Background: Abiotic stresses, particularly drought and heavy metal toxicity, have presented a significant risk to long-term agricultural output around the world. Although the heavy-metal-associated domain (HMA) gene family has been widely explored in Arabidopsis and other plants, it has not been thoroughly studied in wheat (Triticum aestivum). This study was proposed to investigate the HMA gene family in wheat. Methods: To analyze the phylogenetic relationships, gene structure, gene ontology, and conserved motifs, a comparative study of wheat HMA genes with the Arabidopsis genome was performed. Results: A total of 27 T. aestivum proteins belonging to the HMA gene family were identified in this study, with amino acid counts ranging from 262 to 1,071. HMA proteins were found to be grouped into three subgroups in a phylogenetic tree, and closely related proteins in the tree showed the same expression patterns as motifs found in distinct subgroups. Gene structural study elucidated that intron and exon arrangement differed by family. Conclusion: As a result, the current work offered important information regarding HMA family genes in the T. aestivum genome, which will be valuable in understanding their putative functions in other wheat species.

The SPL gene family (for Squamosa Promoter-binding like Proteins) represents specific transcription factors that have significant roles in abiotic stress tolerance, development and the growth processes of different plants, including initiation of the leaf, branching and development of shoot and fruits. The SPL gene family has been studied in different plant species; however, its role is not yet fully explored in pigeon pea (Cajanus cajan). In the present study, 11 members of the CcSPL gene family were identified in C. cajan. The identified SPLs were classified into nine groups based on a phylogenetic analysis involving SPL protein sequences from C. cajan, Arabidopsis thaliana, Cicer arietinum, Glycine max, Phaseolus vulgaris, Vigna unguiculata and Arachis hypogaea. Further, the identification of gene structure, motif analysis, domain analysis and presence of cis-regulatory elements in the SPL family members were studied. Based on RNA-sequencing data, gene expression analysis was performed, revealing that CcSPL2.1, 3 and 13A were significantly upregulated for salt-tolerance and CcSPL14 and 15 were upregulated in a salt-susceptible cultivar. Real-time qPCR validation indicated that CcSPL3, 4, 6 and 13A were upregulated under salt stress conditions. Therefore, molecular docking was performed against the proteins of two highly expressed genes (CcSPL3 and CcSPL14) with three ligands: abscisic acid, gibberellic acid and indole-3-acetic acid. Afterward, their binding affinity was obtained and three-dimensional structures were predicted. In the future, our study may open avenues for harnessing CcSPL genes in pigeon pea for enhanced abiotic stress resistance and developmental traits.

Conserved nature of genomes can be used advantageously to study the landscape of allelic diversity in understudied species of the same genus or family. In the present studies, a total of 54 SSRs regions including both EST and genomic belonging to G. raimondii, G. barbadense and G. hirsutum were selected from the available database for studying the cross-species transferability to 12 understudied species of the family Malvaceae and G. hirsutum (upland cotton). In total 24 SSRs (44.44%) including 5 gSSRs and 19 EST-SSRs showed amplification in the species used in the study depicting a higher amplification ratio of EST-SSRS as compared to genomic SSRs. BNL4037 and BNL3089 both have shown maximum transferability (69.23 %) followed by HAU1980 (61.5%) among all markers tested, while NAU2679, NAU3206, NAU3538, NAU3793, NAU3903, NAU5423 and BNL150 shown 7.69% transferability. In all 13 species allele amplification ranged from 1 to 12 and maximum number of alleles (12) were amplified by primer BNL 3089. Among the species used in study highest transferability rate (100 %) was observed in G. hirsutum followed by Malvaviscus arboreus (45.83 %). However, none of the primer amplified SSR regions in Grewia asiatica and Malva parviflora. The results of this study demonstrated a notable SSR region transferability from cotton to other members of Malvaceae. These findings can contribute to the development of an SSR marker pool, which may aid genetic analysis as well as the allelic diversity assessment of species within the Malvaceae that possess less available genomic information.