Association mapping of soybean seed germination under salt stress

Stress salinity in plants: New strategies to cope with in the foreseeable scenario

The excess of salts in soils causes stress in most plants, except for some halophytes that can tolerate higher levels of salinity. The excess of Na+ generates an ionic imbalance, reducing the K+ content and altering cellular metabolism, thus impacting in plant growth and development. Additionally, salinity in soil induces water stress due to osmotic effects and increments the production of reactive oxygen species (ROS) that affect the cellular structure, damaging membranes and proteins, and altering the electrochemical potential of H+, which directly affects nutrient absorption by membrane transporters. However, plants possess mechanisms to overcome the toxicity of the sodium ions, such as internalization into the vacuole or exclusion from the cell, synthesis of enzymes or protective compounds against ROS, and the synthesis of metabolites that help to regulate the osmotic potential of plants. Physiologic and molecular mechanisms of salinity tolerance in plants will be addressed in this review. Furthermore, a revision of strategies taken by researchers to confer salt stress tolerance on agriculturally important species are discussed. These strategies include conventional breeding and genetic engineering as transgenesis and genome editing by CRISPR/Cas9.

Identification of Single Nucleotide Polymorphic Loci and Candidate Genes for Seed Germination Percentage in Okra under Salt and No-Salt Stresses by Genome-Wide Association Study

Excessive soil salinity is a major stressor inhibiting crops' growth, development, and yield. Seed germination is a critical stage of crop growth and development, as well as one of the most salt-sensitive stages. Salt stress has a significant inhibitory effect on seed germination. Okra is a nutritious vegetable, but its seed germination percentage (GP) is low, whether under salt stress conditions or suitable conditions. In this study, we used 180 okra accessions and conducted a genome-wide association study (GWAS) on the germination percentage using 20,133,859 single nucleotide polymorphic (SNP) markers under 0 (CK, diluted water), 70 (treatment 1, T1), and 140 mmol/L (treatment 2, T2) NaCl conditions. Using the mixed linear model (MLM) in Efficient Mixed-model Association eXpedated (EMMAX) and Genome-wide Efficient Mixed Model Association (GEMMA) software, 511 SNP loci were significantly associated during germination, of which 167 SNP loci were detected simultaneously by both programs. Among the 167 SNPs, SNP2619493 on chromosome 59 and SNP2692266 on chromosome 44 were detected simultaneously under the CK, T1, and T2 conditions, and were key SNP loci regulating the GP of okra seeds. Linkage disequilibrium block analysis revealed that nsSNP2626294 (C/T) in Ae59G004900 was near SNP2619493, and the amino acid changes caused by nsSNP2626294 led to an increase in the phenotypic values in some okra accessions. There was an nsSNP2688406 (A/G) in Ae44G005470 near SNP2692266, and the amino acid change caused by nsSNP2688406 led to a decrease in phenotypic values in some okra accessions. These results indicate that Ae59G004900 and Ae44G005470 regulate the GP of okra seeds under salt and no-salt stresses. The gene expression analysis further demonstrated these results. The SNP markers and genes that were identified in this study will provide reference for further research on the GP of okra, as well as new genetic markers and candidate genes for cultivating new okra varieties with high GPs under salt and no-salt stress conditions.

A genome-wide association analysis for salt tolerance during the soybean germination stage and development of KASP markers

Salt stress poses a significant challenge to crop productivity, and understanding the genetic basis of salt tolerance is paramount for breeding resilient soybean varieties. In this study, a soybean natural population was evaluated for salt tolerance during the germination stage, focusing on key germination traits, including germination rate (GR), germination energy (GE), and germination index (GI). It was seen that under salt stress, obvious inhibitions were found on these traits, with GR, GE, and GI diminishing by 32% to 54% when compared to normal conditions. These traits displayed a coefficient of variation (31.81% to 50.6%) and a substantial generalized heritability (63.87% to 86.48%). Through GWAS, a total of 1841 significant single-nucleotide polymorphisms (SNPs) were identified to be associated with these traits, distributed across chromosome 2, 5, 6, and 20. Leveraging these significant association loci, 12 candidate genes were identified to be associated with essential functions in coordinating cellular responses, regulating osmotic stress, mitigating oxidative stress, clearing reactive oxygen species (ROS), and facilitating heavy metal ion transport - all of which are pivotal for plant development and stress tolerance. To validate the candidate genes, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was conducted, revealing three highly expressed genes (Glyma.02G067700, Glyma.02G068900, and Glyma.02G070000) that play pivotal roles in plant growth, development, and osmoregulation. In addition, based on these SNPs related with salt tolerance, KASP (Kompetitive Allele-Specific PCR)markers were successfully designed to genotype soybean accessions. These findings provide insight into the genetic base of soybean salt tolerance and candidate genes for enhancing soybean breeding programs in this study.

Salt Tolerance in Soybeans: Focus on Screening Methods and Genetics

Salinity greatly affects the production of soybeans in arid and semi-arid lands around the world. The responses of soybeans to salt stress at germination, emergence, and other seedling stages have been evaluated in multitudes of studies over the past decades. Considerable salt-tolerant accessions have been identified. The association between salt tolerance responses during early and later growth stages may not be as significant as expected. Genetic analysis has confirmed that salt tolerance is distinctly tied to specific soybean developmental stages. Our understanding of salt tolerance mechanisms in soybeans is increasing due to the identification of key salt tolerance genes. In this review, we focus on the methods of soybean salt tolerance screening, progress in forward genetics, potential mechanisms involved in salt tolerance, and the importance of translating laboratory findings into field experiments via marker-assisted pyramiding or genetic engineering approaches, and ultimately developing salt-tolerant soybean varieties that produce high and stable yields. Progress has been made in the past decades, and new technologies will help mine novel salt tolerance genes and translate the mechanism of salt tolerance into new varieties via effective routes.

Genome-wide analysis of cold imbibition stress in soybean, Glycine max

In Canada, the length of the frost-free season necessitates planting crops as early as possible to ensure that the plants have enough time to reach full maturity before they are harvested. Early planting carries inherent risks of cold water imbibition (specifically less than 4°C) affecting seed germination. A marker dataset developed for a previously identified Canadian soybean GWAS panel was leveraged to investigate the effect of cold water imbibition on germination. Seed from a panel of 137 soybean elite cultivars, grown in the field at Ottawa, ON, over three years, were placed on filter paper in petri dishes and allowed to imbibe water for 16 hours at either 4°C or 20°C prior to being transferred to a constant 20°C. Observations on seed germination, defined as the presence of a 1 cm radicle, were done from day two to seven. A three-parameter exponential rise to a maximum equation (3PERM) was fitted to estimate germination, time to the one-half maximum germination, and germination uniformity for each cultivar. Genotype-by-sequencing was used to identify SNPs in 137 soybean lines, and using genome-wide association studies (GWAS - rMVP R package, with GLM, MLM, and FarmCPU as methods), haplotype block analysis, and assumed linkage blocks of ±100 kbp, a threshold for significance was established using the qvalue package in R, and five significant SNPs were identified on chromosomes 1, 3, 4, 6, and 13 for maximum germination after cold water imbibition. Percent of phenotypic variance explained (PVE) and allele substitution effect (ASE) eliminated two of the five candidate SNPs, leaving three QTL regions on chromosomes 3, 6, and 13 (Chr3-3419152, Chr6-5098454, and Chr13-29649544). Based on the gene ontology (GO) enrichment analysis, 14 candidate genes whose function is predicted to include germination and cold tolerance related pathways were identified as candidate genes. The identified QTLs can be used to select future soybean cultivars tolerant to cold water imbibition and mitigate risks associated with early soybean planting.

Comparing the Salt Tolerance of Different Spring Soybean Varieties at the Germination Stage

Salinization is a global agricultural problem with many negative effects on crops, including delaying germination, inhibiting growth, and reducing crop yield and quality. This study compared the salt tolerance of 20 soybean varieties at the germination stage to identify soybean germplasm with a high salt tolerance. Germination tests were conducted in Petri dishes containing 0, 50, 100, 150, and 200 mmol L-1 NaCl. Each Petri dish contained 20 soybean seeds, and each treatment was repeated five times. The indicators of germination potential, germination rate, hypocotyl length, and radicle length were measured. The salt tolerance of 20 soybean varieties was graded, and the theoretical identification concentration was determined by cluster analysis, the membership function method, one-way analysis of variance, and quadratic equation analysis. The relative germination rate, relative germination potential, relative root length, and relative bud length of the 20 soybean germplasms decreased when the salt concentration was >50 mmol L-1, compared with that of the Ctrl. The half-lethal salt concentration of soybean was 164.50 mmol L-1, and the coefficient of variation was 18.90%. Twenty soybean varieties were divided into three salt tolerance levels following cluster analysis: Dongnong 254, Heike 123, Heike 58, Heihe 49, and Heike 68 were salt-tolerant varieties, and Xihai 2, Suinong 94, Kenfeng 16, and Heinong 84 were salt-sensitive varieties, respectively. This study identified suitable soybean varieties for planting in areas severely affected by salt and provided materials for screening and extracting parents or genes to breed salt-tolerant varieties in areas where direct planting is impossible. It assists crop breeding at the molecular level to cope with increasingly serious salt stress.

Application of SVR-Mediated GWAS for Identification of Durable Genetic Regions Associated with Soybean Seed Quality Traits

Soybean (Glycine max L.) is an important food-grade strategic crop worldwide because of its high seed protein and oil contents. Due to the negative correlation between seed protein and oil percentage, there is a dire need to detect reliable quantitative trait loci (QTL) underlying these traits in order to be used in marker-assisted selection (MAS) programs. Genome-wide association study (GWAS) is one of the most common genetic approaches that is regularly used for detecting QTL associated with quantitative traits. However, the current approaches are mainly focused on estimating the main effects of QTL, and, therefore, a substantial statistical improvement in GWAS is required to detect associated QTL considering their interactions with other QTL as well. This study aimed to compare the support vector regression (SVR) algorithm as a common machine learning method to fixed and random model circulating probability unification (FarmCPU), a common conventional GWAS method in detecting relevant QTL associated with soybean seed quality traits such as protein, oil, and 100-seed weight using 227 soybean genotypes. The results showed a significant negative correlation between soybean seed protein and oil concentrations, with heritability values of 0.69 and 0.67, respectively. In addition, SVR-mediated GWAS was able to identify more relevant QTL underlying the target traits than the FarmCPU method. Our findings demonstrate the potential use of machine learning algorithms in GWAS to detect durable QTL associated with soybean seed quality traits suitable for genomic-based breeding approaches. This study provides new insights into improving the accuracy and efficiency of GWAS and highlights the significance of using advanced computational methods in crop breeding research.

Identification of a key locus, qNL3.1, associated with seed germination under salt stress via a genome-wide association study in rice

Two causal OsTTL and OsSAPK1 genes of the key locus qNL3.1 significantly associated with seed germination under salt stress were identified via a genome-wide association study, which could improve rice seed germination under salt stress. Rice is a salt-sensitive crop, and its seed germination determines subsequent seedling establishment and yields. In this study, 168 accessions were investigated for the genetic control of seed germination under salt stress based on the germination rate (GR), germination index (GI), time at which 50% germination was achieved (T₅₀) and mean level (ML). Extensive natural variation in seed germination was observed among accessions under salt stress. Correlation analysis showed significantly positive correlations among GR, GI and ML and a negative correlation with T₅₀ during seed germination under salt stress. Forty-nine loci significantly associated with seed germination under salt stress were identified, and seven of these were identified in both years. By comparison, 16 loci were colocated with the previous QTLs, and the remaining 33 loci might be novel. qNL3.1, colocated with qLTG-3, was simultaneously identified with the four indices in two years and might be a key locus for seed germination under salt stress. Analysis of candidate genes showed that two genes, the similar to transthyretin-like protein OsTTL and the serine/threonine protein kinase OsSAPK1, were the causal genes of qNL3.1. Germination tests indicated that both Osttl and Ossapk1 mutants significantly reduced seed germination under salt stress compared to the wild type. Haplotype analysis showed that Hap.1 of OsTTL and Hap.1 of OsSAPK1 genes were excellent alleles, and their combination resulted in high seed germination under salt stress. Eight accessions with elite performance of seed germination under salt stress were identified, which could improve rice seed germination under salt stress.

Genome-wide association studies for soybean epicotyl length in two environments using 3VmrMLM

Germination of soybean seed is the imminent vital process after sowing. The status of plumular axis and radicle determine whether soybean seed can emerge normally. Epicotyl, an organ between cotyledons and first functional leaves, is essential for soybean seed germination, seedling growth and early morphogenesis. Epicotyl length (EL) is a quantitative trait controlled by multiple genes/QTLs. Here, the present study analyzes the phenotypic diversity and genetic basis of EL using 951 soybean improved cultivars and landraces from Asia, America, Europe and Africa. 3VmrMLM was used to analyze the associations between EL in 2016 and 2020 and 1,639,846 SNPs for the identification of QTNs and QTN-by-environment interactions (QEIs)".A total of 180 QTNs and QEIs associated with EL were detected. Among them, 74 QTNs (ELS_Q) and 16 QEIs (ELS_QE) were identified to be associated with ELS (epicotyl length of single plant emergence), and 60 QTNs (ELT_Q) and 30 QEIs (ELT_QE) were identified to be associated with ELT (epicotyl length of three seedlings). Based on transcript abundance analysis, GO (Gene Ontology) enrichment and haplotype analysis, ten candidate genes were predicted within nine genic SNPs located in introns, upstream or downstream, which were supposed to be directly or indirectly involved in the process of seed germination and seedling development., Of 10 candidate genes, two of them (Glyma.04G122400 and Glyma.18G183600) could possibly affect epicotyl length elongation. These results indicate the genetic basis of EL and provides a valuable basis for specific functional studies of epicotyl traits.

The central role of GmGLP20.4 in root architecture modifications of soybean under low-nitrogen stress

KEY MESSAGE

The GmGLP20.4 candidate gene plays an important role to improve soybean root architecture under low-nitrogen stress. The results lay the foundation for breeding low-nitrogen-tolerant soybean. Roots are fundamentally important for plant growth and development, facilitating water and nutrient uptake. Various abiotic and biotic factors significantly affect the root system architecture, especially low nitrogen (LN), but the molecular mechanism remains unclear. In this study, we identified GmGLP20.4, a germin-like protein (ubiquitous plant glycoproteins belonging to the Cupin superfamily) crucial for lateral root development and highly induced by LN stress in lateral roots of soybean. GmGLP20.4 overexpression increased root biomass through development of an improved root system in soybean under LN, whereas a significant decrease in root biomass was observed in the gmglp20.4 knockout mutant. Overexpression of GmGLP20.4 improved plant growth and root architecture in transgenic tobacco (Nicotiana tabacum) under LN. Natural variation of the GT-1 cis-element in the promoter (T to A) of GmGLP20.4 was strongly associated with its expression level under LN, and significantly increased LN-sensitive variation (type A) was observed in wild soybean compared to that in elite cultivars. Thus, type A variation in the promoter of GmGLP20.4 may have been a site of artificial selection during domestication. The GmGT1-16g gene was highly expressed under LN and showed an expression pattern opposite to that of GmGLP20.4. A luciferase complementation imaging assay revealed that the GmGLP20.4 promoter specifically binds to GmGT1-16g. In conclusion, GmGLP20.4 is involved in soybean root development and the natural variation of its promoter will be useful in modern intercropping systems or to improve nitrogen-use efficiency.

Seed Priming with Devosia sp. Cell-Free Supernatant (CFS) and Citrus Bioflavonoids Enhance Canola and Soybean Seed Germination

Climate change, environmental pollution and associated abiotic stresses are beginning to meaningfully affect agricultural production worldwide. Salt stress is, however, one of the most important threats that significantly impairs plant growth and development. Plants in their early growth stages such as seed germination, seed emergence and early seedling growth are very sensitive to salt stress. Among the range of sustainable techniques adopted to improve seed germination and early plant growth is seed priming; however, with the use of ecofriendly substances, this is one of the most effective and economically viable techniques to improve seed tolerance against such environmental stresses. For instance, priming with appropriate non-synthetic compounds including microbial biostimulants are prominent ways to sustainably address these challenges. Therefore, in this research, by using the "priming technique", two biostimulants were tested for their potential as sustainable approaches to improve canola and soybean seed germination under salt stress and optimal growth conditions. Canola and soybean seeds were primed with flavonoids extracted from citrus fruits (flavopriming) and cell-free supernatant (CFS; produced by a novel strain of Devosia sp.-SL43), alone and in combination, and exposed to low-higher levels of salt stress and ideal growth conditions. Both biostimulants showed promising effects by significantly improving seed germination of soybean and canola under both ideal and stressful conditions. However, increases in seed germination were greater under salinity stress as flavonoids and CFS with stress amelioration effects showed substantial and statistically significant improvements in seed germination under varying levels of salt stress. In addition, combinations (mixtures) of both biostimulants were tested to determine if their effects might be more additive or multiplicative than the individual applications. However, results suggested incompatibility of both biostimulants as none of the combinations showed better results than that of the individual applications of either flavonoids or CFS. Conceivably, the use of flavonoids and this novel Devosia sp. CFS could be significant plant growth enhancers, perhaps much better than the few other biostimulants and bacterial-based compounds currently in use.

Machine-Learning-Based Genome-Wide Association Studies for Uncovering QTL Underlying Soybean Yield and Its Components

A genome-wide association study (GWAS) is currently one of the most recommended approaches for discovering marker-trait associations (MTAs) for complex traits in plant species. Insufficient statistical power is a limiting factor, especially in narrow genetic basis species, that conventional GWAS methods are suffering from. Using sophisticated mathematical methods such as machine learning (ML) algorithms may address this issue and advance the implication of this valuable genetic method in applied plant-breeding programs. In this study, we evaluated the potential use of two ML algorithms, support-vector machine (SVR) and random forest (RF), in a GWAS and compared them with two conventional methods of mixed linear models (MLM) and fixed and random model circulating probability unification (FarmCPU), for identifying MTAs for soybean-yield components. In this study, important soybean-yield component traits, including the number of reproductive nodes (RNP), non-reproductive nodes (NRNP), total nodes (NP), and total pods (PP) per plant along with yield and maturity, were assessed using a panel of 227 soybean genotypes evaluated at two locations over two years (four environments). Using the SVR-mediated GWAS method, we were able to discover MTAs colocalized with previously reported quantitative trait loci (QTL) with potential causal effects on the target traits, supported by the functional annotation of candidate gene analyses. This study demonstrated the potential benefit of using sophisticated mathematical approaches, such as SVR, in a GWAS to complement conventional GWAS methods for identifying MTAs that can improve the efficiency of genomic-based soybean-breeding programs.

High-LD SNP markers exhibiting pleiotropic effects on salt tolerance at germination and seedlings stages in spring wheat

Salt tolerance at germination and seedling growth stages was investigated. GWAS revealed nine genomic regions with pleiotropic effects on salt tolerance. Salt tolerant genotypes were identified for future breeding program. With 20% of the irrigated land worldwide affected by it, salinity is a serious threat to plant development and crop production. While wheat is the most stable food source worldwide, it has been classified as moderately tolerant to salinity. In several crop plants; such as barley, maize and rice, it has been shown that salinity tolerance at seed germination and seedling establishment is under polygenic control. As yield was the ultimate goal of breeders and geneticists, less attention has been paid to understanding the genetic architecture of salt tolerance at early stages. Thus, the genetic control of salt tolerance at these stages is poorly understood relative to the late stages. In the current study, 176 genotypes of spring wheat were tested for salinity tolerance at seed germination and seedling establishment. Genome-Wide Association Study (GWAS) has been used to identify the genomic regions/genes conferring salt tolerance at seed germination and seedling establishment. Salinity stress negatively impacted all germination and seedling development parameters. A set of 137 SNPs showed significant association with the traits of interest. Across the whole genome, 33 regions showed high linkage disequilibrium (LD). These high LD regions harbored 15 SNPs with pleiotropic effect (i.e. SNPs that control more than one trait). Nine genes belonging to different functional groups were found to be associated with the pleiotropic SNPs. Noteworthy, chromosome 2B harbored the gene TraesCS2B02G135900 that acts as a potassium transporter. Remarkably, one SNP marker, reported in an early study, associated with salt tolerance was validated in this study. Our findings represent potential targets of genetic manipulation to understand and improve salinity tolerance in wheat.

Association analysis of GmMAPKs and functional characterization of GmMMK1 to salt stress response in soybean

Salinity is one of the major abiotic constraints affecting the growth and yield of plants including soybean. In this context, the previous studies have documented the role of the mitogen-activated protein kinase (MAPK) cascade in the regulation of salt signaling in model plants. However, there is not a systematic analysis of salt-related MAPKs in soybean. Hence, in this study, we identified a total of 32 GmMAPKs via., genome-wide reanalysis of the MAPK family using the soybean genome v4.0. Based on the transcriptome datasets in the public database, we observed that GmMAPKs are induced by different abiotic stresses, especially salt stress. Furthermore, based on the candidate gene association mapping and haplotype analysis of the GmMAPKs, we identified a salt-related MAPK member, GmMMK1. GmMMK1 possesses significant sequence variations, which affect salt tolerance in soybean at the germination stage. Besides, the overexpression of the GmMMK1 in soybean hairy roots has a significant negative effect on the root growth, leading to increased sensitivity of the GmMMK1-OE plants to salt stress. Moreover, the heterologous expression of the GmMMK1 in Arabidopsis has been also observed to have a negative effect on the germination and root growth under salt stress. The transcriptome analysis and yeast two-hybrid screening showed that hormone signaling and the homeostasis of reactive oxygen species are involved in the GmMMK1 regulation network. In conclusion, the results of this work demonstrated that GmMMK1 is an important negative regulator of the salt stress response, and provides better insights for understanding the role of the MAPKs in soybean salt signaling.

A stress-responsive transcription factor PeNAC1 regulating beta-D-glucan biosynthetic genes enhances salt tolerance in oat

A Populus euphratica NAC gene regulates (1,3; 1,4)-β-D-glucan content in oat developing seed and improves the spikelet number and grain number per spike in transgenic oat under salinity conditions Salinity is the major factor affecting the production and quality of oat, and improving oat salt tolerance to increase yield and quality is vital. (1,3;1,4)-β-D-glucan in Gramineae is the key component in response to various environmental signals, and it is the most important functional ingredient in oat grain. The NAC transcription factors are important candidate genes used in genetic engineering to improve plant abiotic stress tolerance. In this study, we introduced Populus euphratica PeNAC1, controlled by its own promoter, into hexaploid cultivated oat and produced six transgenic lines. Compared to the non-transgenic control, the expression of PeNAC1 significantly improved the seed germination rate, seedling survival rate, and leaf chlorophyll content in the transgenic plants under salt stress. These physiological changes increased the spikelet number and grain number per spike in the transgenic oat under salinity conditions and reduced the yield loss per plant. The results indicated that the heterologous expression of PeNAC1 plays an effective role in improving the salt tolerance in transgenic oat. In addition, overexpressing PeNAC1 significantly increased the (1,3;1,4)-β-D-glucan content as well as the expression level of the (1,3;1,4)-β-D-glucan biosynthetic genes AsCslF3, AsCslF6, and AsCslF9 in the transgenic lines under salt stress, which suggested that PeNAC1 regulates the synthesis of (1,3;1,4)-β-D-glucan. Our research should assist in the discovery of the diverse action modes of NAC proteins, while PeNAC1 will be useful for improving the salt tolerance and quality of oat through molecular breeding.

Natural variation in the promoter of GsERD15B affects salt tolerance in soybean

Salt stress has detrimental effects on crop growth and yield, and the area of salt-affected land is increasing. Soybean is a major source of vegetable protein, oil and feed, but considered as a salt-sensitive crop. Cultivated soybean (Glycine max) is domesticated from wild soybean (G. soja) but lost considerable amount of genetic diversity during the artificial selection. Therefore, it is important to exploit the gene pool of wild soybean. In this study, we identified 34 salt-tolerant accessions from wild soybean germplasm and found that a 7-bp insertion/deletion (InDel) in the promoter of GsERD15B (early responsive to dehydration 15B) significantly affects the salt tolerance of soybean. GsERD15B encodes a protein with transcriptional activation function and contains a PAM2 domain to mediate its interaction with poly(A)-binding (PAB) proteins. The 7-bp deletion in GsERD15B promoter enhanced the salt tolerance of soybean, with increased up-regulation of GsERD15B, two GmPAB genes, the known stress-related genes including GmABI1, GmABI2, GmbZIP1, GmP5CS, GmCAT4, GmPIP1:6, GmMYB84 and GmSOS1 in response to salt stress. We propose that natural variation in GsERD15B promoter affects soybean salt tolerance, and overexpression of GsERD15B enhanced salt tolerance probably by increasing the expression levels of genes related to ABA-signalling, proline content, catalase peroxidase, dehydration response and cation transport.

Genome-Wide Association Study Uncover the Genetic Architecture of Salt Tolerance-Related Traits in Common Wheat (Triticum aestivum L.)

Soil salinity is a serious threat to wheat yield affecting sustainable agriculture. Although salt tolerance is important for plant establishment at seedling stage, its genetic architecture remains unclear. In the present study, we have evaluated eight salt tolerance-related traits at seedling stage and identified the loci for salt tolerance by genome-wide association study (GWAS). This GWAS panel comprised 317 accessions and was genotyped with the wheat 90 K single-nucleotide polymorphism (SNP) chip. In total, 37 SNPs located at 16 unique loci were identified, and each explained 6.3 to 18.6% of the phenotypic variations. Among these, six loci were overlapped with previously reported genes or quantitative trait loci, whereas the other 10 were novel. Besides, nine loci were detected for two or more traits, indicating that the salt-tolerance genetic architecture is complex. Furthermore, five candidate genes were identified for salt tolerance-related traits, including kinase family protein, E3 ubiquitin-protein ligase-like protein, and transmembrane protein. SNPs identified in this study and the accessions with more favorable alleles could further enhance salt tolerance in wheat breeding. Our results are useful for uncovering the genetic mechanism of salt tolerance in wheat at seeding stage.

ABA Metabolism and Homeostasis in Seed Dormancy and Germination

Abscisic acid (ABA) is a key hormone that promotes dormancy during seed development on the mother plant and after seed dispersal participates in the control of dormancy release and germination in response to environmental signals. The modulation of ABA endogenous levels is largely achieved by fine-tuning, in the different seed tissues, hormone synthesis by cleavage of carotenoid precursors and inactivation by 8'-hydroxylation. In this review, we provide an overview of the current knowledge on ABA metabolism in developing and germinating seeds; notably, how environmental signals such as light, temperature and nitrate control seed dormancy through the adjustment of hormone levels. A number of regulatory factors have been recently identified which functional relationships with major transcription factors, such as ABA INSENSITIVE3 (ABI3), ABI4 and ABI5, have an essential role in the control of seed ABA levels. The increasing importance of epigenetic mechanisms in the regulation of ABA metabolism gene expression is also described. In the last section, we give an overview of natural variations of ABA metabolism genes and their effects on seed germination, which could be useful both in future studies to better understand the regulation of ABA metabolism and to identify candidates as breeding materials for improving germination properties.

Jasmonates and Plant Salt Stress: Molecular Players, Physiological Effects, and Improving Tolerance by Using Genome-Associated Tools

Soil salinity is one of the most limiting stresses for crop productivity and quality worldwide. In this sense, jasmonates (JAs) have emerged as phytohormones that play essential roles in mediating plant response to abiotic stresses, including salt stress. Here, we reviewed the mechanisms underlying the activation and response of the JA-biosynthesis and JA-signaling pathways under saline conditions in Arabidopsis and several crops. In this sense, molecular components of JA-signaling such as MYC2 transcription factor and JASMONATE ZIM-DOMAIN (JAZ) repressors are key players for the JA-associated response. Moreover, we review the antagonist and synergistic effects between JA and other hormones such as abscisic acid (ABA). From an applied point of view, several reports have shown that exogenous JA applications increase the antioxidant response in plants to alleviate salt stress. Finally, we discuss the latest advances in genomic techniques for the improvement of crop tolerance to salt stress with a focus on jasmonates.

Rhizobacteria From Root Nodules of an Indigenous Legume Enhance Salinity Stress Tolerance in Soybean

Soybean is the most widely grown legume worldwide, but it is a glycophyte and salinity stress can decrease its yield potential up to 50%. Plant growth promoting rhizobacteria (PGPR) are known to enhance growth and induce tolerance to abiotic stresses including salinity. The aim of this study was to isolate such PGPR from the root nodules of Amphicarpaea bracteata, a North American relative of soybean. Isolated strains were identified, and 15 strains were screened for potential utilization as PGPR of soybean through a series of greenhouse trials. Four isolates that greatly improved shoot and root growth were further selected and screened under a range of salt concentrations. Two of the most promising strains, Rhizobium sp. SL42 and Hydrogenophaga sp. SL48 were ascertained to exert the greatest beneficial effects on soybean growth and salinity tolerance. They were co-inoculated with Bradyrhizobium japonicum 532C (Bj) and the plants were grown up to the harvest stage. The treatment of Bj+SL42 resulted in higher shoot biomass than the control, 18% at the vegetative stage, 16% at flowering, 7.5% at pod-filling, and 4.6% at harvest and seed weight was increased by 4.3% under salt stress (ECe = 7.4 ds/m). Grain yield was raised under optimal conditions by 7.4 and 8.1% with treatments Bj+SL48 and Bj+SL42+SL48, respectively. Nitrogen assimilation and shoot K+/Na+ ratio were also higher in the co-inoculation treatments. This study suggested that inoculation with bacteria from an indigenous legume can induce stress tolerance, improve growth and yield to support sustainability, and encourage ecological adaptability of soybean.

Mutation of GmAITR Genes by CRISPR/Cas9 Genome Editing Results in Enhanced Salinity Stress Tolerance in Soybean

Breeding of stress-tolerant plants is able to improve crop yield under stress conditions, whereas CRISPR/Cas9 genome editing has been shown to be an efficient way for molecular breeding to improve agronomic traits including stress tolerance in crops. However, genes can be targeted for genome editing to enhance crop abiotic stress tolerance remained largely unidentified. We have previously identified abscisic acid (ABA)-induced transcription repressors (AITRs) as a novel family of transcription factors that are involved in the regulation of ABA signaling, and we found that knockout of the entire family of AITR genes in Arabidopsis enhanced drought and salinity tolerance without fitness costs. Considering that AITRs are conserved in angiosperms, AITRs in crops may be targeted for genome editing to improve abiotic stress tolerance. We report here that mutation of GmAITR genes by CRISPR/Cas9 genome editing leads to enhanced salinity tolerance in soybean. By using quantitative RT-PCR analysis, we found that the expression levels of GmAITRs were increased in response to ABA and salt treatments. Transfection assays in soybean protoplasts show that GmAITRs are nucleus proteins, and have transcriptional repression activities. By using CRISPR/Cas9 to target the six GmAITRs simultaneously, we successfully generated Cas9-free gmaitr36 double and gmaitr23456 quintuple mutants. We found that ABA sensitivity in these mutants was increased. Consistent with this, ABA responses of some ABA signaling key regulator genes in the gmaitr mutants were altered. In both seed germination and seedling growth assays, the gmaitr mutants showed enhanced salt tolerance. Most importantly, enhanced salinity tolerance in the mutant plants was also observed in the field experiments. These results suggest that mutation of GmAITR genes by CRISPR/Cas9 is an efficient way to improve salinity tolerance in soybean.

Plant growth promotion by Pseudomonas putida KT2440 under saline stress: role of eptA

New strategies to improve crop yield include the incorporation of plant growth-promoting bacteria in agricultural practices. The non-pathogenic bacterium Pseudomonas putida KT2440 is an excellent root colonizer of crops of agronomical importance and has been shown to activate the induced systemic resistance of plants in response to certain foliar pathogens. In this work, we have analyzed additional plant growth promotion features of this strain. We show it can tolerate high NaCl concentrations and determine how salinity influences traits such as the production of indole compounds, siderophore synthesis, and phosphate solubilization. Inoculation with P. putida KT2440 significantly improved seed germination and root and stem length of soybean and corn plants under saline conditions compared to uninoculated plants, whereas the effects were minor under non-saline conditions. Also, random transposon mutagenesis was used for preliminary identification of KT2440 genes involved in bacterial tolerance to saline stress. One of the obtained mutants was analyzed in detail. The disrupted gene encodes a predicted phosphoethanolamine-lipid A transferase (EptA), an enzyme described to be involved in the modification of lipid A during lipopolysaccharide (LPS) biosynthesis. This mutant showed changes in exopolysaccharide (EPS) production, low salinity tolerance, and reduced competitive fitness in the rhizosphere.

Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height

Plant height is an important target for soybean breeding. It is a typical quantitative trait controlled by multiple genes and is susceptible to environmental influences. Here, we carried out phenotypic analysis of 156 recombinant inbred lines derived from "Dongnong L13" and "Henong 60" in nine environments at four locations over 6 years using interval mapping and inclusive composite interval mapping methods. We performed quantitative trait locus (QTL) analysis by applying pre-built simple-sequence repeat maps. We detected 48 QTLs, including nine significant QTLs detected by multiple methods and in multiple environments. Meanwhile, genotyping of all lines using the SoySNP660k BeadChip produced 54,836 non-redundant single-nucleotide polymorphism (SNP) genotypes. We used five multi-locus genome-wide association analysis methods to locate 10 quantitative trait nucleotides (QTNs), four of which overlap with previously located QTLs. Five candidate genes related to plant height are predicted to lie within 200 kb of these four QTNs. We identified 19 homologous genes in Arabidopsis, two of which may be associated with plant height. These findings further our understanding of the multi-gene regulatory network and genetic determinants of soybean plant height, which will be important for breeding high-yielding soybean.

Genome-wide association study of inflorescence length of cultivated soybean based on the high-throughout single-nucleotide markers

As an important and complex trait, inflorescence length (IL) of soybean [Glycine max (L.) Merr.] significantly affected seed yields. Therefore, elucidating molecular basis of inflorescence architecture, especially for IL, was important for improving soybean yield potentials. Longer IL meaned to have more pod and seed in soybean. Hence, increasing IL and improving yield are targets for soybean breeding. In this study, a association panel, comprising 283 diverse samples, was used to dissect the genetic basis of IL based on genome-wide association analysis (GWAS) and haplotype analysis. GWAS and haplotype analysis were conducted through high-throughout single-nucleotide polymorphisms (SNP) developed by SLAF-seq methodology. A total of 39, 057 SNPs (minor allele frequency ≥ 0.2 and missing data ≤ 10%) were utilized to evaluate linkage disequilibrium (LD) level in the tested association panel. A total of 30 association signals were identified to be associated with IL via GWAS. Among them, 13 SNPs were novel, and another 17 SNPs were overlapped or located near the linked regions of known quantitative trait nucleotide (QTN) with soybean seed yield or yield component. The functional genes, located in the 200-kb genomic region of each peak SNP, were considered as candidate genes, such as the cell division/ elongation, specific enzymes, and signaling or transport of specific proteins. These genes have been reported to participant in the regulation of IL. Ten typical long-IL lines and ten typical short-IL lines were re-sequencing, and then, six SNPs from five genes were obtained based on candidate gene-based association. In addition, 42 haplotypes were defined based on haplotype analysis. Of them, 11 haplotypes were found to regulate long IL (> 14 mm) in soybean. The identified 30 QTN with beneficial alleles and their candidate genes might be valuable for dissecting the molecular mechanisms of IL and further improving the yield potential of soybean.

Electrospun Microbial-Encapsulated Composite-Based Plasticized Seed Coat for Rhizosphere Stabilization and Sustainable Production of Canola ( Brassica napus L.)

Plant-growth-promoting bacteria show promises in crop production; nevertheless, innovation in their stable delivery is required for practical use by farmers. Herein, the composite of poly(vinyl alcohol)/poly(vinylpyrrolidone) plasticized with glycerol and loaded with the microbial consortium ( Bacillus subtilis plus Seratia marcescens) was fabricated and engineered onto canola ( Brassica napus L.) seed via electrospinning. Scanning electron microscopy showed that the biocomposite is a one-dimensional membrane, which encapsulated microbes in a multilayered nanostructure, and their interfacial behavior between microorganism and seed is beneficial for safer farming. A universal testing machine and thermogravimetric analysis demonstrated that the biocomposite holds sufficient thermomechanical properties for stable handling and practical management. A spectroscopic study resolved the living hybrid-polymer structure of the biocomposite and proved the plasticizing role of glycerol. A swelling study supports the degradation of the biocomposite in the hydrophilic environment as a result of the leaching of the plasticizer, which is important for the sustained release of microbial cells. A shelf life study supported that the biocomposite seed coat placed a threshold level of microbes [5.675 ± 0.48 log₁₀ colony forming units (CFU)/seed] and maintained their satisfactory viability for 15 days at room temperature. An antifungal and nutrient-solubilizing study supported that the biocomposite seed coat could provide opportunities to biocontrol diseases and improve nutrient acquisition by the plant. A pot study documents the better performance of the biocomposite seed coat on seed germination, seedling growth, leaf area, plant dry biomass, and root system. A chemical and microbial study demonstrated that the biocomposite seed coat improved the effectiveness of the bioinoculant in the root-soil interface, where they survive, flourish, and increase the nutrient pool status. In particular, this study presents advances in the fabrication of the biocomposite for encapsulation, preservation, sustained release, and efficacious use of microorganisms onto seeds for precision farming.

Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping

BACKGROUND

Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplasm. In this study, a genome-wide association study (GWAS) was performed to map genomic regions for salt tolerance in a diverse panel of 305 soybean accessions using a single nucleotide polymorphism (SNP) dataset derived from the SoySNP50K iSelect BeadChip. A second GWAS was also conducted in a subset of 234 accessions using another 3.7 M SNP dataset derived from a whole-genome resequencing (WGRS) study. In addition, three gene-based markers (GBM) of the known gene, Glyma03g32900, on Chr. 3 were also integrated into the two datasets. Salt tolerance among soybean lines was evaluated by leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC).

RESULTS

For both association studies, a major locus for salt tolerance on Chr. 3 was confirmed by a number of significant SNPs, of which three gene-based SNP markers, Salt-20, Salt14056 and Salt11655, had the highest association with all four traits studied. Also, additional genomic regions on Chrs. 1, 8, and 18 were found to be associated with various traits measured in the second GWAS using the WGRS-derived SNP dataset.

CONCLUSIONS

A region identified on Chr. 8 was identified to be associated with all four traits and predicted as a new minor locus for salt tolerance in soybean. The candidate genes harbored in this minor locus may help reveal the molecular mechanism involved in salt tolerance and to improve tolerance in soybean cultivars. The significant SNPs will be useful for marker-assisted selection for salt tolerance in soybean breeding programs.

Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes

Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.

Identification of favorable SNP alleles and candidate genes responsible for inflorescence-related traits via GWAS in chrysanthemum

81 SNPs were identified for three inflorescence-related traits, in which 15 were highly favorable. Two dCAPS markers were developed for future MAS breeding, and six candidate genes were predicted. Chrysanthemum is a leading ornamental species worldwide and demonstrates a wealth of morphological variation. Knowledge about the genetic basis of its phenotypic variation for key horticultural traits can contribute to its effective management and genetic improvement. In this study, we conducted a genome-wide association study (GWAS) based on two years of phenotype data and a set of 92,617 single nucleotide polymorphisms (SNPs) using a panel of 107 diverse cut chrysanthemums to dissect the genetic control of three inflorescence-related traits. A total of 81 SNPs were significantly associated with the three inflorescence-related traits (capitulum diameter, number of ray florets and flowering time) in at least one environment, with an individual allele explaining 22.72-38.67% of the phenotypic variation. Fifteen highly favorable alleles were identified for the three target traits by computing the phenotypic effect values for the stable associations detected in 2 year-long trials at each locus. Dosage pyramiding effects of the highly favorable SNP alleles and significant linear correlations between highly favorable allele numbers and corresponding phenotypic performance were observed. Two highly favorable SNP alleles correlating to flowering time and capitulum diameter were converted to derived cleaved amplified polymorphic sequence (dCAPS) markers to facilitate future breeding. Finally, six putative candidate genes were identified that contribute to flowering time and capitulum diameter. These results serve as a foundation for analyzing the genetic mechanisms underlying important horticultural traits and provide valuable insights into molecular marker-assisted selection (MAS) in chrysanthemum breeding programs.

Genome-wide association and transcriptional studies reveal novel genes for unsaturated fatty acid synthesis in a panel of soybean accessions

BACKGROUND

The nutritional value of soybean oil is largely influenced by the proportions of unsaturated fatty acids (FAs), including oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). Genome-wide association (GWAS) studies along with gene expression studies in soybean [Glycine max (L.) Merr.] were leveraged to dissect the genetics of unsaturated FAs.

RESULTS

A association panel of 194 diverse soybean accessions were phenotyped in 2013, 2014 and 2015 to identify Single Nucleotide Polymorphisms (SNPs) associated with OA, LLA, and LNA content, and determine putative candidate genes responsible for regulating unsaturated FAs composition. 149 SNPs that represented 73 genomic regions were found to be associated with the unsaturated FA contents in soybean seeds according to the results of GWAS. Twelve novel genes were predicted to be involved in unsaturated FA synthesis in soybean. The relationship between expression pattern of the candidate genes and the accumulation of unsaturated FAs revealed that multiple genes might be involved in unsaturated FAs regulation simultaneously but work in very different ways: Glyma.07G046200 and Glyma.20G245500 promote the OA accumulation in soybean seed in all the tested accessions; Glyma.13G68600 and Glyma.16G200200 promote the OA accumulation only in high OA germplasms; Glyma.07G151300 promotes OA accumulation in higher OA germplasms and suppresses that in lower OA germplasms; Glyma.16G003500 has the effect of increasing LLA accumulation in higher LA germplasms; Glyma.07G254500 suppresses the accumulation of LNA in lower OA germplasms; Glyma.14G194300 might be involved in the accumulation of LNA content in lower LNA germplasms.

CONCLUSIONS

The beneficial alleles and candidate genes identified might be valuable for improving marker-assisted breeding efficiency and exploring the molecular mechanisms underlying unsaturated fatty acid of soybean.

Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums

Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r ² = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.

A cation diffusion facilitator, GmCDF1, negatively regulates salt tolerance in soybean

Salt stress is one of the major abiotic factors that affect the metabolism, growth and development of plants, and soybean [Glycine max (L.) Merr.] germination is sensitive to salt stress. Thus, to ensure the successful establishment and productivity of soybeans in saline soil, the genetic mechanisms of salt tolerance at the soybean germination stage need to be explored. In this study, a population of 184 recombinant inbred lines (RILs) was utilized to map quantitative trait loci (QTLs) related to salt tolerance. A major QTL related to salt tolerance at the soybean germination stage named qST-8 was closely linked with the marker Sat_162 and detected on chromosome 8. Interestingly, a genome-wide association study (GWAS) identified several single nucleotide polymorphisms (SNPs) significantly associated with salt tolerance in the same genetic region on chromosome 8. Resequencing, bioinformatics and gene expression analyses were implemented to identify the candidate gene Glyma.08g102000, which belongs to the cation diffusion facilitator (CDF) family and was named GmCDF1. Overexpression and RNA interference of GmCDF1 in soybean hairy roots resulted in increased sensitivity and tolerance to salt stress, respectively. This report provides the first demonstration that GmCDF1 negatively regulates salt tolerance by maintaining K+-Na+ homeostasis in soybean. In addition, GmCDF1 affected the expression of two ion homeostasis-associated genes, salt overly sensitive 1 (GmSOS1) and Na+/H+ exchanger 1 (GmNHX1), in transgenic hairy roots. Moreover, a haplotype analysis detected ten haplotypes of GmCDF1 in 31 soybean genotypes. A candidate-gene association analysis showed that two SNPs in GmCDF1 were significantly associated with salt tolerance and that Hap1 was more sensitive to salt stress than Hap2. The results demonstrated that the expression level of GmCDF1 was negatively correlated with salt tolerance in the 31 soybean accessions (r = -0.56, P < 0.01). Taken together, these results not only indicate that GmCDF1 plays a negative role in soybean salt tolerance but also help elucidate the molecular mechanisms of salt tolerance and accelerate the breeding of salt-tolerant soybean.

Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums

Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r ² = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.

Mapping and confirmation of loci for salt tolerance in a novel soybean germplasm, Fiskeby III

KEY MESSAGE

The confirmation of a major locus associated with salt tolerance and mapping of a new locus, which could be beneficial for improving salt tolerance in soybean. Breeding soybean for tolerance to high salt conditions is important in some regions of the USA and world. Soybean cultivar Fiskeby III (PI 438471) in maturity group 000 has been reported to be highly tolerant to multiple abiotic stress conditions, including salinity. In this study, a mapping population of 132 F2 families derived from a cross of cultivar Williams 82 (PI 518671, moderately salt sensitive) and Fiskeby III (salt tolerant) was analyzed to map salt tolerance genes. The evaluation for salt tolerance was performed by analyzing leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC) after treatment with 120 mM NaCl under greenhouse conditions. Genotypic data for the F2 population were obtained using the SoySNP6K Illumina Infinium BeadChip assay. A major allele from Fiskeby III was significantly associated with LSS, CCR, LSC, and LCC on chromosome (Chr.) 03 with LOD scores of 19.1, 11.0, 7.7 and 25.6, respectively. In addition, a second locus associated with salt tolerance for LSC was detected and mapped on Chr. 13 with an LOD score of 4.6 and an R 2 of 0.115. Three gene-based polymorphic molecular markers (Salt-20, Salt14056 and Salt11655) on Chr.03 showed a strong predictive association with phenotypic salt tolerance in the present mapping population. These molecular markers will be useful for marker-assisted selection to improve salt tolerance in soybean.

Association analysis of salt tolerance in cowpea (Vigna unguiculata (L.) Walp) at germination and seedling stages

This is the first report on association analysis of salt tolerance and identification of SNP markers associated with salt tolerance in cowpea. Cowpea (Vigna unguiculata (L.) Walp) is one of the most important cultivated legumes in Africa. The worldwide annual production in cowpea dry seed is 5.4 million metric tons. However, cowpea is unfavorably affected by salinity stress at germination and seedling stages, which is exacerbated by the effects of climate change. The lack of knowledge on the genetic underlying salt tolerance in cowpea limits the establishment of a breeding strategy for developing salt-tolerant cowpea cultivars. The objectives of this study were to conduct association mapping for salt tolerance at germination and seedling stages and to identify SNP markers associated with salt tolerance in cowpea. We analyzed the salt tolerance index of 116 and 155 cowpea accessions at germination and seedling stages, respectively. A total of 1049 SNPs postulated from genotyping-by-sequencing were used for association analysis. Population structure was inferred using Structure 2.3.4; K optimal was determined using Structure Harvester. TASSEL 5, GAPIT, and FarmCPU involving three models such as single marker regression, general linear model, and mixed linear model were used for the association study. Substantial variation in salt tolerance index for germination rate, plant height reduction, fresh and dry shoot biomass reduction, foliar leaf injury, and inhibition of the first trifoliate leaf was observed. The cowpea accessions were structured into two subpopulations. Three SNPs, Scaffold87490_622, Scaffold87490_630, and C35017374_128 were highly associated with salt tolerance at germination stage. Seven SNPs, Scaffold93827_270, Scaffold68489_600, Scaffold87490_633, Scaffold87490_640, Scaffold82042_3387, C35069468_1916, and Scaffold93942_1089 were found to be associated with salt tolerance at seedling stage. The SNP markers were consistent across the three models and could be used as a tool to select salt-tolerant lines for breeding improved cowpea tolerance to salinity.

GWAS of agronomic traits in soybean collection included in breeding pool in Kazakhstan

BACKGROUND

In recent years soybean is becoming one of the most important oilseed crops in Kazakhstan. Only within the last ten years (2006-2016), the area under soybean is expanded from 45 thousand hectares (ha) in 2006 to 120 thousand ha in 2016. The general trend of soybean expansion is from south-eastern to eastern and northern regions of the country, where average temperatures are lower and growing seasons are shorter. These new soybean growing territories were poorly examined in terms of general effects on productivity level among the diverse sample of soybean accessions. In this study, phenotypic data were collected in three separate regions of Kazakhstan and entire soybean sample was genotyped for identification of marker-trait associations (MTA).

RESULTS

In this study, the collection of 113 accessions representing five different regions of the World was planted in 2015-2016 in northern, eastern, and south-eastern regions of Kazakhstan. It was observed that North American accessions showed the highest yield in four out of six trials especially in Northern Kazakhstan in both years. The entire sample was genotyped with 6 K SNP Illumina array. 4442 SNPs found to be polymorphic and were used for whole genome genotyping purposes. Obtained SNP markers data and field data were used for GWAS (genome-wide association study). 30 SNPs appear to be very significant in 42 MTAs in six studied environments.

CONCLUSIONS

The study confirms the efficiency of GWAS for the identification of molecular markers which tag important agronomic traits. Overall thirty SNP markers associated with time to flowering and maturation, plant height, number of fertile nodes, seeds per plant and yield were identified. Physical locations of 32 identified out of 42 total MTAs coincide well with positions of known analogous QTLs. This result indicates importance of revealed MTAs for soybean growing regions in Kazakhstan. Obtained results would serve as required prerequisite for forming and realization of specific breeding programs towards effective adaptation and increased productivity of soybean in three different regions of Kazakhstan.

Salt responsive physiological, photosynthetic and biochemical attributes at early seedling stage for screening soybean genotypes

Salt stress affects all the stages of plant growth however seed germination and early seedling growth phases are more sensitive and can be used for screening of crop germplasm. In this study, we aimed to find the most effective indicators of salt tolerance for screening ten genotypes of soybean (SL-295, Gujosoya-2, PS-1042, PK-1029, ADT-1, RKS-18, KDS-344, MAUS-47, Bragg and PK-416). The principal component analysis (PCA) resulted in the formation of three different clusters, salt sensitive (SL-295, Gujosoya-2, PS-1042 and ADT-1), salt tolerant (MAUS-47, Bragg and PK-416) and moderately tolerant/sensitive (RKS-18, PK-1029 and KDS-344) suggesting that there was considerable genetic variability for salt tolerance in the soybean genotypes. Subsequently, genotypes contrasting in salt tolerance were analyzed for their physiological traits, photosynthetic efficiency and mitochondrial respiration at seedling and early germination stages under different salt (NaCl) treatments. It was found that salt mediated increase in AOX-respiration, root and shoot K+/Na+ ratio, improved leaf area and water use efficiency were the key determinants of salinity tolerance, which could modulate the net photosynthesis (carbon assimilation) and growth parameters (carbon allocation). The results suggest that these biomarkers could be can be useful for screening soybean genotypes for salt tolerance.

Beneficial rhizobacteria immobilized in nanofibers for potential application as soybean seed bioinoculants

Seed inoculation with plant growth promoting rhizobacteria (PGPR) is an ideal tool to supply the soil with a high density of beneficial microorganisms. However, maintaining viable microorganisms is a major problem during seed treatment and storage. In this work, an evaluation was made of the effect of bacterial immobilization in nanofibers on the stability (viability and maintenance of beneficial properties) of two potential PGPR, Pantoea agglomerans ISIB55 and Burkholderia caribensis ISIB40. Moreover, the impact of soybean seed coating with nanofiber-immobilized rhizobacteria on bacterial survival during seed storage and on germination and plant growth parameters was determined. Bacterial nanoimmobilization and subsequent seed coating with nanofiber-immobilized rhizobacteria were carried out by electrospinning. The results demonstrate that this technique successfully immobilized P. agglomerans ISIB55 and B. caribensis ISIB40 because it did not affect the viability or beneficial properties of either rhizobacteria. Seed coating with nanofiber-immobilized rhizobacteria improved P. agglomerans ISIB55 and B. caribensis ISIB40 survival on seeds stored for 30 days and contributed to the successful colonization of both bacteria on the plant root. Moreover, seed coating with P. agglomerans ISIB55 increased germination, length and dry weight of the root. Furthermore, seed coating with B. caribensis ISIB40 increased leaf number and dry weight of the shoot. Therefore, the technique applied in the present work to coat seeds with nanofiber-immobilized PGPR could be considered a promising eco-friendly approach to improve soybean production using a microbial inoculant.

Improvement of Soybean Products Through the Response Mechanism Analysis Using Proteomic Technique

Soybean is rich in protein/vegetable oil and contains several phytochemicals such as isoflavones and phenolic compounds. Because of the predominated nutritional values, soybean is considered as traditional health benefit food. Soybean is a widely cultivated crop; however, its growth and yield are markedly affected by adverse environmental conditions. Proteomic techniques make it feasible to map protein profiles both during soybean growth and under unfavorable conditions. The stress-responsive mechanisms during soybean growth have been uncovered with the help of proteomic studies. In this review, the history of soybean as food and the morphology/physiology of soybean are described. The utilization of proteomics during soybean germination and development is summarized. In addition, the stress-responsive mechanisms explored using proteomic techniques are reviewed in soybean.

Genome-Wide Association Study Reveals the Genetic Architecture Underlying Salt Tolerance-Related Traits in Rapeseed (Brassica napus L.)

Soil salinity is a serious threat to agriculture sustainability worldwide. Salt tolerance at the seedling stage is crucial for plant establishment and high yield in saline soils; however, little information is available on rapeseed (Brassica napus L.) salt tolerance. We evaluated salt tolerance in different rapeseed accessions and conducted a genome-wide association study (GWAS) to identify salt tolerance-related quantitative trait loci (QTL). A natural population comprising 368 B. napus cultivars and inbred lines was genotyped with a Brassica 60K Illumina Infinium SNP array. The results revealed that 75 single-nucleotide polymorphisms (SNPs) distributed across 14 chromosomes were associated with four salt tolerance-related traits. These SNPs integrated into 25 QTLs that explained 4.21-9.23% of the phenotypic variation in the cultivars. Additionally, 38 possible candidate genes were identified in genomic regions associated with salt tolerance indices. These genes fell into several functional groups that are associated with plant salt tolerance, including transcription factors, aquaporins, transporters, and enzymes. Thus, salt tolerance in rapeseed involves complex molecular mechanisms. Our results provide valuable information for studying the genetic control of salt tolerance in B. napus seedlings and may facilitate marker-based breeding for rapeseed salt tolerance.

Salt Stress Represses Soybean Seed Germination by Negatively Regulating GA Biosynthesis While Positively Mediating ABA Biosynthesis

Soybean is an important and staple oilseed crop worldwide. Salinity stress has adverse effects on soybean development periods, especially on seed germination and post-germinative growth. Improving seed germination and emergence will have positive effects under salt stress conditions on agricultural production. Here we report that NaCl delays soybean seed germination by negatively regulating gibberellin (GA) while positively mediating abscisic acid (ABA) biogenesis, which leads to a decrease in the GA/ABA ratio. This study suggests that fluridone (FLUN), an ABA biogenesis inhibitor, might be a potential plant growth regulator that can promote soybean seed germination under saline stress. Different soybean cultivars, which possessed distinct genetic backgrounds, showed a similar repressed phenotype during seed germination under exogenous NaCl application. Biochemical analysis revealed that NaCl treatment led to high MDA (malondialdehyde) level during germination and the post-germinative growth stages. Furthermore, catalase, superoxide dismutase, and peroxidase activities also changed after NaCl treatment. Subsequent quantitative Real-Time Polymerase Chain Reaction analysis showed that the transcription levels of ABA and GA biogenesis and signaling genes were altered after NaCl treatment. In line with this, phytohormone measurement also revealed that NaCl considerably down-regulated active GA₁, GA₃, and GA₄ levels, whereas the ABA content was up-regulated; and therefore ratios, such as GA₁/ABA, GA₃/ABA, and GA₄/ABA, are decreased. Consistent with the hormonal quantification, FLUN partially rescued the delayed-germination phenotype caused by NaCl-treatment. Altogether, these results demonstrate that NaCl stress inhibits soybean seed germination by decreasing the GA/ABA ratio, and that FLUN might be a potential plant growth regulator that could promote soybean seed germination under salinity stress.

Genetic variation and association mapping of waterlogging tolerance in chrysanthemum

Forty-five molecular markers were detected significantly associated with chrysanthemum' waterlogging tolerance, and four favorable parental lines were identified as potential donors for improving waterlogging tolerance in chrysanthemum. The productivity of chrysanthemum is downgraded by waterlogging soils, which has driven a search for germplasm showing an enhanced level of waterlogging tolerance (WT). As yet little is known regarding the mode of inheritance of WT in chrysanthemum. The study set out to characterize the extent of genetic variation for WT represented in a collection of one hundred chrysanthemum accessions by testing them under both greenhouse and field conditions. A membership function value of waterlogging (MFVW), which integrated a wilting index, a chlorosis score and the proportion of dead leaf in waterlogged plants, was used as a measure of WT. The variation for MFVW among plants grown in the greenhouse (two experiments) was generally higher than that generated in field-grown (one experiment) plants. The MFVW broad sense heritability was 0.82, and the phenotypic coefficient of variation (31.8 %) was larger than the genetic one (28.8 %). Association mapping (AM) identified 45 markers related to WT: 25 by applying the general linear model (GLM) + principal component (PC) model, 16 by applying the mixed linear model (MLM), 31 by applying the MLM + Q matrix model and 12 by applying the MLM + PC model. Of the associated markers, eight and two were predictive in two and three experiments within all models, respectively; the proportion of the phenotypic variance explained by the eight associations ranged from 6.3 to 16.4 %. On the basis of their harboring all four of the leading markers E2M16-2, SSR150-6, E19M16-1 and E10M10-12, the varieties 'Nannong Xuefeng', 'Qx097', 'Nannong Xunzhang' and 'Finch' were identified as potential donors for future improvement of WT in chrysanthemum.

Identification of novel loci for salt stress at the seed germination stage in soybean

Salt tolerance in soybean [Glycine max (L.) Merr.] at the seed germination stage is a critical determinant of stable stand establishment in saline soil. This study examined one population of 184 recombinant inbred lines (RILs, F_7:11) derived from a cross between Kefeng1 and Nannong1138-2 and one natural population consisting of 196 soybean landraces. A total of 11 quantitative trait loci (QTLs) and 22 simple sequence repeat (SSR) loci associated with three salt tolerance indices were detected by linkage and association mapping. The SSR marker Sat_162 was found to be closely linked to the co-localized QTLs at a site 792,811 bp from the gene Glyma08g12400.1, which was verified in response to salt stress at the germination stage. Five SSR markers, Satt201, BE475343, CSSR306, Satt664 and Satt567, were co-associated with two of the salt tolerance indices, and two SSR markers, Satt156 and Satt636, were co-associated with all three salt tolerance indices. Furthermore, elite alleles and their carrier materials were identified by analyzing alleles at the loci associated with these salt tolerance indices. These results may be beneficial for the future breeding of soybean salt tolerance at the germination stage using marker-assisted selection and molecular pyramiding breeding.

Shotgun proteomic analysis of soybean embryonic axes during germination under salt stress

Seed imbibition and radicle emergence are generally less affected by salinity in soybean than in other crop plants. In order to unveil the mechanisms underlying this remarkable salt tolerance of soybean at seed germination, a comparative label-free shotgun proteomic analysis of embryonic axes exposed to salinity during germination sensu stricto (GSS) was conducted. The results revealed that the application of 100 and 200 mmol/L NaCl stress was accompanied by significant changes (>2-fold, P<0.05) of 97 and 75 proteins, respectively. Most of these salt-responsive proteins (70%) were classified into three major functional categories: disease/defense response, protein destination and storage and primary metabolism. The involvement of these proteins in salt tolerance of soybean was discussed, and some of them were suggested to be potential salt-tolerant proteins. Furthermore, our results suggest that the cross-protection against aldehydes, oxidative as well as osmotic stress, is the major adaptive response to salinity in soybean.

Karrikins delay soybean seed germination by mediating abscisic acid and gibberellin biogenesis under shaded conditions

Karrikins (KAR) are a class of signal compounds, discovered in wildfire smoke, which affect seed germination. Currently, numerous studies have focused on the model plant Arabidopsis in the KAR research field, rather than on crops. Thus the regulatory mechanisms underlying KAR regulation of crop seed germination are largely unknown. Here, we report that KAR delayed soybean seed germination through enhancing abscisic acid (ABA) biosynthesis, while impairing gibberellin (GA) biogenesis. Interestingly, KAR only retarded soybean seed germination under shaded conditions, rather than under dark and white light conditions, which differs from in Arabidopsis. Phytohormone quantification showed that KAR enhanced ABA biogenesis while impairing GA biosynthesis during the seed imbibition process, and subsequently, the ratio of active GA4 to ABA was significantly reduced. Further qRT-PCR analysis showed that the transcription pattern of genes involved in ABA and GA metabolic pathways are consistent with the hormonal measurements. Finally, fluridone, an ABA biogenesis inhibitor, remarkably rescued the delayed-germination phenotype of KAR-treatment; and paclobutrazol, a GA biosynthesis inhibitor, inhibited soybean seed germination. Taken together, these evidences suggest that KAR inhibit soybean seed germination by mediating the ratio between GA and ABA biogenesis.

GmSALT3, Which Confers Improved Soybean Salt Tolerance in the Field, Increases Leaf Cl- Exclusion Prior to Na+ Exclusion But Does Not Improve Early Vigor under Salinity

Soil salinity reduces soybean growth and yield. The recently identified GmSALT3 (Glycine max salt Tolerance-associated gene on chromosome 3) has the potential to improve soybean yields in salinized conditions. Here we evaluate the impact of GmSALT3 on soybean performance under saline or non-saline conditions. Three sets of near isogenic lines (NILs), with genetic similarity of 95.6-99.3% between each pair of NIL-T and NIL-S, were generated from a cross between two varieties 85-140 (salt-sensitive, S) and Tiefeng 8 (salt-tolerant, T) by using marker-assisted selection. Each NIL-T; 782-T, 820-T and 860-T, contained a common ~1000 kb fragment on chromosome 3 where GmSALT3 was located. We show that GmSALT3 does not contribute to an improvement in seedling emergence rate or early vigor under salt stress. However, when 12-day-old seedlings were exposed to NaCl stress, the NIL-T lines accumulated significantly less leaf Na⁺ compared with their corresponding NIL-S, while no significant difference of K⁺ concentration was observed between NIL-T and NIL-S; the magnitude of Na⁺ accumulation within each NIL-T set was influenced by the different genetic backgrounds. In addition, NIL-T lines accumulated less Cl^- in the leaf and more in the root prior to any difference in Na⁺; in the field they accumulated less pod wall Cl^- than the corresponding NIL-S lines. Under non-saline field conditions, no significant differences were observed for yield related traits within each pair of NIL-T and NIL-S lines, indicating there was no yield penalty for having the GmSALT3 gene. In contrast, under saline field conditions the NIL-T lines had significantly greater plant seed weight and 100-seed weight than the corresponding NIL-S lines, meaning GmSALT3 conferred a yield advantage to soybean plants in salinized fields. Our results indicated that GmSALT3 mediated regulation of both Na⁺ and Cl^- accumulation in soybean, and contributes to improved soybean yield through maintaining a higher seed weight under saline stress.