CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals

Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggests a negative selection during domestication and breeding

KEY MESSAGE

Sustainable winter production in lettuce requires freezing tolerant varieties. This study identified a wild-type allele of LsCBF7 that could contribute to freezing tolerance improvement in lettuce. Lettuce is one of the most consumed vegetables globally. While ideally grown in 13-21 °C, its cultivation extends into winter in milder climates. However, occasional freezing temperatures can significantly reduce yields. Therefore, the development of freezing-tolerant lettuce varieties has become a long-term goal of lettuce breeding programs. Despite its significance, our understanding of freezing tolerance in lettuce remains limited. Plants have evolved a coping mechanism against freezing, known as cold acclimation, whereby they can increase freezing tolerance when pre-exposed to low nonfreezing temperatures. The CBF pathway is well-known for its central role in cold acclimation. Previously, we identified 14 CBF genes in lettuce and discovered that one of them, LsCBF7, had a loss-of-function mutation. In this study, we uncovered that accessions from colder regions carried the wild-type allele of LsCBF7 and this allele likely contributed to increased freezing tolerance, with 14% of the lettuce population carrying this allele. Interestingly, in wild lettuce (L. serriola) that is considered a progenitor of cultivated lettuce, this wild-type allele was much more common, with a frequency of 90%. This finding suggests that this wild-type allele may have undergone negative selection during the domestication or breeding of lettuce. Our data strongly indicate that this allele could be linked to early bolting, an undesirable trait in lettuce, which may have driven the negative selection. While this wild-type allele shows promise for improving freezing tolerance in lettuce, it is crucial to decouple it from the early bolting trait to fully harness its potential in lettuce breeding.

Integrating genomics and genome editing for orphan crop improvement: a bridge between orphan crops and modern agriculture system

Domestication of orphan crops could be explored by editing their genomes. Genome editing has a lot of promise for enhancing agricultural output, and there is a lot of interest in furthering breeding in orphan crops, which are sometimes plagued with unwanted traits that resemble wild cousins. Consequently, applying model crop knowledge to orphan crops allows for the rapid generation of targeted allelic diversity and innovative breeding germplasm. We explain how plant breeders could employ genome editing as a novel platform to accelerate the domestication of semi-domesticated or wild plants, resulting in a more diversified base for future food and fodder supplies. This review emphasizes both the practicality of the strategy and the need to invest in research that advances our understanding of plant genomes, genes, and cellular systems. Planting more of these abandoned orphan crops could help alleviate food scarcities in the challenge of future climate crises.

The Triticeae CBF Gene Cluster-To Frost Resistance and Beyond

The pivotal role of CBF/DREB1 transcriptional factors in Triticeae crops involved in the abiotic stress response has been highlighted. The CBFs represent an important hub in the ICE-CBF-COR pathway, which is one of the most relevant mechanisms capable of activating the adaptive response to cold and drought in wheat, barley, and rye. Understanding the intricate mechanisms and regulation of the cluster of CBF genes harbored by the homoeologous chromosome group 5 entails significant potential for the genetic improvement of small grain cereals. Triticeae crops seem to share common mechanisms characterized, however, by some peculiar aspects of the response to stress, highlighting a combined landscape of single-nucleotide variants and copy number variation involving CBF members of subgroup IV. Moreover, while chromosome 5 ploidy appears to confer species-specific levels of resistance, an important involvement of the ICE factor might explain the greater tolerance of rye. By unraveling the genetic basis of abiotic stress tolerance, researchers can develop resilient varieties better equipped to withstand extreme environmental conditions. Hence, advancing our knowledge of CBFs and their interactions represents a promising avenue for improving crop resilience and food security.

Importance of genetic architecture in marker selection decisions for genomic prediction

KEY MESSAGE

We demonstrate potential for improved multi-environment genomic prediction accuracy using structural variant markers. However, the degree of observed improvement is highly dependent on the genetic architecture of the trait. Breeders commonly use genetic markers to predict the performance of untested individuals as a way to improve the efficiency of breeding programs. These genomic prediction models have almost exclusively used single nucleotide polymorphisms (SNPs) as their source of genetic information, even though other types of markers exist, such as structural variants (SVs). Given that SVs are associated with environmental adaptation and not all of them are in linkage disequilibrium to SNPs, SVs have the potential to bring additional information to multi-environment prediction models that are not captured by SNPs alone. Here, we evaluated different marker types (SNPs and/or SVs) on prediction accuracy across a range of genetic architectures for simulated traits across multiple environments. Our results show that SVs can improve prediction accuracy, but it is highly dependent on the genetic architecture of the trait and the relative gain in accuracy is minimal. When SVs are the only causative variant type, 70% of the time SV predictors outperform SNP predictors. However, the improvement in accuracy in these instances is only 1.5% on average. Further simulations with predictors in varying degrees of LD with causative variants of different types (e.g., SNPs, SVs, SNPs and SVs) showed that prediction accuracy increased as linkage disequilibrium between causative variants and predictors increased regardless of the marker type. This study demonstrates that knowing the genetic architecture of a trait in deciding what markers to use in large-scale genomic prediction modeling in a breeding program is more important than what types of markers to use.

Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes

The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novel genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding to mitigate the impact of global climate change. Here, we summarize the tools used for pan-genome assembly and annotations, web-portals hosting plant pan-genomes, etc. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and future potential of this emerging field of study.

Molecular and genetic perspectives of cold tolerance in wheat

Environmental variation is the most crucial problem as it is causing food insecurity and negatively impacts food availability, utilization, assessment, and stability. Wheat is the largest and extensively cultivated staple food crop for fulfilling global food requirements. Abiotic stresses including salinity, heavy metal toxicity, drought, extreme temperatures, and oxidative stresses being the primary cause of productivity loss are a serious threat to agronomy. Cold stress is a foremost ecological constraint that is extremely influencing plant development, and yield. It is extremely hampering the propagative development of plant life. The structure and function of plant cells depend on the cell's immune system. The stresses due to cold, affect fluid in the plasma membrane and change it into crystals or a solid gel phase. Plants being sessile in nature have evolved progressive systems that permit them to acclimatize the cold stress at the physiological as well as molecular levels. The phenomenon of acclimatisation of plants to cold stress has been investigated for the last 10 years. Studying cold tolerance is critical for extending the adaptability zones of perennial grasses. In the present review, we have elaborated the current improvement of cold tolerance in plants from molecular and physiological viewpoints, such as hormones, the role of the posttranscriptional gene, micro RNAs, ICE-CBF-COR signaling route in cold acclimatization and how they are stimulating the expression of underlying genes encoding osmoregulatory elements and strategies to improve cold tolerance in wheat.

Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat

Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications.

Identification of structural variations related to drought tolerance in wheat (Triticum aestivum L.)

Structural variations are common in plant genomes, affecting meiotic recombination and distorted segregation in wheat. And presence/absence variations can significantly affect drought tolerance in wheat. Drought is a major abiotic stress limiting wheat production. Common wheat has a complex genome with three sub-genomes, which host large numbers of structural variations (SVs). SVs play critical roles in understanding the genetic contributions of plant domestication and phenotypic plasticity, but little is known about their genomic characteristics and their effects on drought tolerance. In the present study, high-resolution karyotypes of 180 doubled haploids (DHs) were developed. Signal polymorphisms between the parents involved with 8 presence-absence variations (PAVs) of tandem repeats (TR) distributed on the 7 (2A, 4A, 5A, 7A, 3B, 7B, and 2D) of 21 chromosomes. Among them, PAV on chromosome 2D showed distorted segregation, others transmit normal conforming to a 1:1 segregation ration in the population; and a PAVs recombination occurred on chromosome 2A. Association analysis of PAV and phenotypic traits under different water regimes, we found PAVs on chromosomes 4A, 5A, and 7B showed negative effect on grain length (GL) and grain width (GW); PAV.7A had opposite effect on grain thickness (GT) and spike length (SL), with the effect on traits differing under different water regimes. PAVs on linkage group 2A, 4A, 7A, 2D, and 7B associated with the drought tolerance coefficients (DTCs), and significant negative effect on drought resistance values (D values) were detected in PAV.7B. Additionally, quantitative trait loci (QTL) associated with phenotypic traits using the 90 K SNP array showed QTL for DTCs and grain-related traits in chromosomes 4A, and 5A, 3B were co-localized in differential regions of PAVs. These PAVs can cause the differentiation of the target region of SNP and could be used for genetic improvement of agronomic traits under drought stress via marker-assisted selection (MAS) breeding.

FER and LecRK show haplotype-dependent cold-responsiveness and mediate freezing tolerance in Lotus japonicus

Many plant species have succeeded in colonizing a wide range of diverse climates through local adaptation, but the underlying molecular genetics remain obscure. We previously found that winter survival was a direct target of selection during colonization of Japan by the perennial legume Lotus japonicus and identified associated candidate genes. Here, we show that two of these, FERONIA-receptor like kinase (LjFER) and a S-receptor-like kinase gene (LjLecRK), are required for non-acclimated freezing tolerance and show haplotype-dependent cold-responsive expression. Our work suggests that recruiting a conserved growth regulator gene, FER, and a receptor-like kinase gene, LecRK, into the set of cold-responsive genes has contributed to freezing tolerance and local climate adaptation in L. japonicus, offering functional genetic insight into perennial herb evolution.

Computational genomics insights into cold acclimation in wheat

Development of cold acclimation in crops involves transcriptomic reprograming, metabolic shift, and physiological changes. Cold responses in transcriptome and lipid metabolism has been examined in separate studies for various crops. In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in four wheat genotypes of distinct cold tolerance. Differential expression was investigated between cold treated and control samples and between the winter-habit and spring-habit wheat genotypes. Collectively, 12,676 differentially expressed genes (DEGs) were identified. Principal component analysis of these DEGs indicated that the first, second, and third principal components (PC1, PC2, and PC3) explained the variance in cold treatment, vernalization and cold hardiness, respectively. Differential expression feature extraction (DEFE) analysis revealed that the winter-habit wheat genotype Norstar had high number of unique DEGs (1884 up and 672 down) and 63 winter-habit genes, which were clearly distinctive from the 64 spring-habit genes based on PC1, PC2 and PC3. Correlation analysis revealed 64 cold hardy genes and 39 anti-hardy genes. Cold acclimation encompasses a wide spectrum of biological processes and the involved genes work cohesively as revealed through network propagation and collective association strength of local subnetworks. Integration of transcriptomics and lipidomics data revealed that the winter-habit genes, such as COR413-TM1, CIPKs and MYB20, together with the phosphatidylglycerol lipids, PG(34:3) and PG(36:6), played a pivotal role in cold acclimation and coordinated cohesively associated subnetworks to confer cold tolerance.

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.

Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution

Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least two species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene–Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.

Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley

Exome sequencing-based allele mining for frost tolerance suggests HvCBF14 rather than CNV at Fr-H2 locus is the main responsible of frost tolerance in barley. Wild relatives, landraces and old cultivars of barley represent a reservoir of untapped and potentially important genes for crop improvement, and the recent sequencing technologies provide the opportunity to mine the existing genetic diversity and to identify new genes/alleles for the traits of interest. In the present study, we use frost tolerance and vernalization requirement as case studies to demonstrate the power of allele mining carried out on exome sequencing data generated from > 400 barley accessions. New deletions in the first intron of VRN-H1 were identified and linked to a reduced vernalization requirement, while the allelic diversity of HvCBF2a, HvCBF4b and HvCBF14 was investigated by combining the analysis of SNPs and read counts. This approach has proven very effective to identify gene paralogs and copy number variants of HvCBF2 and the HvCBF4b-HvCBF2a segment. A multiple linear regression model which considers allelic variation at these genes suggests a major involvement of HvCBF14, rather than copy number variation of HvCBF4b-HvCBF2a, in controlling frost tolerance in barley. Overall, the present study provides powerful resource and tools to discover novel alleles at relevant genes in barley.

Cold Conditioned: Discovery of Novel Alleles for Low-Temperature Tolerance in the Vavilov Barley Collection

Climate changes leading to higher summer temperatures can adversely affect cool season crops like spring barley. In the Upper Midwest region of the United States, one option for escaping this stress factor is to plant winter or facultative type cultivars in the autumn and then harvest in early summer before the onset of high-temperature stress. However, the major challenge in breeding such cultivars is incorporating sufficient winter hardiness to survive the extremely low temperatures that commonly occur in this production region. To broaden the genetic base for winter hardiness in the University of Minnesota breeding program, 2,214 accessions from the N. I. Vavilov Institute of Plant Industry (VIR) were evaluated for winter survival (WS) in St. Paul, Minnesota. From this field trial, 267 (>12%) accessions survived [designated as the VIR-low-temperature tolerant (LTT) panel] and were subsequently evaluated for WS across six northern and central Great Plains states. The VIR-LTT panel was genotyped with the Illumina 9K SNP chip, and then a genome-wide association study was performed on seven WS datasets. Twelve significant associations for WS were identified, including the previously reported frost resistance gene FR-H2 as well as several novel ones. Multi-allelic haplotype analysis revealed the most favorable alleles for WS in the VIR-LTT panel as well as another recently studied panel (CAP-LTT). Seventy-eight accessions from the VIR-LTT panel exhibited a high and consistent level of WS and select ones are being used in winter barley breeding programs in the United States and in a multiparent population.

Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene

Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.

Defence by duplication: The relation between phenotypic glyphosate resistance and EPSPS gene copy number variation in Amaranthus palmeri

Gene copy number variation (CNV) has been increasingly associated with organismal responses to environmental stress, but we know little about the quantitative relation between CNV and phenotypic variation. In this study we quantify the relation between variation in EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) copy number using digital drop PCR and variation in phenotypic glyphosate resistance in 22 populations of Amaranthus palmeri (Palmer Amaranth), a range-expanding agricultural weed. Overall, we detected a significant positive relation between population mean copy number and resistance. The majority of populations exhibited high glyphosate resistance yet maintained low-resistance individuals, resulting in bimodality in many populations. We also investigated threshold models for the relation between copy number and resistance, and found evidence for a threshold of ~15 EPSPS copies: there was a steep increase in resistance below the threshold, followed by a much shallower increase. Across 924 individuals, as copy number increased the range of variation in resistance decreased, yielding an increasing frequency of high phenotypic resistance individuals. Among populations we detected a decline in variation (s.d.) as mean phenotypic resistance increased from moderate to high, consistent with the prediction that as phenotypic resistance increases in populations, stabilizing selection decreases variation in the trait. Our study demonstrates that populations of A. palmeri can harbour wide variation in EPSPS copy number and phenotypic glyphosate resistance, reflecting the history of, and template for future, resistance evolution.

Quantitative trait loci and candidate genes associated with freezing tolerance of winter triticale (× Triticosecale Wittmack)

Freezing tolerance of triticale is a major trait contributing to its winter hardiness. The identification of genomic regions — quantitative trait loci (QTL) and molecular markers associated with freezing tolerance in winter hexaploid triticale — was the aim of this study. For that purpose, a new genetic linkage map was developed for the population of 92 doubled haploid lines derived from ‘Hewo’ × ‘Magnat’ F₁ hybrid. Those lines, together with parents were subjected to freezing tolerance test three times during two winter seasons. Plants were grown and cold-hardened under natural fall/winter conditions and then subjected to freezing in controlled conditions. Freezing tolerance was assessed as the plants recovery (REC), the electrolyte leakage (EL) from leaves and chlorophyll fluorescence parameters (JIP) after freezing. Three consistent QTL for several fluorescence parameters, electrolyte leakage, and the percentage of the survived plants were identified with composite interval mapping (CIM) and single marker analysis (SMA). The first locus Qfr.hm-7A.1 explained 9% of variation of both electrolyte leakage and plants recovery after freezing. Two QTL explaining up to 12% of variation in plants recovery and shared by selected chlorophyll fluorescence parameters were found on 4R and 5R chromosomes. Finally, main locus Qchl.hm-5A.1 was detected for chlorophyll fluorescence parameters that explained up to 19.6% of phenotypic variation. The co-located QTL on chromosomes 7A.1, 4R and 5R, clearly indicated physiological and genetic relationship of the plant survival after freezing with the ability to maintain optimal photochemical activity of the photosystem II and preservation of the cell membranes integrity. The genes located in silico within the identified QTL include those encoding BTR1-like protein, transmembrane helix proteins like potassium channel, and phosphoric ester hydrolase involved in response to osmotic stress as well as proteins involved in the regulation of the gene expression, chloroplast RNA processing, and pyrimidine salvage pathway. Additionally, our results confirm that the JIP test is a valuable tool to evaluate freezing tolerance of triticale under unstable winter environments.

A 24,482-bp deletion is associated with increased seed weight in Brassica napus L

A major QTL for seed weight was fine-mapped in rapeseed, and a 24,482-bp deletion likely mediates the effect through multiple pathways. Exploration of the genes controlling seed weight is critical to the improvement of crop yield and elucidation of the mechanisms underlying seed formation in rapeseed (Brassica napus L.). We previously identified the quantitative trait locus (QTL) qSW.C9 for the thousand-seed weight (TSW) in a double haploid population constructed from F₁ hybrids between the parental accessions HZ396 and Y106. Here, we confirmed the phenotypic effects associated with qSW.C9 in BC₃F₂ populations and fine-mapped the candidate causal locus to a 266-kb interval. Sequence and expression analyses revealed that a 24,482-bp deletion in HZ396 containing six predicted genes most likely underlies qSW.C9. Differential gene expression analysis and cytological observations suggested that qSW.C9 affects both cell proliferation and cell expansion through multiple signaling pathways. After genotyping of a rapeseed diversity panel to define the haplotype structure, it could be concluded that the selection of germplasm with two specific markers may be effective in improving the seed weight of rapeseed. This study provides a solid foundation for the identification of the causal gene of qSW.C9 and offers a promising target for the breeding of higher-yielding rapeseed.

The Breeding of Winter-Hardy Malting Barley

In breeding winter malting barley, one recurring strategy is to cross a current preferred spring malting barley to a winter barley. This is because spring malting barleys have the greatest amalgamation of trait qualities desirable for malting and brewing. Spring barley breeding programs can also cycle their material through numerous generations each year-some managing even six-which greatly accelerates combining desirable alleles to generate new lines. In a winter barley breeding program, a single generation per year is the limit when the field environment is used and about two generations per year if vernalization and greenhouse facilities are used. However, crossing the current favored spring malting barley to a winter barley may have its downsides, as winter-hardiness too may be an amalgamation of desirable alleles assembled together that confers the capacity for prolonged cold temperature conditions. In this review I touch on some general criteria that give a variety the distinction of being a malting barley and some of the general trends made in the breeding of spring malting barleys. But the main objective of this review is to pull together different aspects of what we know about winter-hardiness from the seemingly most essential aspect, which is survival in the field, to molecular genetics and gene regulation, and then finish with ideas that might help further our insight for predictability purposes.

Genome-wide identification of the histone acetyltransferase gene family in Triticum aestivum

Background

Histone acetylation is a ubiquitous and reversible post-translational modification in eukaryotes and prokaryotes that is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT activity is important for the modification of chromatin structure in eukaryotic cells, affecting gene transcription and thereby playing a crucial regulatory role in plant development. Comprehensive analyses of HAT genes have been performed in Arabidopsis thaliana, Oryza sativa, barley, grapes, tomato, litchi and Zea mays, but comparable identification and analyses have not been conducted in wheat (Triticum aestivum).

Results

In this study, 31 TaHATs were identified and divided into six groups with conserved gene structures and motif compositions. Phylogenetic analysis was performed to predict functional similarities between Arabidopsis thaliana, Oryza sativa and Triticum aestivum HAT genes. The TaHATs appeared to be regulated by cis-acting elements such as LTR and TC-rich repeats. The qRT–PCR analysis showed that the TaHATs were differentially expressed in multiple tissues. The TaHATs in expression also responded to temperature changes, and were all significantly upregulated after being infected by barley streak mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV) and wheat yellow mosaic virus (WYMV).

Conclusions

These results suggest that TaHATs may have specific roles in the response to viral infection and provide a basis for further study of TaHAT functions in T. aestivum plant immunity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07348-6.

How the pan-genome is changing crop genomics and improvement

Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.

How the pan-genome is changing crop genomics and improvement

Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.

Natural variation in glycine-rich region of Brassica oleracea cold shock domain protein 5 (BoCSDP5) is associated with low temperature tolerance

BACKGROUND

Low temperature (LT) or cold stress is a major environmental stress that seriously affects plant growth and development, limiting crop productivity. Cold shock domain proteins (CSDPs), which are present in most living organism, are involved in RNA metabolisms influencing abiotic stress tolerance.

OBJECTIVE

The aims of this study are to identify target gene for LT-tolerance, like CSDPs, characterize genetics, and develop molecular marker distinguishing LT-tolerance in cabbage (Brassica oleracea var. capitata).

METHODS

Semi-quantitative RT-PCR or qRT-PCR was used in gene expression study. LT-tolerance was determined by electrolyte leakage and PCR with allelic specific primers.

RESULTS

Allelic variation was found in BoCSDP5 coding sequence (CDs) between LT-tolerant (BN106 and BN553) and -susceptible inbred lines (BN107 and BN554). LT-tolerant inbred lines contained variant type of BoCSDP5 (named as BoCSDP5v) which encodes extra CCHC zinc finger domain at C-terminus. Association of LT-tolerance with BoCSDP5v was confirmed by electrolyte leakage and segregation using genetic population derived from BN553 and BN554 cross. Allelic variation in BoCSDP5 gene does not influence the rate of gene expression, but produces different proteins with different number of CCHC zinc finger domains. LT-tolerance marker designed on the basis of polymorphism between BoCSDP5 and BoCSDP5v was confirmed with samples used in previous B. oleracea CIRCADIAN CLOCK ASSOCIATED 1 (BoCCA1) marker validation.

CONCLUSIONS

LT-tolerant allele (BoCSDP5v) is dominant and independent of CBF pathway, and sufficient to generate molecular markers to identify LT-tolerant cabbage when it is used in combination with another marker, like BoCCA1-derived one. Production and analysis of overexpressing plants of BoCSDP1, BoCSDP3, BoCSDP5 and BoCSDP5v will be required for elucidating the function of CCHC zinc finger domains in LT-tolerance.

Isolation and expression analysis of a CBF transcriptional factor gene from the mangrove Bruguiera gymnorrhiza

The present work isolated a CBF/DREB1 gene from mangrove Bruguiera gymnorrhiza (BgCBF1) and compared its expression levels in various tissues under normal condition and cold stress, and in leaves exposed to various environmental stimuli. Results showed that the BgCBF1 deduced protein showed almost 100% similarities to that of AcCBF1 from Aegiceras corniculatum and AmCBF1 from Avicennia marina. Real-time quantitative PCR analysis showed that BgCBF1 gene displayed constitute expression in leaf, stem and root samples of plantlets under normal condition, but with different expression levels and tissue preference. When exposed to cold, BgCBF1 could be rapidly, slightly and transiently induced in all tissues. Furthermore, the BgCBF1 gene in leaves displayed a transient and small induction after salt and drought (PEG) exposure, while exhibited relatively high up-regulated expression after the phytohormone abscisic acid (ABA) treatment. These results suggest that the BgCBF1 gene may participate in the ABA mediated development and protection of plant against cold and drought. Further studies on its promoters and downstream genes will be needed to better understand its functions.

Isolation and expression analysis of two novel C-repeat binding factor (CBF) genes involved in plant growth and abiotic stress response in mangrove Kandelia obovata

Kandelia obovata is one of the cold tolerant mangrove plants along the China coast. To reveal the cold tolerant mechanism of K. obovata, the present work isolated two CBF/DREB1 genes (designated KoCBF1 and KoCBF3) from cold-stressed K. obovata and characterized their expression profiles in various organs and in response to multiple abiotic stresses. The deduced proteins of KoCBF1 and 3 all contain specific features of CBFs, and show high similarity to AmCBF1 and 3 from Avicennia marina, respectively. Different expression patterns of the two CBF orthologous under various abiotic stresses and exogenous hormone suggested that they may have different regulators and be involved in different regulatory pathway. The high basal and cold induced expression of the two genes indicated that they may all play important roles in growth and cold resistance of plants. The significant induction of KoCBF3 after salt and lead (Pb²⁺) treatments suggested that this CBF gene may also participate in response to salinity and heavy metal stresses. This study will provide a better understanding of CBF-regulated stress-resistant mechanism, which may be benefit in mangrove biotechnological breeding, high-latitude transplanting, and bioremediation of heavy metal pollutions.

Early Drought-Responsive Genes Are Variable and Relevant to Drought Tolerance

Drought stress is an important crop yield limiting factor worldwide. Plant physiological responses to drought stress are driven by changes in gene expression. While drought-responsive genes (DRGs) have been identified in maize, regulation patterns of gene expression during progressive water deficits remain to be elucidated. In this study, we generated time-series transcriptomic data from the maize inbred line B73 under well-watered and drought conditions. Comparisons between the two conditions identified 8,626 DRGs and the stages (early, middle, and late drought) at which DRGs occurred. Different functional groups of genes were regulated at the three stages. Specifically, early and middle DRGs display higher copy number variation among diverse Zea mays lines, and they exhibited stronger associations with drought tolerance as compared to late DRGs. In addition, correlation of expression between small RNAs (sRNAs) and DRGs from the same samples identified 201 negatively sRNA/DRG correlated pairs, including genes showing high levels of association with drought tolerance, such as two glutamine synthetase genes, gln2 and gln6 The characterization of dynamic gene responses to progressive drought stresses indicates important adaptive roles of early and middle DRGs, as well as roles played by sRNAs in gene expression regulation upon drought stress.

Perspectives on Low Temperature Tolerance and Vernalization Sensitivity in Barley: Prospects for Facultative Growth Habit

One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT-assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit.

Influence of CNV on transcript levels of HvCBF genes at Fr-H2 locus revealed by resequencing in resistant barley cv. 'Nure' and expression analysis

Resequencing in resistant cultivar 'Nure' and structural comparison with the same region of susceptible 'Morex' was performed in order to gain a better insight into barley Frost-resistance-H2 locus. Accurate annotation showed copy number variation (CNV) in the proximal part of the locus. In 'Nure', two exact copies of the HvCBF4-HvCBF2A region and one of the HvCBF4-HvCBF2B segment were observed, while in 'Morex' the corresponding region harboured a single HvCBF4-HvCBF2A (22 kb) segment. Abundance and diversity of repetitive element classes, gene function gain/losses, regulatory motifs and SNPs in gene sequences were identified. An expression study of key HvCBFs with/without CNV on selected genotypes contrasting for frost resistance and estimated HvCBF4-HvCBF2B copy number (2-10 copies) was also performed. Under light stimulus at warm temperature (23 °C), CNV of HvCBF2A and HvCBF4 correlated with their expression levels and reported frost resistance of genotypes; moreover, expression levels of HvCBF2A and HvCBF14 were strongly correlated (r = 0.908, p < 0.01). On the other hand, frost resistance correlated to HvCBF14 expression (r = 0.871, p < 0.01) only after cold induction (6°C) in the dark. A complex interplay of HvCBFs expression levels under different light/temperature stimuli is discussed in light of CNV and presence/number of regulatory elements that integrate different signal transduction pathways.

A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits in Populus trees

Gene dosage variation and the associated changes in gene expression influence a wide variety of traits, ranging from cancer in humans to yield in plants. It is also expected to affect important traits of ecological and agronomic importance in forest trees, but this variation has not been systematically characterized or exploited. Here we performed a comprehensive scan of the Populus genome for dosage-sensitive loci affecting quantitative trait variation for spring and fall phenology and biomass production. The study population was a large collection of clonally propagated F1 hybrid lines of Populus that saturate the genome 10-fold with deletions and insertions (indels) of known sizes and positions. As a group, the phenotypic means of the indel lines consistently differed from control nonindel lines, with an overall negative effect of both insertions and deletions on all biomass-related traits but more diverse effects and an overall wider phenotypic distribution of the indel lines for the phenology-related traits. We also investigated the correlation between gene dosage at specific chromosomal locations and phenotype, to identify dosage quantitative trait loci (dQTL). Such dQTL were detected for most phenotypes examined, but stronger effect dQTL were identified for the phenology-related traits than for the biomass traits. Our genome-wide screen for dosage sensitivity in a higher eukaryote demonstrates the importance of global genomic balance and the impact of dosage on life history traits.

De Novo Domestication: An Alternative Route toward New Crops for the Future

Current global agricultural production must feed over 7 billion people. However, productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental deterioration. Moreover, the increase in human population size and dietary changes are putting an ever greater burden on agriculture. The majority of this burden is met by the cultivation of a very small number of species, largely in locations that differ from their origin of domestication. Recent technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable low-input agriculture. Here we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.

Genetic association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

Landraces are local populations of crop plants adapted to a particular environment. Extant landraces are surviving genetic archives, keeping signatures of the selection processes experienced by them until settling in their current niches. This study intends to establish relationships between genetic diversity of barley (Hordeum vulgare L.) landraces collected in Spain and the climate of their collection sites. A high-resolution climatic data set (5 × 5 km spatial, 1-day temporal grid) was computed from over 2,000 temperature and 7,000 precipitation stations across peninsular Spain. This data set, spanning the period 1981-2010, was used to derive agroclimatic variables meaningful for cereal production at the collection sites of 135 barley landraces. Variables summarize temperature, precipitation, evapotranspiration, potential vernalization and frost probability at different times of the year and time scales (season and month). SNP genotyping of the landraces was carried out combining Illumina Infinium assays and genotyping-by-sequencing, yielding 9,920 biallelic markers (7,479 with position on the barley reference genome). The association of these SNPs with agroclimatic variables was analysed at two levels of genetic diversity, with and without taking into account population structure. The whole data sets and analysis pipelines are documented and available at https://eead-csic-compbio.github.io/barley-agroclimatic-association. We found differential adaptation of the germplasm groups identified to be dominated by reactions to cold temperature and late-season frost occurrence, as well as to water availability. Several significant associations pointing at specific adaptations to agroclimatic features related to temperature and water availability were observed, and candidate genes underlying some of the main regions are proposed.

Copy Number Variation in Domestication

Domesticated plants have long served as excellent models for studying evolution. Many genes and mutations underlying important domestication traits have been identified, and most causal mutations appear to be SNPs. Copy number variation (CNV) is an important source of genetic variation that has been largely neglected in studies of domestication. Ongoing work demonstrates the importance of CNVs as a source of genetic variation during domestication, and during the diversification of domesticated taxa. Here, we review how CNVs contribute to evolutionary processes underlying domestication, and review examples of domestication traits caused by CNVs. We draw from examples in plant species, but also highlight cases in animal systems that could illuminate the roles of CNVs in the domestication process.

Connecting genome structural variation with complex traits in crop plants

Structural genome variation is a major determinant of useful trait diversity. We describe how genome analysis methods are enabling discovery of trait-associated structural variants and their potential impact on breeding. As our understanding of complex crop genomes continues to grow, there is growing evidence that structural genome variation plays a major role in determining traits important for breeding and agriculture. Identifying the extent and impact of structural variants in crop genomes is becoming increasingly feasible with ongoing advances in the sophistication of genome sequencing technologies, particularly as it becomes easier to generate accurate long sequence reads on a genome-wide scale. In this article, we discuss the origins of structural genome variation in crops from ancient and recent genome duplication and polyploidization events and review high-throughput methods to assay such variants in crop populations in order to find associations with phenotypic traits. There is increasing evidence from such studies that gene presence-absence and copy number variation resulting from segmental chromosome exchanges may be at the heart of adaptive variation of crops to counter abiotic and biotic stress factors. We present examples from major crops that demonstrate the potential of pangenomic diversity as a key resource for future plant breeding for resilience and sustainability.

Prospects of pan-genomics in barley

The concept of a pan-genome refers to intraspecific diversity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover and genotype structural variants. The large size and complex structure of Triticeae genomes were for a long time an obstacle for genomic research in barley and its relatives. Now that a reference genome is available, computational pipelines for high-quality sequence assembly are in place, and sequence costs continue to drop, investigations into the structural diversity of the barley genome seem within reach. Here, we review the recent progress on pan-genomics in the model grass Brachypodium distachyon, and the cereal crops rice and maize, and devise a multi-tiered strategy for a pan-genome project in barley. Our design involves: (1) the construction of high-quality de novo sequence assemblies for a small core set of representative genotypes, (2) short-read sequencing of a large diversity panel of genebank accessions to medium coverage and (3) the use of complementary methods such as chromosome-conformation capture sequencing and k-mer-based association genetics. The in silico representation of the barley pan-genome may inform about the mechanisms of structural genome evolution in the Triticeae and supplement quantitative genetics models of crop performance for better accuracy and predictive ability.

Exploring and Exploiting Pan-genomics for Crop Improvement

Genetic variation ranging from single-nucleotide polymorphisms to large structural variants (SVs) can cause variation of gene content among individuals within the same species. There is an increasing appreciation that a single reference genome is insufficient to capture the full landscape of genetic diversity of a species. Pan-genome analysis offers a platform to evaluate the genetic diversity of a species via investigation of its entire genome repertoire. Although a recent wave of pan-genomic studies has shed new light on crop diversity and improvement using advanced sequencing technology, the potential applications of crop pan-genomics in crop improvement are yet to be fully exploited. In this review, we highlight the progress achieved in understanding crop pan-genomics, discuss biological activities that cause SVs, review important agronomical traits affected by SVs, and present our perspective on the application of pan-genomics in crop improvement.

Improving and Maintaining Winter Hardiness and Frost Tolerance in Bread Wheat by Genomic Selection

Winter hardiness is a major constraint for autumn sown crops in temperate regions, and thus an important breeding goal in the development of new winter wheat varieties. Winter hardiness is though influenced by many environmental factors rendering phenotypic selection under field conditions a difficult task due to irregular occurrence or absence of winter damage in field trials. Controlled frost tolerance tests in growth chamber experiments are, on the other hand, even with few genotypes, often costly and laborious, which makes a genomic breeding strategy for early generation selection an attractive alternative. The aims of this study were thus to compare the merit of marker-assisted selection using the major frost tolerance QTL Fr-A2 with genomic prediction for winter hardiness and frost tolerance, and to assess the potential of combining both measures with a genomic selection index using a high density marker map or a reduced set of pre-selected markers. Cross-validation within two training populations phenotyped for frost tolerance and winter hardiness underpinned the importance of Fr-A2 for frost tolerance especially when upweighting its effect in genomic prediction models, while a combined genomic selection index increased the prediction accuracy for an independent validation population in comparison to training with winter hardiness data alone. The prediction accuracy could moreover be maintained with pre-selected marker sets, which is highly relevant when employing cost reducing fingerprinting techniques such as targeted genotyping-by-sequencing. Genomic selection showed thus large potential to improve or maintain the performance of winter wheat for these difficult, costly, and laborious to phenotype traits.

Hotspots in the genomic architecture of field drought responses in wheat as breeding targets

Wheat can adapt to most agricultural conditions across temperate regions. This success is the result of phenotypic plasticity conferred by a large and complex genome composed of three homoeologous genomes (A, B, and D). Although drought is a major cause of yield and quality loss in wheat, the adaptive mechanisms and gene networks underlying drought responses in the field remain largely unknown. Here, we addressed this by utilizing an interdisciplinary approach involving field water status phenotyping, sampling, and gene expression analyses. Overall, changes at the transcriptional level were reflected in plant spectral traits amenable to field-level physiological measurements, although changes in photosynthesis-related pathways were found likely to be under more complex post-transcriptional control. Examining homoeologous genes with a 1:1:1 relationship across the A, B, and D genomes (triads), we revealed a complex genomic architecture for drought responses under field conditions, involving gene homoeolog specialization, multiple gene clusters, gene families, miRNAs, and transcription factors coordinating these responses. Our results provide a new focus for genomics-assisted breeding of drought-tolerant wheat cultivars.

Evidence of cyclical light/dark-regulated expression of freezing tolerance in young winter wheat plants

The ability of winter wheat (Triticum aestivum L.) plants to develop freezing tolerance through cold acclimation is a complex rait that responds to many environmental cues including day length and temperature. A large part of the freezing tolerance is conditioned by the C-repeat binding factor (CBF) gene regulon. We investigated whether the level of freezing tolerance of 12 winter wheat lines varied throughout the day and night in plants grown under a constant low temperature and a 12-hour photoperiod. Freezing tolerance was significantly greater (P<0.0001) when exposure to subfreezing temperatures began at the midpoint of the light period, or the midpoint of the dark period, compared to the end of either period, with an average of 21.3% improvement in survival. Thus, freezing survival was related to the photoperiod, but cycled from low, to high, to low within each 12-hour light period and within each 12-hour dark period, indicating ultradian cyclic variation of freezing tolerance. Quantitative real-time PCR analysis of expression levels of CBF genes 14 and 15 indicated that expression of these two genes also varied cyclically, but essentially 180° out of phase with each other. Proton nuclear magnetic resonance analysis (¹H-NMR) showed that the chemical composition of the wheat plants' cellular fluid varied diurnally, with consistent separation of the light and dark phases of growth. A compound identified as glutamine was consistently found in greater concentration in a strongly freezing-tolerant wheat line, compared to moderately and poorly freezing-tolerant lines. The glutamine also varied in ultradian fashion in the freezing-tolerant wheat line, consistent with the ultradian variation in freezing tolerance, but did not vary in the less-tolerant lines. These results suggest at least two distinct signaling pathways, one conditioning freezing tolerance in the light, and one conditioning freezing tolerance in the dark; both are at least partially under the control of the CBF regulon.

Association genetics studies on frost tolerance in wheat (Triticum aestivum L.) reveal new highly conserved amino acid substitutions in CBF-A3, CBF-A15, VRN3 and PPD1 genes

BACKGROUND

Understanding the genetic basis of frost tolerance (FT) in wheat (Triticum aestivum L.) is essential for preventing yield losses caused by frost due to cellular damage, dehydration and reduced metabolism. FT is a complex trait regulated by a number of genes and several gene families. Availability of the wheat genomic sequence opens new opportunities for exploring candidate genes diversity for FT. Therefore, the objectives of this study were to identity SNPs and insertion-deletion (indels) in genes known to be involved in frost tolerance and to perform association genetics analysis of respective SNPs and indels on FT.

RESULTS

Here we report on the sequence analysis of 19 candidate genes for FT in wheat assembled using the Chinese Spring IWGSC RefSeq v1.0. Out of these, the tandem duplicated C-repeat binding factors (CBF), i.e. CBF-A3, CBF-A5, CBF-A10, CBF-A13, CBF-A14, CBF-A15, CBF-A18, the vernalisation response gene VRN-A1, VRN-B3, the photoperiod response genes PPD-B1 and PPD-D1 revealed association to FT in 235 wheat cultivars. Within six genes (CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1) amino acid (AA) substitutions in important protein domains were identified. The amino acid substitution effect in VRN-A1 on FT was confirmed and new AA substitutions in CBF-A3, CBF-A15, VRN-B3, PPD-B1 and PPD-D1 located at highly conserved sites were detected. Since these results rely on phenotypic data obtained at five locations in 2 years, detection of significant associations of FT to AA changes in CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1 may be exploited in marker assisted breeding for frost tolerance in winter wheat.

CONCLUSIONS

A set of 65 primer pairs for the genes mentioned above from a previous study was BLASTed against the IWGSC RefSeq resulting in the identification of 39 primer combinations covering the full length of 19 genes. This work demonstrates the usefulness of the IWGSC RefSeq in specific primer development for highly conserved gene families in hexaploid wheat and, that a candidate gene association genetics approach based on the sequence data is an efficient tool to identify new alleles of genes important for the response to abiotic stress in wheat.

Gene Regulatory Networks Mediating Cold Acclimation: The CBF Pathway

Under low nonfreezing temperature conditions, plants from temperate climates undergo physiological and biochemical adjustments that increase their tolerance to freezing temperatures. This response, termed cold acclimation, is largely regulated by changes in gene expression. Molecular and genetic studies have identified a small family of transcription factors, called C-repeat binding factors (CBFs), as key regulators of the transcriptomic rearrangement that leads to cold acclimation. The function of these proteins is tightly controlled, and an inadequate supply of CBF activity may be detrimental to the plant. Accumulated evidence has revealed an extremely intricate network of positive and negative regulators of cold acclimation that coalesce at the level of CBF promoters constituting a central hub where multiple internal and external signals are integrated. Moreover, CBF expression is also controlled at posttranscriptional and posttranslational levels further refining CBF regulation. Recently, natural variation studies in Arabidopsis have demonstrated that mutations resulting in changes in CBF expression have an adaptive value for wild populations. Intriguingly, CBF genes are also present in plant species that do not cold acclimate, which suggest that they may also have additional functions. For instance, CBFs are required for some cold-related abiotic stress responses. In addition, their involvement in plant development deserves further study. Although more studies are necessary to fully harness CBF biotechnological potential, these transcription factors are meant to be key for a rational design of crops with enhanced tolerance to abiotic stress.

Exploring new alleles for frost tolerance in winter rye

Rye genetic resources provide a valuable source of new alleles for the improvement of frost tolerance in rye breeding programs. Frost tolerance is a must-have trait for winter cereal production in northern and continental cropping areas. Genetic resources should harbor promising alleles for the improvement of frost tolerance of winter rye elite lines. For frost tolerance breeding, the identification of quantitative trait loci (QTL) and the choice of optimum genome-based selection methods are essential. We identified genomic regions involved in frost tolerance of winter rye by QTL mapping in a biparental population derived from a highly frost tolerant selection from the Canadian cultivar Puma and the European elite line Lo157. Lines per se and their testcrosses were phenotyped in a controlled freeze test and in multi-location field trials in Russia and Canada. Three QTL on chromosomes 4R, 5R, and 7R were consistently detected across environments. The QTL on 5R is congruent with the genomic region harboring the Frost resistance locus 2 (Fr-2) in Triticeae. The Puma allele at the Fr-R2 locus was found to significantly increase frost tolerance. A comparison of predictive ability obtained from the QTL-based model with different whole-genome prediction models revealed that besides a few large, also small QTL effects contribute to the genomic variance of frost tolerance in rye. Genomic prediction models assigning a high weight to the Fr-R2 locus allow increasing the selection intensity for frost tolerance by genome-based pre-selection of promising candidates.

Nuclear localization and transactivation by Vitis CBF transcription factors are regulated by combinations of conserved amino acid domains

The highly conserved CBF pathway is crucial in the regulation of plant responses to low temperatures. Extensive analysis of Arabidopsis CBF proteins revealed that their functions rely on several conserved amino acid domains although the exact function of each domain is disputed. The question was what functions similar domains have in CBFs from other, overwintering woody plants such as Vitis, which likely have a more involved regulation than the model plant Arabidopsis. A total of seven CBF genes were cloned and sequenced from V. riparia and the less frost tolerant V. vinifera. The deduced species-specific amino acid sequences differ in only a few amino acids, mostly in non-conserved regions. Amino acid sequence comparison and phylogenetic analysis showed two distinct groups of Vitis CBFs. One group contains CBF1, CBF2, CBF3 and CBF8 and the other group contains CBF4, CBF5 and CBF6. Transient transactivation assays showed that all Vitis CBFs except CBF5 activate via a CRT or DRE promoter element, whereby Vitis CBF3 and 4 prefer a CRT element. The hydrophobic domains in the C-terminal end of VrCBF6 were shown to be important for how well it activates. The putative nuclear localization domain of Vitis CBF1 was shown to be sufficient for nuclear localization, in contrast to previous reports for AtCBF1, and also important for transactivation. The latter highlights the value of careful analysis of domain functions instead of reliance on computer predictions and published data for other related proteins.

Circadian and Light Regulated Expression of CBFs and their Upstream Signalling Genes in Barley

CBF (C-repeat binding factor) transcription factors show high expression levels in response to cold; moreover, they play a key regulatory role in cold acclimation processes. Recently, however, more and more information has led to the conclusion that, apart from cold, light-including its spectra-also has a crucial role in regulating CBF expression. Earlier, studies established that the expression patterns of some of these regulatory genes follow circadian rhythms. To understand more of this complex acclimation process, we studied the expression patterns of the signal transducing pathways, including signal perception, the circadian clock and phospholipid signalling pathways, upstream of the CBF gene regulatory hub. To exclude the confounding effect of cold, experiments were carried out at 22 °C. Our results show that the expression of genes implicated in the phospholipid signalling pathway follow a circadian rhythm. We demonstrated that, from among the tested CBF genes expressed in Hordeumvulgare (Hv) under our conditions, only the members of the HvCBF4-phylogenetic subgroup showed a circadian pattern. We found that the HvCBF4-subgroup genes were expressed late in the afternoon or early in the night. We also determined the expression changes under supplemental far-red illumination and established that the transcript accumulation had appeared four hours earlier and more intensely in several cases. Based on our results, we propose a model to illustrate the effect of the circadian clock and the quality of the light on the elements of signalling pathways upstream of the HvCBFs, thus integrating the complex regulation of the early cellular responses, which finally lead to an elevated abiotic stress tolerance.

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.

CBF2A-CBF4B genomic region copy numbers alongside the circadian clock play key regulatory mechanisms driving expression of FR-H2 CBFs

The C-Repeat Binding Factors (CBFs) are DNA-binding transcriptional activators that were identified using Arabidopsis thaliana. In barley, Hordeum vulgare, a cluster of CBF genes reside at FROST RESISTANCE-H2, one of two loci having major effects on winter-hardiness. FR-H2 was revealed in a population derived from the winter barley 'Nure' and the spring barley 'Trèmois'. 'Nure' harbors two to three copies of CBF2A and CBF4B as a consequence of tandem iteration of the genomic region encompassing these genes whereas 'Trèmois' harbors single copies, and these copy number differences are associated with their transcript level differences. Here we explore further the relationship between FR-H2 CBF gene copy number and transcript levels using 'Admire', a winter barley accumulating FR-H2 CBF gene transcripts to very high levels, and a group of lines related to 'Admire' through descent. DNA blot hybridization indicated the CBF2A-CBF4B genomic region is present in 7-8 copies in 'Admire' and is highly variable in copy number across the lines related to 'Admire'. At normal growth temperatures transcript levels of CBF12, CBF14, and CBF16 were higher in lines having greater CBF2A-CBF4B genomic region copy numbers than in lines having fewer copy numbers at peak expression level time points controlled by the circadian clock. Chromatin immunoprecipitation indicated CBF2 was at the CBF12 and CBF16 promoters at normal growth temperatures. These data support a scenario in which CBF2A-CBF4B genomic region copy numbers affect expression of other FR-H2 CBFs through a mechansim in which these other FR-H2 CBFs are activated by those in the copy number variable unit.

Wheat genomics comes of age

Advances in wheat genomics have lagged behind other major cereals (e.g., rice and maize) due to its highly repetitive and large polyploid genome. Recent technological developments in sequencing and assembly methods, however, have largely overcome these barriers. The community now moves to an era centred on functional characterisation of the genome. This includes understanding sequence and structural variation as well as how information is integrated across multiple homoeologous genomes. This understanding promises to uncover variation previously hidden from natural and human selection due to the often observed functional redundancy between homoeologs. Key functional genomic resources will enable this, including sequenced mutant populations and gene editing technologies which are now available in wheat. Training the next-generation of genomics-enabled researchers will be essential to ensure these advances are quickly translated into farmers' fields.

Response of microRNAs to cold treatment in the young spikes of common wheat

Background

MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important roles in biotic and abiotic stresses by regulating their target genes. For common wheat, spring frost damage frequently occurs, especially when low temperature coincides with plants at early floral organ differentiation, which may result in significant yield loss. Up to date, the role of miRNAs in wheat response to frost stress is not well understood.

Results

We report here the sequencing of small RNA transcriptomes from the young spikes that were treated with cold stress and the comparative analysis with those of the control. A total of 192 conserved miRNAs from 105 families and nine novel miRNAs were identified. Among them, 34 conserved and five novel miRNAs were differentially expressed between the cold-stressed samples and the controls. The expression patterns of 18 miRNAs were further validated by quantitative real time polymerase chain reaction (qRT-PCR). Moreover, nearly half of the miRNAs were cross inducible by biotic and abiotic stresses when compared with previously published work. Target genes were predicted and validated by degradome sequencing. Gene Ontology (GO) enrichment analysis showed that the target genes of differentially expressed miRNAs were enriched for response to the stimulus, regulation of transcription, and ion transport functions. Since many targets of differentially expressed miRNAs were transcription factors that are associated with floral development such as ARF, SPB (Squamosa Promoter Binding like protein), MADS-box (MCM1, AG, DEFA and SRF), MYB, SPX (SYG1, Pho81 and XPR1), TCP (TEOSINTE BRANCHED, Cycloidea and PCF), and PPR (PentatricoPeptide Repeat) genes, cold-altered miRNA expression may cause abnormal reproductive organ development.

Conclusion

Analysis of small RNA transcriptomes and their target genes provide new insight into miRNA regulation in developing wheat inflorescences under cold stress. MiRNAs provide another layer of gene regulation in cold stress response that can be genetically manipulated to reduce yield loss in wheat.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3556-2) contains supplementary material, which is available to authorized users.

CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation

Background

Copy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays. Gene CNVs were assessed in three full-sib families from species with 20 Gb genomes, i.e., white and black spruce, and interior spruce - a natural hybrid.

Results

We discovered hundreds of gene CNVs in each species, 3612 in total, which were enriched in functions related to stress and defense responses and narrow expression profiles, indicating a potential role in adaptation. The number of shared CNVs was in accordance with the degree of relatedness between individuals and species. The genetically mapped subset of these genes showed a wide distribution across the genome, implying numerous structural variations. The hybrid family presented significantly fewer CNVs, suggesting that the admixture of two species within one genome reduces the occurrence of CNVs.

Conclusions

The approach we developed is of particular interest in non-model species lacking a reference genome. Our findings point to a role for CNVs in adaptation. Their reduced abundance in the hybrid may limit genetic variability and evolvability of hybrids. We propose that CNVs make a qualitatively distinct contribution to adaptation which could be important for short term change.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3458-8) contains supplementary material, which is available to authorized users.

Breeding approaches and genomics technologies to increase crop yield under low-temperature stress

Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders' toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.