Salinity, a major abiotic stress, significantly impairs crop productivity by inducing osmotic, ionic, and secondary stresses that disrupt metabolic processes. Chickpea (Cicer arietinum L.), a diploid annual legume of the Fabaceae family, is one of the major pulse crops cultivated by farmers with limited resources. While previous studies have explored salt tolerance in chickpeas, this study provides a comprehensive multi-omics perspective. Exploring the mechanism of chickpea adaptation to the saline environment can effectively supplement the problem of single source of plant protein. The present study analyzed the transcriptomic and metabolomic profiles of two distinct chickpea varieties, DY3 and DY1, with contrasting salinity tolerance capacities. The salinity tolerance of DY3 was associated with greater biomass, higher antioxidant enzyme activity, and higher photosynthetic efficiency. Transcriptomic analysis revealed that the genes induced in DY3 under salinity stress were associated with ion homeostasis, antioxidant defense system, and plant hormone signaling. Metabolomics analysis revealed significant enrichment of components of diverse secondary metabolites pathways, as well as carbohydrate metabolism. Integrated multi-omics analysis highlighted the anthocyanin biosynthesis pathway, functioning within the broader flavonoid metabolic network, as a key regulator of salt tolerance in the chickpea. Subsequent, RT-qPCR confirmed the upregulation of key genes associated with anthocyanin metabolism. These findings reveal the key regulatory role of the flavonoid pathway in salt tolerance of chickpeas, offering insights for breeding improved varieties.

Soybean is an important crop worldwide that provides ~ 50% oil for humans. Salinity is a major abiotic stress that inhibits soybean growth and yield. Dissecting the genetic basis of salt tolerance is an effective way for soybean plants to combat salt-related yield losses. In this study, the variety salt tolerance index (STIv) of a natural population of 140 soybean germplasms was calculated in terms of plant height (PH), leaf area (LA), shoot fresh weight (SFW) and shoot dry weight (SDW), which were measured under normal condition and in a 1.50% NaCl solution. GWAS analysis was subsequently conducted on the basis of STIv and 150 K SNP markers of “Zhongdouxin-1”. The results revealed that 365 significant SNPs located on 19 chromosomes (excluding Gm03) were associated with STIv. Among them, 108 SNPs were associated with LA-STIv, 71 SNPs associated with PH-STIv, 95 SNPs associated with SDW-STIv and 91 SNPs associated with SFW-STIv. A total of 333 genes were identified according to the flanking region (150 kb) of the significant SNPs. 333 genes were identified. Based on gene functional annotations, SNP mutations, and RNA expressions, nine causal genes responsible for soybean salt tolerance were identified. Thus, the significantly associated SNPs and candidate genes detected in this study might provide novel insights into soybean salt tolerance in breeding programs.

This study evaluated 362 chickpea accessions by analyzing the phenotypic variation of 17 major traits. The main agronomic traits and quality traits were comprehensively evaluated using principal component analysis (PCA) and cluster analysis. The results revealed a Shannon diversity index (H’) for the five qualitative traits ranging from 0.76 to 1.20, while for the twelve quantitative traits, it ranged from 1.45 to 2.07. The coefficient of variation (CV) ranged from 7.63% to 41.69%, demonstrating substantial variation and significant differences among the 362 germplasm resources. Correlation analysis revealed that traits such as growth period, plant height, seed weight per plant, and hundred-seed weight were closely correlated with yield. PCA extracted five principal components, collectively explaining 76.06% of the total variance, representing most of the agronomic traits and quality traits. Cluster analysis categorized the accessions into five distinct groups, which can be used as germplasm alternative materials with high yield, mechanization potential, large grain size, early maturity, stress resistance, and high protein content. Using a membership function, a comprehensive evaluation score (F-value) was calculated, leading to the identification of ten accessions with superior overall traits. These could be used as materials for breeding and germplasm creation of new chickpea varieties. This research provides a scientific basis for future parental selection in chickpea breeding programs and for the screening of specific chickpea germplasm resources.