Soil salinity is an increasing threat to global food production systems. As such, there is a need for salt tolerant plant model systems in order to understand salt stress regulation and response. Salicornia bigelovii , a succulent obligatory halophyte, is one of the most salt tolerant plant species in the world. It possesses distinctive characteristics that make it a candidate plant model for studying salt stress regulation and tolerance, showing promise as an economical non-crop species that can be used for saline land remediation and for large-scale biofuel production. However, available S. bigelovii genomic and transcriptomic data are insufficient to reveal its molecular mechanism of salt tolerance. We performed transcriptome analysis of S. bigelovii flowers, roots, seeds and shoots tissues cultivated under desert conditions and irrigated with saline aquaculture effluent. We identified a unique set of tissue specific transcripts present in this non-model crop. A total of 66,943 transcripts (72.63%) were successfully annotated through the GO database with 18,321 transcripts (27.38%) having no matches to known transcripts. Excluding non-plant transcripts, differential expression analysis of 49,914 annotated transcripts revealed differentially expressed transcripts (DETs) between the four tissues and identified shoots and flowers as the most transcriptionally similar tissues relative to roots and seeds. The DETs between above and below ground tissues, with the exclusion of seeds, were primarily involved in osmotic regulation and ion transportation. We identified DETs between shoots and roots implicated in salt tolerance including Sb SOS1, Sb NHX, Sb HKT6 upregulated in shoots relative to roots, while aquaporins (AQPs) were up regulated in roots. We also noted that DETs implicated in osmolyte regulation exhibit a different profile among shoots and roots. Our study provides the first report of a highly upregulated HKT6 from S. bigelovii shoot tissue. Furthermore, we identified two BADH transcripts with divergent sequence and tissue specific expression pattern. Overall, expression of the ion transport transcripts suggests Na ⁺ accumulation in S. bigelovii shoots. Our data led to novel insights into transcriptional regulation across the four tissues and identified a core set of salt stress-related transcripts in S. bigelovii .

Salicornia bigelovii is a promising oilseed crop known for its high yield potential and exceptional salt tolerance, ranking among the most salt-resistant vascular plants. Although previous studies have investigated individual phenotypic and genetic characteristics of S. bigelovii, integrated assessments combining agronomic performance, seed morphometric variation, and genetic relationships among geographically distinct accessions remain limited. This study evaluated six S. bigelovii accessions from the Texas Gulf coastline, focusing on phenotypic and morphometric traits, geographic origins, and genomic distances. Significant variability was observed among accessions in key traits, such as plant height, spike number, root length, and seed yield. Notably, the South Padre and Boca Chica accessions demonstrated superior growth and higher seed productivity compared with Corpus Christi Bridge and Galveston accessions, indicating substantial phenotypic diversity and potential for selecting high-performing accessions for breeding. Morphological analysis revealed minor but distinct differences among the six seed accessions. The southern accessions, SPN and SP, exhibited advantageous traits, including a high surface area, circularity values close to 1, and increased seed volume, suggesting favorable dispersal and flow characteristics. Multivariate analyses and hierarchal clustering showed significant relationships among accessions, providing insights for breeding programs. Phylogenetic analysis indicated the divergence of CCB and G accessions from BC, BCW, SP, and SPN. This morphological and genetic assessment establishes a foundation for accelerated molecular breeding and genomic-assisted improvement of S. bigelovii as an industrial crop.