Combined QTL mapping and RNA-Seq profiling reveals candidate genes associated with cadmium tolerance in barley

Smart reprogramming of plants against cadmium toxicity using membrane transporters and modern tools

Cadmium (Cd) in soil and water streams is now recognized as a significant environmental issue that harms plants and animals. Plants damaged by Cd toxicity experience various effects, from germination to yield reduction. Plant- and animal-based goods are allowing more Cd to enter our food chain, which could harm human health. Therefore, this urgent global concern must be addressed by implementing appropriate remedial measures. Plant-based phytoremediation is one safe, economical, and environmentally acceptable way to remove hazardous metals from the environment. Hyperaccumulator plants possess specialized transport proteins, such as metal transporters located in membranes of roots, as well as they facilitate Cd uptake from soil. This review outlines the latest findings about these membrane transporters. Moreover, we also discuss how innovative modern tools such as microbiomes, omics, nanotechnology, and genome editing have revealed molecular regulators connected to Cd tolerance, which may be employed to develop Cd-tolerant future plants. We can develop effective solutions to enhance tolerance of plant to Cd toxicity by leveraging membrane transporters and modern biotechnological tools. Additionally, implementing strategies to increase tolerance of Cd and restrict its bioavailability in plants' edible parts is crucial for improving food safety. These combined efforts will lead to the cultivation of safer food crops and support sustainable agricultural practices in contaminated environments.

Integrated endogenous hormones and transcriptome analysis contribute to fruit development related gene mining in Eriobotrya japonica

Loquat has both a delicious taste and natural medicinal effects. Fruit yield is the foundation of loquat production. However, as loquat fruits ripen, the time course changes in endogenous hormones and the transcriptome are still unclear, and the mining of loquat fruit development-related genes is still limited. Pulps from four stages of fruit development, including 70 days after full-blooming (DAF) (Z01), 90 DAF (Z02), 110 DAF (Z03), and 130 DAF (Z04), were collected to detect the contents of endogenous hormones and conduct transcriptome analysis. The results revealed that the pulps thickened continuously at a steady speed, whereas the rapid fruit expansion before the Z02 stage could be attributed to a sharp expansion of seeds. In addition, the endogenous hormone levels of the pulps tended to differ among these four stages. A total of 39,051 genes were obtained, and each sample was compared. Z01-VS-Z02, Z01-VS-Z03, and Z01-VS-Z04 presented 2611, 12,594, and 19,214 differentially expressed genes (DEGs), respectively. We found that there were 259, 49, 47, 70, 169, 47, 22 and 33 DEGs related to Aux, GA, CTK, ABA, Eth, BR, SA and JA, respectively. GO and KEGG enrichment analyses revealed that the most obviously enriched terms were photosynthesis-antenna proteins, starch and sucrose metabolism, and photosynthesis. Cluster analysis of the expression trends of the DEGs revealed that 25 clusters were obtained, 16 of which were highly correlated with 1 to 5 hormones. A total of 25 and 28 core genes were systematically identified from clusters 21 and 25, respectively. Heterologous expression revealed that EjHsc70, a selected core gene, promoted Arabidopsis growth and could be involved in the development process of loquat fruit. This study provides new insights into fruit development in Eriobotrya japonica.

Fine mapping and candidate gene analysis of the major QTL qSW-A03 for seed weight in Brassica napus

Seed weight is a determining factor for improving rapeseed productivity. In the present study, a high-density genetic map was constructed via genome resequencing in an RIL population derived from a cross of two rapeseed varieties, ZS11 and DL704, with great differences in thousand-seed weight (TSW). A total of 1,306 bins involving 1,261,526 markers were used to construct the bin map. On the basis of the genetic map, QTL mapping for seed weight was performed. In total, 15 QTLs associated with TSW were detected. A major and stable QTL, qSW-A03, was mapped to a 2.8 cM interval on chromosome A03. Fine mapping delimited the qSW-A03 locus into a 59-kb region, and 11 genes within this region were predicted. By employing a combination of gene variation, gene expression difference and gene coexpression network analysis of seed weight, BnaDUF1666 was identified as a promising candidate gene. This study provides useful information for the genetic dissection of seed weight and promotes the molecular breeding of high-yield rapeseed.

Different nontarget-site mechanisms underlie resistance to dicamba and 2,4-D in an Amaranthus tuberculatus population

BACKGROUND

Amaranthus tuberculatus (Moq.) Sauer (waterhemp) has emerged as one of several weed species that is resistant to synthetic auxin herbicides (SAHs). Among the mechanisms of resistance to SAHs, nontarget-site resistance (NTSR) has been of particular concern owing to its complexity. Here, we integrated linkage mapping with transcriptome analysis to explore NTSR mechanisms to two SAHs, dicamba and 2,4-D, in a multiple-herbicide-resistant A. tuberculatus population (CHR).

RESULTS

Phenotypic evaluations of an F2 mapping population indicated a polygenic basis for both dicamba and 2,4-D resistance in CHR. A weak correlation was observed between phenotypic responses to dicamba and 2,4-D treatments. Linkage mapping analyses revealed eight quantitative trait loci (QTL) regions associated with dicamba and 2,4-D resistance mapped to seven A. tuberculatus chromosomes. Together, these QTL regions explained 24.2 and 23.1% of the variation in dicamba- and 2,4-D-resistant phenotypes, respectively. Only one co-localized QTL region was found between the two resistance traits.

CONCLUSION

The results of this study demonstrated that resistance to dicamba and 2,4-D in the CHR population is under the control of genes at multiple loci. The weak phenotypic and genetic associations of resistance traits indicate that more than one NTSR mechanism confers resistance to dicamba and 2,4-D in this A. tuberculatus population. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Identification of Key Genes and Pathways for Anaerobic Germination Tolerance in Rice Using Weighted Gene Co-Expression Network Analysis (WGCNA) in Association with Quantitative Trait Locus (QTL) Mapping

BACKGROUND

Rice is one of the most important food crops in the world, and with the development of direct seeding methods for rice, exposure to anaerobic stress has become a major factor limiting its growth.

RESULTS

In this experiment, we tested the tolerance to anaerobic germination of rice varieties NIP and HD84, and they were used as parents to construct a DH (doubled-haploid) population. The transcriptomes of NIP (highly tolerant) and HD86 (intolerant), and their progeny HR (highly tolerant) and NHR (intolerant) were sequenced from normal and anaerobic environments. The differentially-expressed genes (DEGs) were subjected to GO (Gene ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), and WGCNA analyses. QTL mapping of the DH population identified tolerance to anaerobic germination-related chromosomal segments. The transcriptome results from 24 samples were combined with the anaerobic stress QTL results for 159 DH population lines to construct a metabolic network to identify key pathways and a gene interaction network to study the key genes. Essential genes were initially subjected to rigorous functional validation, followed by a comprehensive analysis aimed at elucidating their potential utility in domestication and breeding practices, particularly focusing on the exploitation of dominant haplotypes.

CONCLUSION

The results show that pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) are the starting signals of energy metabolism for coleoptile length growth, the auxin transporter EXPA is the determining signal for coleoptile length growth. The pivotal genes Os05g0498700 and Os01g0866100 exert a negative regulatory influence on coleoptile length, ultimately enhancing tolerance to anaerobic germination in rice. Analyses of breeding potential underscore the additional value of Os05g0498700-hyp2 and Os01g0866100-hyp2, highlighting their potential utility in further improving rice through breeding programs. The results of our study will provide a theoretical basis for breeding anaerobic-tolerant rice varieties.

Unveiling Innovative Approaches to Mitigate Metals/Metalloids Toxicity for Sustainable Agriculture

Due to anthropogenic activities, environmental pollution of heavy metals/metalloids (HMs) has increased and received growing attention in recent decades. Plants growing in HM-contaminated soils have slower growth and development, resulting in lower agricultural yield. Exposure to HMs leads to the generation of free radicals (oxidative stress), which alters plant morpho-physiological and biochemical pathways at the cellular and tissue levels. Plants have evolved complex defense mechanisms to avoid or tolerate the toxic effects of HMs, including HMs absorption and accumulation in cell organelles, immobilization by forming complexes with organic chelates, extraction via numerous transporters, ion channels, signaling cascades, and transcription elements, among others. Nonetheless, these internal defensive mechanisms are insufficient to overcome HMs toxicity. Therefore, unveiling HMs adaptation and tolerance mechanisms is necessary for sustainable agriculture. Recent breakthroughs in cutting-edge approaches such as phytohormone and gasotransmitters application, nanotechnology, omics, and genetic engineering tools have identified molecular regulators linked to HMs tolerance, which may be applied to generate HMs-tolerant future plants. This review summarizes numerous systems that plants have adapted to resist HMs toxicity, such as physiological, biochemical, and molecular responses. Diverse adaptation strategies have also been comprehensively presented to advance plant resilience to HMs toxicity that could enable sustainable agricultural production.

Research progress of the detection and analysis methods of heavy metals in plants

Heavy metal (HM)-induced stress can lead to the enrichment of HMs in plants thereby threatening people's lives and health via the food chain. For this reason, there is an urgent need for some reliable and practical techniques to detect and analyze the absorption, distribution, accumulation, chemical form, and transport of HMs in plants for reducing or regulating HM content. Not only does it help to explore the mechanism of plant HM response, but it also holds significant importance for cultivating plants with low levels of HMs. Even though this field has garnered significant attention recently, only minority researchers have systematically summarized the different methods of analysis. This paper outlines the detection and analysis techniques applied in recent years for determining HM concentration in plants, such as inductively coupled plasma mass spectrometry (ICP-MS), atomic absorption spectrometry (AAS), atomic fluorescence spectrometry (AFS), X-ray absorption spectroscopy (XAS), X-ray fluorescence spectrometry (XRF), laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), non-invasive micro-test technology (NMT) and omics and molecular biology approaches. They can detect the chemical forms, spatial distribution, uptake and transport of HMs in plants. For this paper, the principles behind these techniques are clarified, their advantages and disadvantages are highlighted, their applications are explored, and guidance for selecting the appropriate methods to study HMs in plants is provided for later research. It is also expected to promote the innovation and development of HM-detection technologies and offer ideas for future research concerning HM accumulation in plants.

Plant response to heavy metal stress toxicity: the role of metabolomics and other omics tools

Metabolomic investigations offers a significant foundation for improved comprehension of the adaptability of plants to reconfigure the key metabolic pathways and their response to changing climatic conditions. Their application to ecophysiology and ecotoxicology help to assess potential risks caused by the contaminants, their modes of action and the elucidation of metabolic pathways associated with stress responses. Heavy metal stress is one of the most significant environmental hazards affecting the physiological and biochemical processes in plants. Metabolomic tools have been widely utilised in the massive characterisation of the molecular structure of plants at various stages for understanding the diverse aspects of the cellular functioning underlying heavy metal stress-responsive mechanisms. This review emphasises on the recent progressions in metabolomics in plants subjected to heavy metal stresses. Also, it discusses the possibility of facilitating effective management strategies concerning metabolites for mitigating the negative impacts of heavy metal contaminants on the growth and productivity of plants.

Molecular-Assisted Breeding of Cadmium Pollution-Safe Cultivars

Cadmium (Cd) contamination in edible agricultural products, especially in crops intended for consumption, has raised worldwide concerns regarding food safety. Breeding of Cd pollution-safe cultivars (Cd-PSCs) is an effective solution to preventing the entry of Cd into the food chain from contaminated agricultural soil. Molecular-assisted breeding methods, based on molecular mechanisms for cultivar-dependent Cd accumulation and bioinformatic tools, have been developed to accelerate and facilitate the breeding of Cd-PSCs. This review summarizes the recent progress in the research of the low Cd accumulation traits of Cd-PSCs in different crops. Furthermore, the application of molecular-assisted breeding methods, including transgenic approaches, genome editing, marker-assisted selection, whole genome-wide association analysis, and transcriptome, has been highlighted to outline the breeding of Cd-PSCs by identifying critical genes and molecular biomarkers. This review provides a comprehensive overview of the development of Cd-PSCs and the potential future for breeding Cd-PSC using modern molecular technologies.

Growth, antioxidant system, and phytohormonal status of barley cultivars contrasting in cadmium tolerance

Cadmium leads to disturbance of plant growth, and the manifestation of toxicity can vary greatly in different genotypes within one species. In this work we studied the effect of Cd on growth, antioxidant enzyme activity, and phytohormonal status of four barley cultivars (cvs. Simfoniya, Mestnyj, Ca 220702, Malva). According to the earlier study on seedlings, these cultivars were contrast in tolerance to Cd: Simfoniya and Mestnyj are Cd-tolerant and Ca 220702 and Malva are Cd-sensitive. The results presented showed that barley plants accumulated more Cd in straw than in grain. Tolerant cultivars accumulated significantly less Cd in grain than sensitive ones. The leaf area appeared to be a growth parameter susceptible to Cd treatment. The significant differences in leaf area values depended on Cd contamination and were not associated with cultivars' tolerance. Tolerance of cultivars was contingent on the activity of the antioxidant defense system. Indeed, activity of enzymes decreased in sensitive cultivars Ca 220702 and Malva under Cd stress. In contrast, in tolerant cultivars, increased activity of guaiacol peroxidase was revealed. The concentrations of abscisic acid and salicylic acid mostly increased as a result of Cd treatment, while the concentrations of auxins and trans-zeatin either decreased or did not change. The results obtained indicate that antioxidant enzymes and phytohormones play an important role in the response of barley plants to elevated concentrations of cadmium; however, these parameters are not able to explain the differentiation of barley cultivars in terms of tolerance to cadmium at the seedling stage. Therefore, barley intraspecific polymorphism for cadmium resistance is determined by the interplay of antioxidant enzymes, phytohormones, and other factors that require further elucidation.

Low-level cadmium exposure induced hormesis in peppermint young plant by constantly activating antioxidant activity based on physiological and transcriptomic analyses

As one of the most toxic environmental pollutants, cadmium (Cd) has lastingly been considered to have negative influences on plant growth and productivity. Recently, increasing studies have shown that low level of Cd exposure could induce hormetic effect which benefits to plants. However, the underlying mechanisms of Cd-triggered hormesis are poorly understood. In this study, we found that Cd stress treatment showed a hormetic effect on peppermint and Cd treatment with 1.6 mg L-1 concertation manifested best stimulative effects. To explore the hormesis mechanisms of Cd treatment, comparative transcriptome analysis of peppermint young plants under low (1.6 mg L-1) and high (6.5 mg L-1) level of Cd exposure at 0 h, 24 h and 72 h were conducted. Twelve of differentially expressed genes (DEGs) were selected for qRT-PCR validation, and the expression results confirmed the credibility of transcriptome data. KEGG analysis of DEGs showed that the phenylpropanoid biosynthesis and photosynthesis were important under both low and high level of Cd treatments. Interestingly, GO and KEGG analysis of 99 DEGs specifically induced by low level of Cd treatment at 72 h indicated that these DEGs were mainly involved in the pathway of phenylpropanoid biosynthesis and their functions were associated with antioxidant activity. The expression pattern of those genes in the phenylpropanoid biosynthesis pathway and encoding antioxidant enzymes during 72 h of Cd exposure showed that low level of Cd treatment induced a continuation in the upward trend but high level of Cd treatment caused an inverted V-shape. The changes of physiological parameters during Cd exposure were highly consistent with gene expression pattern. These results strongly demonstrate that low level of Cd exposure constantly enhanced antioxidant activity of peppermint to avoid oxidative damages caused by Cd ion, while high level of Cd stress just induced a temporary increase in antioxidant activity which was insufficient to cope with lasting Cd toxicity. Overall, the results presented in this study shed a light on the underlying mechanisms of the Cd-mediated hormesis in plant. Moreover, our study provided a safe method for the efficient utilization of mild Cd-contaminated soil as peppermint is an important cash plant.

Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses

Abiotic stresses cause a significant decrease in productivity and growth in agricultural products, especially barley. Breeding has been considered to create resistance against abiotic stresses. Pyramiding genes for tolerance to abiotic stresses through selection based on molecular markers connected to Mega MQTLs of abiotic tolerance can be one of the ways to reach Golden Barley. In this study, 1162 original QTLs controlling 116 traits tolerant to abiotic stresses were gathered from previous research and mapped from various populations. A consensus genetic map was made, including AFLP, SSR, RFLP, RAPD, SAP, DArT, EST, CAPS, STS, RGA, IFLP, and SNP markers based on two genetic linkage maps and 26 individual linkage maps. Individual genetic maps were created by integrating individual QTL studies into the pre-consensus map. The consensus map covered a total length of 2124.43 cM with an average distance of 0.25 cM between markers. In this study, 585 QTLs and 191 effective genes related to tolerance to abiotic stresses were identified in MQTLs. The most overlapping QTLs related to tolerance to abiotic stresses were observed in MQTL6.3. Furthermore, three MegaMQTL were identified, which explained more than 30% of the phenotypic variation. MQTLs, candidate genes, and linked molecular markers identified are essential in barley breeding and breeding programs to develop produce cultivars resistant to abiotic stresses.

Identification of QTL and candidate genes associated with biomass yield and Feed Quality in response to water deficit in alfalfa (Medicago sativa L.) using linkage mapping and RNA-Seq

Biomass yield and Feed Quality are the most important traits in alfalfa (Medicago sativa L.), which directly affect its economic value. Drought stress is one of the main limiting factors affecting alfalfa production worldwide. However, the genetic and especially the molecular mechanisms for drought tolerance in alfalfa are poorly understood. In this study, linkage mapping was performed in an F1 population by combining 12 phenotypic data (biomass yield, plant height, and 10 Feed Quality-related traits). A total of 48 significant QTLs were identified on the high-density genetic linkage maps that were constructed in our previous study. Among them, nine main QTLs, which explained more than 10% phenotypic variance, were detected for biomass yield (one), plant height (one), CP (two), ASH (one), P (two), K(one), and Mg (one). A total of 31 candidate genes were identified in the nine main QTL intervals based on the RNA-seq analysis under the drought condition. Blast-P was further performed to screen candidate genes controlling drought tolerance, and 22 functional protein candidates were finally identified. The results of the present study will be useful for improving drought tolerance of alfalfa varieties by marker-assisted selection (MAS), and provide promising candidates for further gene cloning and mechanism study.

Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

BACKGROUND

Leaf size affects crop canopy morphology and photosynthetic efficiency, which can influence forage yield and quality. It is of great significance to mine the key genes controlling leaf development for breeding new alfalfa varieties. In this study, we mapped leaf length (LL), leaf width (LW), and leaf area (LA) in an F1 mapping population derived from a cultivar named ZhongmuNo.1 with larger leaf area and a landrace named Cangzhou with smaller leaf area.

RESULTS

This study showed that the larger LW was more conducive to increasing LA. A total of 24 significant quantitative trait loci (QTL) associated with leaf size were identified on both the paternal and maternal linkage maps. Among them, nine QTL explained about 11.50-22.45% phenotypic variation. RNA-seq analysis identified 2,443 leaf-specific genes and 3,770 differentially expressed genes. Combining QTL mapping, RNA-seq alalysis, and qRT-PCR, we identified seven candidate genes associated with leaf development in five major QTL regions.

CONCLUSION

Our study will provide a theoretical basis for marker-assisted breeding and lay a foundation for further revealing molecular mechanism of leaf development in alfalfa.

State-of-the-art OMICS strategies against toxic effects of heavy metals in plants: A review

Environmental pollution of heavy metals (HMs), mainly due to anthropogenic activities, has received growing attention in recent decades. HMs, especially the non-essential carcinogenic ones, including chromium (Cr), cadmium (Cd), mercury (Hg), aluminum (Al), lead (Pb), and arsenic (As), have appeared as the most significant air, water, and soil pollutants, which adversely affect the quantity, quality, and security of plant-based food all over the world. Plants exposed to HMs could experience significant decline in growth and yield. To avoid or tolerate the toxic effects of HMs, plants have developed complicated defense mechanisms, including absorption and accumulation of HMs in cell organelles, immobilization by forming complexes with organic chelates, extraction by using numerous transporters, ion channels, signalling cascades, and transcription elements, among others. OMICS strategies have developed significantly to understand the mechanisms of plant transcriptomics, genomics, proteomics, metabolomics, and ionomics to counter HM-mediated stress stimuli. These strategies have been considered to be reliable and feasible for investigating the roles of genomics (genomes), transcriptomic (coding), mRNA transcripts (non-coding), metabolomics (metabolites), and ionomics (metal ions) to enhance stress resistance or tolerance in plants. The recent developments in the mechanistic understandings of the HMs-plant interaction in terms of their absorption, translocation, and toxicity invasions at the molecular and cellular levels, as well as plants' response and adaptation strategies against these stressors, are summarized in the present review. Transcriptomics, genomics, metabolomics, proteomics, and ionomics for plants against HMs toxicities are reviewed, while challenges and future recommendations are also discussed.

Identification of Novel Genes Associated with Partial Resistance to Aphanomyces Root Rot in Field Pea by BSR-Seq Analysis

Aphanomyces root rot, caused by Aphanomyces euteiches, causes severe yield loss in field pea (Pisum sativum). The identification of a pea germplasm resistant to this disease is an important breeding objective. Polygenetic resistance has been reported in the field pea cultivar '00-2067'. To facilitate marker-assisted selection (MAS), bulked segregant RNA-seq (BSR-seq) analysis was conducted using an F8 RIL population derived from the cross of 'Carman' × '00-2067'. Root rot development was assessed under controlled conditions in replicated experiments. Resistant (R) and susceptible (S) bulks were constructed based on the root rot severity in a greenhouse study. The BSR-seq analysis of the R bulks generated 44,595,510~51,658,688 reads, of which the aligned sequences were linked to 44,757 genes in a reference genome. In total, 2356 differentially expressed genes were identified, of which 44 were used for gene annotation, including defense-related pathways (jasmonate, ethylene and salicylate) and the GO biological process. A total of 344.1 K SNPs were identified between the R and S bulks, of which 395 variants were located in 31 candidate genes. The identification of novel genes associated with partial resistance to Aphanomyces root rot in field pea by BSR-seq may facilitate efforts to improve management of this important disease.

Seed Priming with ZnO and Fe3O4 Nanoparticles Alleviate the Lead Toxicity in Basella alba L. through Reduced Lead Uptake and Regulation of ROS

The increased lead (Pb) content in the environment has an impact on all living beings, including plant growth and quality. The present study aims to investigate the protective roles of zinc (Zn)- and iron (Fe)- nanoparticles (NPs) in alleviating stress symptoms caused by lead (Pb) exposure in Basella alba seedlings. For this purpose, 15 different treatment combinations of seed priming with two NPs at 0 and 200 mg L−1, and five Pb levels (0, 4, 8, 15, 20 mM) were chosen. Pb stress (20 mM) was found to reduce seed germination by 72.8% and seedling growth, particularly root length, by 92% when compared to the control. Under different Pb concentrations, seed priming with ZnNPs (200 mg L−1) and FeNPs (200 mg L−1) increased seed germination by 34.7% and 54.9%, respectively, and root length by 152.9% and 252.9%, respectively. In 20 mM Pb stress, NPs primed seedling showed decrease in Pb content by 33.7% with ZnNPs and 32.6% with FeNPs. Increased Pb stress resulted in increased reactive oxygen species (ROS) generation (H2O2) and lipid peroxidation (MDA) compared to non-Pb stressed seedlings. However, increased antioxidants in the NPs treatments such as SOD, CAT, POD and proline content, scavenged these ROS. Considering all the parameters under study, priming alleviated Pb stress in the following order: FeNPs > ZnNPs > hydropriming > control. To summarise, seed priming with Zn- and Fe-NPs has the potential to alleviate Pb toxicity via reduced Pb uptake, ROS generation and lipid peroxidation as well as increased proline content and activation of antioxidant enzymatic system.

Identification of Heat-Tolerant Genes in Non-Reference Sequences in Rice by Integrating Pan-Genome, Transcriptomics, and QTLs

The availability of large-scale genomic data resources makes it very convenient to mine and analyze genes that are related to important agricultural traits in rice. Pan-genomes have been constructed to provide insight into the genome diversity and functionality of different plants, which can be used in genome-assisted crop improvement. Thus, a pan-genome comprising all genetic elements is crucial for comprehensive variation study among the heat-resistant and -susceptible rice varieties. In this study, a rice pan-genome was firstly constructed by using 45 heat-tolerant and 15 heat-sensitive rice varieties. A total of 38,998 pan-genome genes were identified, including 37,859 genes in the reference and 1141 in the non-reference contigs. Genomic variation analysis demonstrated that a total of 76,435 SNPs were detected and identified as the heat-tolerance-related SNPs, which were specifically present in the highly heat-resistant rice cultivars and located in the genic regions or within 2 kbp upstream and downstream of the genes. Meanwhile, 3214 upregulated and 2212 downregulated genes with heat stress tolerance-related SNPs were detected in one or multiple RNA-seq datasets of rice under heat stress, among which 24 were located in the non-reference contigs of the rice pan-genome. We then mapped the DEGs with heat stress tolerance-related SNPs to the heat stress-resistant QTL regions. A total of 1677 DEGs, including 990 upregulated and 687 downregulated genes, were mapped to the 46 heat stress-resistant QTL regions, in which 2 upregulated genes with heat stress tolerance-related SNPs were identified in the non-reference sequences. This pan-genome resource is an important step towards the effective and efficient genetic improvement of heat stress resistance in rice to help meet the rapidly growing needs for improved rice productivity under different environmental stresses. These findings provide further insight into the functional validation of a number of non-reference genes and, especially, the two genes identified in the heat stress-resistant QTLs in rice.

Comparative Plasticity Responses of Stable Isotopes of Carbon (δ13C) and Nitrogen (δ15N), Ion Homeostasis and Yield Attributes in Barley Exposed to Saline Environment

Salinity is a major threat to agricultural productivity worldwide. The selection and evaluation of crop varieties that can tolerate salt stress are the main components for the rehabilitation of salt-degraded marginal soils. A field experiment was conducted to evaluate salinity tolerance potential, growth performance, carbon (δ13C) and nitrogen isotope composition (δ15N), intrinsic water use efficiency (iWUE), harvest index, and yield stability attributes in six barley genotypes (113/1B, 59/3A, N1-10, N1-29, Barjouj, Alanda01) at three salinity levels (0, 7, and 14 dS m-1). The number of spikes m-2 was highest in Alanda01 (620.8) while the lowest (556.2) was exhibited by Barjouj. Alanda01 produced the highest grain yield (3.96 t ha-1), while the lowest yield was obtained in 59/3A (2.31 t ha-1). Genotypes 113/1B, Barjouj, and Alanda01 demonstrate the highest negative δ13C values (-27.10‱, -26.49‱, -26.45‱), while the lowest values were obtained in N1-29 (-21.63‱) under salt stress. The δ15N was increased (4.93‱ and 4.59‱) after 7 and 14 dS m-1 as compared to control (3.12‱). The iWUE was higher in N1-29 (144.5) and N1-10 (131.8), while lowest in Barjouj (81.4). Grain protein contents were higher in 113/1B and Barjouj than other genotypes. We concluded that salt tolerant barley genotypes can be cultivated in saline marginal soils for food and nutrition security and can help in the rehabilitation of marginal lands.

RAD-Seq-Based High-Density Linkage Maps Construction and Quantitative Trait Loci Mapping of Flowering Time Trait in Alfalfa (Medicago sativa L.)

Alfalfa (Medicago sativa L.) is a perennial forage crop known as the "Queen of Forages." To dissect the genetic mechanism of flowering time (FT) in alfalfa, high-density linkage maps were constructed for both parents of an F1 mapping population derived from a cross between Cangzhou (P1) and ZhongmuNO.1 (P2), consisting of 150 progenies. The FT showed a transgressive segregation pattern in the mapping population. A total of 13,773 single-nucleotide polymorphism markers was obtained by using restriction-site associated DNA sequencing and distributed on 64 linkage groups, with a total length of 3,780.49 and 4,113.45 cM and an average marker interval of 0.58 and 0.59 cM for P1 and P2 parent, respectively. Quantitative trait loci (QTL) analyses were performed using the least square means of each year as well as the best linear unbiased prediction values across 4 years. Sixteen QTLs for FT were detected for P1 and 22 QTLs for P2, accounting for 1.40-16.04% of FT variation. RNA-Seq analysis at three flowering stages identified 5,039, 7,058, and 7,996 genes that were differentially expressed between two parents, respectively. Based on QTL mapping, DEGs analysis, and functional annotation, seven candidate genes associated with flowering time were finally detected. This study discovered QTLs and candidate genes for alfalfa FT, making it a useful resource for breeding studies on this essential crop.

Overview of Identified Genomic Regions Associated with Various Agronomic and Physiological Traits in Barley under Abiotic Stresses

Climate change has caused breeders to focus on varieties that are able to grow under unfavorable conditions, such as drought, high and low temperatures, salinity, and other stressors. In recent decades, progress in biotechnology and its related tools has provided opportunities to dissect and decipher the genetic basis of tolerance to various stress conditions. One such approach is the identification of genomic regions that are linked with specific or multiple characteristics. Cereal crops have a key role in supplying the energy required for human and animal populations. However, crop products are dramatically affected by various environmental stresses. Barley (Hordeum vulgare L.) is one of the oldest domesticated crops that is cultivated globally. Research has shown that, compared with other cereals, barley is well adapted to various harsh environmental conditions. There is ample literature regarding these responses to abiotic stressors, as well as the genomic regions associated with the various morpho-physiological and biochemical traits of stress tolerance. This review focuses on (i) identifying the tolerance mechanisms that are important for stable growth and development, and (ii) the applicability of QTL mapping and association analysis in identifying genomic regions linked with stress-tolerance traits, in order to help breeders in marker-assisted selection (MAS) to quickly screen tolerant germplasms in their breeding cycles. Overall, the information presented here will inform and assist future barley breeding programs.

The influence of barley genotype and growing conditions on zinc and cadmium accumulation

Zinc and cadmium accumulation of in plant tissues of barley of the line 999-93 and of its regenerant forms resulting from cell selection was assessed. The scheme of the experiment: 1) control; 2) acidic; 3) cadmium. We used the method of inversion voltammetry to assess the share of zinc and cadmium in plant samples. To assess the share of active and total forms of zinc and cadmium in soil samples collected from root rhizosphere we used the method of atomic absorption spectroscopy. Barley plants accumulated zinc from 0.2 to 79.7 mg∙kg-1 of dry phytomass. The genotype of plants has little influence on zinc accumulation, and plant organs participate in equal measure in zinc accumulation. As for the soil background with cadmium excess, there is a tendency to lessening zinc absorption in all the plant organs, and it is not connected with the plant’s genotype. Unlike zinc, cadmium gets accumulated mostly in the root system. In the control background the share of cadmium in roots was 0.2–0.4 mg∙kg-1; in the acidic one – 0.2–3.6 mg∙kg-1; in the cadmium one – 5.5–9.5 mg∙kg-1. In barley grain grown on soil with excess of cadmium we did not find any IPC excess of cadmium. On backgrounds of the same acidity, the more cadmium concentration grew, the less zinc concentration in grain was, mostly it concerns the original genotype, to a smaller degree it concerns the regenerant line on the selective medium with cadmium and aluminum. Coupling accumulation of zinc and cadmium took place mostly on acidic background, it was characteristic of barley with the original genotype and the regenerant selected in vitro as cadmium-resistant; on control background coupling accumulation is characteristic of aluminum-resistant regenerant. These regenerant genotypes had a tendency to eliminating cadmium and absorbing zinc.

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.

Transcriptome Response to Cadmium Exposure in Barley (Hordeum vulgare L.)

Cadmium is an environmental pollutant with high toxicity that negatively affects plant growth and development. To understand the molecular mechanisms of plant response to cadmium stress, we have performed a genome-wide transcriptome analysis on barley plants treated with an increased concentration of cadmium. Differential gene expression analysis revealed 10,282 deregulated transcripts present in the roots and 7,104 in the shoots. Among them, we identified genes related to reactive oxygen species metabolism, cell wall formation and maintenance, ion membrane transport and stress response. One of the most upregulated genes was PLANT CADMIUM RESISTACE 2 (HvPCR2) known to be responsible for heavy metal detoxification in plants. Surprisingly, in the transcriptomic data we identified four different copies of the HvPCR2 gene with a specific pattern of upregulation in individual tissues. Heterologous expression of all five barley copies in a Cd-sensitive yeast mutant restored cadmium resistance. In addition, four HvPCR2 were located in tandem arrangement in a single genomic region of the barley 5H chromosome. To our knowledge, this is the first example showing multiplication of the PCR2 gene in plants.