Identification and fine mapping of a major locus controlling branching in Brassica napus

Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield

Silique number is a crucial yield-related trait for the genetic enhancement of rapeseed (Brassica napus L.). The intricate molecular process governing the regulation of silique number involves various factors. Despite advancements in understanding the mechanisms regulating silique number in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the molecular processes involved in controlling silique number in rapeseed remain largely unexplored. In this review, we identify candidate genes and review the roles of genes and environmental factors in regulating rapeseed silique number. We use genetic regulatory networks for silique number in Arabidopsis and grain number in rice to uncover possible regulatory pathways and molecular mechanisms involved in regulating genes associated with rapeseed silique number. A better understanding of the genetic network regulating silique number in rapeseed will provide a theoretical basis for the genetic improvement of this trait and genetic resources for the molecular breeding of high-yielding rapeseed.

3D genome structural variations play important roles in regulating seed oil content of Brassica napus

Dissecting the complex regulatory mechanism of seed oil content (SOC) is one of the main research goals in Brassica napus. Increasing evidence suggests that genome architecture is linked to multiple biological functions. However, the effect of genome architecture on SOC regulation remains unclear. Here, we used high-throughput chromatin conformation capture to characterize differences in the three-dimensional (3D) landscape of genome architecture of seeds from two B. napus lines, N53-2 (with high SOC) and Ken-C8 (with low SOC). Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci (QTLs)/associated genomic regions (AGRs) for SOC. A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural variations in QTLs/AGRs of B. napus. The candidate gene BnaA09g48250D, which showed structural variation in a QTL/AGR on chrA09, was identified by fine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8. Overexpression and knockout of BnaA09g48250D led to significant increases and decreases in SOC, respectively, in the transgenic lines. Taken together, our results reveal the 3D genome architecture of B. napus seeds and the roles of genome structural variations in SOC regulation, enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.

Transcriptomic Profiling of Shoot Apical Meristem Aberrations in the Multi-Main-Stem Mutant (ms) of Brassica napus L

Rapeseed (Brassica napus L.) is a globally important oilseed crop with various uses, including the consumption of its succulent stems as a seasonal vegetable, but its uniaxial branching habit limits the stem yield. Therefore, developing a multi-stem rapeseed variety has become increasingly crucial. In this study, a natural mutant of the wild type (ZY511, Zhongyou511) with stable inheritance of the multi-stem trait (ms) was obtained, and it showed abnormal shoot apical meristem (SAM) development and an increased main stem number compared to the WT. Histological and scanning electron microscopy analyses revealed multiple SAMs in the ms mutant, whereas only a single SAM was found in the WT. Transcriptome analyses showed significant alterations in the expression of genes involved in cytokinin (CK) biosynthesis and metabolism pathways in the ms mutant. These findings provide insight into the mechanism of multi-main-stem formation in Brassica napus L. and lay a theoretical foundation for breeding multi-main-stem rapeseed vegetable varieties.

Fine mapping of BnDM1-the gene regulating indeterminate inflorescence in Brassica napus

KEY MESSAGE

A candidate gene Bndm1 related to determinate inflorescence was mapped to a 128-kb interval on C02 in Brassica napus. Brassica napus plants with determinate inflorescence exhibit improved traits in field production, such as lower plant height, improved lodging resistance, and consistent maturity. Compared to plants with indeterminate inflorescence, such features are favorable for mechanized harvesting techniques. Here, using a natural mutant 6138 with determinate inflorescence, it is demonstrated that determinate inflorescence reduces plant height significantly without affecting thousand-grain weight and yield per plant. Determinacy was regulated by a single recessive gene, Bndm1. Using a combination of SNP arrays and map-based cloning, we mapped the locus of determinacy to a 128-kb region on C02. Based on sequence comparisons and the reported functions of candidate genes in this region, we predicted BnaC02.knu (a homolog of KNU in Arabidopsis) as a possible candidate gene of Bndm1 for controlling determinate inflorescence. We found a 623-bp deletion in a region upstream of the KNU promoter in the mutant. This deletion led to the significant overexpression of BnaC02.knu in the mutant compared to that in the ZS11 line. The correlation between this deletion and determinate inflorescence was examined in natural populations. The results indicated that the deletion affected the normal transcription of BnaC02.knu in the plants with determinate inflorescence and played an important role in maintaining flower development. This study presents as a new material for optimizing plant architecture and breeding novel canola varieties suitable for mechanized production. Moreover, our findings provide a theoretical basis for analyzing the molecular mechanisms underlying the formation of determinate inflorescence in B. napus.

Discovery of common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits in Brassica napus L

KEY MESSAGE

Common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits were identified in Brassica napus combining QTL mapping with transcriptome under salt and alkaline stresses. The yield of rapeseed (Brassica napus L.) is determined by multiple yield-related traits, which are susceptible to environmental factors. Many yield-related quantitative trait loci (QTLs) have been reported in Brassica napus; however, no studies have been conducted to investigate both salt-alkali tolerance and yield-related traits simultaneously. Here, specific-locus amplified fragment sequencing (SLAF-seq) technologies were utilized to map the QTLs for salt-alkali tolerance and yield-related traits. A total of 65 QTLs were identified, including 30 QTLs for salt-alkali tolerance traits and 35 QTLs for yield-related traits, accounting for 7.61-27.84% of the total phenotypic variations. Among these QTLs, 18 unique QTLs controlling two to four traits were identified by meta-analysis. Six novel and unique QTLs were detected for salt-alkali tolerance traits. By comparing these unique QTLs for salt-alkali tolerance traits with those previously reported QTLs for yield-related traits, seven co-localized chromosomal regions were identified on A09 and A10. Combining QTL mapping with transcriptome of two parents under salt and alkaline stresses, thirteen genes were identified as the candidates controlling both salt-alkali tolerance and yield. These findings provide useful information for future breeding of high-yield cultivars resistant to alkaline and salt stresses.

BnaC01.BIN2, a GSK3-like kinase, modulates plant height and yield potential in Brassica napus

Using map-based cloning and transgenic transformation, we revealed that glycogen kinase synthase 3-like kinase, BnaC01.BIN2, modulates plant height and yield in rapeseed. The modification of plant height is one of the most important goals in rapeseed breeding. Although several genes that regulate rapeseed plant height have been identified, the genetics mechanisms underlying rapeseed plant height regulation remain poorly understood, and desirable genetic resources for rapeseed ideotype breeding are scarce. Here, we map-based cloned and functionally verified that the rapeseed semi-dominant gene, BnDF4, greatly affects rapeseed plant height. Specifically, BnDF4 encodes brassinosteroid (BR)-insensitive 2, a glycogen synthase kinase 3 primarily expressed in the lower internodes to modulate rapeseed plant height by blocking basal internode-cell elongation. Transcriptome data showed that several cell expansion-related genes involving auxin and BRs pathways were significantly downregulated in the semi-dwarf mutant. Heterozygosity in the BnDF4 allele results in small stature with no marked differences in other agronomic traits. Using BnDF4 in the heterozygous condition, the hybrid displayed strong yield heterosis through optimum intermediate plant height. Our results provide a desirable genetic resource for breeding semi-dwarf rapeseed phenotypes and support an effective strategy for breeding rapeseed hybrid varieties with strong yield heterosis.

Identification of two tandem genes associated with primary rosette branching in flowering Chinese cabbage

Branching is an important agronomic trait determining plant architecture and yield; however, the molecular mechanisms underlying branching in the stalk vegetable, flowering Chinese cabbage, remain unclear. The present study identified two tandem genes responsible for primary rosette branching in flowering Chinese cabbage by GradedPool-Seq (GPS) combined with Kompetitive Allele Specific PCR (KASP) genotyping. A 900 kb candidate region was mapped in the 28.0-28.9 Mb interval of chromosome A07 through whole-genome sequencing of three graded-pool samples from the F₂ population derived by crossing the branching and non-branching lines. KASP genotyping narrowed the candidate region to 24.6 kb. Two tandem genes, BraA07g041560.3C and BraA07g041570.3C, homologous to AT1G78440 encoding GA2ox1 oxidase, were identified as the candidate genes. The BraA07g041560.3C sequence was identical between the branching and non-branching lines, but BraA07g041570.3C had a synonymous single nucleotide polymorphic (SNP) mutation in the first exon (290^th bp, A to G). In addition, an ERE cis-regulatory element was absent in the promoter of BraA07g041560.3C, and an MYB cis-regulatory element in the promoter of BraA07g041570.3C in the branching line. Gibberellic acid (GA₃) treatment decreased the primary rosette branch number in the branching line, indicating the significant role of GA in regulating branching in flowering Chinese cabbage. These results provide valuable information for revealing the regulatory mechanisms of branching and contributing to the breeding programs of developing high-yielding species in flowering Chinese cabbage.

Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits in Brassica napus L

Salt stress severely affects crop growth and development and reduces the yield of Brassica napus. Exploring natural genetic variations for high salt tolerance in B. napus seedlings is an effective approach to improve productivity under salt stress. Using 10,658 high-quality single nucleotide polymorphic (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, genome-wide association studies (GWAS) were performed to investigate the genetic basis of salt tolerance and yield-related traits of B. napus. The results revealed that 77 and 497 SNPs were significantly associated with salt tolerance and yield-related traits, of which 40 and 58 SNPs were located in previously reported QTLs/SNPs, respectively. We identified nineteen candidate genes orthologous with Arabidopsis genes known to be associated with salt tolerance and seven potential candidates controlling both salt tolerance and yield. Our study provides a novel genetic resource for the breeding of high-yield cultivars resistant to salt stress.

Prioritized candidate causal haplotype blocks in plant genome-wide association studies

Genome wide association studies (GWAS) can play an essential role in understanding genetic basis of complex traits in plants and animals. Conventional SNP-based linear mixed models (LMM) that marginally test single nucleotide polymorphisms (SNPs) have successfully identified many loci with major and minor effects in many GWAS. In plant, the relatively small population size in GWAS and the high genetic diversity found in many plant species can impede mapping efforts on complex traits. Here we present a novel haplotype-based trait fine-mapping framework, HapFM, to supplement current GWAS methods. HapFM uses genotype data to partition the genome into haplotype blocks, identifies haplotype clusters within each block, and then performs genome-wide haplotype fine-mapping to prioritize the candidate causal haplotype blocks of trait. We benchmarked HapFM, GEMMA, BSLMM, GMMAT, and BLINK in both simulated and real plant GWAS datasets. HapFM consistently resulted in higher mapping power than the other GWAS methods in high polygenicity simulation setting. Moreover, it resulted in smaller mapping intervals, especially in regions of high LD, achieved by prioritizing small candidate causal blocks in the larger haplotype blocks. In the Arabidopsis flowering time (FT10) datasets, HapFM identified four novel loci compared to GEMMA’s results, and the average mapping interval of HapFM was 9.6 times smaller than that of GEMMA. In conclusion, HapFM is tailored for plant GWAS to result in high mapping power on complex traits and improved on mapping resolution to facilitate crop improvement.

Genome-wide association studies (GWAS) are commonly used in human and plant studies to identify genetic variants responsible for the phenotype of interest and provide foundations for studying disease mechanisms and crop improvement. Most GWAS models are developed and optimized using human datasets. However, the difference between human and plant datasets essentially limits their applications in plant studies, especially when mapping complex traits such as drought resistance and yield. In this study, we present a novel GWAS method, HapFM, tailored for plant datasets to overcome the difficulties of many conventional GWAS methods. HapFM resulted in higher statistical power than conventional GWAS methods for mapping complex traits in our simulation and real dataset analyses. In addition, HapFM reduced the mapping interval by prioritizing candidate causal regions in the genome, which benefits the downstream experimental studies. Last but not least, HapFM can incorporate biological annotations to increase statistical power further. Overall, HapFM balances statistical power, result interpretability, and downstream experimental verifiability.

Bulk segregant analysis-sequencing and RNA-Seq analyses reveal candidate genes associated with albino phenotype in Brassica napus

Inheritable albino mutants are excellent models for exploring the mechanism of chloroplast biogenesis and development. However, only a few non-lethal albino mutations have been reported to date in Brassica species. Here, we describe a resynthesized Brassica napus mutant, whose leaf, stem, and silique tissues showed an inheritable albino phenotype under field conditions after the bud stage but green phenotype in the greenhouse during the whole growing season, indicating that the albino phenotype depends on environmental conditions. Compared with the green leaves of the field-grown wild-type (GL) and greenhouse-grown mutant (WGL) plants, white leaves of the field-grown mutant (WL) showed significantly lower chlorophyll contents and structural defects in chloroplasts. Genetic analysis revealed that the albino phenotype of WL is recessive and is controlled by multiple genes. Bulk segregant analysis-sequencing (BSA-Seq) indicated that the candidate regions responsible for the albino phenotype spanned a total physical distance of approximately 49.68 Mb on chromosomes A03, A07, A08, C03, C04, C06, and C07. To gain insights into the molecular mechanisms that control chloroplast development in B. napus, we performed transcriptome (RNA-Seq) analysis of GL, WGL, and WL samples. GO and KEGG enrichment analyses suggested that differentially expressed genes (DEGs) associated with leaf color were significantly enriched in photosynthesis, ribosome biogenesis and chlorophyll metabolism. Further analysis indicated that DEGs involved in chloroplast development and chlorophyll metabolism were likely the main factors responsible for the albino phenotype in B. napus. A total of 59 DEGs were screened in the candidate regions, and four DEGs (BnaC03G0522600NO, BnaC07G0481600NO, BnaC07G0497800NO, and BnaA08G0016300NO) were identified as the most likely candidates responsible for the albino phenotype. Altogether, this study provides clues for elucidating the molecular mechanisms underlying chloroplast development in B. napus.

Identification and Fine Mapping of the Candidate Gene Controlling Multi-Inflorescence in Brassica napus

As a desirable agricultural trait, multi-inflorescence (MI) fulfills the requirement of mechanized harvesting and yield increase in rapeseed (Brassica napus L.). However, the genetic mechanism underlying the multi-inflorescence trait remain poorly understood. We previously identified a difference of one pair of dominant genes between the two mapping parental materials. In this study, phenotype and expression analysis indicated that the imbalance of the CLAVATA (CLV)-WUSCHEL (WUS) feedback loop may contribute to the abnormal development of the shoot apical meristem (SAM). BnaMI was fine-mapped to a 55 kb genomic region combining with genotype and phenotype of 5768 BCF₁ individuals using a traditional mapping approach. Through comparative and expression analyses, combined with the annotation in Arabidopsis, five genes in this interval were identified as candidate genes. The present findings may provide assistance in functional analysis of the mechanism associated with multi-inflorescence and yield increase in rapeseed.

Receptor-like cytoplasmic kinases PBL34/35/36 are required for CLE peptide-mediated signaling to maintain shoot apical meristem and root apical meristem homeostasis in Arabidopsis

Shoot apical meristem (SAM) and root apical meristem (RAM) homeostasis is tightly regulated by CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-related (CLE) peptide signaling. However, the intracellular signaling components after CLV3 is perceived by the CLV1-CLV3-INSENSITIVE KINASE (CIK) receptor complex and CLE25/26/45 are sensed by the BARELY ANY MERISTEM (BAM)-CIK receptor complex are unknown. Here, we report that PBS1-LIKE34/35/36 (PBL34/35/36), a clade of receptor-like cytoplasmic kinases, are required for both CLV3-mediated signaling in the SAM and CLE25/26/45-mediated signaling in the RAM. Physiological assays showed that the SAM and RAM of pbl34 pbl35 pbl36 were resistant to CLV3 and CLE25/26/45 treatment, respectively. Genetic analyses indicated that pbl34 pbl35 pbl36 greatly enhanced the SAM defects of clv2 and rpk2 but not clv1, and did not show additive effects with bam3 and cik2 in the RAM. Further biochemical assays revealed that PBL34/35/36 interacted with CLV1, BAM1/3, and CIKs, and were phosphorylated by CLV1 and BAM1. All these results suggest that PBL34/35/36 act downstream of CLV1 and BAM1/3 to mediate the CLV3 and CLE25/26/45 signals in maintaining SAM and RAM homeostasis, respectively. Our findings shed light on how CLE signals are transmitted intracellularly after being perceived by cell surface receptor complexes.

Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus

Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.

Combined BSA-Seq Based Mapping and RNA-Seq Profiling Reveal Candidate Genes Associated with Plant Architecture in Brassica napus

Plant architecture involves important agronomic traits affecting crop yield, resistance to lodging, and fitness for mechanical harvesting in Brassica napus. Breeding high-yield varieties with plant architecture suitable for mechanical harvesting is the main goal of rapeseed breeders. Here, we report an accession of B. napus (4942C-5), which has a dwarf and compact plant architecture in contrast to cultivated varieties. A BC₈ population was constructed by crossing a normal plant architecture line, 8008, with the recurrent parent 4942C-5. To investigate the molecular mechanisms underlying plant architecture, we performed phytohormone profiling, bulk segregant analysis sequencing (BSA-Seq), and RNA sequencing (RNA-Seq) in BC₈ plants with contrasting plant architecture. Genetic analysis indicated the plant architecture traits of 4942C-5 were recessive traits controlled by multiple genes. The content of auxin (IAA), gibberellin (GA), and abscisic acid (ABA) differed significantly between plants with contrasting plant architecture in the BC₈ population. Based on BSA-Seq analysis, we identified five candidate intervals on chromosome A01, namely those of 0 to 6.33 Mb, 6.45 to 6.48 Mb, 6.51 to 6.53 Mb, 6.77 to 6.79 Mb, and 7 to 7.01 Mb regions. The RNA-Seq analysis revealed a total of 4378 differentially expressed genes (DEGs), of which 2801 were up-regulated and 1577 were down-regulated. There, further analysis showed that genes involved in plant hormone biosynthesis and signal transduction, cell structure, and the phenylpropanoid pathway might play a pivotal role in the morphogenesis of plant architecture. Association analysis of BSA-Seq and RNA-Seq suggested that seven DEGs involved in plant hormone signal transduction and a WUSCHEL-related homeobox (WOX) gene (BnaA01g01910D) might be candidate genes responsible for the dwarf and compact phenotype in 4942C-5. These findings provide a foundation for elucidating the mechanisms underlying rapeseed plant architecture and should contribute to breed new varieties suitable for mechanization.

Different Shades of Kale-Approaches to Analyze Kale Variety Interrelations

Brassica oleracea is a vegetable crop with an amazing morphological diversity. Among the various crops derived from B. oleracea, kale has been in the spotlight globally due to its various health-benefitting compounds and many different varieties. Knowledge of the existing genetic diversity is essential for the improved breeding of kale. Here, we analyze the interrelationships, population structures, and genetic diversity of 72 kale and cabbage varieties by extending our previous diversity analysis and evaluating the use of summed potential lengths of shared haplotypes (SPLoSH) as a new method for such analyses. To this end, we made use of the high-density Brassica 60K SNP array, analyzed SNPs included in an available Brassica genetic map, and used these resources to generate and evaluate the information from SPLoSH data. With our results we could consistently differentiate four groups of kale across all analyses: the curly kale varieties, Italian, American, and Russian varieties, as well as wild and cultivated types. The best results were achieved by using SPLoSH information, thus validating the use of this information in improving analyses of interrelations in kale. In conclusion, our definition of kale includes the curly varieties as the kales in a strict sense, regardless of their origin. These results contribute to a better understanding of the huge diversity of kale and its interrelations.

The branchless gene Clbl in watermelon encoding a TERMINAL FLOWER 1 protein regulates the number of lateral branches

A SNP mutation in Clbl gene encoding TERMINAL FLOWER 1 protein is responsible for watermelon branchless. Lateral branching is one of the most important traits, which directly determines plant architecture and crop productivity. Commercial watermelon has the characteristics of multiple lateral branches, and it is time-consuming and labor-costing to manually remove the lateral branches in traditional watermelon cultivation. In our present study, a lateral branchless trait was identified in watermelon material WCZ, and genetic analysis revealed that it was controlled by a single recessive gene, which named as Clbl (Citrullus lanatus branchless). A bulked segregant sequencing (BSA-seq) and linkage analysis was conducted to primarily map Clbl on watermelon chromosome 4. Next-generation sequencing-aided marker discovery and a large mapping population consisting of 1406 F₂ plants were used to further map Clbl locus into a 9011-bp candidate region, which harbored only one candidate gene Cla018392 encoding a TERMINAL FLOWER 1 protein. Sequence comparison of Cla018392 between two parental lines revealed that there was a SNP detected from C to A in the coding region in the branchless inbred line WCZ, which resulted in a mutation from alanine (GCA) to glutamate (GAA) at the fourth exon. A dCAPS marker was developed from the SNP locus, which was co-segregated with the branchless phenotype in both BC₁ and F₂ population, and it was further validated in 152 natural watermelon accessions. qRT-PCR and in situ hybridization showed that the expression level of Cla018392 was significantly reduced in the axillary bud and apical bud in branchless line WCZ. Ectopic expression of ClTFL1 in Arabidopsis showed an increased number of lateral branches. The results of this study will be helpful for better understanding the molecular mechanism of lateral branch development in watermelon and for the development of marker-assisted selection (MAS) for new branchless watermelon cultivars.

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

BACKGROUND

Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F₂ mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type.

RESULTS

Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC.

CONCLUSIONS

These findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F₂ populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.