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Key Message: Recent developments in understanding the distribution and distinctive features of recombination hotspots are reviewed and approaches are proposed to increase recombination frequency in coldspot regions. Recombination events during meiosis provide the foundation and premise for creating new varieties of crops. The frequency of recombination in different genomic regions differs across eukaryote species, with recombination generally occurring more frequently at the ends of chromosomes. In most crop species, recombination is rare in centromeric regions. If a desired gene variant is linked in repulsion with an undesired variant of a second gene in a region with a low recombination rate, obtaining a recombinant plant combining two favorable alleles will be challenging. Traditional crop breeding involves combining desirable genes from parental plants into offspring. Therefore, understanding the mechanisms of recombination and factors affecting the occurrence of meiotic recombination is important for crop breeding. Here, we review chromosome recombination types, recombination mechanisms, genes and proteins involved in the meiotic recombination process, recombination hotspots and their regulation systems and discuss how to increase recombination frequency in recombination coldspot regions., (© 2024. Crown.)

Developing climate-resilient crops is critical for future food security and sustainable agriculture under current climate scenarios. Of specific importance are drought and soil salinity. Tolerance traits to these stresses are highly complex, and the progress in improving crop tolerance is too slow to cope with the growing demand in food production unless a major paradigm shift in crop breeding occurs. In this work, we combined bioinformatics and physiological approaches to compare some of the key traits that may differentiate between xerophytes (naturally drought-tolerant plants) and mesophytes (to which the majority of the crops belong). We show that both xerophytes and salt-tolerant mesophytes have a much larger number of copies in key gene families conferring some of the key traits related to plant osmotic adjustment, abscisic acid (ABA) sensing and signalling, and stomata development. We show that drought and salt-tolerant species have (i) higher reliance on Na for osmotic adjustment via more diversified and efficient operation of Na + /H + tonoplast exchangers (NHXs) and vacuolar H + - pyrophosphatase (VPPases); (ii) fewer and faster stomata; (iii) intrinsically lower ABA content; (iv) altered structure of pyrabactin resistance/pyrabactin resistance-like (PYR/PYL) ABA receptors; and (v) higher number of gene copies for protein phosphatase 2C (PP2C) and sucrose non-fermenting 1 (SNF1)-related protein kinase 2/open stomata 1 (SnRK2/OST1) ABA signalling components. We also show that the past trends in crop breeding for Na + exclusion to improve salinity stress tolerance are counterproductive and compromise their drought tolerance. Incorporating these genetic insights into breeding practices could pave the way for more drought-tolerant and salt-resistant crops, securing agricultural yields in an era of climate unpredictability., (© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Residual transpiration (RT) is defined as a loss of water through the leaf cuticle while stomata are closed. Reduced RT might be a potentially valuable trait for improving plant performance under water deficit conditions imposed by either drought or salinity. Due to the presence of stomata on the leaf surface, it is technically challenging to measure RT. RT has been estimated by the water loss through either astomatous leaf surface or isolated astomatous cuticular layers. This approach is not suitable for all species (e.g. not applicable to grasses) and is difficult and too time consuming for large-scale screening in breeding programs. Several alternative methods may be used to quantify the extent of RT; each of them comes with its own advantages and limitations. In this study, we have undertaken a comparative assessment of eight various methods of assessing RT, using barley (Hordeum vulgare ) plants as a model species. RT measured by water retention curves and a portable gas exchange (infrared gas analyser; IRGA) system had low resolution and were not able to differentiate between RT rates from young and old leaves. Methods based on quantification of the water loss at several time-points were found to be the easiest and least time-consuming compared to others. Of these, the 'three time-points water loss' method is deemed as the most suitable for the high throughput screening of plant germplasm for RT traits.

The global population is projected to experience a rapid increase in the future, which poses a challenge to global food sustainability. The "Green Revolution" beginning in the 1960s allowed grain yield to reach two billion tons in 2000 due to the introduction of semi-dwarfing genes in cereal crops. Semi-dwarfing genes reduce the gibberellin (GA) signal, leading to short plant stature, which improves the lodging resistance and harvest index under modern fertilization practices. Here, we reviewed the literature on the function of GA in plant growth and development, and the role of GA-related genes in controlling key agronomic traits that contribute to grain yield in cereal crops. We showed that: (1) GA is a significant phytohormone in regulating plant development and reproduction; (2) GA metabolism and GA signalling pathways are two key components in GA-regulated plant growth; (3) GA interacts with other phytohormones manipulating plant development and reproduction; and (4) targeting GA signalling pathways is an effective genetic solution to improve agronomic traits in cereal crops. We suggest that the modification of GA-related genes and the identification of novel alleles without a negative impact on yield and adaptation are significant in cereal crop breeding for plant architecture improvement. We observed that an increasing number of GA-related genes and their mutants have been functionally validated, but only a limited number of GA-related genes have been genetically modified through conventional breeding tools and are widely used in crop breeding successfully. New genome editing technologies, such as the CRISPR/Cas9 system, hold the promise of validating the effectiveness of GA-related genes in crop development and opening a new venue for efficient and accelerated crop breeding.

Climate change (CC) in central China will change seasonal patterns of agricultural production through increasingly frequent extreme climatic events (ECEs). Breeding climate-resilient wheat (Triticum aestivum L.) genotypes may mitigate adverse effects of ECEs on crop productivity. To reveal crop traits conducive to long-term yield improvement in the target population of environments, we created 8,192 virtual genotypes with contrasting but realistic ranges of phenology, productivity and waterlogging tolerance. Using these virtual genotypes, we conducted a genotype (G) by environment (E) by management (M) factorial analysis (G×E×M) using locations distributed across the entire cereal cropping zone in mid-China. The G×E×M invoked locally-specific sowing dates under future climates that were premised on shared socioeconomic pathways SSP5-8.5, with a time horizon centred on 2080. Across the simulated adaptation landscape, productivity was primarily driven by yield components and phenology (average grain yield increase of 6-69% across sites with optimal combinations of these traits). When incident solar radiation was not limiting carbon assimilation, ideotypes with higher grain yields were characterised by earlier flowering, higher radiation-use efficiency and larger maximum kernel size. At sites with limited solar radiation, crops required longer growing periods to realise genetic yield potential, although higher radiation-use efficiency and larger maximum kernel size were again prospective traits enabling higher rates of yield gains. By 2080, extreme waterlogging stress in some regions of mid-China will impact substantially on productivity, with yield penalties of up to 1,010 kg ha -1 . Ideotypes with optimal G×M could mitigate yield penalty caused by waterlogging by up to 15% under future climates. These results help distil promising crop trait by best management practice combinations that enable higher yields and robust adaptation to future climates and more frequent extreme climatic events, including flash flooding and soil waterlogging., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

To match predicted population growth, annual food production should be doubled by 2050. This is not achievable by current agronomical and breeding practices, due to the impact of climate changes and associated abiotic stresses on agricultural production systems. Here, we analyze the impact of global climate trends on crop productivity and show that the overall loss in crop production from climate-driven abiotic stresses may exceed US$170 billion year-1 and represents a major threat to global food security. We also show that abiotic stress tolerance had been present in wild progenitors of modern crops but was lost during their domestication. We argue for a major shift in our paradigm of crop breeding, focusing on climate resilience, and call for a broader use of wild relatives as a major tool in this process. We argue that, while molecular tools are currently in place to harness the potential of climate-resilient genes present in wild relatives, the complex polygenic nature of tolerance traits remains a major bottleneck in this process. Future research efforts should be focused not only on finding appropriate wild relatives but also on development of efficient cell-based high-throughput phenotyping platforms allowing assessment of the in planta operation of key genes., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Background: China has diverse wheat varieties that adapt to very different environments divided into ten agro-ecological zones. A better understanding of genomic differences and patterns of selection among agro-ecological zones could provide useful information in selection of specific adaptive traits in breeding., Results: We genotyped 438 wheat accessions from ten zones with kompetitive allele specific PCR (KASP) markers specific to 47 cloned genes for grain yield, quality, adaptation and stress resistance. Phylogenetic trees and principle component analysis revealed clear differences in winter and spring growth habits. Nucleotide diversity (π) and π ratio (π CL /π MCC ) suggested that genetic diversity had increased during breeding, and that Chinese landraces (CL) from Zones I-V contributed little to modern Chinese cultivars (MCC). π ratio and Fst identified 24 KASP markers with 53 strong selection signals specific to Zones I (9 signals), II (12), III (5), IV (5), V (6), and VI (6). Genes with clear genetic differentiation and strong response to selection in at least three zones were leaf rust resistance gene Lr34 (I, II, III and IV), photoperiod sensitivity gene Ppd-D1 (I, II, III, IV and V), vernalization gene Vrn-B1 (V, VII, VIII and X), quality-related gene Glu-B1 (I, II and III) and yield-related genes Sus1-7B (I, II, III, IV and IX), Sus2-2A (I, II, III., IV and VI) and GW2-6B (II, V and VI)., Conclusions: This study examined selection of multiple genes in each zone, traced the distribution of important genetic variations and provided useful information for ecological genomics and enlightening future breeding goals for different agro-ecological zones.

Key Message: This study demonstrates the feasibility of developing co-segregating markers and identifying candidate genes for Fusarium crown rot resistance in barley based on the generation and exploitation of a near-isogenic line-derived large population. Fusarium crown rot (FCR) is a chronic and severe disease in cereals in semi-arid regions worldwide. Previous studies showed that FCR assessment could be affected by many factors including plant height, growth rate as well as drought stress. Thus, accurate assessment, which is essential for detailed mapping of any locus conferring FCR resistance, is difficult. Targeting one of the resistance loci reported earlier, we developed a near-isogenic line-derived population consisting of 1820 F9 lines. By analysing this population, the Qcrs.cpi-4H locus was mapped to an interval of 0.09 cM covering a physical distance of about 637 kb and 13 markers co-segregating with the targeted locus were developed. Candidate genes underlying the resistance locus were identified by analysing the expression and sequence variation of genes in the targeted interval. The accurate localization and the development of co-segregating markers should facilitate the incorporation of this large-effect QTL into breeding programmes as well as the cloning of gene(s) underlying the locus.

Key Message: Aerenchyma formation after 7 days of waterlogging in commercial potting mixture can be a reliable, fast, and widely utilized approach for the selection of waterlogging tolerant barley genotypes. One major QTL for aerenchyma formation after 7 days of waterlogging treatment was identified and the newly developed markers explained 44 % of the phenotypic variance. This QTL can now be effectively used in barley breeding programs. Waterlogging is one of the important limiting conditions for crop yield and productivity. The main feature of waterlogged soils is oxygen deprivation, due to slow gas diffusion in water. Decreased oxygen content in waterlogged soils leads to the oxygen deficiency in plant tissues, resulting in reduced energy availability for plants. Rapidly induced aerenchyma formation is critical to maintaining adequate oxygen supply and overall waterlogging tolerance in barley. In this study, we have proved that quantifying aerenchyma formation after 7 days of waterlogging in commercial potting mixture can be a reliable, fast, and widely utilised approach for the selection of waterlogging tolerant barley genotypes, which is supported by measurements of redox potential (an indicator of anaerobic conditions). This protocol was also used to identify quantitative trait loci (QTL) in a doubled haploid population of barley from the cross between Yerong (tolerant) and Franklin (sensitive) genotypes. The QTL for aerenchyma formation and root porosity were at the same location as the waterlogging tolerance QTL. Seven new markers were developed and added onto this region on chromosome 4H. One major QTL for aerenchyma formation after 7 days waterlogging treatment explained 44.0 % of the phenotypic variance. This successful QTL for aerenchyma formation can be effectively used in the marker assisted selection to improve waterlogging tolerance in barley.

High sensitivity and rapid closure of wheat stomata to environmental stimuli make it difficult and inconvenient when investigating stomatal physiology and morphology using epidermal peels. This is due to inevitable mechanical stress to stomatal guard cells when separating epidermis from mesophyll cells, which induced a vast majority of stomatal closure in wheat. Stomata are more open and active in detached leaves than in epidermal peels. Based on these observations, we proposed a simple method, which promotes stomatal opening using detached leaves rather than epidermis for physiological observations. Stomatal response to stimuli was significantly increased when using intact leaf segment. The method was used to investigate stomatal behaviours of two wheat genotypes with contrasting salt tolerance to salinity stress. The effects of salt stress and exogenous abscisic acid (ABA) treatment on stomatal behaviours were also assessed. The salt-tolerant genotype, H-135, demonstrated a greater stomatal closure rate than the salt-sensitive genotype, H-093, in response to exogenous ABA under salt stress, highlighting the potential of stomatal responsiveness as an indicator for breeding salt-resistant crops. This method not only facilitates the effective initiation of stomatal opening but also ensures the continued responsiveness of stomata to subsequent treatments in wheat. [ABSTRACT FROM AUTHOR]

Oxygen depletion under waterlogged conditions results in a compromised operation of H+-ATPase, with strong implications for membrane potential maintenance, cytosolic pH homeostasis, and transport of all nutrients across membranes. The above effects, however, are highly tissue specific and time dependent, and the causal link between hypoxia-induced changes to the cell's ionome and plant adaptive responses to hypoxia is not well established. This work aimed to fill this gap and investigate the effects of oxygen deprivation on K+ signalling and homeostasis in plants, and potential roles of GORK (depolarization-activated outward-rectifying potassium) channels in adaptation to oxygen-deprived conditions in barley. A significant K+ loss was observed in roots exposed to hypoxic conditions; this loss correlated with the cell's viability. Stress-induced K+ loss was stronger in the root apex immediately after stress onset, but became more pronounced in the root base as the stress progressed. The amount of K+ in shoots of plants grown in waterlogged soil correlated strongly with K+ flux under hypoxia measured in laboratory experiments. Hypoxia induced membrane depolarization; the severity of this depolarization was less pronounced in the tolerant group of cultivars. The expression of GORK was down-regulated by 1.5-fold in mature root but it was up-regulated by 10-fold in the apex after 48 h hypoxia stress. Taken together, our results suggest that the GORK channel plays a central role in K+ retention and signalling under hypoxia stress, and measuring hypoxia-induced K+ fluxes from the mature root zone may be used as a physiological marker to select waterlogging-tolerant varieties in breeding programmes. [ABSTRACT FROM AUTHOR]

Introduction: Reducing plant height has played an important role in improving crop yields. The success of a breeding program relies on the source of dwarfing genes. For a dwarfing or semi-dwarfing gene to be successfully used in a breeding program, the gene should have minimal negative effects on yield and perform consistently in different environments. Methods: In this study, 182 doubled haploid lines, generated from a cross between TX9425 and Naso Nijo, were grown in six different environments to identify quantitative trait loci (QTL) controlling plant height and investigate QTL × environments interaction. Results: A QTL for plant was identified on 7H. This QTL showed no significant effects on other agronomic traits and yield components and consistently expressed in the six environments. A sufficient allelic effect makes it possible for this QTL to be successfully used in breeding programs. [ABSTRACT FROM AUTHOR]

Background: Resistance to soil waterlogging stress is an important plant breeding objective in high rainfall or poorly drained areas across many countries in the world. The present study was conducted to identify quantitative trait loci (QTLs) associated with waterlogging tolerance (e.g. leaf chlorosis, plant survival and biomass reduction) in barley and compare the QTLs identified across two seasons and in two different populations using a composite map constructed with SSRs, RFLP and Diversity Array Technology (DArT) markers. Results: Twenty QTLs for waterlogging tolerance related traits were found in the two barley double haploid (DH) populations. Several of these QTLs were validated through replication of experiments across seasons or by co-location across populations. Some of these QTLs affected multiple waterlogging tolerance related traits, for example, QTL Qwt4-1 contributed not only to reducing barley leaf chlorosis, but also increasing plant biomass under waterlogging stress, whereas other QTLs controlled both leaf chlorosis and plant survival. Conclusion: Improving waterlogging tolerance in barley is still at an early stage compared with other traits. QTLs identified in this study have made it possible to use marker assisted selection (MAS) in combination with traditional field selection to significantly enhance barley breeding for waterlogging tolerance. There may be some degree of homoeologous relationship between QTLs controlling barley waterlogging tolerance and that in other crops as discussed in this study. [ABSTRACT FROM AUTHOR]

Soil salinity is one of the major abiotic stresses restricting plant growth and development. Application of plant growth regulators (PGRs) is a possible practical means for minimizing salinity-induced yield losses, and can be used in addition to or as an alternative to crop breeding for enhancing salinity tolerance. The PGRs auxin, cytokinin, nitric oxide, brassinosteroid, gibberellin, salicylic acid, abscisic acid, jasmonate, and ethylene have been advocated for practical use to improve crop performance and yield under saline conditions. This review summarizes the current knowledge of the effectiveness of various PGRs in ameliorating the detrimental effects of salinity on plant growth and development, and elucidates the physiological and genetic mechanisms underlying this process by linking PGRs with their downstream targets and signal transduction pathways. It is shown that, while each of these PGRs possesses an ability to alter plant ionic and redox homeostasis, the complexity of interactions between various PGRs and their involvement in numerous signaling pathways makes it difficult to establish an unequivocal causal link between PGRs and their downstream effectors mediating plants' adaptation to salinity. The beneficial effects of PGRs are also strongly dependent on genotype, the timing of application, and the concentration used. The action spectrum of PGRs is also strongly dependent on salinity levels. Taken together, this results in a rather narrow "window" in which the beneficial effects of PGR are observed, hence limiting their practical application (especially under field conditions). It is concluded that, in the light of the above complexity, and also in the context of the cost–benefit analysis, crop breeding for salinity tolerance remains a more reliable avenue for minimizing the impact of salinity on plant growth and yield. Further progress in the field requires more studies on the underlying cell-based mechanisms of interaction between PGRs and membrane transporters mediating plant ion homeostasis. [ABSTRACT FROM AUTHOR]

Genome-wide association study (GWAS) is an effective approach for the identification of marker-trait associations (MTA) using more diverse germplasm not constrained by specific crossing. This study used a collection of 327 advanced indica breeding lines and varieties genotyped using a genotyping-by-sequencing method and phenotyped in eight environments to identify MTA for grain yield (GY) and 10 related traits. The current panel of indica breeding lines were divided into two subpopulations by three analytical methods including STRUCTURE, principal component analysis (PCA) and neighbour joining (NJ) tree. STRUCTURE and PCA gave the same classification of genotypes while the NJ tree results are slight difference in assigning genotypes to subpopulation from STRCUTURE and PCA. Wide variation was observed for all the 11 traits in the whole panel and the two subpopulations inferred by STRUCTURE analysis. Linkage disequilibrium (LD) analysis showed that LD decay varied across the chromosomes and average pairwise squared correlation coefficient (r 2 ) dropped to half of its maximum value (r 2 = 0.25) within a physical distance of 200 kb in the whole population. A MLM model controlling both population structure and cryptic relatedness was chosen to identify MTA for all the 11 tested traits. A total of 452 MTA that were delineated into 43 QTL were identified for all traits but PB, SB, and SR with 39 QTL being not reported before. Three QTL on chromosome 6, 9 and 12 were identified for GY but only in DS2. The numbers of QTL identified for the remaining traits varied from two to 26. Most of the detected QTL were found in only one environment. Four QTL were located in the regions containing genes/QTL previously identified for other related traits. The effects of identified QTL were relatively small with the highest percentage of phenotypic variance explained by a single QTL being 9.6%. The identified QTL are directly relevant to and can be more effectively used in breeding programs. [ABSTRACT FROM AUTHOR]