Genetic dissection of the shoot and root ionomes of Brassica napus grown with contrasting phosphate supplies

Quantitative Proteomic Analysis of Brassica Napus Reveals Intersections Between Nutrient Deficiency Responses

Macronutrients such as nitrogen (N), phosphorus (P), potassium (K) and sulphur (S) are critical for plant growth and development. Field-grown canola (Brassica napus L.) is supplemented with fertilizers to maximize plant productivity, while deficiency in these nutrients can cause significant yield loss. A holistic understanding of the interplay between these nutrient deficiency responses in a single study and canola cultivar is thus far lacking, hindering efforts to increase the nutrient use efficiency of this important oil seed crop. To address this, we performed a comparative quantitative proteomic analysis of both shoot and root tissue harvested from soil-grown canola plants experiencing either nitrogen, phosphorus, potassium or sulphur deficiency. Our data provide critically needed insights into the shared and distinct molecular responses to macronutrient deficiencies in canola. Importantly, we find more conserved responses to the four different nutrient deficiencies in canola roots, with more distinct proteome changes in aboveground tissue. Our results establish a foundation for a more comprehensive understanding of the shared and distinct nutrient deficiency response mechanisms of canola plants and pave the way for future breeding efforts.

Genetic analysis of the variation for mineral accumulation in the leaves and seeds of natural germplasm of Brassica rapa L. (AA) and the its derived forms extracted from an allotetraploid B.juncea L.(AABB)

Brassica rapa L. (2n = 20; AA) is a vegetable and oilseed crop that is grown all over the world. Its leaves, shoots, and seeds store significant amounts of minerals. We used inductively coupled plasma-optical emission spectroscopy (ICP-OES) to determine the concentrations of eleven minerals in the leaves and seeds of 195 advanced generation inbred lines, of which 92 represented natural (NR) B. rapa and the remaining 103 were derived (DR) from a set of mother genotypes originally extracted from an allotetraploid B. juncea (2n = 36; AABB). The inbred lines differed for the composition of leaf and seed minerals. Leaf concentrations of N, K, Zn, and Se were higher in the DR subpanel as compared to NR subpanel, along with high seed accumulations of K and Se. DArT genotyping and genome wide association mapping led to the identification of SNPs associated with leaf and seed mineral compositions. Chromosomes A03, A05, and A10 harboured the most associated loci. Annotations of the regions adjacent to respective GWAS peaks allowed prediction of genes known for acquisition, transport, and accumulation of minerals and heavy metal detoxification. Transcriptome analysis revealed differential expression patterns of the predicted candidates, with most genes either down-regulated in derived genotypes relative to natural forms or their expression being comparable between the two. General downregulation may be a consequence of extracting B. rapa from allotetraploid B. juncea through genome resection. Some of the identified SNPs may be used as DNA markers for breeding programmes designed to modify the leaf and seed mineral compositions.

Silicon modifies leaf nutriome and improves growth of oak seedlings exposed to phosphorus deficiency and Phytophthora plurivora infection

Beneficial effects of silicon (Si) on plants have primarily been studied in crop species under single stress. Moreover, nutrient acquisition-based responses to combination of biotic and abiotic stresses (a common situation in natural habitats) have rarely been reported, in particular in conjunction with soil amendments with Si. Pedunculate oak (Quercus robur L.), one of the ecologically and economically most important tree species in Europe, is facing a severe decline due to combined stresses, but also problems in assisted regeneration in nurseries. Here, we studied the effect of Si supply on the leaf nutriome, root traits and overall growth of 12-weeks-old oak seedlings exposed to abiotic stress [low phosphorus (P) supply], biotic stress (Phytophthora plurivora root infection), and their combination. The application of Si had the strongest ameliorative effect on growth, root health and root phenome under the most severe stress conditions (i.e., combination of P deficiency and P. plurivora root infection), where it differentially affected the uptake and leaf accumulation in 11 out of 13 analysed nutrients. Silicon supply tended to reverse the pattern of change of some, but not all, leaf nutrients affected by stresses: P, boron (B) and magnesium (Mg) under P deficiency, and P, B and sulphur (S) under pathogen attack, but also nickel (Ni) and molybdenum (Mo) under all three stresses. Surprisingly, Si affected some nutrients that were not changed by a particular stress itself and decreased leaf Mg levels under all the stresses. On the other hand, pathogen attack increased leaf accumulation of Si. This exploratory work presents the complexity of nutrient crosstalk under three stresses, and opens more questions about genetic networks that control plant physiological responses. Practically, we show a potential of Si application to improve P status and root health in oak seedlings, particularly in nurseries.

Genetic dissection of seed yield and yield-related traits in Brassica napus grown with contrasting nitrogen supplies

Oilseed rape (B. napus) is the main oil crop in China as well as in the world. Nitrogen (N) deficiency significantly reduces the seed yield of B. napus. However, a very few studies involved in the genetic mechanism of seed yield and SY-related traits of B. napus in response to N deficiency. In this study, plant height (PH), branch number per plant (BN), pod number per plant (PN), seed number per pod (SN), 1000-seed weight (SW), and seed yield per plant (SY) were investigated using a B. napus double haploid (BnaTNDH) population derived from a cross between cultivars "Tapidor" and "Ningyou7" grown at an optimal N (ON) and a low N (LN) supplies in three-year field trials. Great variations of SY and related traits were observed in BnaTNDH population under contrasting N supplies. A total of 106 and 110 significant quantitative trait loci (QTLs) were detected for six traits at ON and LN in three field trials, respectively. All of these significant QTLs for the same trait identified in two or three trials were integrated into 20 stable QTLs. A total of 50 consensus QTLs and 53 unique QTLs were obtained from 172 significant QTLs and 20 stable QTLs, including 35 ON-specific QTLs, 29 LN-specific QTLs and 39 constitutive QTLs detected at both ON and LN. cqA3l was integrated from four QTLs for PN, PH, SN, SY at LN, cqC9c was integrated from QTLs for BN, SY, PN at ON and LN. Both cqA3l and cqC9c were detected in three trials. In addition, a total of 194 epistatic interactions, inculding 15 pleiotropic epistatic interactions, were identified. Eight of the 15 pleiotropic epistatic interactions were detected to affect SY. This result may help to better understand the genetic mechanism of yield traits in response to low N and promote the breeding of N-efficient varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01281-0.

Advances in "Omics" Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants' demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.

Genome-wide association mapping identifies HvNIP2;2/HvLsi6 accounting for efficient boron transport in barley

Boron (B) is an essential mineral element for plant growth, and the seed B pool of crops can be crucial when seedlings need to establish on low-B soils. To date, it is poorly understood how B accumulation in grain crops is genetically controlled. Here, we assessed the genotypic variation of the B concentration in grains of a spring barley (Hordeum vulgare L.) association panel that represents broad genetic diversity. We found a large genetic variation of the grain B concentration and detected in total 23 quantitative trait loci (QTLs) using genome-wide association mapping. HvNIP2;2/HvLsi6, encoding a potential B-transporting membrane protein, mapped closely to a major-effect QTL accounting for the largest proportion of grain B variation. Based on transport studies using heterologous expression systems and gene expression analysis, we demonstrate that HvNIP2;2/HvLsi6 represents a functional B channel and that expression variation in its transcript level associates with root and shoot B concentrations as well as with root dry mass formation under B-deficient conditions.

Identification of QTLs associated with potassium use efficiency and underlying candidate genes by whole-genome resequencing of two parental lines in Brassica napus

Breeding crops that acquire and/or utilize potassium (K) more effectively could reduce the use of K fertilizers. Sixteen traits affecting K use efficiency (KUE) at the seedling stage were investigated in a B. napus double haploid population grown at an optimal K supply (OK) and a low K supply (LK) in a hydroponic culture system. In total, 50 and 62 QTLs associated with these traits were identified at OK and LK, respectively. A total of 25 orthologues of 23 Arabidopsis genes regulating K transport were identified in the confidence intervals of nine QTLs impacting shoot dry weight at LK, and 22 of these showed variations in coding sequences and/or exhibited significant differences in mRNA abundances in roots at LK between the two parental lines. This study provided insights to the genetic basis of KUE in B. napus, which will accelerate the breeding of K-efficient rapeseed cultivars by marker-assisted selection.