Genome-wide characterization of soybean RALF genes and their expression responses to Fusarium oxysporum

Genome-wide exploration and characterization of the RALFs and analysis of its role in peanut (Arachis hypogaea L.)

BACKGROUND

Rapid alkalinization factors (RALFs) are small peptides hormones that regulate plant growth and stress responses. Although RALFs have been identified in a broad range of land plant species, their roles in peanuts (Arachis hypogaea L.) remain largely unexplored.

RESULT

A total of 24 AhRALF genes we identified in the peanut genome and classified them into three clades through phylogenetic analysis. Whole genome duplication (WGD) or segmental duplication primarily drives the expansion of AhRALFs. Gene transcription analysis revealed that two genes from clade II (AhRALF1 and AhRALF12) and three from clade III (AhRALF8, AhRALF10, and AhRALF21) are highly expressed across 18 different tissues. Notably, AhRALF11 and AhRALF24, paralogous genes from clade II, are specifically expressed in immature buds and flowers. Additionally, AhRALF1, AhRALF12, AhRALF8, and AhRALF21 exhibited elevated expression under aluminum (Al) stress. Functional analysis of AhRALF1 confirmed its secretory function and inhibitory effect on root growth in Arabidopsis. Moreover, AhRALF1-silenced plants displayed reduced tolerance to Al stress, with altered antioxidant enzyme activities and increased oxidative damage.

CONCLUSION

This study provides a comprehensive analysis of the AhRALF gene family in peanut, highlighting their roles in growth regulation and stress responses. The function of AhRALF1 in enhancing peanut tolerance to Al stress was preliminary revealed. Our findings provide valuable insights into the roles of AhRALFs in peanuts and lay the groundwork for future functional studies and breeding programs.

Genome-Wide Association Study and Marker Development for Fusarium Oxysporum Root Rot Resistance in Soybean

Fusarium oxysporum root rot (FORR) is an important disease threatening soybean production. The development of marker-assisted selection (MAS) molecular markers will help accelerate the disease resistance breeding process and achieve the breeding goal of improving soybean disease resistance. This study evaluated the FORR disease resistance of 356 soybean germplasm accessions (SGAs) and screened resistance-related loci using genome-wide association analysis (GWAS) to develop molecular markers for MAS. A total of 1,355,930 high-quality SNPs were analyzed, 150 SNP sites significantly associated with FORR resistance were identified, and these sites were distributed within 41 QTLs. Additionally, 240 candidate genes were screened near these QTL regions, involving multiple functions such as hormone metabolism, signal transduction, stress defense, and growth regulation. Cleaved amplified polymorphic sequence (CAPS) and Kompetitive Allele-Specific PCR (KASP) molecular markers were developed based on candidate genes with significant SNP loci and beneficial haplotypes. The CAPS markers, S15_50486939-CAPS1 and S15_50452626-CAPS2, can effectively distinguish resistant and sensitive genotypes through enzyme digestion. The KASP marker is based on S07_19078765-G/T and exhibits a genotype clustering pattern consistent with disease resistance, demonstrating its application value in breeding. The CAPS and KASP markers developed in this study can provide reliable tools for MAS in FORR disease-resistant varieties. The research results will help reveal the genetic structure of FORR disease resistance and provide support for efficient breeding.

Rapid alkalinization factor: function, regulation, and potential applications in agriculture

Rapid alkalinization factor (RALF) is widespread throughout the plant kingdom and controls many aspects of plant life. Current studies on the regulatory mechanism underlying RALF function mainly focus on Arabidopsis, but little is known about the role of RALF in crop plants. Here, we systematically and comprehensively analyzed the relation between RALF family genes from five important crops and those in the model plant Arabidopsis thaliana. Simultaneously, we summarized the functions of RALFs in controlling growth and developmental behavior using conservative motifs as cues and predicted the regulatory role of RALFs in cereal crops. In conclusion, RALF has considerable application potential in improving crop yields and increasing economic benefits. Using gene editing technology or taking advantage of RALF as a hormone additive are effective way to amplify the role of RALF in crop plants.

Genome-Wide Identification and Comparative Analysis of RALF Gene Family in Legume and Non-Legume Species

Rapid alkalinization factor (RALF) are small secreted peptide hormones that can induce rapid alkalinization in a medium. They act as signaling molecules in plants, playing a critical role in plant development and growth, especially in plant immunity. Although the function of RALF peptides has been comprehensively analyzed, the evolutionary mechanism of RALFs in symbiosis has not been studied. In this study, 41, 24, 17 and 12 RALFs were identified in Arabidopsis, soybean, Lotus and Medicago, respectively. A comparative analysis including the molecular characteristics and conserved motifs suggested that the RALF pre-peptides in soybean represented a higher value of isoelectric point and more conservative motifs/residues composition than other species. All 94 RALFs were divided into two clades according to the phylogenetic analysis. Chromosome distribution and synteny analysis suggested that the expansion of the RALF gene family in Arabidopsis mainly depended on tandem duplication, while segment duplication played a dominant role in legume species. The expression levels of most RALFs in soybean were significantly affected by the treatment of rhizobia. Seven GmRALFs are potentially involved in the release of rhizobia in the cortex cells. Overall, our research provides novel insights into the understanding of the role of the RALF gene family in nodule symbiosis.