From QTL to candidate genes: a data-driven approach to unravel the genetic architecture of yellow rust resistance in central European wheat

Genome wide association studies and expression analyses identify candidate genes for spot blotch resistance in bread wheat

Genome-wide association identifies and validates genomic region controlling grain yield and agronomic traits in extra-early orange maize inbred lines under drought

In order to meet the expected maize yield by 2050, breeders must work to improve breeding program efficiency by intensifying the implementation of new and improved technologies such as marker-assisted selection (MAS). Dissecting the genomic regions associated with drought tolerance is the first step forward in MAS program deployment for maize improvement under drought stress. Genome-wide association studies (GWAS) were used to investigate and identify quantitative trait loci (QTLs) associated with six traits under drought stress. One hundred and eighty-seven extra-early orange maize inbred lines were evaluated under managed drought stress at Ikenne, in Nigeria, during the 2022 and 2023 dry seasons. The materials were also genotyped using 9355 DArTseq SNP markers and analyzed using the enriched compressed mixed linear model (ECMLM). Enriched compressed mixed linear model was used for association-trait analysis. The ECMLM-based GWAS identified 45 candidate genomic loci associated with the six traits, including five for grain yield, with R2 ranging from 8.79 to 25.3%. Independent validation using the multi-locus 3VmrMLM approach confirmed seven high-confidence genomic loci consistently detected by both methods across grain yield, anthesis-silking interval, ear aspect, and ears per plant, providing additional statistical support for these genomic regions. Candidate gene annotation identified biologically relevant genes underlying the validated loci, including Zm00001eb238250 (protein-serine/threonine phosphatase), Zm00001eb040940 (trehalose-phosphatase), Zm00001eb117820 (homeobox protein knotted-1-like 4), Zm00001eb145560 (zinc ion-binding protein), and Zm00001eb294180 (WRKY DNA-binding domain protein), suggesting their potential roles in drought adaptation and grain productivity. These findings improve our understanding of the genetic architecture of drought tolerance in extra-early orange maize and provide valuable genomic resources for accelerating drought-resilient maize breeding.

Genomic Insights into the Genetic Diversity, Selection Signals, and Agronomic Traits of Rice (Oryza sativa L.) Germplasm in Zhejiang Province

Elucidating the evolutionary trajectories and genetic basis of critical agronomic traits in regional rice germplasm is paramount for discovering elite allelic variations for crop improvement. Here, we systematically characterized a panel of 109 rice accessions from Zhejiang Province through whole-genome resequencing (~10× coverage) coupled with two years of rigorous field phenotypic evaluations. A total of 4,753,071 high-quality genomic variants, including 4,147,316 SNPs, were identified across the genome. Population structure and evolutionary analyses revealed sharp genetic differentiation at the subspecies level, partitioning the panel into distinct indica and japonica clusters accompanied by intricate subpopulation stratification and historical gene flow. Through a joint scanning of the fixation index (Fst) and nucleotide diversity (Pi) ratios, three prominent selective sweep regions (qSS1, qSS10, and qSS12) driving subspecific differentiation were captured on chromosomes 1, 10, and 12. Notably, the qSS12 locus harbors the sucrose transporter gene OsSUT2, indicating that carbohydrate transport and energy metabolism served as core genomic targets driving the indica–japonica divergence. Furthermore, genome-wide association studies (GWAS) successfully mapped 9 significant loci modulating heading date, effective tiller number, and grain size. Subsequent gene-based haplotype analyses within these target intervals pinpointed elite allelic variations in core candidate genes, including OsSPX1 (phosphate homeostasis, 1000-grain weight), Chl9 (chlorophyll synthesis, grain width), and OsCER1 (wax biosynthesis, panicle length). Collectively, this study deciphers the genomic landscape and subspecies differentiation patterns of Zhejiang rice germplasm, providing pivotal molecular targets and invaluable genomic resources for germplasm conservation and precision molecular breeding.

QTL rich genomic clusters in wheat: a catalogue for resistance to Puccinia striiformis f. sp. tritici

Wheat stripe/yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), remains one of the most significant constraints to global wheat production. Genetic resistance breeding is the most effective, economical, and environmentally sustainable strategy for controlling stripe rust. Over the past two decades, advances in genome sequencing, molecular markers and high-throughput genotyping have led to the reporting of numerous Yr genes and an even greater number of quantitative trait loci (QTL, QYr). Alignment of QYr onto a common refence map is therefore required to consolidate dispersed reports, identify regions of co-localization, and define stable genomic regions underlying stripe rust resistance. In this review, catalogued Yr genes and published stripe rust QTL were systematically compiled from 142 studies and, where sufficient marker information was available, physically re-anchored to the IWGSC RefSeq v2.1 wheat reference genome. This integrative approach enabled consolidation of overlapping loci and delineation of 42 QTL-rich clusters (QRCs). The B-sub genome had the highest number of clusters (20), followed by the A-sub genome (16). The D-sub genome had the least number of clusters (6), with two chromosomes, 5D and 6D, lacking any clusters. Thirteen cloned Yr genes were mapped within these clusters, thereby providing functional validation of QRCs as biologically meaningful reservoirs of resistance. This cluster-based framework provides a practical roadmap for consolidating Yr/QYr loci, prioritizing novel genomic targets, and deploying resistance strategically against evolving pathogen populations.

Multiple environmental test and genetic mapping jointly reveal genomic loci and associated genes underlying cotton Verticillium wilt resistance

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.