Identification of a major QTL and candidate genes analysis for branch angle in rapeseed (Brassica napus L.) using QTL-seq and RNA-seq
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ABSTRACT:
SUBMITTER: Lei S
PROVIDER: S-EPMC10914954 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:Oilseed rape (Brassica napus L.) is one of the most important oil crops in China as well as worldwide. Branch angle as a plant architecture component trait plays an important role for high density planting and yield performance. In this study, bulked segregant analysis (BSA) combined with next generation sequencing technology was used to fine map QTL for branch angle. A major QTL, designated as branch angle 1 (ba1) was identified on A06 and further validated by Indel marker-based classical QTL mapping in an F2 population. Eighty-two genes were identified in the ba1 region. Among these genes, BnaA0639380D is a homolog of AtYUCCA6. Sequence comparison of BnaA0639380D from small- and big-branch angle oilseed rape lines identified six SNPs and four amino acid variation in the promoter and coding region, respectively. The expression level of BnaA0639380D is significantly higher in the small branch angle line Purler than in the big branch angle line Huyou19, suggesting that the genomic mutations may result in reduced activity of BnaA0639380D in Huyou19. Phytohormone determination showed that the IAA content in Purler was also obviously increased. Taken together, our results suggested BnaA0639380D is a possible candidate gene for branch angle in oilseed rape.
| S-EPMC5138835 | biostudies-literature
Project description:Plant height (PH) is a critical agronomic trait in Brassica napus, significantly impacting yield. Consequently, identifying genes associated with plant height is a pivotal objective in oilseed rape breeding. This study employed a combination of bulk segregant analysis sequencing (BSA-seq) and RNA sequencing (RNA-seq) for analysis. A novel quantitative trait locus (QTL), qPH_C02, was identified between 63,989,634 and 64,945,122 bp on chromosome C02, from which eight candidate genes were screened. The Gene Ontology (GO) analysis revealed enrichment in peroxisomes, while the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated enrichment in the oxidative phosphorylation (OP) pathway. It is hypothesized that the observed differences in plant height and silique length may be attributed to the regulation of peroxidase activity in the OP pathway, which in turn alters plant energy metabolism and controls nutrient uptake. Subsequently, we will further test this hypothesis. The results of this study will contribute to our understanding of the genetic basis for differences in plant height and provide a foundation for the selection and breeding of Brassica napus varieties with desired plant shapes.
| S-EPMC11432562 | biostudies-literature
Project description:Changes in the rapeseed branch angle alter plant architecture, allowing more efficient light capture as planting density increases. In this study, a natural population of rapeseed was grown in three environments and evaluated for branch angle trait to characterize their phenotypic patterns and genotype with a 60K Brassica Infinium SNP array. Significant phenotypic variation was observed from 20 to 70°. As a result, 25 significant quantitative trait loci (QTL) associated with branch angle were identified on chromosomes A2, A3, A7, C3, C5, and C7 by the MLM model in TASSEL 4.0. Orthologs of the functional candidate genes involved in branch angle were identified. Among the key QTL, the peak SNPs were close to the key orthologous genes BnaA.Lazy1 and BnaC.Lazy1 on A3 and C3 homologous genome blocks. With the exception of Lazy (LA) orthologous genes, SQUMOSA PROMOTER BINDING PROTEIN LIKE 14 (SPL14) and an auxin-responsive GRETCHEN HAGEN 3 (GH3) genes from Arabidopsis thaliana were identified close to two clusters of SNPs on the A7 and C7 chromosomes. These findings on multiple novel loci and candidate genes of branch angle will be useful for further understanding and genetic improvement of plant architecture in rapeseed.
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Project description:Seed density per silique (SD) is an important agricultural trait and plays an important role in the yield performance of Brassica napus L. (B. napus). In this study, a genetic linkage map was constructed using a double haploid (DH) population with 213 lines derived from a cross between a low SD line No. 935 and a high SD line No. 3641, and a total of 1,098,259 SNP (single-nucleotide polymorphisms) markers and 2,102 bins were mapped to 19 linkage groups. Twenty-eight QTLs for SD were detected on chromosomes A02, A04, A05, A09, C02, C03, C06, and C09 of B. napus, of which eight QTLs were on chromosome A09 and explained 5.89%-13.24% of the phenotypic variation. Furthermore, a consistent QTL for SD on chromosome A09, cqSD-A9a, was identified in four environments by QTL meta-analysis, explaining 10.68% of the phenotypic variation. In addition, four pairs of epistatic interactions were detected in the DH population via QTL epistasis analysis, indicating that SD is controlled not only by additive effects but also by epistatic effects that play an important role in spring B. napus., but with little environmental effect. Moreover, 18 closely linked SSR markers for cqSD-A9a were developed, as a result, it was mapped to a 1.86Mb (7.80-9.66 Mb) region on chromosome A09. A total of 13 differentially expressed genes (DEGs) were screened in the candidate interval by RNA-seq analysis, which were differentially expressed in buds, leaves and siliques both between and siliques both between two parents and two pools of extremely high-SD and low-SD lines in the DH population. Three of 13 DEGs were possible candidate genes that might control SD: BnaA09g14070D, which encodes a callose synthase that plays an important role in development and stress responses; BnaA09g14800D, a plant synaptic protein that encodes a membrane component; and BnaA09g18250D, which is responsible for DNA binding, transcriptional regulation, and sequence-specific DNA binding and is involved in the response to growth hormone stimulation. Overall, these results lay a foundation for fine mapping and gene cloning for SD in B. napus.
| S-EPMC9987769 | biostudies-literature
Project description:Plant architecture is vital not only for crop yield, but also for field management, such as mechanical harvesting. The branch angle is one of the key factors determining plant architecture. With the aim of revealing the genetic control underlying branch angle in rapeseed (Brassica napus L.), the positional variation of branch angles on individual plants was evaluated, and the branch angle increased with the elevation of branch position. Furthermore, three middle branches of individual plants were selected to measure the branch angle because they exhibited the most representative phenotypic values. An association panel with 472 diverse accessions was estimated for branch angle trait in six environments and genotyped with a 60K Brassica Infinium® SNP array. As a result of association mapping, 46 and 38 significantly-associated loci were detected using a mixed linear model (MLM) and a multi-locus random-SNP-effect mixed linear model (MRMLM), which explained up to 62.2 and 66.2% of the cumulative phenotypic variation, respectively. Numerous highly-promising candidate genes were identified by annotating against Arabidopsis thaliana homologous, including some first found in rapeseed, such as TAC1, SGR1, SGR3, and SGR5. These findings reveal the genetic control underlying branch angle and provide insight into genetic improvements that are possible in the plant architecture of rapeseed.
| S-EPMC5474488 | biostudies-literature
Project description:The rapeseed branch angle is an important morphological trait because an adequate branch angle enables more efficient light capture under high planting densities. Here, we report that the average angle of the five top branches provides a reliable representation of the average angle of all branches. Statistical analyses revealed a significantly positive correlation between the branch angle and multiple plant-type and yield-related traits. The 60 K Brassica Infinium(®) single nucleotide polymorphism (SNP) array was utilized to genotype an association panel with 520 diverse accessions. A genome-wide association study was performed to determine the genetic architecture of branch angle, and 56 loci were identified as being significantly associated with the branch angle trait via three models, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Moreover, these loci explained 51.1% of the phenotypic variation when a simple additive model was applied. Within the linkage disequilibrium (LD) decay ranges of 53 loci, we observed plausible candidates orthologous to documented Arabidopsis genes, such as LAZY1, SGR2, SGR4, SGR8, SGR9, PIN3, PIN7, CRK5, TIR1, and APD7. These results provide insight into the genetic basis of the branch angle trait in rapeseed and might facilitate marker-based breeding for improvements in plant architecture.
| S-EPMC5028734 | biostudies-literature
Project description: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.
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Project description:Elice16Indures® Plant Conditioner combines the effects of a number of herbs to increase the yield of dicotyledonous plants in the field. This crop enhancer can also be used in organic farming applying low doses with ULV spraying by drone. Reducing the ecological footprint is the basis for sustainable crop production. By using the crop enhancer, a better crop can be achieved with less impact on the environment. EU Member States attach great importance to rapeseed (Brassica napus). Due to its versatility, it is one of the supported plants. Plant conditioner applied in different phenological phases (BBCH 51 and BBCH 67) of winter oilseed rape at a dose of 240 g/ha of. By using Elice16Indures, the value of the vegetation index and the yield can be increased. RNA-seq data set of field Elice16Indures-treated and non-treated (control) rapeseed plants are presented. For RNA-seq experiments, two samples were taken from leaf tissues in the phenological phase of BBCH 69 from control and treated plots, 2 days after treatment. Illumina NextSeq 550 sequence reads were uploaded to the NCBI SRA database after preprocessing. Combined read sets were de novo assembled and functional annotation with the output transcripts were performed. The entire dataset of identified coding sequences (transcripts) was deposited in the NCBI TSA database. The SRA and TSA datasets are under the BioProject access PRJNA838472. The data series reported in this study may open up new opportunities to increase the efficiency of organic rapeseed production.
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Project description:Plant architecture is crucial for rapeseed yield and is determined by plant height (PH), branch initiation height (BIH), branch number (BN) and leaf and inflorescence morphology. In this study, we measured three major factors (PH, BIH, and BN) in a panel of 333 rapeseed accessions across 4 years. A genome-wide association study (GWAS) was performed via Q + K model and the panel was genotyped using the 60 k Brassica Infinium SNP array. We identified seven loci for PH, four for BIH, and five for BN. Subsequently, by determining linkage disequilibrium (LD) decay associated with 38 significant SNPs, we gained 31, 15, and 17 candidate genes for these traits, respectively. We also showed that PH is significantly correlated with BIH, while no other correlation was revealed. Notably, a GA signaling gene (BnRGA) and a flowering gene (BnFT) located on chromosome A02 were identified as the most likely candidate genes associated with PH regulation. Furthermore, a meristem initiation gene (BnLOF2) and a NAC domain transcriptional factor (BnCUC3) that may be associated with BN were identified on the chromosome A07. This study reveals novel insight into the genetic control of plant architecture and may facilitate marker-based breeding for rapeseed.
| S-EPMC5513965 | biostudies-literature
Project description:Fruit cracking decreases the total production and the commercial value of watermelon. The molecular mechanisms of fruit cracking are unknown. In this study, 164 recombinant inbred lines (RILs) of watermelon, derived from the crossing of the WQ1 (cracking-sensitive) and WQ2 (cracking-tolerant) lines, were sequenced using specific length amplified fragment sequencing (SLAF-seq). A high-density genetic linkage map was constructed with 3,335 markers spanning 1,322.74 cM, at an average 0.40 cM across whole-genome flanking markers. The cracking tolerance capacity (CTC), depth of fruit cracking (DFC), rind thickness (RT), and rind hardness (RH) were measured for quantitative trait locus (QTL) analysis. Of the four traits analyzed, one major QTL with high phenotypic variation (41.04%-61.37%) was detected at 76.613-76.919 cM on chromosome 2, which contained 104 annotated genes. Differential gene expression analysis with RNA sequencing (RNA-seq) data between the two parents identified 4,508 differentially expressed genes (DEGs). Comparison of the genes between the QTL region and the DEGs obtained eight coexisting genes. Quantitative real-time PCR (qRT-PCR) analysis revealed that these genes were significant differentially expressed between the two parents. These results provide new insights into the identification of QTLs or genes and marker-assisted breeding in watermelon.
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