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Theoretical and Applied Genetics

@theorapplgenet.bsky.social
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Theoretical & Applied Genetics communicates key discoveries and news in plant genetics, genomics and plant breeding link.springer.com/journal/122

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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 30/04/2026
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.
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Structural diversity of Ym2, a gene conferring resistance against Wheat yellow mosaic virus
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 30/04/2026
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.
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The DTH8-SD1 pair regulates panicle architecture in rice
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 29/04/2026
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.
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Natural variation in VrERF088 modulates drought tolerance during mungbean germination
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 29/04/2026
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.
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TaAGL6-B1 identified as a candidate gene for the dominant awn-inhibitor locus B2 in wheat
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 28/04/2026
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.
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Unveiling the genetic architecture of stripe rust resistance in wheat: a region-specific GWAS in Xinjiang, China
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 28/04/2026
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.
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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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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 28/04/2026
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.
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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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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 28/04/2026
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.
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Genome-wide association study (GWAS) identifies genetic loci controlling Distinctness, Uniformity, and Stability (DUS) traits in wheat
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 27/04/2026
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.
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Regulation of grain protein content by the amino acid permease gene OsAAP4 in rice
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 27/04/2026
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.
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Molecular marker development for salt tolerance in cowpea: insights from genome-wide association analysis at the early vegetative stage
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 27/04/2026
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.
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Genome-wide association study and transcriptomic analysis reveal new genes for unsaturated fatty acid contents in soybean
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 26/04/2026
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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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 26/04/2026
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.
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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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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 26/04/2026
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.
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Understanding the genetics of root system architecture in pigeonpea [Cajanus cajan (L.) Millsp.]
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 25/04/2026
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.
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GhTPS11, underlying an early-maturity QTL cluster on Chr. D08, positively regulates flowering through the age pathway in cotton
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 25/04/2026
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.
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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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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 24/04/2026
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.
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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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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 24/04/2026
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.
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Candidate genomic regions underlying capsule shattering in sesame revealed by multi-model GWAS and field-based phenotyping
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 24/04/2026
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.
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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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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 24/04/2026
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.
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Comparative transcriptomics of anthocyanin accumulation in the pericarp of pigmented purple corn
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 23/04/2026
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.
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Characterization of the genetic architecture of adult plant resistance to sharp eyespot in Chinese wheat germplasm
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 23/04/2026
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.
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Content characteristics and genetic architecture of macronutrient signatures in cottonseed
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 23/04/2026
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.
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Identification and validation of novel and stable QTL for Gibberella stalk rot resistance in maize inbred KA105
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 22/04/2026
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.
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Genetic and phenotypic associations between peduncle characteristics and spike productivity in wheat under drought and normal conditions
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 22/04/2026
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.
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Integrated omics and functional validation identify StGDPD1 as a central regulator of salt stress tolerance in potato
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 22/04/2026
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.
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Regression approaches for modeling genotype-environment interaction and making predictions into unseen environments
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 21/04/2026
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.
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Exploring standing genetic variation for barley leaf rust resistance in Australian breeding panel
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 21/04/2026
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.
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Targeted expansion of a barley genebank core collection facilitates the discovery of disease resistance loci
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 21/04/2026
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.
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Bayesian neural networks for genomic prediction: uncertainty quantification and SNP interpretation with SHAP and GWAS
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 20/04/2026
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.
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Genomic approaches to build de novo elite breeding gene pools from locally adapted landraces
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 20/04/2026
Rainfed lowland NERICA varieties harbor substantial genetic variation for stagnant‑flooding tolerance, with some lines showing only modest yield loss. A set of stable QTLs for key traits, such as grain yield, under stagnant flooding provides markers for breeding dual‑tolerant rice.
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Unveiling stagnant flooding tolerance in lowland NERICAs: genomic insights and breeding prospects
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 20/04/2026
A QTL on rye chromosome 5R underpins root‑lesion nematode resistance in triticale and explains around 20% of the phenotypic variation. This rye‑derived locus, plus an associated KASP marker, enables marker‑assisted selection to transfer nematode resistance from triticale into wheat.
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Genetic analysis of a quantitative trait locus associated with resistance to the root-lesion nematode Pratylenchus neglectus in triticale
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 19/04/2026
BrRLP1 enhances downy mildew resistance in B.rapa by acting as a membrane‑localized receptor‑like protein. It interacts with the redox‑related enzyme BrMDAR1, linking immune signaling to the ascorbate pathway and offering new mechanistic insight for breeding resistant brassica crops.
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The BrRLP1–BrMDAR1 module regulates the resistance to downy mildew in Brassica rapa
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 19/04/2026
A core set of 1,008 sequence‑tagged microsatellite markers for the Oryza sativa complex was developed, validated. These cross‑amplifiable markers facilitate chromosome‑segment substitution lines, molecular mapping, and trait introgression from wild species into cultivated rice.
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A robust 1K-core marker set for wild germplasm management and targeted pre-breeding of rice: development and applications
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 19/04/2026
A major locus, CaPAR1, underpins plant growth habit variation in chickpea, distinguishing erect/semi‑erect from spreading types. This gene and its haplotypes open a route to breeding mechanically harvestable, high‑yielding chickpea cultivars.
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A genome-wide association analysis identifies a key candidate gene controlling plant growth habit in chickpea
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 18/04/2026
A retrotransposon insertion in PR1b explains why tasty rice cultivars like Koshihikari are highly susceptible to blast. This mutation appears to be fixed across the top Japanese cultivars and also appears in several Chinese‑bred varieties, underlining its genetic impact.
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Modern Japanese rice cultivars often carry a nonautonomous retrotransposon-insertion mutation at the pathogenesis-related 1b protein gene locus causing reduced resistance to Pyricularia oryzae
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 18/04/2026
AhHAA1 is a promising peanut gene tied to higher antioxidant activity in testaless seeds. Researchers mapped it to chromosome A03 and found markers that could help breed more nutritious peanuts.
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A major qualitative trait locus increases antioxidant activity in testaless peanut seeds
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 17/04/2026
Short-term allopolyploidization reshaped miRNAs in Brassica A genomes, with over half lost in B. juncea and B. napus. Retention varied by genome context and neighboring genes, offering new clues to miRNA evolution in polyploids.
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Allopolyploidization-driven short-term evolution of miRNAs in Brassica A genome
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 17/04/2026
Eggplant begomovirus resistance gene found in No.820: SmNEN3, a DEDDh exonuclease. This gene appears to drive dominant resistance to TYLCKaV. Authors identify new DNA markers to help speed marker-assisted breeding for resistant eggplant lines. rdcu.be/fa4et
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Ey-1 encodes a DEDDh exonuclease in eggplant (Solanum melongena), providing a novel pathway for begomovirus resistance
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 17/04/2026
Stable soybean QTL qPL6 on chromosome 6 is linked to petiole length across three seasons, with two auxin-related candidate genes identified. The finding offers useful targets for improving plant architecture and yield under high-density planting.
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Identification of quantitative trait loci qPL6 for petiole length in soybean
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 17/04/2026
A new interpretable deep-learning model, L-CRE, predicts tomato gene expression from regulatory DNA with up to 86.9% accuracy. It also highlights key non-coding regions, including transcription factor binding sites, that shape expression.
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Investigating cis-regulatory elements and gene expression in multiple tomato varieties using interpretable deep learning
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 16/04/2026
TaTPK1-5D helps wheat cope with low potassium by boosting vacuolar K⁺ efflux. Working with TaCIPK23-4D, it emerges as a promising breeding target for better K⁺-use efficiency and low-K tolerance.
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Vacuolar K⁺ efflux transporter TaTPK1-5D confers low-K⁺ tolerance of ‘Zhengmai 136’ through interaction with TaCIPK23-4D in bread wheat
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 16/04/2026
Researchers identified three novel QTL on chromosomes 3H, 4H, and 6H linked to net-form net blotch resistance in barley. These markers offer new tools to accelerate breeding for improved disease resilience.
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Novel resistance loci against Pyrenophora teres f. teres map to chromosomes 3H and 6H of barley
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 16/04/2026
New wheat genetics insight: a major QTL on chr6A (QWE-AX.haust-6A) increases water-extractable arabinoxylan, a key dietary fiber. Candidate gene TaqW-6AS identified, with markers and haplotypes ready for marker-assisted biofortification.
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Identification of TaqW-6AS, a novel gene controlling WE-AX content in wheat grain
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 15/04/2026
First "barcode" consensus karyotype for peanut using oligonucleotide probes reveals A. duranensis and A. ipaensis as subgenome donors. Analysis suggests outcrossing generated distinct A. duranensis chloroplasts, followed by hybridization with A. ipaensis.
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Chromosomal variations and evolution in Arachis species revealed by single-copy FISH karyotyping
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 15/04/2026
Map-based cloning identified ELP1 from Oryza officinalis, encoding an F-box protein with two alternatively spliced isoforms. Overexpressing the short isoform ELP1S increased tiller number by 37.5%, grain number by 37.6%, and total yield per plant by ~30% in cultivated rice.
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An extra-large panicle gene ELP1 from wild rice Oryza officinalis increases grain number and grain yield
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 15/04/2026
EMS mutagenesis identified a "pendant awn" barley mutant with a premature stop codon in HvEMF1L on chromosome 3H, truncating the protein by 62.3%. Pan-genomic analysis showed high sequence conservation, revealing HvEMF1L as a putative regulator of awn development.
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A pendant awn phenotype linked to the EMBRYONIC FLOWER 1 LIKE (EMF1L) gene in barley
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 14/04/2026
High-resolution mapping in 866 maize-teosinte RILs identified 11 ear shank length QTLs explaining 35.8% of variation, with 10 carrying domestication-selected teosinte alleles. RNA-seq of near-isogenic lines for qESL1-1 identified three candidate genes involved in floral development.
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Integrative QTL mapping and RNA-seq unravel the genetic architecture and candidate genes for ear shank length in a large maize–teosinte population
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 14/04/2026
StAN1 overexpression in potato tubers controls tissue-specific flavonoid diversification, upregulating anthocyanins and flavanones while suppressing flavonols. DAP-seq confirmed direct activation of biosynthetic genes like StDFR for nutraceutical enhancement.
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Integrated multi-omics elucidates StAN1 as a key regulator reprogramming flavonoid partitioning and co-regulatory networks in potato tubers
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 14/04/2026
GWAS in the Global Durum Panel and QTL mapping in two RIL populations identified a major resistance locus at the distal end of chromosome arm 6AS. Modern cultivars and Ethiopian landrace PI 387336 showed high resistance, with SNP markers enabling transfer into elite wheat germplasm.
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Genome-wide association and biparental mapping revealed a major quantitative trait locus associated with seedling resistance to bacterial leaf streak in durum
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