Traits In Rapeseed Research Articles

Mining Candidate Genes for Leaf Angle in Brassica napus L. by Combining QTL Mapping and RNA Sequencing Analysis.

Leaf angle (LA) is an important trait of plant architecture, and individuals with narrow LA can better capture canopy light under high-density planting, which is beneficial for increasing the overall yield per unit area. To study the genetic basis and molecular regulation mechanism of leaf angle in rapeseed, we carried out a series of experiments. Quantitative trait loci (QTL) mapping was performed using the RIL population, and seven QTLs were identified. Transcriptome analysis showed that the cell wall formation/biogenesis processes and biosynthesis/metabolism of cell wall components were the most enrichment classes. Most differentially expressed genes (DEGs) involved in the synthesis of lignin, xylan, and cellulose showed down-regulated expression in narrow leaf material. Microscopic analysis suggested that the cell size affected by the cell wall in the junction area of the stem and petiole was the main factor in leaf petiole angle (LPA) differences. Combining QTL mapping and RNA sequencing, five promising candidate genes BnaA01G0125600ZS, BnaA01G0135700ZS, BnaA01G0154600ZS, BnaA10G0154200ZS, and BnaC03G0294200ZS were identified in rapeseed, and most of them were involved in cell wall biogenesis and the synthesis/metabolism of cell wall components. The results of QTL, transcriptome analysis, and cytological analysis were highly consistent, collectively revealing that genes related to cell wall function played a crucial role in regulating the LA trait in rapeseed. The study provides further insights into LA traits, and the discovery of new QTLs and candidate genes is highly beneficial for genetic improvement.

Genetic dissection of Brassica napus seed vigor after aging.

Stable and novel QTLs that affect seed vigor under different storage durations were discovered, and BnaOLE4, located in the interval of cqSW-C2-3, increased seed vigor after aging. Seed vigor is an important trait in crop breeding; however, the underlying molecular regulatory mechanisms governing this trait in rapeseed remain largely unknown. In the present study, vigor-related traits were analyzed in seeds from a doubled haploid (DH) rapeseed (Brassica napus) population grown in 2 different environments using seeds stored for 7, 5, and 3years under natural storage conditions. A total of 229 quantitative trait loci (QTLs) were identified and were found to explain 3.78%-17.22% of the phenotypic variance for seed vigor-related traits after aging. We further demonstrated that seed vigor-related traits were positively correlated with oil content (OC) but negatively correlated with unsaturated fatty acids (FAs). Some pleiotropic QTLs that collectively regulate OC, FAs, and seed vigor, such as uq.A8, uq.A3-2, uq.A9-2, and uq.C3-1, were identified. The transcriptomic results from extreme pools of DH lines with distinct seed vigor phenotypes during accelerated aging revealed that various biological pathways and metabolic processes (such as glutathione metabolism and reactive oxygen species) were involved in seed vigor. Through integration of QTL analysis and RNA-Seq, a regulatory network for the control of seed vigor was constructed. Importantly, a candidate (BnaOLE4) from cqSW-C2-3 was selected for functional analysis, and transgenic lines overexpressing BnaOLE4 showed increased seed vigor after artificial aging. Collectively, these results provide novel information on QTL and potential candidate genes for molecular breeding for improved seed storability.

Genomic and transcriptome analyses reveal potential contributors to erucic acid biosynthesis in seeds of rapeseed (Brassica napus).

Through comprehensive genomic and transcriptomic analyses, we identified a set of 23 genes that act up- or downstream of erucic acid content (EAC) production in rapeseed seeds. We selected example genes to showcase the distribution of single nucleotide polymorphisms, haplotypes associated with EAC phenotypes, and the creation of molecular markers differentiating low EAC and high EAC genotypes. Erucic acid content (EAC) is a crucial trait in rapeseed, with low LEAC oil recognized for its health benefits and high EA oil holding industrial value. Despite its significance, the genomic consequences of intensive LEAC-cultivar selection and the genetic basis underlying EA regulation remain largely unexplored. To address this knowledge gap, we conducted selective signal analyses, genome-wide association studies (GWAS), and transcriptome analyses. Our investigation unveiled the genetic footprints resulting from LEAC selection in germplasm populations, drawing attention to specific loci that contribute to enriching diversity. By integrating GWAS and transcriptome analyses, we identified a set of 23 genes that play a significant role in determining EAC in seeds or are downstream consequences of EA-level alterations. These genes have emerged as promising candidates for elucidating the potential mechanisms governing EAC in rapeseed. To exemplify the findings, we selected specific genes to demonstrate the distribution of single nucleotide polymorphisms and haplotypes associated with different EAC phenotypes. Additionally, we showcased to develop molecular markers distinguishing between LEAC and high EAC genotypes.

Advancements in Enhancing Oil Quality in Rapeseed and Mustard: A Comprehensive Review

Rapeseed and mustard are important oilseed crops cultivated worldwide for their high oil content and versatile applications in food, feed, and industrial sectors. The quality of oil derived from these crops is influenced by various genetic, environmental, and agronomic factors. Breeding efforts aimed at improving oil quality traits in rapeseed and mustard have garnered significant attention in recent years due to their impact on market value, nutritional attributes, and industrial utility. In this review, we provide a comprehensive overview of breeding strategies and methodologies employed to enhance oil quality traits in rapeseed and mustard. We explore the genetic basis of oil quality traits, including fatty acid composition, erucic acid content, glucosinolate content, and tocopherol content, and discuss the importance of these traits for different end-uses. Furthermore, we highlight the role of molecular markers, genomics-assisted breeding, and biotechnological approaches in accelerating the breeding process and achieving targeted improvements in oil quality. The review also addresses the challenges and constraints associated with breeding for oil quality in rapeseed and mustard, including genotype-environment interactions, trait stability, and regulatory considerations. Additionally, we discuss emerging trends and future prospects in oil quality breeding, such as genome editing, metabolic engineering, and precision breeding, which offer novel avenues for achieving desired oil quality profiles while addressing sustainability and consumer preferences. Overall, this review underscores the significance of breeding for oil quality in rapeseed and mustard and provides insights into the latest advancements, challenges, and opportunities in this field. By integrating multidisciplinary approaches and harnessing the power of modern breeding tools and technologies, rapeseed and mustard breeders can continue to drive innovation and deliver oilseed crops with enhanced nutritional value, functional properties, and market competitiveness.

Selection of Suitable Genotypes Based on Physiological and Morphological Traits in Rapeseed (Brassica napus L.)

Aims: Rapeseed (Brassica napus L.) as one of the most important oilseeds in the world, has a special role in cultivation and plant breeding research. Especially, the properties of rapeseed oil compounds, which have high oleic acid, antioxidant and positive effects on cholesterol, blood sugar control, blood pressure and cancer, make it one of the healthiest and most important edible oils in the world and an alternative to use Other vegetable oils have been introduced in recent years. Evaluation of different genotypes of Rapeseed in terms of different traits and selection of the most appropriate genotypes can be effective in realizing the goals of plant breeding.
 Study Design: In order to conduct the experiment, a randomized complete block design (RCBD) was used in three replications.
 Place and Duration of Study: This study was conducted in Varamin region of Iran in 2019-2020.
 Methodology: Each experimental plot had 4 rows of cultivation at a distance of 50 cm. The seeds were planted at a distance of 10 cm from each other and all steps such as watering and weeding were done regularly and manually.
 Results: The results of analysis of variance at the level of 0.01 indicated that the evaluated genotypes have significant differences in terms of all traits except the number of grains in the pod. In the means comparison of the traits, grain yield and oil percentage traits, which were selected as the most important traits, the Licord genotype was selected as the most favorable genotype. Based on the correlation analysis between the traits, the trait of grain yield had a positive and significant correlation with the traits of thousand grain weight, number of pods in the main stem, pod weight, days to flowering and oil percentage. Based on analysis of the main components, the first five components accounted for more than 74% of the variance of the total data. The drawn polygon diagram also identified Licord, Hyola-401, SLM046, Modena and Option 500 genotypes as desirable genotypes.
 Conclusion: Non-invasive independent predictors for screening esophageal varices may decrease medical as well as financial burden, hence improving the management of cirrhotic patients. These predictors, however, need further work to validate reliability.

Analysis of Altered Flowering Related Genes in a Multi-Silique Rapeseed (Brassica napus L.) Line zws-ms Based on Combination of Genome, Transcriptome and Proteome Data

Based on previous researches, we further investigated the multi-silique trait in rapeseed (Brassica napus L.) line zws-ms. In this study, we used a relatively comprehensive list of flowering related genes in rapeseed and compared them between zws-ms and its near-isogenic line (NIL) zws-217. Genes were studied on genome, transcriptome and proteome levels and then we focused on genes with non-synonymous single nucleotide polymorphism (SNP) or frame-shift insertion-deletion (InDel), finding some genes on the list which changes their sequences. Then, combined with their annotation and the information of their orthologs, certain genes such as BnaA09g05900D, ortholog of AGAMOUS-LIKE 42 (AGL42), which encodes an MADS-box protein, were assumed as probably responsible for the multi-silique trait. Also, we analyzed the Differentially Accumulated Proteins (DAPs) between zws-ms and zws-217, revealing some genes involved in homologous recombination and mismatch repair pathways. Since the development of flowers/siliques is crucial to crops and it influences the yield of rapeseed, this study paved a way to deeply understand the mechanism of the multi-pistil flower formation, which may facilitate researches on rapeseed production in future.

Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed.

Yellow seed coat in rapeseed (Brassica napus) is a desirable trait that can be targeted to improve the quality of this oilseed crop. To better understand the inheritance mechanism of the yellow-seeded trait, we performed transcriptome profiling of developing seeds in yellow- and black-seeded rapeseed with different backgrounds. The differentially expressed genes (DEGs) during seed development showed significant characteristics, these genes were mainly enriched for the Gene Ontology (GO) terms carbohydrate metabolic process, lipid metabolic process, photosynthesis, and embryo development. Moreover, 1206 and 276 DEGs, which represent candidates to be involved in seed coat color, were identified between yellow- and black-seeded rapeseed during the middle and late stages of seed development, respectively. Based on gene annotation, GO enrichment analysis, and protein-protein interaction network analysis, the downregulated DEGs were primarily enriched for the phenylpropanoid and flavonoid biosynthesis pathways. Notably, 25 transcription factors (TFs) involved in regulating flavonoid biosynthesis pathway, including known (e.g., KNAT7, NAC2, TTG2 and STK) and predicted TFs (e.g., C2H2-like, bZIP44, SHP1, and GBF6), were identified using integrated gene regulatory network (iGRN) and weight gene co-expression networks analysis (WGCNA). These candidate TF genes had differential expression profiles between yellow- and black-seeded rapeseed, suggesting they might function in seed color formation by regulating genes in the flavonoid biosynthesis pathway. Thus, our results provide in-depth insights that facilitate the exploration of candidate gene function in seed development. In addition, our data lay the foundation for revealing the roles of genes involved in the yellow-seeded trait in rapeseed.

Genome-Wide Identification and Posttranscriptional Regulation Analyses Elucidate Roles of Key Argonautes and Their miRNA Triggers in Regulating Complex Yield Traits in Rapeseed.

Argonautes (AGOs) interact with microRNAs (miRNAs) to form the RNA-induced silencing complex (RISC), which can posttranscriptionally regulate the expression of targeted genes. To date, however, the AGOs and their miRNA triggers remain elusive in rapeseed (Brassica napus). Here, we systematically performed a phylogenetic analysis and examined the collinear relationships of the AGOs among four Brassicaceae species. Their physicochemical properties, gene structures, and expression patterns among 81 tissues from multiple materials and developmental stages were further analyzed. Additionally, their posttranscriptional regulation was analyzed using psRNATarget prediction, miRNA-/mRNA-Seq analyses, and a qRT-PCR verification. We finally identified 10 AtAGOs, 13 BolAGOs, 11 BraAGOs, and 24 BnaAGOs. An expression analysis of the BnaAGOs in the B. napus cultivar ZS11, as well as genotypes with extreme phenotypes in various yield-related traits, revealed the conservation and diversity of these genes. Furthermore, we speculated the posttranscriptional regulation of the B. napus miR168a-AGO1s and miR403-AGO2s modules. Combining miRNA-Seq and mRNA-Seq analyses, we found that the B. napus miR168a-AGO1s module may play an essential role in negatively regulating yield traits, whereas the miR403-AGO2s module positively impacts yield. This is the first attempt to comprehensively analyze the AGOs and their miRNA triggers in B. napus and provides a theoretical basis for breeding high-yielding varieties through the manipulation of the miRNA-AGOs modules.

QTL mapping for seed density per silique in Brassica napus

Seed density per silique (SDPS) and valid silique length (VSL) are two important yield-influencing traits in rapeseed. SDPS has a direct or indirect effect on rapeseed yield through its effect on seed per silique. In this study, a quantitative trait locus (QTL) for SDPS was detected on chromosome A09 using the QTL-seq approach and confirmed via linkage analysis in the mapping population obtained from 4263 × 3001 cross. Furthermore, one major QTL for SDPS (qSD.A9-1) was mapped to a 401.8 kb genomic interval between SSR markers Nys9A190 and Nys9A531. In the same genomic region, a QTL (qSL.A9) linked to VSL was also detected. The phenotypic variation of qSD.A9-1 and qSL.A9 was 53.1% and 47.6%, respectively. Results of the additive and dominant effects demonstrated that the expression of genes controlling SDPS and VSL were derived from a different parent in this population. Subsequently, we identified 56 genes that included 45 specific genes with exonic (splicing) variants. Further analysis identified specific genes containing mutations that may be related to seed density as well as silique length. These genes could be used for further studies to understand the details of these traits of rapeseed.

Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus.

The online version contains supplementary material available at 10.1007/s11032-022-01337-1.

Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress.

An excellent root system is responsible for crops with high nitrogen-use efficiency (NUE). The current study evaluated the natural variations in 13 root- and biomass-related traits under a low nitrogen (LN) treatment in a rapeseed association panel. The studied traits exhibited significant phenotypic differences with heritabilities ranging from 0.53 to 0.66, and most of the traits showed significant correlations with each other. The genome-wide association study (GWAS) found 51 significant and 30 suggestive trait–SNP associations that integrated into 14 valid quantitative trait loci (QTL) clusters and explained 5.7–21.2% phenotypic variance. In addition, RNA sequencing was performed at two time points to examine the differential expression of genes (DEGs) between high and low NUE lines. In total, 245, 540, and 399 DEGs were identified as LN stress-specific, high nitrogen (HN) condition-specific, and HNLN common DEGs, respectively. An integrated analysis of GWAS, weighted gene co-expression network, and DEGs revealed 16 genes involved in rapeseed root development under LN stress. Previous studies have reported that the homologs of seven out of sixteen potential genes control root growth and NUE. These findings revealed the genetic basis underlying nitrogen stress and provided worthwhile SNPs/genes information for the genetic improvement of NUE in rapeseed.

Identification of SSR Markers Associated with Yield-Related Traits and Heterosis Effect in Winter Oilseed Rape (Brassica Napus L.)

The identification of markers responsible for regulating important agronomic traits in rapeseed supports breeding and increases the seed yield. Microsatellite (SSR) markers are mainly used as ‘neutral’ genetic markers but are also linked with many biological functions. The objective of this study was identification of microsatellite markers associated with important agronomic traits affecting the seed yield of winter oilseed rape and with the heterosis effect for these traits. The plant material consists of four parental lines, 60 doubled haploid (DH) lines, 60 single cross hybrids, and 60 three-way cross hybrids. The association between molecular markers and observed traits was estimated using regression analysis. Among 89 SSR markers, 43 were polymorphic, and 15 were selected for mapping because they demonstrated stability in both years of observation. These markers were physically mapped in the rapeseed reference genomes and their immediate vicinity was searched to identify candidate genes associated with the studied traits. Six markers (BrGMS3837, BnEMS1119, BrGMS2901, BnGMS0509, BrGMS3688, BrGMS4057), which showed a positive estimation effect in our association analysis, and thus increased the value of a given trait or heterosis effect, turned out to be linked with genes that could be responsible for the development and growth of plants.

A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L.

BackgroundAllotetraploid oilseed rape (Brassica napus L.) is an important worldwide oil-producing crop. The origin of rapeseed is still undetermined due to the lack of wild resources. Despite certain genetic architecture and phylogenetic studies have been done focus on large group of Brassica nuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies of B. napus. Here, based on de novo assemblies of 1,579 B. napus accessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes of B. napus, and investigated the genetic diversity, phylogenetic relationships of B. napus, B. rapa and B. oleracea.ResultsBased on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding the nap, pol, ole, and cam mitotypes, among which the structure of chloroplast genomes was more conserved without any rearrangement than mitochondrial genomes. A total of 2,092 variants were detected in chloroplast genomes, whereas only 326 in mitochondrial genomes, indicating that chloroplast genomes exhibited a higher level of single-base polymorphism than mitochondrial genomes. Based on whole-genome variants diversity analysis, eleven genetic difference regions among different cytoplasmic haplotypes were identified on chloroplast genomes. The phylogenetic tree incorporating accessions of the B. rapa, B. oleracea, natural and synthetic populations of B. napus revealed multiple origins of B. napus cytoplasm. The cam-type and pol-type were both derived from B. rapa, while the ole-type was originated from B. oleracea. Notably, the nap-type cytoplasm was identified in both the B. rapa population and the synthetic B. napus, suggesting that B. rapa might be the maternal ancestor of nap-type B. napus.ConclusionsThe phylogenetic results provide novel insights into the organelle genomic evolution of Brassica species. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominant nap-type might be originated from B. rapa. Besides, the organelle pan-genomes and the overall variation data offered useful resources for analysis of cytoplasmic inheritance related agronomical important traits of rapeseed, which can substantially facilitate the cultivation and improvement of rapeseed varieties.

Yield performance of radiation induced rapeseed mutants at M8 generation

Rapeseed is the most potential oil seed crops of Indian sub-continent. So higher seed yield potential variety is central choice of rapeseed grower. To verify the yield performances of rapeseed mutants an experiment was conducted at various locations of Bangladesh. Four true breeding (homozygous) mutants obtain from three different radiation doses (600, 800 and 900 Gy) along with the mother variety BARI Sarisha-15 and check variety BARI Sarisha-17 were used for each condition. The experiment was laid out in a randomized complete block design with three replications. Interaction between genotype and location showed significant variations for all the agronomic traits, whereas only non-significant variations were provided from branch plant-1 and siliquae length for location. Mutant RM-20 produces the highest plant height (101.1cm) and matures earlier than all other mutants’ parent and check. At Magura and Ishurdi all the mutants produce significantly higher number of siliquae plant-1 then parent BARI Sarisha-15 and check BARI Sarisha-17. RM-18 and RM-20 produce maximum seeds siliquae-1 (30) whereas the mutant RM-07 produced lowest number of seeds siliquae-1 (22). Combined means over locations showed that mutants namely RM-18 and RM-20 produced significantly higher seed yield (1551.1 and 1385 kg/ha, respectively). This suggests that gamma ray’s irradiation can be fruitfully applied to develop mutants with higher seed yield and other agronomic traits in rapeseed

Meta-analysis of QTLs controlling seed quality traits based on QTL alignment in Brassica napus

A growing demand in oilseed use for food, feed and fuel has caused added pressure on rapeseed breeders to improve higher-quality cultivars. To gain a better understanding of the genetics of oil, fatty acids, sterols, protein and amino acids contents in Brassica napus, 2138 QTLs in 16 populations were collected from 22 studies published since 2000. The physical position of 1567 initial QTLs could be found in the physical map of Darmor-bzh that finally revealed 294 QTL overlapping regions from different populations potentially associated with seed quality traits, distributed unequally in most of the chromosomes. We detected enrichment regions with more than 10 initial QTLs in some traits, which could provide clues in discovering varied or protected areas. Additionally, 111 overlapping QTLs regions were found, controlling at least two traits. These regions with broad pleiotropic effects or tight linkages might have merit in improving B. napus in targeting more than one desirable trait simultaneously. Furthermore, to validate our findings, candidate genes were subjected to three types of gene set analyses: KEGG pathway and interaction networks for Arabidopsis thaliana genes, and expression enrichment analysis for candidate genes of B. napus. The results indicated key known genes, novel genes, and genes with unknown functions in the overlapping regions that were involved in different biological processes of quality traits, such as highly expressed genes in seed, including BnaA08g13680D, BnaA08g13750D, BnaA08g13730D, BnaA08g14030D, BnaA08g14060D, BnaA08g12340D and BnaC05g42910D, which were observed in overlapping QTLs of multiple traits. Further validation also depicted that 107 overlapping QTLs were co-located with 366 SNP peak positions reported based on the genome-wide association studies (GWAS) for quality traits in rapeseed. Our results will serve as a resource for future researches in functional gene analysis, genetic engineering and breeding programs.

Genetic Dissection of Mature Root Characteristics by Genome-Wide Association Studies in Rapeseed (Brassica napus L.).

Roots are complicated quantitative characteristics that play an essential role in absorbing water and nutrients. To uncover the genetic variations for root-related traits in rapeseed, twelve mature root traits of a Brassica napus association panel were investigated in the field within three environments. All traits showed significant phenotypic variation among genotypes, with heritabilities ranging from 55.18% to 79.68%. Genome-wide association studies (GWAS) using 20,131 SNPs discovered 172 marker-trait associations, including 103 significant SNPs (−log10 (p) > 4.30) that explained 5.24–20.31% of the phenotypic variance. With the linkage disequilibrium r2 > 0.2, these significant associations were binned into 40 quantitative trait loci (QTL) clusters. Among them, 14 important QTL clusters were discovered in two environments and/or with phenotypic contributions greater than 10%. By analyzing the genomic regions within 100 kb upstream and downstream of the peak SNPs within the 14 loci, 334 annotated genes were found. Among these, 32 genes were potentially associated with root development according to their expression analysis. Furthermore, the protein interaction network using the 334 annotated genes gave nine genes involved in a substantial number of interactions, including a key gene associated with root development, BnaC09g36350D. This research provides the groundwork for deciphering B. napus’ genetic variations and improving its root system architecture.

QTL Analysis of Five Silique-Related Traits in Brassica napus L. Across Multiple Environments.

As an important physiological and reproductive organ, the silique is a determining factor of seed yield and a breeding target trait in rapeseed (Brassica napus L.). Genetic studies of silique-related traits are helpful for rapeseed marker-assisted high-yield breeding. In this study, a recombinant inbred population containing 189 lines was used to perform a quantitative trait loci (QTLs) analysis for five silique-related traits in seven different environments. As a result, 120 consensus QTLs related to five silique-related traits were identified, including 23 for silique length, 25 for silique breadth, 29 for silique thickness, 22 for seed number per silique and 21 for silique volume, which covered all the chromosomes, except C5. Among them, 13 consensus QTLs, one, five, two, four and one for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively, were repeatedly detected in multiple environments and explained 4.38–13.0% of the phenotypic variation. On the basis of the functional annotations of Arabidopsis homologous genes and previously reported silique-related genes, 12 potential candidate genes underlying these 13 QTLs were screened and found to be stable in multiple environments by analyzing the re-sequencing results of the two parental lines. These findings provide new insights into the gene networks affecting silique-related traits at the QTL level in rapeseed.

Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed.

MicroRNAs (miRNAs) and their target genes play vital roles in crops. However, the genetic variations in miRNA-targeted sites that affect miRNA cleavage efficiency and their correlations with agronomic traits in crops remain unexplored. On the basis of a genome-wide DNA re-sequencing of 210 elite rapeseed (Brassica napus) accessions, we identified the single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) in miRNA-targeted sites complementary to miRNAs. Variant calling revealed 7.14 million SNPs and 2.89 million INDELs throughout the genomes of 210 rapeseed accessions. Furthermore, we detected 330 SNPs and 79 INDELs in 357 miRNA target sites, of which 33.50% were rare variants. We also analyzed the correlation between the genetic variations in miRNA target sites and 12 rapeseed agronomic traits. Eleven SNPs in miRNA target sites were significantly correlated with phenotypes in three consecutive years. More specifically, three correlated SNPs within the miRNA-binding regions of BnSPL9-3, BnSPL13-2, and BnCUC1-2 were in the loci associated with the branch angle, seed weight, and silique number, respectively; expression profiling suggested that the variation at these 3 miRNA target sites significantly affected the expression level of the corresponding target genes. Taken together, the results of this study provide researchers and breeders with a global view of the genetic variations in miRNA-targeted sites in rapeseed and reveal the potential effects of these genetic variations on elite agronomic traits.

Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.).

Low temperature inhibits rapid germination and successful seedling establishment of rapeseed (Brassica napus L.), leading to significant productivity losses. Little is known about the genetic diversity for seed vigor under low-temperature conditions in rapeseed, which motivated our investigation of 13 seed germination- and emergence-related traits under normal and low-temperature conditions for 442 diverse rapeseed accessions. The stress tolerance index was calculated for each trait based on performance under non-stress and low-temperature stress conditions. Principal component analysis of the low-temperature stress tolerance indices identified five principal components that captured 100% of the seedling response to low temperature. A genome-wide association study using ~8 million SNP (single-nucleotide polymorphism) markers identified from genome resequencing was undertaken to uncover the genetic basis of seed vigor related traits in rapeseed. We detected 22 quantitative trait loci (QTLs) significantly associated with stress tolerance indices regarding seed vigor under low-temperature stress. Scrutiny of the genes in these QTL regions identified 62 candidate genes related to specific stress tolerance indices of seed vigor, and the majority were involved in DNA repair, RNA translation, mitochondrial activation and energy generation, ubiquitination and degradation of protein reserve, antioxidant system, and plant hormone and signal transduction. The high effect variation and haplotype-based effect of these candidate genes were evaluated, and high priority could be given to the candidate genes BnaA03g40290D, BnaA06g07530D, BnaA09g06240D, BnaA09g06250D, and BnaC02g10720D in further study. These findings should be useful for marker-assisted breeding and genomic selection of rapeseed to increase seed vigor under low-temperature stress.

Associative transcriptomics study dissects the genetic architecture of seedling biomass‐related traits in rapeseed (Brassica napus L.)

AbstractIt was observed that the seedling biomass was correlated with final seed yield in many crops. It is helpful to dissect the genetic architecture of seedling biomass‐related traits for high yield breeding of rapeseed (Brassica napus L.). To date, the genetic architecture of seedling biomass‐related traits is still unclear in B. napus. To identify candidate genes associated with high seedling biomass, a genome‐wide association study of seedling biomass‐related traits under normal growth condition and waterlogging stress was conducted with 156 B. napus accessions. We detected six peaks including 55 single‐nucleotide polymorphisms (SNPs) significantly associated with the above‐mentioned traits in SNP association analysis and 142 UniGenes showed significantly associated with traits in gene expression marker (GEM) association analysis. Candidate genes located within the linkage disequilibrium (LD) blocks were identified, such as ADP GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 1 (BnaC2APL1), PS II OXYGEN‐EVOLVING COMPLEX 1 (BnaC9PSBO1), their ortholog in the Arabidopsis thaliana has been shown to play key roles in starch biosynthesis and photosynthesis. Resequencing of genomic regions revealed the non‐synonymous SNPs in coding regions may be the functional polymorphisms in the two candidate genes. Our results provide insight into the molecular mechanisms underlying the establishment of high‐seedling biomass B. napus and lay a foundation for the characterization of candidate genes aimed at developing high‐seedling B. napus varieties.