Phenotypic evaluation and mapping QTLs for drought tolerance in an interspecific RIL population from a Setaria italica × Setaria viridis cross

Genetic Dissection and Fine-Mapping of QTL for Salinity Tolerance at the Reproductive Stage on Chromosome 2 of Rice Variety Nona Bokra

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.

Genomics-Assisted Breeding for Drought Tolerance in Wheat (Triticum aestivum L.): Recent Advances and Future Prospects

Overall, transcription factors from the DREB, NAC, MYB, and WRKY families are still considered the primary regulatory targets, but CRISPR/Cas-based gene editing is now able to provide precise, multiplex gene modifications in polyploid wheat.

Phenotypic variation in drought response for a double-haploid population of bread wheat (Triticum aestivum)

Integrated Genome-Wide Association and QTL Mapping Elucidate the Genetic Basis of Fruit Yield and Quality Traits in Pepper under Water Stress.

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.

Linkage Mapping Study Reveals Conservative QTL and Candidate Genes for Fusarium Ear Rot Resistance in Maize

Fusarium ear rot (FER), caused by Fusarium verticillioides (F. verticillioides), is a major disease of maize that reduces grain yield and quality globally. However, few major loci for FER have been verified and cloned. Resistance to FER is a quantitative trait influenced by environmental conditions, and maize genotypes completely resistant to the pathogen remain unknown. To gain a comprehensive understanding of the genetic basis of natural variation in FER resistance, a recombinant inbred line (RIL) population consisting of 257 progenies was developed by crossing the resistant line BT with the susceptible line Xi502. This population was genotyped using a set of 6807 high-density single nucleotide polymorphism (SNP) markers developed in this study. As a result, a total of five QTLs were identified by linkage mapping across three years, located on five chromosomes, and explaining 4.38–13.13% of the phenotypic variation. Among these was a major QTL, qFER5-2. Located on chromosome 5 within the interval 185568562–185574073, qFER5-2 explained 13.13% of the total phenotypic variance. The two candidate genes within qFER5-2 exhibited distinct expression profiles between the BT and Xi502 inbred lines, suggesting their potential association with FER resistance. Collectively, these findings provide candidate genetic resources for further investigation and offer potentially useful materials for maize disease resistance breeding.

Identification of genetic factors governing drought tolerance in wild and domesticated tetraploid wheat

Germplasm characterization and gene identification are essential first steps in developing drought-resilient cultivars. Evaluation of diverse tetraploid wheat accessions representing cultivated and wild species under severe drought stress using an in-house protocol identified three extremely tolerant genotypes including the CIMMYT-bred durum ( Triticum turgidum ssp. durum ) variety Altar 84 and the two wild emmer ( T. turgidum ssp. dicoccoides ) accessions PI 478742 and PI 481521. Chromosome substitution lines involving individual pairs of chromosomes from PI 478742 and PI 481521 substituted for homologous pairs of chromosomes in drought sensitive durum variety Langdon 16 were evaluated to identify chromosome(s) carrying loci controlling drought tolerance. The 11 chromosome substitution lines available for PI 478742 (2A, 3A, and 3B substitution lines were not available) were all sensitive to drought suggesting tolerance may be conferred by a locus on one of the chromosomes not evaluated. All 14 possible chromosome substitution lines were available for PI 481521, and among these, 13 were drought sensitive. The substitution line involving chromosome 3A (LDN-DIC 3A(521)) was tolerant to drought. QTL mapping in a durum inter-varietal population of 138 recombinant inbred lines (RILs) derived by crossing Altar 84 and Langdon 16 identified a major QTL on the short arm of chromosome 4B explaining 26% of phenotypic variation (PVE). This QTL spans large physical region of approximately 265.52 Mb in the Svevo RefSeq v1.0 genome. Sequence analysis of TRITD4Bv1G024340 , an orthologue of drought tolerance gene ( TaWD40-4B.1 ) cloned and previously reported from same genomic region in hexaploid wheat, suggested that QTL identified in this study in Altar 84 is governed by a different genomic region. Additionally, two drought tolerance regions identified (on chromosome 3A and 4BS) in this study are two independent QTLs originated from different sources, and hence they might have different genetic tolerance mechanism. Drought tolerant lines and the genomic regions identified in this study serve as valuable resources for developing drought-resilient durum wheat varieties.