A global alfalfa diversity panel reveals genomic selection signatures in Chinese varieties and genomic associations with root development

Exogenous NO-mediated microRNA398a-3p -MsCSD2-2 modules negatively regulate the drought stress tolerance of alfalfa

Drought stress is a serious natural challenge facing alfalfa (Medicago sativa L.), seriously affecting its yield and quality. NO can enhance the activity of antioxidant enzymes and reduce oxidative damage, the core mechanism for plants to cope with drought stress. Small RNA and degradome sequencing demonstrated that exogenous NO enhances drought resilience by suppressing Ms-miR398a-3p expression, which directly targets MsCSD2-2 encoding a Cu/Zn superoxide dismutase (SOD). Transient co-expression assays in tobacco confirmed Ms-miR398a-3p-dependent cleavage of MsCSD2-2 transcripts. Strikingly, transgenic alfalfa overexpressing MsCSD2-2 or silencing Ms-miR398a-3p exhibited elevated SOD activity, reduced ROS accumulation, and improved drought tolerance. Conversely, Ms-miR398a-3p overexpression exacerbated drought sensitivity. Our findings establish Ms-miR398a-3p as a negative regulator of drought responses through post-transcriptional repression of MsCSD2-2, while NO acts as an upstream signal to fine-tune this pathway. This study provides actionable targets for engineering drought-resistant alfalfa cultivars.

Simple Sequence Repeat-Based Genetic Diversity Analysis of Alfalfa Varieties

Alfalfa, as a high-quality forage resource, has high nutritional value. Due to the high phenotypic similarity among its varieties and the susceptibility to environmental influences, challenges are encountered in variety identification and breeding. In this study, 23 simple sequence repeat (SSR) markers were screened to distinguish 49 alfalfa varieties, among which 21 SSR markers showed polymorphic fragments. The results indicated that these 21 markers were highly polymorphic, with an average of 5.91 alleles per SSR marker locus and an average polymorphic information content (PIC) of 0.66, suggesting a strong discriminatory efficiency. The results of a population genetic diversity analysis showed that there was a relatively high level of genetic diversity among the tested materials. The analysis of molecular variance (AMOVA) results indicated that the genetic variation within the population of the 49 alfalfa germplasm samples was the main source of the total variation. The results of genetic distance and genetic identity analyses showed that the genetic relationship between population 1 and population 4 was the most distant, while the relationship between population 2 and population 3 was the closest. The cluster analysis results showed that samples S16 and S55 formed a separate branch; that is, there were two main genetic subgroups. These results confirm that SSR markers are effective tools for genetic characterization and precise discrimination of alfalfa varieties and have important application values in breeding, variety registration, and germplasm resource conservation.

Complete mitochondrial genome of Medicago sativa ssp. falcata (Papilionoideae, Fabaceae): characterization and phylogenetic analysis

MAIN CONCLUSION

The first mitogenome of Medicago sativa ssp. falcata complete assembly and a comparative analysis of the four Medicago species base on mitogenome reveal taxonomic insights. Medicago sativa ssp. falcata is primarily distributed in the northern part of the geographical range where alfalfa grows and is a subspecies of the Medicago sativa complex (also called Mediacago falacta). However, compared to M. sativa, M. falcata has better performance in cold resistance and drought tolerance, making it a high-quality gene source for the breeding improvement of Medicago species. We sequenced and assembled the mitochondrial genome of M. falcata with a length of 307,026 bp and successfully annotated 50 genes, of which nad2 exhibited high nucleotide polymorphism in four Medicago species. A total of 197 RNA-editing sites were predicted across 24 protein-coding genes, with alterations at these editing sites resulting in a substantial number of leucine-coding sites, which is consistent with the results of codon usage bias. In addition, we conducted a horizontal comparison of four types of Medicago, including Medicago truncatula, and found that repetitive sequences in their mitogenomes exhibited consistent distribution characteristics. Phylogenetic trees generated through two methods indicated the independent genetic status of M. falcata within the Medicago genus and its partial kinship relationships within the Fabaceae family. The analysis of non-synonymous and synonymous substitution rates of shared protein-coding genes in different plants, along with gene transfer results, suggests that the mitogenome of M. falcata evolved smoothly without showing phases of intense change. This study provides useful information for further understanding the genetic background of M. falcata, with the expectation of contributing to the genomic mining and utilization of germplasm resources in the Medicago genus.

Systematic characterization of the calmodulin-like (CML) gene family in alfalfa and functional analysis of MsCML70 under salt stress

Calmodulin-like proteins (CMLs), which are widely involved in various abiotic stress responses, are important calcium ion sensors in plants. However, systematic identification and functional analysis of these proteins have not been performed in alfalfa. Here, a total of 211 MsCMLs were identified in the alfalfa genome. Conserved domain analysis revealed that most MsCMLs contained three EF-hand domains. A total of 17 tandem duplication events and 292 segmental duplication events were identified, indicating that segmental duplications were the major factor in the expansion of MsCMLs. There were 28, 36 and 18 MsCMLs that responded to drought, salt and cold stress, respectively, in alfalfa. In addition, MsCML70 overexpression significantly increased salt tolerance in Arabidopsis. MsCML70 participates in the plant salt stress response through various biological pathways, including transcriptional regulation, protein modification, plant hormone metabolism and secondary metabolism. Moreover, MsCML70 significantly increased the expression of HKT1 (high-affinity K+transporter 1), DREB19 (dehydration responsive element binding protein 19), PRX32 (peroxidase 32), JAL10 (jacalin-associated lectins 10), HB17 (homeobox 17), and NPF2.3 (nitrate transporter 2.3) under salt stress to promote tolerance to salt stress in Arabidopsis. The results of this study help elucidate the function of alfalfa CML genes and provide a new gene resource for the breeding of stress-resistant alfalfa.

Genome-wide characterization and expression analysis of the ADF gene family in response to salt and drought stress in alfalfa (Medicago sativa)

The microfilament cytoskeleton, formed by the process of actin polymerization, serves not only to support the morphology of the cell, but also to regulate a number of cellular activities. Actin-depolymerizing factors (ADFs) represent a significant class of actin-binding proteins that regulate the dynamic alterations in the microfilament framework, thereby playing a pivotal role in plant growth and development. Additionally, they are instrumental in modulating stress responses in plants. The ADF gene family has been explored in various plants, but there was a paucity of knowledge regarding the ADF gene family in alfalfa (Medicago sativa), which is one of the most significant leguminous forage crops globally. In this study, a total of nine ADF genes (designated MsADF1 through MsADF9) were identified in the alfalfa genome and mapped to five different chromosomes. A phylogenetic analysis indicated that the MsADF genes could be classified into four distinct groups, with members within the same group exhibiting comparable gene structures and conserved motifs. The analysis of the Ka/Ks ratios indicated that the MsADF genes underwent purity-based selection during its evolutionary expansion. The promoter region of these genes was found to contain multiple cis-acting elements related to hormone responses, defence, and stress, indicating that they may respond to a variety of developmental and environmental stimuli. Gene expression profiles analyzed by RT-qPCR experiments demonstrated that MsADF genes exhibited distinct expression patterns among different organs. Furthermore, the majority of MsADF genes were induced by salt and drought stress by more than two-fold, with MsADF1, 2/3, 6, and 9 being highly induced, suggesting their critical role in resistance to abiotic stress. These results provide comprehensive information on the MsADF gene family in alfalfa and lay a solid foundation for elucidating their biological function.

Genome-wide identification and expression analysis of CBF/DREB1 gene family in Medicago sativa L. and functional verification of MsCBF9 affecting flowering time

BACKGROUND

The C-repeat binding factor (CBF)/dehydration-responsive element binding (DREB1) belongs to a subfamily of the AP2/ERF (APETALA2/ethylene-responsive factor) superfamily, which can regulate many physiological and biochemical processes in plants, such as plant growth and development, hormone signal transduction and response to abiotic stress. Although the CBF/DREB1 family has been identified in many plants, studies of the CBF/DREB1 family in alfalfa are insufficient.

RESULTS

In this study, 25 MsCBF genes were identified in the genome of alfalfa ("Zhongmu No. 4"). These genes were distributed on chromosomes 1, 5, 6 and unassembled scaffolds. Phylogenetics divided the CBF members of Medicago sativa, Arabidopsis thaliana, and Medicago truncatula into six groups, of which group VI had the most MsCBFs members, reaching 52% (13/25). Gene duplication analysis showed that 64% (16/25) of MsCBFs formed tandem duplications, and 32% (8/25) formed segment duplications. The expression pattern of MsCBF9 under different hormone treatments was verified by RT-qPCR, and it was found that MsCBF9 responded to GA3, IAA, SA, and MeJA. Overexpression of MsCBF9 in Arabidopsis significantly delayed the flowering time of Arabidopsis. In contrast, the flowering time of the cbfs mutant was earlier, and overexpression of MsCBF9 also increased the number and size of Arabidopsis rosette leaves.

CONCLUSION

In this study, the CBF/DREB1 family of alfalfa was comprehensively identified and analyzed, and the function of MsCBF9 in regulating flowering time was studied. This study laid a foundation for further analysis of the function of the CBF family in alfalfa.

CLINICAL TRIAL NUMBER

Not applicable.

Comprehensive analysis of epigenetic modifications in alfalfa under cadmium stress

Epigenetics plays an important role in plant growth and development and in environmental adaptation. Alfalfa, an important forage crop, is rich in nutrients. However, little is known about the molecular regulatory mechanisms underlying the response of alfalfa to cadmium (Cd) stress. Here, we performed DNA methylation (5mC), RNA methylation (m6A) and transcriptomic sequencing analyses of alfalfa roots under Cd stress. Whole-genome methylation sequencing and transcriptomic sequencing revealed that Cd stress reduced DNA methylation levels. Moreover, a reduced 5mC methylation level was associated with decreased expression of several DNA methyltransferase genes. Compared with those under normal (CK) conditions, the m6A modification levels under Cd stress were greater and were positively correlated with gene expression in alfalfa roots. We also found a negative correlation between the 5mC level and the m6A level, especially in CG and CHG contexts. In yeast, the overexpression of MsNARMP5 (natural resistance-associated macrophage protein) and MsPCR2 (plant cadmium resistance 2), which are modified by 5mC or m6A, significantly increased Cd stress tolerance. These results provide candidate genes for future studies on the mechanism of Cd stress tolerance in alfalfa roots and valuable information for studying heavy metal stress in alfalfa breeding.

Refining polyploid breeding in sweet potato through allele dosage enhancement

Allele dosage plays a key role in the phenotypic variation of polyploids. Here we present a genome-wide variation map of hexaploid sweet potato that captures allele dosage information, constructed from deep sequencing of 294 hexaploid accessions. Genome-wide association studies identified quantitative trait loci with dosage effects on 23 agronomic traits. Our analyses reveal that sweet potato breeding has progressively increased the dosage of favourable alleles to enhance trait performance. Notably, the Mesoamerican gene pool has evolved towards higher dosages of favourable alleles at multiple loci, which have been increasingly introgressed into modern Chinese cultivars. We substantiated the breeding-driven dosage accumulation through transgenic validation of IbEXPA4, an expansin gene influencing tuberous root weight. In addition, we explored causative sequence variations that alter the expression of the Orange gene, which regulates flesh colour. Our findings illuminate the breeding history of sweet potato and establish a foundation for leveraging allele dosages in polyploid breeding practices.

Genome-wide identification and analysis of expression patterns of the ABC1K gene family members in Medicago sativa

The ABC1K (activity of bc1 complex kinase) atypical protein kinase family regulates diverse physiological functions in plants, including the development, growth, and response of plants to various stress stimuli. However, to date, only a few members of the alfalfa (Medicago sativa) ABC1K gene family have been identified, which severely limits the exploration of the functional mechanism of alfalfa ABC1K. Here, we identified 22 ABC1K genes from the alfalfa genome and categorized them into four types on the basis of phylogenetic analysis results and gene structure. We then characterized the physical and biochemical properties, chromosomal location, subcellular localization, cis-regulatory elements, and conserved motifs of these genes. Transcript profiling analysis confirmed that MsABC1Ks were widely expressed in various alfalfa tissues, with tissue-specific expression. We also found that salt and drought conditions significantly regulated MsABC1K gene expression, thus indicating that MsABC1K genes perform critical functions in alfalfa's response to abiotic stress. In summary, the findings of our study serve as an important basis to enhance the stress resistance of alfalfa and provide valuable insights to better comprehend the functions of the MsABC1K gene family.

Multi-omics integrative analysis provided new insights into alkaline stress in alfalfa

Saline-alkali stress is one of the main abiotic stresses that limits plant growth. Salt stress has been widely studied, but alkaline salt degradation caused by NaHCO3 has rarely been investigated. In the present study, the alfalfa cultivar 'Zhongmu No. 1' was treated with 50 mM NaHCO3 (0, 4, 8, 12 and 24 h) to study the resulting enzyme activity and changes in mRNA, miRNA and metabolites in the roots. The results showed that the enzyme activity changed significantly after alkali stress treatment. The genomic analysis revealed 14,970 differentially expressed mRNAs (DEMs), 53 differentially expressed miRNAs (DEMis), and 463 differentially accumulated metabolites (DAMs). Combined analysis of DEMs and DEMis revealed that 21 DEMis negatively regulated 42 DEMs. In addition, when combined with Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEMs and DAMs, we found that phenylpropanoid biosynthesis, flavonoid biosynthesis, starch and sucrose metabolism and plant hormone signal transduction played important roles in the alkali stress response. The results of this study further elucidated the regulatory mechanism underlying the plant response to alkali stress and provided valuable information for the breeding of new saline-alkaline tolerance plant varieties.

Genome-Wide Identification, Phylogenetic, and Expression Analysis of Jasmonate ZIM-Domain Gene Family in Medicago Sativa L

JASMONATE ZIM domain (JAZ) proteins, inhibitors of the jasmonic acid (JA) signaling pathway, are identified in different plants, such as rice and Arabidopsis. These proteins are crucial for growth, development, and abiotic stress responses. However, limited information is available regarding the JAZ family in alfalfa. This study identified 11 JAZ genes (MsJAZs) in the "Zhongmu No.1" reference genome of alfalfa. The physical and chemical properties, chromosome localization, phylogenetic relationships, gene structure, cis-acting elements, and collinearity of the 11 MsJAZ genes were subsequently analyzed. Tissue-specific analysis revealed distinct functions of different MsJAZ genes in growth and development. The expression patterns of MsJAZ genes under salt stress conditions were validated using qRT-PCR. All MsJAZ genes responded to salt stress, with varying levels of upregulation over time, highlighting their role in stress responses. Furthermore, heterogeneous expression of MsJAZ1 in Arabidopsis resulted in significantly lower seed germination and survival rates in OE-2 and OE-4 compared to the WT under 150 mM NaCl treatment. This study establishes a foundation for further exploration of the function of the JAZ family and provides significant insights into the genetic improvement of alfalfa.

Genome-wide association analysis reveal candidate genes and haplotypes related to root weight in cucumber (Cucumis sativus L.)

Background

The plant root system is critical for the absorption of water and nutrients, and have a direct influence on growth and yield. In cucumber, a globally consumed crop, the molecular mechanism of root development remains unclear, and this has implications for developing stress tolerant varieties. This study sought to determine the genetic patterns and related genes of cucumber root weight. A core cucumber germplasms population was used to do the GWAS analysis in three environments.

Results

Here, we investigated four root-weight related traits including root fresh weight (RFW), root dry weight (RDW), ratio of root dry weight to root fresh weight (RDFW) and the comprehensive evaluation index, D-value of root weight (DRW) deduced based on the above three traits for the core germplasm of the cucumber global repository. According to the D-value, we identified 21 and 16 accessions with light and heavy-root, respectively. We also found that the East Asian ecotype accessions had significantly heavier root than other three ecotypes. The genome-wide association study (GWAS) for these four traits reveals that 4 of 10 significant loci (gDRW3.1, gDRW3.2, gDRW4.1 and gDRW5.1) were repeatedly detected for at least two traits. Further haplotype and expression analysis for protein-coding genes positioned within these 4 loci between light and heavy-root accessions predicted five candidate genes (i.e., Csa3G132020 and Csa3G132520 both encoding F-box protein PP2-B1 for gDRW3.1, Csa3G629240 encoding a B-cell receptor-associated protein for gDRW3.2, Csa4G499330 encodes a GTP binding protein for gDRW4.1, and Csa5G286040 encodes a proteinase inhibitor for gDRW5.1).

Conclusions

We conducted a systematic analysis of the root genetic basis and characteristics of cucumber core germplasms population. We detected four novel loci, which regulate the root weight in cucumber. Our study provides valuable candidate genes and haplotypes for the improvement of root system in cucumber breeding.

A genome-wide association study reveals novel loci and candidate genes associated with plant height variation in Medicago sativa

BACKGROUND

Plant height (PH) is an important agronomic trait influenced by a complex genetic network. However, the genetic basis for the variation in PH in Medicago sativa remains largely unknown. In this study, a comprehensive genome-wide association analysis was performed to identify genomic regions associated with PH using a diverse panel of 220 accessions of M. sativa worldwide.

RESULTS

Our study identified eight novel single nucleotide polymorphisms (SNPs) significantly associated with PH evaluated in five environments, explaining 8.59-12.27% of the phenotypic variance. Among these SNPs, the favorable genotype of chr6__31716285 had a low frequency of 16.4%. Msa0882400, located proximal to this SNP, was annotated as phosphate transporter 3;1, and its role in regulating alfalfa PH was supported by transcriptome and candidate gene association analysis. In addition, 21 candidate genes were annotated within the associated regions that are involved in various biological processes related to plant growth and development.

CONCLUSIONS

Our findings provide new molecular markers for marker-assisted selection in M. sativa breeding programs. Furthermore, this study enhances our understanding of the underlying genetic and molecular mechanisms governing PH variations in M. sativa.

Genome-wide identification of B-box zinc finger (BBX) gene family in Medicago sativa and their roles in abiotic stress responses

BACKGROUND

B-box (BBX) family is a class of zinc finger transcription factors (TFs) that play essential roles in regulating plant growth, development, as well as abiotic stress. However, no systematic analysis of BBX genes has yet been conducted in alfalfa (Medica go sativa L.), and their functions have not been elucidated up to now.

RESULTS

In this study, 28 MsBBX genes were identified from the alfalfa genome, which were clustered into 4 subfamilies according to an evolutionary tree of BBX proteins. Exon-intron structure and conserved motif analysis reflected the evolutionary conservation of MsBBXs in alfalfa. Collinearity analysis showed that segmental duplication promoted the expansion of the MsBBX family. Analysis of cis-regulatory elements suggested that the MsBBX genes possessed many growth/development-, light-, phytohormone-, and abiotic stress-related elements. MsBBX genes were differentially expressed in leaves, flowers, pre-elongated stems, elongated stems, roots and nodules, and most MsBBXs were remarkably induced by drought, salt and various plant growth regulators (ABA, JA, and SA). Further functional verification demonstrated that overexpressing of the MsBBX11 gene clearly promoted salt tolerance in transgenic Arabidopsis by regulating growth and physiological processes of seedlings.

CONCLUSIONS

This research provides insights into further functional research and regulatory mechanisms of MsBBX family genes under abiotic stress of alfalfa.

Genome-wide identification and expression analysis of the glycosyl hydrolase family 1 genes in Medicago sativa revealed their potential roles in response to multiple abiotic stresses

Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs), are encoded by a large number of genes, which participate in the development and stress response of plants, particularly under biotic and abiotic stresses through the activation of phytohormones. However, there are few studies systematically analyzing stress or hormone-responsive BGLU genes in alfalfa. In this study, a total of 179 BGLU genes of the glycoside hydrolase family 1 were identified in the genome of alfalfa, and then were classified into five distinct clusters. Sequence alignments revealed several conserved and unique motifs among these MsBGLU proteins. Many cis-acting elements related to abiotic stresses and phytohormones were identified in the promoter of some MsBGLUs. Moreover, RNA-seq and RT-qPCR analyses showed that these MsBGLU genes exhibited distinct expression patterns in response to different abiotic stress and hormonal treatments. In summary, this study suggests that MsBGLU genes play crucial roles in response to various abiotic stresses and hormonal responses, and provides candidate genes for stress tolerance breeding in alfalfa.

MODMS: a multi-omics database for facilitating biological studies on alfalfa (Medicago sativa L.)

Alfalfa (Medicago sativa L.) is a globally important forage crop. It also serves as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Multi-omics data on alfalfa continue to accumulate owing to recent advances in high-throughput techniques, and integrating this information holds great potential for expediting genetic research and facilitating advances in alfalfa agronomic traits. Therefore, we developed a comprehensive database named MODMS (multi-omics database of M. sativa) that incorporates multiple reference genomes, annotations, comparative genomics, transcriptomes, high-quality genomic variants, proteomics, and metabolomics. This report describes our continuously evolving database, which provides researchers with several convenient tools and extensive omics data resources, facilitating the expansion of alfalfa research. Further details regarding the MODMS database are available at https://modms.lzu.edu.cn/.

Resequencing of global Lotus corniculatus accessions reveals population distribution and genetic loci, associated with cyanogenic glycosides accumulation and growth traits

BACKGROUND

Lotus corniculatus is a widely distributed perennial legume whose great adaptability to different environments and resistance to barrenness make it an excellent forage and ecological restoration plant. However, its molecular genetics and genomic relationships among populations are yet to be uncovered.

RESULT

Here we report on a genomic variation map from worldwide 272 L. corniculatus accessions by genome resequencing. Our analysis suggests that L. corniculatus accessions have high genetic diversity and could be further divided into three subgroups, with the genetic diversity centers were located in Transcaucasia. Several candidate genes and SNP site associated with CNglcs content and growth traits were identified by genome-wide associated study (GWAS). A non-synonymous in LjMTR was responsible for the decreased expression of CNglcs synthesis genes and LjZCD was verified to positively regulate CNglcs synthesis gene CYP79D3. The LjZCB and an SNP in LjZCA promoter were confirmed to be involved in plant growth.

CONCLUSION

This study provided a large number of genomic resources and described genetic relationship and population structure among different accessions. Moreover, we attempt to provide insights into the molecular studies and breeding of CNglcs and growth traits in L. corniculatus.

Characterization of the Heat Shock Transcription Factor Family in Medicago sativa L. and Its Potential Roles in Response to Abiotic Stresses

Heat shock transcription factors (HSFs) are important regulatory factors in plant stress responses to various biotic and abiotic stresses and play important roles in growth and development. The HSF gene family has been systematically identified and analyzed in many plants but it is not in the tetraploid alfalfa genome. We detected 104 HSF genes (MsHSFs) in the tetraploid alfalfa genome ("Xinjiangdaye" reference genome) and classified them into three subgroups: 68 in HSFA, 35 in HSFB and 1 in HSFC subgroups. Basic bioinformatics analysis, including genome location, protein sequence length, protein molecular weight and conserved motif identification, was conducted. Gene expression analysis revealed tissue-specific expression for 13 MsHSFs and tissue-wide expression for 28 MsHSFs. Based on transcriptomic data analysis, 21, 11 and 27 MsHSFs responded to drought stress, cold stress and salt stress, respectively, with seven responding to all three. According to RT-PCR, MsHSF27/33 expression gradually increased with cold, salt and drought stress condition duration; MsHSF6 expression increased over time under salt and drought stress conditions but decreased under cold stress. Our results provide key information for further functional analysis of MsHSFs and for genetic improvement of stress resistance in alfalfa.

Genetic analysis of global faba bean diversity, agronomic traits and selection signatures

KEY MESSAGE

We identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection. Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for sustainable protein production. However, little is known about the genetics underlying trait diversity. In this study, we used 21,345 high-quality SNP markers to genetically characterize 2678 faba bean genotypes. We performed genome-wide association studies of key agronomic traits using a seven-parent-MAGIC population and detected 238 significant marker-trait associations linked to 12 traits of agronomic importance. Sixty-five of these were stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identified three subpopulations differentiated by geographical origin and 33 genomic regions subjected to strong diversifying selection between subpopulations. We found that SNP markers associated with the differentiation of northern and southern accessions explained a significant proportion of agronomic trait variance in the seven-parent-MAGIC population, suggesting that some of these traits were targets of selection during breeding. Our findings point to genomic regions associated with important agronomic traits and selection, facilitating faba bean genomics-based breeding.

Transcriptome and GWAS Analyses Reveal Candidate Gene for Root Traits of Alfalfa during Germination under Salt Stress

Alfalfa growth and production in China are negatively impacted by high salt concentrations in soils, especially in regions with limited water supplies. Few reliable genetic markers are currently available for salt tolerance selection. As a result, molecular breeding strategies targeting alfalfa are hindered. Therefore, with the continuous increase in soil salinity in agricultural lands, it is indispensable that a salt-tolerant variety of alfalfa is produced. We collected 220 alfalfa varieties around the world for resequencing and performed genome-wide association studies (GWASs). Alfalfa seeds were germinated in saline water with different concentrations of NaCl, and the phenotypic differences in several key root traits were recorded. In the phenotypic analysis, the breeding status and geographical origin strongly affected the salt tolerance of alfalfa. Forty-nine markers were significantly associated with salt tolerance, and 103 candidate genes were identified based on linkage disequilibrium. A total of 2712 differentially expressed genes were upregulated and 3570 were downregulated based on transcriptomic analyses. Some candidate genes that affected root development in the seed germination stage were identified through the combination of GWASs and transcriptome analyses. These genes could be used for molecular breeding strategies to increase alfalfa’s salt tolerance and for further research on salt tolerance in general.

Exogenous application of salicylic acid improves freezing stress tolerance in alfalfa

Freezing stress is one of the most detrimental environmental factors that can seriously impact the growth, development, and distribution of alfalfa (Medicago sativa L.). Exogenous salicylic acid (SA) has been revealed as a cost-effective method of improving defense against freezing stress due to its predominant role in biotic and abiotic stress resistance. However, how the molecular mechanisms of SA improve freezing stress resistance in alfalfa is still unclear. Therefore, in this study, we used leaf samples of alfalfa seedlings pretreatment with 200 μM and 0 μM SA, which were exposed to freezing stress (-10°C) for 0, 0.5, 1, and 2h and allowed to recover at normal temperature in a growth chamber for 2 days, after which we detect the changes in the phenotypical, physiological, hormone content, and performed a transcriptome analysis to explain SA influence alfalfa in freezing stress. The results demonstrated that exogenous SA could improve the accumulation of free SA in alfalfa leaves primarily through the phenylalanine ammonia-lyase pathway. Moreover, the results of transcriptome analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway-plant play a critical role in SA alleviating freezing stress. In addition, the weighted gene co-expression network analysis (WGCNA) found that MPK3, MPK9, WRKY22 (downstream target gene of MPK3), and TGACG-binding factor 1 (TGA1) are candidate hub genes involved in freezing stress defense, all of which are involved in the SA signaling pathway. Therefore, we conclude that SA could possibly induce MPK3 to regulate WRKY22 to participate in freezing stress to induced gene expression related to SA signaling pathway (NPR1-dependent pathway and NPR1-independent pathway), including the genes of non-expresser of pathogenesis-related gene 1 (NPR1), TGA1, pathogenesis-related 1 (PR1), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), glutathione-S-transferase (GST), and heat shock protein (HSP). This enhanced the production of antioxidant enzymes such as SOD, POD, and APX, which increases the freezing stress tolerance of alfalfa plants.

Genome-Wide Identification and Phylogenetic and Expression Analyses of the PLATZ Gene Family in Medicago sativa L

The PLATZ family is a novel class of plant-specific zinc finger transcription factors with important roles in plant growth and development and abiotic stress responses. PLATZ members have been identified in many plants, including Oryza sativa, Zea mays, Triticum aestivum, Fagopyrum tataricum, and Arabidopsis thaliana; however, due to the complexity of the alfalfa reference genome, the members of the PLATZ gene family in alfalfa (Medicago sativa L.) have not been systematically identified and analyzed. In this study, 55 Medicago sativa PLATZ genes (MsPLATZs) were identified in the alfalfa "Xinjiangdaye" reference genome. Basic bioinformatic analysis was performed, including the characterization of sequence lengths, protein molecular weights, genomic positions, and conserved motifs. Expression analysis reveals that 7 MsPLATZs are tissue-specifically expressed, and 10 MsPLATZs are expressed in all examined tissues. The transcriptomic expression of these genes is obvious, indicating that these MsPLATZs have different functions in the growth and development of alfalfa. Based on transcriptome data analysis and real-time quantitative PCR (RT-qPCR), we identified 22, 22, and 21 MsPLATZ genes that responded to salt, cold, and drought stress, respectively, with 20 MsPLATZs responding to all three stresses. This study lays a foundation for further exploring the functions of MsPLATZs, and provides ideas for the improvement of alfalfa varieties and germplasm innovation.

Genome-wide identification and characterization of NHL gene family in response to alkaline stress, ABA and MEJA treatments in wild soybean (Glycine soja)

Background

NDR1/HIN1-like (NHL) family genes are known to be involved in pathogen induced plant responses to biotic stress. Even though the NHL family genes have been identified and characterized in plant defense responses in some plants, the roles of these genes associated with the plant abiotic stress tolerance in wild soybean is not fully established yet, especially in response to alkaline stress.

Methods

We identified the potential NHL family genes by using the Hidden Markov model and wild soybean genome. The maximum-likelihood phylogenetic tree and conserved motifs were generated by using the MEME online server and MEGA 7.0 software, respectively. Furthermore, the syntenic analysis was generated with Circos-0.69. Then we used the PlantCARE online software to predict and analyze the regulatory cis-acting elements in promoter regions. Hierarchical clustering trees was generated using TM4: MeV4.9 software. Additionally, the expression levels of NHL family genes under alkaline stress, ABA and MEJA treatment were identified by qRT-PCR.

Results

In this study, we identified 59 potential NHL family genes in wild soybean. We identified that wild soybean NHL family genes could be mainly classified into five groups as well as exist with conserved motifs. Syntenic analysis of NHL family genes revealed genes location on 18 chromosomes and presence of 65 pairs of duplication genes. Moreover, NHL family genes consisted of a variety of putative hormone-related and abiotic stress responsive elements, where numbers of methyl jasmonate (MeJA) and abscisic acid (ABA) responsive elements were significantly larger than other elements. We confirmed the regulatory roles of NHL family genes in response to alkaline stress, ABA and MEJA treatment. In conclusion, we identified and provided valuable information on the wild soybean NHL family genes, and established a foundation to further explore the potential roles of NHL family genes in crosstalk with MeJA or ABA signal transduction mechanisms under alkaline stress.

Genome-Wide Identification and Expression Analysis of the NAC Gene Family in Alfalfa Revealed Its Potential Roles in Response to Multiple Abiotic Stresses

NAC (NAM, ATAF1/2, and CUC2) transcription factors compose one of the largest families of plant-specific transcription factors; they are widely involved in plant growth and development and have especially important roles in improving stress resistance in plants. However, NAC gene family members in alfalfa (Medicago sativa L.) have not been systematically identified and analyzed genome-wide due to the complexity of the alfalfa reference genome. In this study, a total of 421 M. sativa NAC genes (MsNACs) were identified from the alfalfa “Xinjiangdaye” reference genome. Basic bioinformatics analysis, including characterization of sequence length, protein molecular weight and genome position and conserved motif analysis, was conducted. Expression analysis showed that 47 MsNACs had tissue-specific expression, and 64 MsNACs were expressed in all tissues. The transcriptomic profiles of the genes were very different, indicating that these MsNACs have various functions in alfalfa growth and development. We identified 25, 42 and 47 MsNACs that respond to cold, drought and salt stress based on transcriptome data analysis and real-time quantitative PCR (RT−qPCR). Furthermore, 22 MsNACs were found to respond to both salt and drought stress, and 15 MsNACs were found to respond to cold, salt and drought stress. The results of this study could provide valuable information for further functional analysis of MsNACs and for the improvement of stress resistance in alfalfa.

A Genome-Wide Association Study Coupled With a Transcriptomic Analysis Reveals the Genetic Loci and Candidate Genes Governing the Flowering Time in Alfalfa (Medicago sativa L.)

The transition to flowering at the right time is very important for adapting to local conditions and maximizing alfalfa yield. However, the understanding of the genetic basis of the alfalfa flowering time remains limited. There are few reliable genes or markers for selection, which hinders progress in genetic research and molecular breeding of this trait in alfalfa. We sequenced 220 alfalfa cultivars and conducted a genome-wide association study (GWAS) involving 875,023 single-nucleotide polymorphisms (SNPs). The phenotypic analysis showed that the breeding status and geographical origin strongly influenced the alfalfa flowering time. Our GWAS revealed 63 loci significantly related to the flowering time. Ninety-five candidate genes were detected at these SNP loci within 40 kb (20 kb up- and downstream). Thirty-six percent of the candidate genes are involved in development and pollen tube growth, indicating that these genes are key genetic mechanisms of alfalfa growth and development. The transcriptomic analysis showed that 1,924, 2,405, and 3,779 differentially expressed genes (DEGs) were upregulated across the three growth stages, while 1,651, 2,613, and 4,730 DEGs were downregulated across the stages. Combining the results of our GWAS and transcriptome analysis, in total, 38 candidate genes (7 differentially expressed during the bud stage, 13 differentially expressed during the initial flowering stage, and 18 differentially expressed during the full flowering stage) were identified. Two SNPs located in the upstream region of the Msa0888690 gene (which is involved in isop renoids) were significantly related to flowering. The two significant SNPs within the upstream region of Msa0888690 existed as four different haplotypes in this panel. The genes identified in this study represent a series of candidate targets for further research investigating the alfalfa flowering time and could be used for alfalfa molecular breeding.

Genome-Wide Identification and Analysis of the NF-Y Transcription Factor Family Reveal Its Potential Roles in Salt Stress in Alfalfa (Medicago sativa L.)

Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor that plays an important role in various biological processes in plants, such as flowering regulation, drought resistance, and salt stress. However, few in-depth studies investigated the alfalfa NF-Y gene family. In this study, in total, 60 MsNF-Y genes, including 9 MsNF-YAs, 26 MsNF-YBs, and 25 MsNF-YCs, were identified in the alfalfa genome. The genomic locations, gene structures, protein molecular weights, conserved domains, phylogenetic relationships, and gene expression patterns in different tissues and under different stresses (cold stress, drought stress, and salt stress) of these NF-Y genes were analyzed. The illustration of the conserved domains and specific domains of the different subfamilies of the MsNF-Y genes implicates the conservation and diversity of their functions in alfalfa growth, development, and stress resistance. The gene expression analysis showed that 48 MsNF-Y genes (7 MsNF-YAs, 22 MsNF-YBs, and 19 MsNF-YCs) were expressed in all tissues at different expression levels, indicating that these genes have tissue expression specificity and different biological functions. In total, seven, seven, six, and eight MsNF-Y genes responded to cold stress, the ABA treatment, drought stress, and salt stress in alfalfa, respectively. According to the WGCNA, molecular regulatory networks related to salt stress were constructed for MsNF-YB2, MsNF-YB5, MsNF-YB7, MsNF-YB15, MsNF-YC5, and MsNF-YC6. This study could provide valuable information for further elucidating the biological functions of MsNF-Ys and improving salt tolerance and other abiotic stress resistance in alfalfa.

Genome-Wide Association Analysis Coupled With Transcriptome Analysis Reveals Candidate Genes Related to Salt Stress in Alfalfa (Medicago sativa L.)

Salt stress is the main abiotic factor affecting alfalfa yield and quality. However, knowledge of the genetic basis of the salt stress response in alfalfa is still limited. Here, a genome-wide association study (GWAS) involving 875,023 single-nucleotide polymorphisms (SNPs) was conducted on 220 alfalfa varieties under both normal and salt-stress conditions. Phenotypic analysis showed that breeding status and geographical origin play important roles in the alfalfa salt stress response. For germination ability under salt stress, a total of 15 significant SNPs explaining 9%-14% of the phenotypic variation were identified. For tolerance to salt stress in the seedling stage, a total of 18 significant SNPs explaining 12%-23% of the phenotypic variation were identified. Transcriptome analysis revealed 2,097 and 812 differentially expressed genes (DEGs) that were upregulated and 2,445 and 928 DEGs that were downregulated in the leaves and roots, respectively, under salt stress. Among these DEGs, many encoding transcription factors (TFs) were found, including MYB-, CBF-, NAC-, and bZIP-encoding genes. Combining the results of our GWAS analysis and transcriptome analysis, we identified a total of eight candidate genes (five candidate genes for tolerance to salt stress and three candidate genes for germination ability under salt stress). Two SNPs located within the upstream region of MsAUX28, which encodes an auxin response protein, were significantly associated with tolerance to salt stress. The two significant SNPs within the upstream region of MsAUX28 existed as three different haplotypes in this panel. Hap 1 (G/G, A/A) was under selection in the alfalfa domestication and improvement process.