The seed constitutes the main vector of plant propagation and it is a critical development stage with many specificities. Seed longevity is a major challenge for the conservation of plant biodiversity and for crop success. Seeds possess a wide range of systems (protection, detoxification, repair) allowing them to survive in the dry state and to preserve a high germination ability. Therefore, the seed system provides an appropriate model to study longevity and aging.

Iconography : Seed longevity: Survival and maintenance of high germination ability of dry seeds

Advancements in Genome editing technologies have revolutionized the fields of functional genomics and crop improvement. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat)-Cas9 is a multipurpose technology for genetic engineering that relies on the complementarity of the guideRNA (gRNA) to a specific sequence and the Cas9 endonuclease activity. It has broadened the agricultural research area, bringing in new opportunities to develop novel plant varieties with deletion of detrimental traits or addition of significant characters. This RNA guided genome editing technology is turning out to be a groundbreaking innovation in distinct branches of plant biology. CRISPR technology is constantly advancing including options for various genetic manipulations like generating knockouts; making precise modifications, multiplex genome engineering, and activation and repression of target genes. The review highlights the progression throughout the CRISPR legacy. We have studied the rapid evolution of CRISPR/Cas9 tools with myriad functionalities, capabilities, and specialized applications. Among varied diligences, plant nutritional improvement, enhancement of plant disease resistance and production of drought tolerant plants are reviewed. The review also includes some information on traditional delivery methods of Cas9-gRNA complexes into plant cells and incorporates the advent of CRISPR ribonucleoproteins (RNPs) that came up as a solution to various limitations that prevailed with plasmid-based CRISPR system.

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Gene Editing and Crop Improvement Using CRISPR-Cas9 System.

Plant-lead interactions: Transport, toxicity, tolerance, and detoxification mechanisms.

Cadmium (Cd) is one of the most toxic metals in the environment, and has noxious effects on plant growth and production. Cd-accumulating plants showed reduced growth and productivity. Therefore, remediation of this non-essential and toxic pollutant is a prerequisite. Plant-based phytoremediation methodology is considered as one a secure, environmentally friendly, and cost-effective approach for toxic metal remediation. Phytoremediating plants transport and accumulate Cd inside their roots, shoots, leaves, and vacuoles. Phytoremediation of Cd-contaminated sites through hyperaccumulator plants proves a ground-breaking and profitable choice to combat the contaminants. Moreover, the efficiency of Cd phytoremediation and Cd bioavailability can be improved by using plant growth-promoting bacteria (PGPB). Emerging modern molecular technologies have augmented our insight into the metabolic processes involved in Cd tolerance in regular cultivated crops and hyperaccumulator plants. Plants’ development via genetic engineering tools, like enhanced metal uptake, metal transport, Cd accumulation, and the overall Cd tolerance, unlocks new directions for phytoremediation. In this review, we outline the physiological, biochemical, and molecular mechanisms involved in Cd phytoremediation. Further, a focus on the potential of omics and genetic engineering strategies has been documented for the efficient remediation of a Cd-contaminated environment.

Phytoremediation of Cadmium: Physiological, Biochemical, and Molecular Mechanisms

Clubroot disease is one of the major diseases affecting Brassicaceae crops, and a number of these crops grown commercially, such as Chinese cabbage (Brassica rapa L. ssp. pekinensis), are known to be highly susceptible to clubroot disease. To provide protection from this disease, plant breeders have introduced genes for resistance to clubroot from the European turnip into susceptible lines. The CRa gene confers specific resistance to the clubroot pathogen Plasmodiophora brassicae isolate M85. Fine mapping of the CRa locus using synteny to the Arabidopsis thaliana genome and partial genome sequences of B. rapa revealed a candidate gene encoding a TIR-NBS-LRR protein. Several structural differences in this candidate gene were found between susceptible and resistant lines, and CRa expression was observed only in the resistant line. Four mutant lines lacking clubroot resistance were obtained by the UV irradiation of pollen from a resistant line, and all of these mutant lines carried independent mutations in the candidate TIR-NBS-LRR gene. This genetic and molecular evidence strongly suggests that the identified gene is CRa. This is the first report on the molecular characterization of a clubroot Resistance gene in Brassicaceae and of the disease resistance gene in B. rapa.

Molecular Characterization of the CRa Gene Conferring Clubroot Resistance in Brassica rapa

Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. However, the yield and quality of rapeseed were largely decreased by clubroot (Plasmodiophora brassicae Woronin). Therefore, it is of great importance for screening more resistant germplasms or genes and improving the resistance to P. brassicae in rapeseed breeding. In this study, a massive resistant identification for a natural global population was conducted in two environments with race/pathotype 4 of P. brassicae which was the most predominant in China, and a wide range of phenotypic variation was found in the population. In addition, a genome-wide association study of 472 accessions for clubroot resistance (CR) was performed with 60K Brassica Infinium SNP arrays for the first time. In total, nine QTLs were detected, seven of which were novel through integrative analysis. Furthermore, additive effects in genetic control of CR in rapeseed among the above loci were found. By bioinformatic analyses, the candidate genes of these loci were predicted, which indicated that TIR-NBS gene family might play an important role in CR. It is believable that the results presented in our study could provide valuable information for understanding the genetic mechanism and molecular regulation of CR.

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A Genome-Wide Association Study Reveals New Loci for Resistance to Clubroot Disease in Brassica napus.

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.

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Genome-Wide Association Mapping Reveals the Genetic Control Underlying Branch Angle in Rapeseed (Brassica napus L.)

The non-random three-dimensional (3D) organization of the genome in the nucleus is critical to gene regulation and genome function. Using high-throughput chromatin conformation capture, we generated chromatin interaction maps for Brassica rapa and Brassica oleracea at a high resolution and characterized the conservation and divergence of chromatin organization in these two species. Large-scale chromatin structures, including A/B compartments and topologically associating domains, are notably conserved between B. rapa and B. oleracea, yet their KNOT structures are highly divergent. We found that genes retained in less fractionated subgenomes exhibited stronger interaction strengths, and diploidization-resistant duplicates retained in pairs or triplets are more likely to be colocalized in both B. rapa and B. oleracea. These observations suggest that spatial constraint in duplicated genes is correlated to their biased retention in the diploidization process. In addition, we found strong similarities in the epigenetic modification and Gene Ontology terms of colocalized paralogues, which were largely conserved across B. rapa and B. oleracea, indicating functional constraints on their 3D positioning in the nucleus. This study presents an investigation of the spatial organization of genomes in Brassica and provides insights on the role of 3D organization in the genome evolution of this genus.

Fugui Zhang

Papers

A Genome-Wide Association Study Reveals New Loci for Resistance to Clubroot Disease in Brassica napus.

Genome-Wide Association Mapping Reveals the Genetic Control Underlying Branch Angle in Rapeseed (Brassica napus L.)

Biased gene retention during diploidization in Brassica linked to three-dimensional genome organization.

Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding

Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding