Allelic diversity in the Ym2 locus offers a rich reservoir of WYMV‑resistant haplotypes for breeding bread wheat in China, but the absence of functional Ym2 haplotypes in Chinese germplasm so far reveals that this resource has yet to be tapped by Chinese breeding programs.

Structural diversity of Ym2, a gene conferring resistance against Wheat yellow mosaic virus

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DTH8 is a major‑effect QTL that reshapes rice panicle architecture—boosting branch number, panicle length, and grains per panicle. Yet its action is partly mediated by SD1, revealing how QTL interactions can either amplify or constrain yield gains in breeding.

The DTH8-SD1 pair regulates panicle architecture in rice

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Natural variation in a mungbean ERF gene shapes seed‑germination responses under drought, with a mutation in the promoter linked to higher germination. GWAS plus KASP markers and transgenic validation in Arabidopsis show that this gene modulates ABA‑responsive‑gene expression.

Natural variation in VrERF088 modulates drought tolerance during mungbean germination

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TaAGL6‑B1, an AGAMOUS‑LIKE 6 transcription factor, is the likely B2‑locus gene behind awn suppression in wheat. A nonsynonymous change causes ectopic lemma expression that represses TaDL and shortens awns, defining a core genetic module for awn development.

TaAGL6-B1 identified as a candidate gene for the dominant awn-inhibitor locus B2 in wheat

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Genome‑wide association in 300 winter wheat lines maps 20 seedling‑ and 12 adult‑plant‑stage QTLs for stripe rust resistance, including 11 and 7 potentially novel loci. A favorable haplotype (Hap2) provide practical tools for breeding more resistant wheat cultivars.

Unveiling the genetic architecture of stripe rust resistance in wheat: a region-specific GWAS in Xinjiang, China

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Genomic‑selection design matters: in unconstrained rice breeding, large progenies best capture additive and epistatic effects, whereas smaller progenies with more crosses deliver higher long‑term gain. These simulations offer practical rules for optimizing GS schemes.

Optimizing progeny size and number of crosses under genomic selection: insights into additive and epistatic contributions to long-term genetic gain

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Leaf and panicle blast resistances in rice are moderately correlated and co‑controlled by several genes. Integrating GWAS‑based marker weights into GBLUP lifted genomic‑prediction accuracy up to 37%, offering a practical route to improve selection for complex blast‑resistance traits.

Enhancing genomic prediction ability of blast resistance using genome-wide association study-derived marker weights in two rice (Oryza sativa L.) populations

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A GWAS in 412 European wheat varieties links 57 loci to 15 Distinctness, Uniformity, and Stability (DUS) traits, with a strong marker near Ppo‑A1 predicting seed colouration. This marker set supports marker‑aided variety identification and DUS‑test optimization.

Genome-wide association study (GWAS) identifies genetic loci controlling Distinctness, Uniformity, and Stability (DUS) traits in wheat

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The amino acid transporter OsAAP4 regulates grain protein content in rice by mediating amino‑acid translocation into the grain via vascular‑bundle‑localized plasma‑membrane transport. Mutants show lower yield and protein, while overexpression boosts both grain protein and yield.

Regulation of grain protein content by the amino acid permease gene OsAAP4 in rice

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A GWAS in 401 cowpea lines under salt stress identifies several marker–trait associations, with a SNP pair forming an efficient marker combination for distinguishing salt‑tolerant germplasm. The GC haplotype at these sites links to salt improved tolerance.

Molecular marker development for salt tolerance in cowpea: insights from genome-wide association analysis at the early vegetative stage

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Integrated GWAS and RNA‑seq in soybean link 52 stable QTLs to unsaturated fatty acids, with three prioritized genes, confirmed by heterologous overexpression in Arabidopsis to shift seed fatty acid profiles. These resources provide a genetic toolkit for improving soybean oil quality.

Genome-wide association study and transcriptomic analysis reveal new genes for unsaturated fatty acid contents in soybean

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Seed oil content in rapeseed is shaped by complex genetics, with 142 GWAS‑linked QTLs and the HD‑ZIP transcription factor BnaC.GL2.b standing out as a key regulator. Combining GWAS with TILLING identified several BnaC.GL2.b alleles that increase oil content. rdcu.be/fa4fU

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Stable QTL for wheat spike traits were identified and validated across 15 environments, with 14 major loci linked to thermotolerance, grain yield, and floret fertility. New KASP and gene‑based markers give breeders a genomic toolkit for developing heat‑tolerant wheat.

Investigations into genetic control of six spike traits with a focus on breeding for terminal heat stress tolerance in common wheat

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Field‑based “shovelomics” in a pigeonpea diversity panel reveals deep, spreading, and dimorphic root‑system types linked to RSA traits like tap‑ and lateral‑root length. GWAS pinpoints 45 marker‑trait associations for marker‑assisted breeding of stress‑resilient pigeonpea.

Understanding the genetics of root system architecture in pigeonpea [Cajanus cajan (L.) Millsp.]

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GhTPS11, a trehalose‑6‑phosphate synthase gene, acts as a positive regulator of flowering in cotton. Early‑maturity QTLs on chromosome D08 plus functional tests in Arabidopsis and cotton establish GhTPS11 as a key target for breeding faster‑maturing cotton lines.

GhTPS11, underlying an early-maturity QTL cluster on Chr. D08, positively regulates flowering through the age pathway in cotton

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Sweetpotato has at least five IbMYB1 copies, with the newly characterized IbMYB1‑4 driving purple‑to‑black vine color via stem‑ and leaf‑specific expression. This locus plus its regulatory partners offer a clear handle for breeding pigmented, ornamental‑quality sweetpotato lines.

IbMYB1-4 positively regulates purple stem and influences leaf color via dosage effect of gene expression in sweetpotato (Ipomoea batatas (L.) Lam.)

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Seven QTL for adult‑plant crown rust resistance in oat were mapped in Australian field trials, with a major locus on chromosome 4A overlapping Pc61‑linked regions. KASP markers for four key QTL enable marker‑assisted stacking of resistance alleles in new cultivars.

QTL mapping of oat crown rust resistance in Australian fields and identification of a seedling resistance locus in oat line GS7

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Multi‑model GWAS in Sudanese sesame reveals several marker‑trait associations for capsule shattering, including SNPs on chromosomes 1, 2, and 8, plus candidate genes. These loci provide targets for marker‑assisted breeding of non‑shattering, machine‑harvest‑ready sesame cultivars.

Candidate genomic regions underlying capsule shattering in sesame revealed by multi-model GWAS and field-based phenotyping

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Natural variation of SmFAP1, an R2R3‑MYB gene, controls anthocyanin‑deficient green peel in eggplant, with a 6‑bp deletion and a second loss‑of‑function allele disrupting DNA binding. A co‑dominant marker enables efficient marker‑assisted selection for purple‑peel breeding.

A 6-bp deletion in the R2R3-MYB domain of the SmFAP1 gene disrupts DNA-binding capacity and leads to anthocyanin deficiency in eggplant peels

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RNA‑seq and WGCNA in purple maize pericarp pinpoint Pl1, Lc1, P1, and Wrky33 as key regulators of anthocyanin content. These genes offer breeders clear targets to boost natural pigment levels for food‑colorant‑focused corn lines.

Comparative transcriptomics of anthocyanin accumulation in the pericarp of pigmented purple corn

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Four QTLs for sharp eyespot resistance in wheat were identified via genome‑wide association, and genomic prediction using just 35 key SNPs achieved high accuracy. Pyramiding favorable QTLs reduced disease index by 22%, giving breeders tools for developing more resistant wheat lines.

Characterization of the genetic architecture of adult plant resistance to sharp eyespot in Chinese wheat germplasm

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This study uncovers the genetic architecture of potassium, calcium, and magnesium content in cottonseeds, identifying 159 QTLs across 276 accessions. A key candidate gene linked to both K and Mg levels, offers a clear path for breeding more nutritious cottonseed.

Content characteristics and genetic architecture of macronutrient signatures in cottonseed

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Four novel and stable QTL for Gibberella stalk rot resistance in maize were identified, with a major locus qGSR8.08 fine‑mapped to a 1.34 Mb region. Pyramiding these QTLs significantly enhanced stalk and ear rot resistance and reduced yield loss.

Identification and validation of novel and stable QTL for Gibberella stalk rot resistance in maize inbred KA105

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Wheat peduncle traits, especially weight and diameter, strongly link to spike and grain traits under both normal and drought conditions. Genome‑wide analysis shows peduncle and spike traits are genetically distinct, with one key SNP in a peduncle‑ and spike‑expressed gene.

Genetic and phenotypic associations between peduncle characteristics and spike productivity in wheat under drought and normal conditions

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Hydroponic screening identifies potato variety Dongnong 303 as highly salt tolerant, with StGDPD1 being upregulated under stress. Overexpression enhances salt tolerance, while knockout lines become hypersensitive, pointing to StGDPD1 as a key genetic target for salt tolerance.

Integrated omics and functional validation identify StGDPD1 as a central regulator of salt stress tolerance in potato

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Several regression methods for GxE prediction are closely linked, with environmental covariates improving forecasts and a new approach enhancing uncertainty estimation. The framework unifies Finlay‑Wilkinson, random‑coefficient, and kernel‑based models for more robust predictions.

Regression approaches for modeling genotype-environment interaction and making predictions into unseen environments

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A genotype‑by‑environment analysis and haplotype mapping in barley identifies five stable haplo‑blocks linked to adult‑plant leaf rust resistance, including the Rph20 region. Stacking favorable haplotypes boosts resistance and helps breed more resilient cultivars.

Exploring standing genetic variation for barley leaf rust resistance in Australian breeding panel

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Genome‑wide prediction can unlock hidden disease‑resistance diversity in barley genebanks by imputing resistance for thousands of unphenotyped accessions. Models predicted multiple disease resistance across 20,458 lines and revealed new resistance‑associated markers.

Targeted expansion of a barley genebank core collection facilitates the discovery of disease resistance loci

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Bayesian neural networks with LASSO and a new SHAP‑GWAS tool, GSMeSP, enable accurate, uncertainty‑aware genomic prediction in cotton. The framework improves accuracy and pinpoints trait‑linked SNPs, especially on the D‑subgenome, to support transparent breeding decisions.

Bayesian neural networks for genomic prediction: uncertainty quantification and SNP interpretation with SHAP and GWAS

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Many nascent breeding programs cross locally‑elite lines but lack structured gene‑pool design. This study compares genomic approaches to infer elite gene pools, showing that QTL‑based inference plus iso‑elite crosses boosts genetic gain in simulated forward‑breeding programs.

Genomic approaches to build de novo elite breeding gene pools from locally adapted landraces

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