Role of BrSDG8 on bolting in Chinese cabbage (Brassica rapa)

Differential gene expression during floral transition in pineapple

Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up-regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS-like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up-regulated within a day of treatment, their predicted targets being the up-regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS-like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up-regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted DE target genes was developed to give focus to future research. The identified candidate genes are potential targets for genetic manipulation to determine their molecular role in flower transition.

BrKCS6 mutation conferred a bright glossy phenotype to Chinese cabbage

KEY MESSAGE

BrKCS6 encoding 3-ketoacyl-CoA synthases was cloned through MutMap and KASP analysis, and its function was verified via allelic mutants in Chinese cabbage. Bright and glossy green appearance is an attractive commodity character for leafy vegetables and is mainly caused by the absence of epicuticular wax crystals. In this study, two allelic epicuticular wax crystal deficiency mutants, wdm9 and wdm10, were obtained from an EMS mutagenesis population of Chinese cabbage (Brassica rapa L. ssp. pekinensis). Genetic analysis revealed that the mutant phenotype was controlled by a recessive nuclear gene. BrKCS6 encoding 3-ketoacyl-CoA synthases was identified as the candidate gene by MutMap and KASP analysis. A SNP (G to A) on BrKCS6 in wdm9 led to the amino acid substitution from serine (S) to phenylalanine (F), and another SNP (G to A) in wdm10 resulted in the amino acid substitution from serine (S) to leucine (L). Both SNPs are located in the ACP_syn_III_C conserved domain, corresponding to two highly conserved sites among BrKCS6 and its homologs. These two amino acid substitutions changed the secondary structure and the three-dimensional structure of BrKCS6 protein. qRT-PCR results showed that the relative expression of BrKCS6 significantly decreased in the flower, stem, and leaves in mutant, and the relative expressions of the downstream key genes of BrKCS6 were down-regulated in mutant. We were the first to clone the precious glossy bright gene BrKCS6 which has a great potential for commodity quality breeding in Chinese cabbage.

Role of Brassica orphan gene BrLFM on leafy head formation in Chinese cabbage (Brassica rapa)

Brassica orphan gene BrFLM, identified by two allelic mutants, was involved in leafy head formation in Chinese cabbage. Leafy head formation is a unique agronomic trait of Chinese cabbage that determines its yield and quality. In our previous study, an EMS mutagenesis Chinese cabbage mutant library was constructed using the heading Chinese cabbage double haploid (DH) line FT as the wild-type. Here, we screened two extremely similar leafy head deficiency mutants lfm-1 and lfm-2 with geotropic growth leaves from the library to investigate the gene(s) related to leafy head formation. Reciprocal crossing results showed that these two mutants were allelic. We utilized lfm-1 to identify the mutant gene(s). Genetic analysis showed that the mutated trait was controlled by a single nuclear gene Brlfm. Mutmap analysis showed that Brlfm was located on chromosome A05, and BraA05g012440.3C or BraA05g021450.3C were the candidate gene. Kompetitive allele-specific PCR analysis eliminated BraA05g012440.3C from the candidates. Sanger sequencing identified an SNP from G to A at the 271st nucleotide on BraA05g021450.3C. The sequencing of lfm-2 detected another non-synonymous SNP (G to A) located at the 266st nucleotide on BraA05g021450.3C, which verified its function on leafy head formation. We blasted BraA05g021450.3C on database and found that it belongs to a Brassica orphan gene encoding an unknown 13.74 kDa protein, named BrLFM. Subcellular localization showed that BrLFM was located in the nucleus. These findings reveal that BrLFM is involved in leafy head formation in Chinese cabbage.

Identification of an epicuticular wax crystal deficiency gene Brwdm1 in Chinese cabbage (Brassica campestris L. ssp. pekinensis)

Introduction

The cuticle wax covering the plant surface is a whitish hydrophobic protective barrier in Chinese cabbage, and the epicuticular wax crystal deficiency normally has higher commodity value for a tender texture and glossy appearance. Herein, two allelic epicuticular wax crystal deficiency mutants, wdm1 and wdm7, were obtained from the EMS mutagenesis population of a Chinese cabbage DH line 'FT'.

Methods

The cuticle wax morphology was observed by Cryo-scanning electron microscopy (Cryo-SEM) and the composition of wax was determined by GC-MS. The candidate mutant gene was found by MutMap and validated by KASP. The function of candidate gene was verified by allelic variation.

Results

The mutants had fewer wax crystals and lower leaf primary alcohol and ester content. Genetic analysis revealed that the epicuticular wax crystal deficiency phenotype was controlled by a recessive nuclear gene, named Brwdm1. MutMap and KASP analyses indicated that BraA01g004350.3C, encoding an alcohol-forming fatty acyl-CoA reductase, was the candidate gene for Brwdm1. A SNP 2,113,772 (C to T) variation in the 6^th exon of Brwdm1 in wdm1 led to the 262^nd amino acid substitution from threonine (T) to isoleucine (I), which existed in a rather conserved site among the amino acid sequences from Brwdm1 and its homologs. Meanwhile, the substitution changed the three-dimensional structure of Brwdm1. The SNP 2,114,994 (G to A) in the 10^th exon of Brwdm1 in wdm7 resulted in the change of the 434^th amino acid from valine (V) to isoleucine (I), which occurred in the STERILE domain. KASP genotyping showed that SNP 2,114,994 was co-segregated with glossy phenotype. Compared with the wild type, the relative expression of Brwdm1 was significantly decreased in the leaves, flowers, buds and siliques of wdm1.

Discussion

These results indicated that Brwdm1 was indispensable for the wax crystals formation and its mutation resulted in glossy appearance in Chinese cabbage.

Brassica rapa orphan gene BR1 delays flowering time in Arabidopsis

Orphan genes are essential to the emergence of species-specific traits and the process of evolution, lacking sequence similarity to any other identified genes. As they lack recognizable domains or functional motifs, however, efforts to characterize these orphan genes are often difficult. Flowering is a key trait in Brassica rapa, as premature bolting can have a pronounced adverse impact on plant quality and yield. Bolting resistance-related orphan genes, however, have yet to be characterized. In this study, an orphan gene designated BOLTING RESISTANCE 1 (BR1) was identified and found through gene structural variation analyses to be more highly conserved in Chinese cabbage than in other available accessions. The expression of BR1 was increased in bolting resistant Chinese cabbage and decreased in bolting non-resistant type, and the expression of some mark genes were consist with bolting resistance phenotype. BR1 is primarily expressed in leaves at the vegetative growth stage, and the highest BR1 expression levels during the flowering stage were observed in the flower buds and silique as compared to other tissue types. The overexpression of BR1 in Arabidopsis was associated with enhanced bolting resistance under long day (LD) conditions, with these transgenic plants exhibiting significant decreases in stem height, rosette radius, and chlorophyll content. Transcriptomic sequencing of WT and BR1OE plants showed the association of BR1 with other bolting resistance genes. Transcriptomic sequencing and qPCR revealed that six flowering integrator genes and one chlorophyll biosynthesis-related gene were downregulated following BR1 overexpression. Six key genes in photoperiodic flowering pathway exhibited downward expression trends in BR1OE plants, while the expression of floral repressor AtFLC gene was upregulated. The transcripts of these key genes were consistent with observed phenotypes in BR1OE plants, and the results indicated that BR1 may function through vernalization and photoperiodic pathway. Instead, the protein encoded by BR1 gene was subsequently found to localize to the nucleus. Taken together, we first propose that orphan gene BR1 functions as a novel regulator of flowering time, and these results suggested that BR1 may represent a promising candidate gene to support the selective breeding of Chinese cabbage cultivars with enhanced bolting resistance.

BrAN contributes to leafy head formation by regulating leaf width in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Leafy head is an important agronomic trait that determines the yield and quality of Chinese cabbage. The molecular mechanism underlying heading in Chinese cabbage has been the focus of research, and wide leaves are a prerequisite for leafy head formation. In our study, two allelic leafy heading-deficient mutants (lhd1 and lhd2) with narrow leaf phenotypes were screened in an ethyl methanesulfonate mutagenized population from a heading Chinese cabbage double haploid line 'FT'. Genetic analysis revealed that the mutant trait was controlled by a recessive nuclear gene, which was found to be BraA10g000480.3C by MutMap and Kompetitive allele-specific PCR analyses. As BraA10g000480.3C was the ortholog of ANGUSTIFOLIA in Arabidopsis, which has been found to regulate leaf width by controlling cortical microtubule arrangement and pavement cell shape, we named it BrAN. BrAN in mutant lhd1 carried an SNP (G to A) on intron 2 that co-segregated with the mutant phenotype, and disrupted the exon-intron splice junction generating intron retention and a putative truncated protein. BrAN in mutant lhd2 carried an SNP (G to A) on exon 4 leading to a premature stop codon. The ectopic overexpression of BrAN restored normal leaf phenotype due to abnormal cortical microtubule arrangement and pavement cell shape in the Arabidopsis an-t1 mutant. However, transformation of Bran did not rescue the an-t1 phenotype. These results indicate that BrAN contributes to leafy head formation of Chinese cabbage.

Fine mapping and analysis of candidate genes for qFT7.1, a major quantitative trait locus controlling flowering time in Brassica rapa L

qFT7.1, a major QTL for flowering time in Brassica rapa was fine-mapped to chromosome A07 in a 56.4-kb interval, in which the most likely candidate gene is BraA07g018240.3C. In Brassica rapa, flowering time (FT) is an important agronomic trait that affects the yield, quality, and adaption. FT is a complicated trait that is regulated by many genes and is affected greatly by the environment. In this study, a chromosome segment substitution line (CSSL), CSSL16, was selected that showed later flowering than the recurrent parent, a rapid-cycling inbred line of B. rapa (RcBr). Using Bulked Segregant RNA sequencing, we identified a late flowering quantitative trait locus (QTL), designated as qFT7.1, on chromosome A07, based on a secondary-F₂ population derived from the cross between CSSL16 and RcBr. qFT7.1 was further validated by conventional QTL mapping. This QTL explained 39.9% (logarithm of odds = 32.2) of the phenotypic variations and was fine mapped to a 56.4-kb interval using recombinant analysis. Expression analysis suggested that BraA07g018240.3C, which is homologous to ATC (encoding Arabidopsis thaliana CENTRORADIALIS homologue), a gene for delayed flowering in Arabidopsis, as the most promising candidate gene. Sequence analysis demonstrated that two synonymous mutations existed in the coding region and numerous bases replacements existed in promoter region between BraA07g018240.3C from CSSL16 and RcBr. The results will increase our knowledge related to the molecular mechanism of late flowering in B. rapa and lays a solid foundation for the breeding of late bolting B. rapa.

Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Bolting in Spinach (Spinacia oleracea L.)

Spinach is a typical light-sensitive plant. Long days can induce early bolting, thereby influencing the regional adaptation, quality, and vegetative yield of spinach. However, the genes and genetic mechanisms underlying this trait in spinach remain unclear. In this study, a major quantitative trait locus (QTL) qBT1.1, was mapped on chromosome 1 using a BC₁ population (BC_1a) derived from 12S3 (late-bolting recurrent lines) and 12S4 (early bolting lines) with specific-locus amplified fragment (SLAF) markers and Kompetitive Allele Specific PCR (KASP) markers. The qBT1.1 locus was further confirmed and narrowed down to 0.56 Mb by using a large BC₁ (BC_1b) population and an F₂ population using the above KASP markers and the other 20 KASP markers. Within this region, two putative genes, namely, SpFLC and SpCOL14, were of interest due to their relationship with flower regulatory pathways. For SpCOL14, we found multiple variations in the promoter, and the expression pattern was consistent with bolting stages. SpCOL14 was therefore assumed to the best candidate gene for bolting. Overall, our results provide a basis for understanding the molecular mechanisms of bolting in spinach and contribute to the breeding of diverse spinach germplasms for adaptation to different regions.

Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes

Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.

Epigenetics and its role in effecting agronomical traits

Climate-resilient crops with improved adaptation to the changing climate are urgently needed to feed the growing population. Hence, developing high-yielding crop varieties with better agronomic traits is one of the most critical issues in agricultural research. These are vital to enhancing yield as well as resistance to harsh conditions, both of which help farmers over time. The majority of agronomic traits are quantitative and are subject to intricate genetic control, thereby obstructing crop improvement. Plant epibreeding is the utilisation of epigenetic variation for crop development, and has a wide range of applications in the field of crop improvement. Epigenetics refers to changes in gene expression that are heritable and induced by methylation of DNA, post-translational modifications of histones or RNA interference rather than an alteration in the underlying sequence of DNA. The epigenetic modifications influence gene expression by changing the state of chromatin, which underpins plant growth and dictates phenotypic responsiveness for extrinsic and intrinsic inputs. Epigenetic modifications, in addition to DNA sequence variation, improve breeding by giving useful markers. Also, it takes epigenome diversity into account to predict plant performance and increase crop production. In this review, emphasis has been given for summarising the role of epigenetic changes in epibreeding for crop improvement.

Mapping of a Pale Green Mutant Gene and Its Functional Verification by Allelic Mutations in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Leaves are the main organ for photosynthesis, and variations in leaf color affect photosynthesis and plant biomass formation. We created two similar whole-plant pale green mutants (pem1 and pem2) from the double haploid (DH) Chinese cabbage line "FT" through ethyl methanesulfonate (EMS) mutagenesis of seeds. Photosynthetic pigment contents and net photosynthetic rates were significantly lower in the mutants than in the wild-type "FT," and the chloroplast thylakoid endomembrane system was poor. Genetic analysis showed that the mutated phenotypes of pem1 and pem2 were caused by a single nuclear gene. Allelism tests showed that pem1 and pem2 were alleles. We mapped Brpem1 to a 64.25 kb region on chromosome A10, using BSR-Seq and map-based cloning of 979 F₂ recessive individuals. Whole-genome re-sequencing revealed a single nucleotide polymorphism (SNP) transition from guanine to adenosine on BraA10g021490.3C in pem1, causing an amino acid shift from glycine to glutamic acid (G to E); in addition, BraA10g021490.3C in pem2 was found to have a single nucleotide substitution from guanine to adenosine, causing an amino acid change from E to lysine (K). BraA10g021490.3C is a homolog of the Arabidopsisdivinyl chlorophyllide a 8-vinyl-reductase (DVR) gene that encodes 3,8-divinyl protochlorophyllide a 8-vinyl reductase, which is a key enzyme in chlorophyll biosynthesis. Enzyme activity assay and chlorophyll composition analysis demonstrated that impaired DVR had partial loss of function. These results provide a basis to understand chlorophyll metabolism and explore the mechanism of a pale green phenotype in Chinese cabbage.

Comparative Transcriptome Analysis of Early- and Late-Bolting Traits in Chinese Cabbage (Brassica rapa)

Chinese cabbage is one of the most important and widely consumed vegetables in China. The developmental transition from the vegetative to reproductive phase is a crucial process in the life cycle of flowering plants. In spring-sown Chinese cabbage, late bolting is desirable over early bolting. In this study, we analyzed double haploid (DH) lines of late bolting (“Y410-1” and “SY2004”) heading Chinese cabbage (Brassica rapa var. pekinensis) and early-bolting Chinese cabbage (“CX14-1”) (B. rapa ssp. chinensis var. parachinensis) by comparative transcriptome profiling using the Illumina RNA-seq platform. We assembled 721.49 million clean high-quality paired-end reads into 47,363 transcripts and 47,363 genes, including 3,144 novel unigenes. There were 12,932, 4,732, and 4,732 differentially expressed genes (DEGs) in pairwise comparisons of Y410-1 vs. CX14-1, SY2004 vs. CX14-1, and Y410-1 vs. SY2004, respectively. The RNA-seq results were confirmed by reverse transcription quantitative real-time PCR (RT-qPCR). A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs revealed significant enrichment for plant hormone and signal transduction as well as starch and sucrose metabolism pathways. Among DEGs related to plant hormone and signal transduction, six unigenes encoding the indole-3-acetic acid-induced protein ARG7 (BraA02g009130), auxin-responsive protein SAUR41 (BraA09g058230), serine/threonine-protein kinase BSK11 (BraA07g032960), auxin-induced protein 15A (BraA10g019860), and abscisic acid receptor PYR1 (BraA08g012630 and BraA01g009450), were upregulated in both late bolting Chinese cabbage lines (Y410-1 and SY2004) and were identified as putative candidates for the trait. These results improve our understanding of the molecular mechanisms underlying flowering in Chinese cabbage and provide a foundation for studies of this key trait in related species.