Amid escalating water scarcity and groundwater depletion, halophytes such as Salicornia (Amaranthaceae) represent valuable models for extreme salt tolerance and hold promise for saltwater-based agriculture. Here, we show chromosome-scale genome assemblies for six Salicornia species, revealing four distinct subgenomes, reconciling our assemblies with two existing reference genomes (S. ramosissima UK and S. europaea China), correcting chromosome numbering and orientation. Comparative analyses across ploidy levels demonstrate genome expansion in North American lineages driven by Gypsy retrotransposons, and lineage-specific expansions of two gene families implicated in stress metabolism. Phylogenetic and population-structure analyses of a global resequencing panel of 318 accessions resolve interspecific relationships and establish curated germplasm collections for future crop breeding. Genetic analyses uncover a contrasting population-genetic signal on chromosome 6A between two species, highlighting an OSCA calcium-permeable channel gene as a candidate locus for osmotic adaptation. Together, these resources establish a genomic framework for Salicornia that supports evolutionary studies of halophyte adaptation and crop development. Salicornia is a halophytic flowering plants in the family Amaranthaceae. Here, the authors report chromosome-scale genome assemblies for six Salicornia species and reveal subgenome diversity, species boundaries and signatures of halophyte adaptation.
Yun-Chuan Wang, Laxman Adhikari, Lina María Cáceres Leal et al.· Nature Communications· 0 citations
Root biomass is an important determinant of seedling vigor that contributes to water and nutrient acquisition in rice (Oryza sativa L.). In this study, we evaluated the total root weight (TRW) of 127 Korean rice cultivars, comprising 110 temperate japonica (TEJ) and 17 Tongil-type cultivars, under hydroponic conditions. Population structure analysis separated the accessions into two major groups corresponding primarily to the TEJ and Tongil-type cultivars. A genome-wide association study (GWAS) was conducted using the FarmCPU, BLINK, and MLM approaches, all three of which detected a common association signal for TRW on chromosome 7. Further GWAS analysis using only the 110 TEJ cultivars revealed an association signal in the same genomic region, thereby providing evidence of a possible relationship between this region and the variation in TRW within the TEJ cultivars. Additionally, by performing linkage disequilibrium block analysis, we identified a candidate region spanning approximately 369 kb, containing 43 genes. On the basis of gene expression and haplotype analyses, Os07g0517000, Os07g0520400, and Os07g0520900 were selected as putative candidate genes. However, given that the observed haplotype differences were partially associated with the varietal-group composition, their effects should be interpreted with caution. These results will provide genomic information for gaining a better understanding of variations in seedling root biomass and contribute to further validation of genes associated with root development in rice.
Junghyun Gong, Han-gyeol Kim, Dongryung Lee et al.· Korean Journal of Breeding S...· 0 citations
It is demonstrated that OsCGT is essential for C-glycosyl flavone biosynthesis in yel-sdj seeds, particularly for isoorientin accumulation in the embryo, and indicate that embryo lethality is a fundamental consequence of the OsDET1 mutation rather than OsCGT-dependent flavone accumulation.
Backki Kim, Hee-Jin Choi, Sangrae Shim et al.· BMC Plant Biology· 0 citations
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