Aug 2026· Molecular breeding· Vol 46· 0 citations· 58 references
Medicine
TL;DR
Transgenic evaluations confirmed that OsSLT1 acts as a positive regulator of salt tolerance at the seedling stage, and no significant changes in Na+ or K+ accumulation were observed in flag leaves under the tested salt-stress condition, suggesting that OsSLT1 may regulate salt tolerance through mechanisms beyond classical shoot ion accumulation.
Water deficit is a major constraint on pepper (Capsicum annuum) yield, yet the genetic architecture of reproductive-stage drought tolerance remains poorly resolved. We phenotyped a Balkan C. annuum diversity panel (n = 133) and an interspecific backcross inbred line (BIL) population (n = 76) under well-watered (WW) and water-stress (WS) conditions. WS was applied from anthesis of the second truss as a stepwise reduction in irrigation volume relative to WW (30% for 7 days, then 60% thereafter), maintained for 90 days across the reproductive period. We assessed yield components, soluble solids, and stress-tolerance (STI) and stress-susceptibility (SSI) indices. Genome-wide association study (GWAS) identified 104 SNP-trait associations (P < 1×10-5), and QTL mapping detected 38 significant QTLs (1,000 permutations, α = 0.01), with the QTL intervals defined at LOD ≥ 8. Integrating GWAS and QTL mapping under WS revealed overlapping loci on chromosomes 5 and 6, harboring two consensus intergenic SNPs associated with yield components and soluble solids. Haplotype analysis linked chromosome 5 alleles to higher fruit number and soluble solids. At chromosome 6, the G allele at SNP 6_28348737 was enriched in tolerant lines for fruit number. These regions harbor candidate genes for reproductive development and stress response, including GREEN RIPE-LIKE1 (GRL1), CYP77A19, Endoglucanase-like, and FLOWERING PROMOTING FACTOR 1 (FPF1), possibly through cis-regulatory variation. Together, these results advance understanding of the genetic basis of pepper yield under drought and identify candidate breeding markers.
Avanish Rai, Emil Vatov, Alicja Wieteska Georgieva et al.· Journal of Experimental Bota...· 0 citations
Soil salinity is a major problem that reduces the growth and yield of rice, particularly in coastal rice-growing regions such as certain provinces of Cambodia. This study evaluated salinity tolerance in 60 Cambodian rice varieties at germination and seedling stages and combined physiological analyses with genome-wide association study (GWAS) to identify traits and genomic regions associated with salinity tolerance. The screening at the seedling stage showed CAR 11 was a highly salt-tolerant variety in response to salt stress, suggesting this variety could be used in actual salt-affected fields using the transplanting method and may also serve as a valuable genetic resource for salt-tolerance breeding. K+ concentration and Na+/K+ ratios in roots and shoots were identified as physiological traits determining salt tolerance of Cambodian rice varieties. Several varieties also exhibited high tolerance during germination under salt stress, suggesting their potential value as genetic resources for salt-tolerance breeding. GWAS identified some marker-trait associations and putative candidate genes associated with salinity tolerance-related traits under salt stress. These findings provide fundamental knowledge regarding salt tolerance and putative genes associated with traits in Cambodian rice varieties, and this knowledge is essential for developing salt-tolerant varieties via breeding programs and extending rice production in salt-affected areas.
Sarin Neang, Bros Kak, Mab Ken et al.· Euphytica· 0 citations
The genetic architecture and core candidate genes for shoot length (SL) and root length (RL) at the germination stage are dissected and seven core candidate genes for SL and 13 for RL are identified, including three pleiotropic genes regulating both traits.
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
Soil salinity is a major constraint limiting rice productivity, particularly at the reproductive stage. To elucidate the genetic basis of reproductive stage salinity tolerance, this study validated and fine-mapped quantitative trait loci (QTL) for yield-related traits using a salinity-tolerant line SL506, identified through screening of Nona Bokra–CSSLs in a Koshihikari background. In 2016, the F2 population derived from SL506/Koshihikari was evaluated under long-term salt stress; three QTLs associated with plant dry weight, panicle number, and grain weight were detected on chromosome 2. In 2023, validation analysis using F3 individuals confirmed the presence of these QTLs. Subsequent fine-mapping using F4 near-isogenic lines (NILs) delimited the QTL to a 1.7 Mb interval and high-resolution mapping using an F5 recombinant population progressively refined it to a 473 kb genomic region containing 69 annotated genes. Variant Effect Predictor analysis identified 15 deleterious nonsynonymous variants (SIFT < 0.05) in six candidate genes. Based on annotated gene functions, predicted variant effects, and their membership in stress-related gene families, OsPP2C24, OsFbox102, and OsWAK14 were suggested as the most promising candidate genes underlying qPDW2. These findings provide insights into the genetic basis of reproductive-stage salinity tolerance from valuable resources for the future improvement of salt tolerance and yield stability in rice.
Farjana Rauf, H. Trần, T. Nguyen et al.· Agronomy· 0 citations
Sweet corn is a globally important dual-purpose crop for both food and fresh vegetables. The plant architecture and ear-related traits directly determine its yield potential and field ecological adaptability. To elucidate the genetic architecture of these traits and identify superior alleles for breeding, we conducted a genome-wide association study (GWAS) on 11 agronomic traits using 30,597 high-quality SNP markers in a panel of 101 elite sweet corn inbred lines. Population genetic structure was analyzed using sparse non-negative matrix factorization (sNMF) and discriminant analysis of principal components (DAPC) algorithms, revealing three main clusters and six subpopulations. The clustering pattern was highly consistent with germplasm origin. Association mapping with the fixed and random Circulating Probability Unification (FarmCPU) model identified 16 significant marker–trait associations (MTAs), distributed across seven target agronomic traits. The phenotypic variance explained (PVE) by individual loci ranged from 8.0% to 16.0%. Among these, five stable MTAs across environments, a novel ERN locus (SNP25518) specific to sweet corn, and most association intervals overlapped with previously reported quantitative trait loci (QTLs). Within the ±0.15 Mb (defined by LD decay) flanking windows around the significant SNP loci, a total of 236 candidate genes were annotated, which are primarily involved in hormone signaling, carbon and nitrogen metabolism, cell division, and plant growth and development. In summary, this study dissected the genetic basis of key agronomic traits in sweet corn and provides a foundation for marker-assisted selection and functional validation.
Yan-Chao Du, Jing-Wen Xu, Huiming Li et al.· Plants· 0 citations
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