Tetralocular ovary and high silique width in yellow sarson lines of Brassica rapa (subspecies trilocularis) are due to a mutation in Bra034340 gene, a homologue of CLAVATA3 in Arabidopsis

A novel CLAVATA1 mutation causes multilocularity in Brassica rapa

Locules are the seed-bearing structure of fruits. Multiple locules are associated with increased fruit size and seed set, and therefore, control of locule number is an important agronomic trait. Locule number is controlled in part by the CLAVATA-WUSCHEL pathway. Disruption of either the CLAVATA1 receptor-like kinase or its ligand CLAVATA3 can cause larger floral meristems and an increased number of locules. In an EMS mutagenized population of Brassica rapa, we identified a mutant allele that raises the number of locules from four to a range of from six to eight. Linkage mapping and genetic analysis support that the mutant phenotype is due to a missense mutation in a CLAVATA 1 (CLV1) homolog. In addition to increased locule number, additional internal gynoecia are formed in brclv1 individuals, suggesting a failure to terminate floral meristem development, which results in decreased seed production.

Biparental genetic mapping reveals that CmCLAVATA3 (CmCLV3) is responsible for the variation in carpel number in melon (Cucumis melo L.)

Genetic analysis revealed that CmCLV3 is a candidate gene for the variation in melon carpel number. Carpel number (CN) is an important trait in melon. Three-CN melon fruit is oval, while 5-CN melon fruit has a round or flat shape. Herein, a genetic analysis of a population in which the CN locus was segregated indicated that 3-CN is controlled by a major dominant effective gene. Bulked segregant analysis and initial linkage mapping placed the CN locus in a 6.67 Mb region on chromosome 12, and it was narrowed to 882.19 kb with molecular markers and recombinant plants. Fine mapping with a large F₂ population containing 1026 individuals further narrowed the locus to an 83.98 kb region harboring five annotated genes. Gene structure alignment between the parental lines revealed MELO3C035640.2 (annotated as CLAVATA3, CmCLV3) as the best candidate gene for the CN trait. CmCLV3 was more highly expressed in 3- than 5-CN lines and specifically expressed in terminal buds rather than in young leaves, hypocotyls, and roots. The CmCLV3 coding region was cloned from eight 3- or 5-CN melon accessions, and a nonsynonymous SNP site was highly correlated with CN variation. This SNP site was also related to CN variations among 40 melon lines according to their resequencing data, causing a helix alteration in the CmCLV3 protein. Promoter region sequence alignment and activity analysis showed that, unlike in cucumber and tomato, CmCLV3 promoter variation and activity were not the main reasons for CN alteration. Overall, this study provides a genetic resource for melon fruit development research and molecular breeding tools for melon CN improvement.

Marker-Assisted Pyramiding of Genes for Multilocular Ovaries, Self-Compatibility, and Clubroot Resistance in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Molecular marker-assisted gene pyramiding combined with backcrossing has been widely applied for crop variety improvement. Molecular marker identification could be used in the early stage of breeding to achieve the rapid and effective pyramiding of multiple genes. To create high-quality germplasm for Chinese cabbage breeding, multi-gene pyramiding for self-compatibility, multilocular, and clubroot resistance was performed through molecular marker-assisted selection. The results showed that self-compatibility and multilocular traits were controlled by a pair of recessive genes. Two flanking markers, sau_um190 and cun_246a, and marker Teo-1, based on the gene sequence related to multilocular ovaries, were used for multilocular ovary trait selection. Two flanking markers, SCF-6 and SC-12, and marker Sal-SLGI /PK1+PK4, based on the gene sequence, were used for self-compatibility selection. Two flanking markers, TCR74 and TCR79, closely linked to clubroot resistance gene CRb, were used as foreground selection markers. Based on Chinese cabbage genomic information, 111 SSR markers covering 10 chromosomes were applied for background selection. After multiple generations of selection, a multi-gene pyramided line from a BC4F2 population with self-compatibility, multilocular ovaries, and clubroot resistance was obtained with a high genomic background recovery rate. The improved pyramided line is expected to be utilized as a potential material in further breeding programs.

Increased seed number per silique in Brassica juncea by deleting cis-regulatory region affecting BjCLV1 expression in carpel margin meristem

Mustard yield per plant is severely restricted by the seed number per silique. The seed number per silique in the Brassica juncea trilocular mutant J163-4 is significantly greater than that in normal bilocular plants. However, how the trilocular silique of J163-4 is formed remains unclear. Here, we studied the gene structure and function of mc2 in B. juncea and Arabidopsis using comparative morphology and molecular genetic experiments. We found that mc2 is a CLV1 ortholog, BjA7.CLV1. The deletion of cis-regulatory region in mc2 promoter, which affects Mc2 expression in carpel margin meristem (CMM), led to trilocular silique formation. The BjCLV1 sequence with its complete promoter containing the cis-regulatory region can restore the Bjclv1 and clv1 mutant phenotypes in B. juncea and Arabidopsis, respectively. Additionally, this cis-regulatory region had a collinear segment in the promoter of CLV1 homologous gene in most Brassicaceae species. Our results are consistent with the report that BjCLV1 represents a conserved pleiotropic role in shoot meristem and CMM development, which contains a cis-regulatory sequence specifically expressed BjCLV1 in CMM in its promoter, and this cis-regulatory region is conserved in Brassicaceae species. These results offer a reliable approach for fine-tuning the traits of seed yield in Brassicaceae crops.

Investigation of Thermomorphogenesis-Related Genes for a Multi-Silique Trait in Brassica napus by Comparative Transcriptome Analysis

In higher plants, the structure of a flower is precisely controlled by a series of genes. An aberrance flower results in abnormal fruit morphology. Previously, we reported multi-silique rapeseed (Brassica napus) line zws-ms. We identified two associated regions and investigated differentially expressed genes (DEGs); thus, some candidate genes underlying the multi-silique phenotype in warm area Xindu were selected. However, this phenotype was switched off by lower temperature, and the responsive genes, known as thermomorphogenesis-related genes, remained elusive. So, based on that, in this study, we further investigated the transcriptome data from buds of zws-ms and its near-isogenic line zws-217 grown in colder area Ma’erkang, where both lines showed normal siliques only, and the DEGs between them analyzed. We compared the 129 DEGs from Xindu to the 117 ones from Ma’erkang and found that 33 of them represented the same or similar expression trends, whereas the other 96 DEGs showed different expression trends, which were defined as environment-specific. Furthermore, we combined this with the gene annotations and ortholog information and then selected BnaA09g45320D (chaperonin gene CPN10-homologous) and BnaC08g41780D [Seryl-tRNA synthetase gene OVULE ABORTION 7 (OVA7)-homologous] the possible thermomorphogenesis-related genes, which probably switched off the multi-silique under lower temperature. This study paves a way to a new perspective into flower/fruit development in Brassica plants.

Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis

Background

Flower and fruit development are vital stages of the angiosperm lifecycle. We previously investigated the multi-silique trait in the rapeseed (Brassica napus) line zws-ms on a genomic and transcriptomic level, leading to the identification of two genomic regions and several candidate genes associated with this trait. However, some events on the transcriptome level, like alternative splicing, were poorly understood.

Methods

Plants from zws-ms and its near-isogenic line (NIL) zws-217 were both grown in Xindu with normal conditions and a colder area Ma'erkang. Buds from the two lines were sampled and RNA was isolated to perform the transcriptomic sequencing. The numbers and types of alternative splicing (AS) events from the two lines were counted and classified. Genes with AS events and expressed differentially between the two lines, as well as genes with AS events which occurred in only one line were emphasized. Their annotations were further studied.

Results

From the plants in Xindu District, an average of 205,496 AS events, which could be sorted into five AS types, were identified. zws-ms and zws-217 shared highly similar ratios of each AS type: The alternative 5' and 3' splice site types were the most common, while the exon skipping type was observed least often. Eleven differentially expressed AS genes were identified, of which four were upregulated and seven were downregulated in zws-ms. Their annotations implied that five of these genes were directly associated with the multi-silique trait. While samples from colder area Ma'erkang generated generally reduced number of each type of AS events except for Intron Retention; but the number of differentially expressed AS genes increased significantly. Further analysis found that among the 11 differentially expressed AS genes from Xindu, three of them maintained the same expression models, while the other eight genes did not show significant difference between the two lines in expression level. Additionally, the 205 line-specific expressed AS genes were analyzed, of which 187 could be annotated, and two were considered to be important.

Discussion

This study provides new insights into the molecular mechanism of the agronomically important multi-silique trait in rapeseed on the transcriptome level and screens out some environment-responding candidate genes.

Comparative Mapping Combined With Map-Based Cloning of the Brassica juncea Genome Reveals a Candidate Gene for Multilocular Rapeseed

Multilocular traits exist in a variety of plants and exert important effects on plant yield. Previous genetic studies have shown that multilocular trait of the Brassica juncea cultivar Duoshi is controlled by two recessive genes, Bjln1 and Bjln2. In previous studies, the Bjln1 gene is located on chromosome A07, and the Bjln1 candidate gene is BjuA07.CLV1. In this study, a BC4 mapping population for the Bjln2 gene was generated. This population was used to construct genetic linkage maps of the Bjln2 gene using amplified fragment length polymorphism (AFLP), intron length polymorphism (IP) and simple sequence repeat (SSR) methodology. The results showed that the Bjln2 gene was restricted to a 0.63 cM interval. BLAST alignment with B. juncea revealed the Bjln2 gene was located within a 11.81-16.65 Mb region on chromosome B07. Moreover, the candidate gene BjuB07.CLV1 (equivalent to Bjln2) was cloned by comparing mapping and map-based cloning, and BjuB07.CLV1 gene was shown to have the ability to restore the bilocular traits in a genetic complementation experiment. The sequencing revealed that a 4961 bp insertion interrupted the coding sequence of the BjuB07.CLV1 gene, resulting in an increase in locule number. Expression analysis revealed that BjuB07.CLV1 was expressed in all tissues and the expression level in bilocular plants was significantly higher than that in multilocular plants. In addition, markers closely linked to the Bjln2 gene were developed and used for molecular marker-assisted breeding of multilocular traits.

Trilocular phenotype in Brassica juncea L. resulted from interruption of CLAVATA1 gene homologue (BjMc1) transcription

As a desirable agricultural trait, multilocular trait of rapeseed (Brassica rapa; Brassica napus; Brassica juncea), always represents higher yield per plant compared with bilocular plants. We previously isolated a trilocular gene locus, Bjmc1, and identified a set of molecular markers linked to the trilocular gene. With a map-based cloning, we identified that the BjMc1 was located in B genome of Brassica juncea, and it was a CLAVATA1 (CLV1) gene homologue. The insertion of a copia-LTR retrotransposable element 1 (RTE1) into the coding region of BjMc1 interrupted its transcription in rapeseed, leading to the trilocular phenotype. Phylogenetic analysis showed that Mc1 genes were conserved and widespread in land plants. Two amino acid sites had undergone positive selection in the ancestor of Mc1 genes, and then purifying selection was the dominant force after the divergence of dicots and monocots from their common ancestor in the evolutionary process, indicating that Mc1 genes are conserved in modern land plants. Our results provided new insights in molecular regulatory mechanism of multilocularity in rapeseed, and better understanding of molecular mechanism in crop yield improvement.

Integrated analysis in bi-parental and natural populations reveals CsCLAVATA3 (CsCLV3) underlying carpel number variations in cucumber

Carpel number variation in cucumber was controlled by a single gene, Cn . Linkage and association analysis revealed CsCLV3 as the candidate gene of the Cn locus. Carpel number (CN) is an important fruit quality trait of cucumber, but the genetic basis of CN variations is largely unknown. In the present study, segregating analysis in multiple bi-parental mapping populations (F2, F3, and RILs) derived from WI2757 (CN = 3) × True Lemon (CN = 5) suggested that CN is controlled by a simply inherited gene, Cn, with CN = 3 being incompletely dominant to CN = 5. Initial linkage mapping located Cn in a 1.9-Mb region of cucumber chromosome 1. Exploration of DNA sequence variations in this region with in silico bulked segregant analysis among eight re-sequenced lines allowed delimiting the Cn locus to a 16-kb region with five predicted genes including CsCLV3, a homolog of the Arabidopsis gene CLAVATA3. Fine genetic mapping in F2 and RIL populations and association analysis in natural populations confirmed CsCLV3 as the candidate gene for Cn, which was further evidenced from gene expression analysis and microscopic examination of floral meristem size in the two parent lines. This study highlights the importance of integrated use of linkage and association analysis as well as next-gen high-throughput sequencing in mapping and cloning genes that are difficult in accurate genotyping. The results provide new insights into the genetic control of CN variations in cucumber, which were discussed in the context of the well-characterized CLAVATA pathway for stem cell homeostasis and regulation of meristem sizes in plants. The associations of carpel number with fruit shape, size, and weight in cucumber and melon are also discussed.