of TaEXPB7-B. Cytological data obtained from the transient expression of 35S::TaEXPB7-B-eYFP in onion epidermal cells indicated that TaEXPB7-B is cell wall localised. Overexpression of TaEXPB7-B in Arabidopsis promoted a significant increase in plant growth and increased lignin and cellulose contents. Moreover, TaEXPB7-B conferred enhanced antioxidant and osmotic regulation in transgenic Arabidopsis, thereby increasing the tolerance and survival of plants under conditions of low-temperature stress.

Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.)

Despite the high accuracy of short read sequencing (SRS), there are still issues with attaining accurate single nucleotide polymorphism (SNP) genotypes at low sequencing coverage and in highly duplicated genomes due to misalignment. Long read sequencing (LRS) systems, including the Oxford Nanopore Technologies (ONT) minION, have become popular options for de novo genome assembly and structural variant characterisation. The current high error rate often requires substantial post-sequencing correction and would appear to prevent the adoption of this system for SNP genotyping, but nanopore sequencing errors are largely random. Using low coverage ONT minION sequencing for genotyping of pre-validated SNP loci was examined in 9 canola doubled haploids. The minION genotypes were compared to the Illumina sequences to determine the extent and nature of genotype discrepancies between the two systems. The significant increase in read length improved alignment to the genome and the absence of classical SRS biases results in a more even representation of the genome. Sequencing errors are present, primarily in the form of heterozygous genotypes, which can be removed in completely homozygous backgrounds but requires more advanced bioinformatics in heterozygous genomes. Developments in this technology are promising for routine genotyping in the future.

Transcriptome Profile Analysis of Winter Rapeseed (Brassica napus L.) in Response to Freezing Stress, Reveal Potentially Connected Events to Freezing Stress

Winter rapeseed is not only an important oilseed crop, but also a winter cover crop in Northern China, where its production was severely limited by freezing stress. As an overwinter crop, the production is severely limited by freezing stress. Therefore, understanding the physiological and molecular mechanism of winter rapeseed (Brassica napus L.) in freezing stress responses becomes essential for the improvement and development of freezing-tolerant varieties of Brassica napus. In this study, morphological, physiological, ultrastructure and transcriptome changes in the Brassica napus line "2016TS(G)10" (freezing-tolerance line) that was exposed to -2 °C for 0 h, 1 h, 3 h and 24 h were characterized. The results showed that freezing stress caused seedling dehydration, and chloroplast dilation and degradation. The content of malondialdehyde (MDA), proline, soluble protein and soluble sugars were increased, as well as the relative electrolyte leakage (REL) which was significantly increased at frozen 24 h. Subsequently, RNA-seq analysis revealed a total of 98,672 UniGenes that were annotated in Brassica napus and 3905 UniGenes were identified as differentially expressed genes after being exposed to freezing stress. Among these genes, 2312 (59.21%) were up-regulated and 1593 (40.79%) were down-regulated. Most of these DEGs were significantly annotated in the carbohydrates and energy metabolism, signal transduction, amino acid metabolism and translation. Most of the up-regulated DEGs were especially enriched in plant hormone signal transduction, starch and sucrose metabolism pathways. Transcription factor enrichment analysis showed that the AP2/ERF, WRKY and MYB families were also significantly changed. Furthermore, 20 DEGs were selected to validate the transcriptome profiles via quantitative real-time PCR (qRT-PCR). In conclusion, the results provide an overall view of the dynamic changes in physiology and insights into the molecular regulation mechanisms of winter Brassica napus in response to freezing treatment, expanding our understanding on the complex molecular mechanism in plant response to freezing stress.

Population-level approaches reveal novel aspects of lignin biosynthesis, content, composition and structure

Population-level studies enabled by high-throughput phenotyping have revealed significant variation in lignin characteristics including content, S:G:H ratio, inter-unit linkage distributions, and molecular weights across multiple plant species. Coupled with genome-wide association mapping studies (GWAS) targeted at linking genetic mutations to phenotype, significant progress has been made in associating putative causal mutations to variation in lignin characteristics. Despite this progress, there are few examples, in which these associations have been molecularly validated to provide new insights into the genetic regulation of lignin biosynthesis. Given a recent report of a GWAS-discovered 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase moonlighting as a transcriptional regulator of lignin biosynthesis, the potential to bridge scientific disciplines in order to uncover hidden elements of lignin biosynthesis has been demonstrated, offering a path to alter lignin characteristics via genetic manipulation in order to expedite lignin valorization. To maximize this potential, however, there is a crucial need for (1) broader surveys of naturally varying diverse plant populations and (2) analytical platforms that can resolve subtle properties at fine chemical and biological scales.

Molecular identification, phylogenomic characterization and expression patterns analysis of the LIM (LIN-11, Isl1 and MEC-3 domains) gene family in pear (Pyrus bretschneideri) reveal its potential role in lignin metabolism

Lignin is the main component of stone cells, which are a key factor in determining pear quality. Therefore, modification of lignin biosynthesis has important implications for regulating stone cell formation. LIMs are involved in plant development, stress response and metabolism. However, there is still a lack of knowledge about the pear LIM family and lignin-related LIMs. To address this problem, we identified 14 LIMs from the pear genome and named them. Phylogenomic and feature domain analysis showed that they were divided into CRP- and DA&DAR-LIM groups and five subclades. LIMs from the genomes of four rosids (Prunus mummer, Prunus persica, Fragaria vesca and Vitis vinifera) were also identified, and microsynteny analysis revealed the most orthologous gene pairs in the cross of pear/grape and pear/mei. The transcript levels of PbLIMs were significantly affected by SA, ABA and MeJA. Spatio-temporal expression analysis showed that PbLIMs of the δLIM2 subfamily were highly expressed in the flowers. Changes in the expression levels of PbWLIM1a and PbWLIM1b during fruit development was consistent with the changes in lignin content. Combining phylogenetic analyses, protein three-dimensional structure determination and sequence alignment analyses, these two genes were suggested as lignin-related PbLIMs. Subcellular localization results showed that PbWLIM1a and PbWLIM1b were located mainly in the chloroplast. This study lays the foundation for revealing the mechanism of LIM-mediated lignin metabolism to regulate stone cell formation.

Morphological, transcriptomics and biochemical characterization of new dwarf mutant of Brassica napus

Plant height is a key trait of plant architecture, and is responsible for both yield and lodging resistance in Brassica napus. A dwarf mutant line (bnaC.dwf) was obtained by chemical mutagenesis of an inbred line T6. However, the molecular mechanisms and changed biological processes of the dwarf mutant remain to be determined. In this study, a comparative transcriptome analysis between bnaC.dwf and T6 plants was performed to identify genome-wide differentially expressed genes (DEGs) and possible biological processes that may explain the phenotype variations in bnaC.dwf. As a result of this analysis, 60,134,746-60,301,384 clean reads were aligned to 60,074 genes in the B. napus genome, and accounted for 60.03% of the annotated genes. In total, 819 differentially expressed genes were used for GO (Gene Ontology) term and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses with a FDR (false discovery rate) criterion of <0.001, |log₂Ratio| ≥ 1. We focused on plant hormone signal transduction pathways, plant-pathogen interaction pathway, protein phosphorylation and degradation pathways and sugar metabolism pathways. Taken together, the decrease in local auxin (IAA) levels, the variation in BnTCH4, BnKAN1, BnERF109, COI1-JAZ9-MYC2, auxin response genes (BnGH3.11, BnSAUR78, and AUX/IAA19), and ABA (abscisic acid) signaling genes (BnADP5, BnSnRK2.1, BnABF3.1) partially accounted for variations of cell proliferation in internodes, shoot and root apical meristem maintenance, abiotic and biotic stress resistance, and pre-harvest sprouting. As a comprehensive consequence of the cross-talk between plant hormones, sugar metabolism, plant-pathogen interactions and protein metabolism, bnaC.dwf presents distinct phenotypes from T6. These results will be helpful for shedding light on molecular mechanisms in the dwarf mutant, and give insight into further molecular breeding of semi-dwarf B. napus.

Major Co-localized QTL for Plant Height, Branch Initiation Height, Stem Diameter, and Flowering Time in an Alien Introgression Derived Brassica napus DH Population

Plant height (PH), branch initiation height (BIH), and stem diameter (SD) are three stem-related traits that play crucial roles in plant architecture and lodging resistance. Herein, we show one doubled haploid (DH) population obtained from a cross between Y689 (one Capsella bursa-pastoris derived Brassica napus intertribal introgression) and Westar (B. napus cultivar) that these traits were significantly positively correlated with one another and with flowering time (FT). Based on a high-density SNP map, a total of 102 additive quantitative trait loci (QTL) were identified across six environments. Seventy-two consensus QTL and 49 unique QTL were identified using a two-round strategy of QTL meta-analysis. Notably, a total of 19 major QTL, including 11 novel ones, were detected for these traits, which comprised two QTL clusters on chromosomes A02 and A07. Conditional QTL mapping was performed to preliminarily evaluate the genetic basis (pleiotropy or tight linkage) of the co-localized QTL. In addition, QTL by environment interactions (QEI) mapping was performed to verify the additive QTL and estimate the QEI effect. In the genomic regions of all major QTL, orthologs of the genes involved in phytohormone biosynthesis, phytohormone signaling, flower development, and cell differentiation in Arabidopsis were proposed as candidate genes. Of these, BnaA02g02560, an ortholog of Arabidopsis GASA4, was suggested as a candidate gene for PH, SD, and FT; and BnaA02g08490, an ortholog of Arabidopsis GNL, was associated with PH, BIH and FT. These results provide useful information for further genetic studies on stem-related traits and plant growth adaptation.

An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus

Lodging is a persistent problem which severely reduce yield and impair seed quality in rapeseed (Brassica napus L.). Enhancing stem strength (SS) has proven to be an effective approach to decrease lodging risk. In the present study, four interrelated stem lodging-related traits, including stem breaking resistance (SBR), stem diameter (SD), SS, and lodging coefficient (LC), were investigated among 472 rapeseed accessions. A genome-wide association study (GWAS) using Brassica 60K SNP array for stem lodging-related traits identified 67 significantly associated quantitative trait loci (QTLs) and 71 candidate genes. In parallel, a gene co-expression network based on transcriptome sequencing was constructed. The module associated with cellulose biosynthesis was highlighted. By integrating GWAS and gene co-expression network analysis, some promising candidate genes, such as ESKIMO1 (ESK1, BnaC08g26920D), CELLULOSE SYNTHASE 6 (CESA6, BnaA09g06990D), and FRAGILE FIBER 8 (FRA8, BnaC04g39510D), were prioritized for further research. These findings revealed the genetic basis underlying stem lodging and provided worthwhile QTLs and genes information for genetic improvement of stem lodging resistance in B. napus.