{"title":"Mining rare haplotypes to accelerate precision breeding in rice.","authors":"Swati Tyagi, Anoop Kishor Singh Gurjar, Sonali Vijay Habde, Krishna Tesman Sundaram, Namrata Devidas Patil, Diksha Rai, Ajay Bogati, Pronob J Paul, Ankur Kumar Singh, Ajay Tripathi, Sanjay Kalia, Ajay Kohli, Arvind Kumar, Pallavi Sinha, Uma Maheshwar Singh, Vikas Kumar Singh","doi":"10.1002/tpg2.70292","DOIUrl":"10.1002/tpg2.70292","url":null,"abstract":"<p><p>Rice (Oryza sativa L.) genomics has made significant progress, with over 13000 genome sequences available and more than 4500 genes functionally characterized. However, limited haplotype-level information has constrained the effective deployment of these genes in breeding programs. Here, we investigated haplotype variation of 1644 functionally characterized genes representing six major trait categories using the 3000 Rice Genome panel. High haplotypic diversity was observed, with more than 300 haplotypes, which clustered into 2-15 major haplogroups. Several haplotypes showed subpopulation or region-specific distributions, whereas others were broadly distributed across the panel. To identify rare haplotypes (frequency < 0.1) with potential breeding value, we prioritized 180 genes relevant to defined product concepts and identified 210 rare haplotypes across 51 genes. Notably, a rare haplotype of DEP1 (DEP1-H2: frequency 0.07) associated with increased panicle length was introgressed into the mega rice variety Swarna through haplotype-based backcross breeding. The resulting introgression lines showed a 29%-34% increase in panicle length compared to the recurrent parent, confirming the functional advantage of the rare haplotype.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 3","pages":"e70292"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13504149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148814665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2026-09-01DOI: 10.1002/tpg2.70289
Asif Bashir Shikari, V Shasi Kiran Reddy, Raheel Shafeeq Khan, Noor Ul-Ain, Gazala H Khan, Najeeb-Ul-Rehman Sofi, Zahoor A Dar, Nazir A Ganai, R K Salgotra, Manmohan Sharma, G A Parray, A K Singh
{"title":"Re-sequencing 142 rice genomes reveals the fine-scale population structure and phylogenetic affinities of landraces of Kashmir Valley: Evidence from domestication and adaptive signatures.","authors":"Asif Bashir Shikari, V Shasi Kiran Reddy, Raheel Shafeeq Khan, Noor Ul-Ain, Gazala H Khan, Najeeb-Ul-Rehman Sofi, Zahoor A Dar, Nazir A Ganai, R K Salgotra, Manmohan Sharma, G A Parray, A K Singh","doi":"10.1002/tpg2.70289","DOIUrl":"10.1002/tpg2.70289","url":null,"abstract":"<p><p>The emergence of rice (Oryza sativa) as a cultivated crop has represented a landmark in the history of agriculture in Kashmir Valley. Unlike winter cereals, such as wheat and barley, which exhibit clear West-Asian origins, rice attained a different domestication trajectory linked to East-Asian Neolithic cultures. However, evidence of such origins and adaptive history of Kashmir's rice landraces have relied on limited archaeo-botanical data, tool typologies, and information pertaining regional cultural exchange. We present the first comprehensive genomics-resource for the region produced through whole genome re-sequencing of 142 rice germplasm lines. By leveraging on the 3000 Rice Genomes Project (3K RGP) database, we analyzed fine-scale population structures and evolutionary relationships. Our findings reveal that local landraces possess temperate japonica (Tej) genetic signatures with the origins having been traced to North-East Asia, while the modern bred varieties in the region often align with indica (derivative) lineages from subtropical India. The sequence data were generated with a mean depth of 13.6x, and 3.94 million high-confidence single nucleotide polymorphisms (SNPs) after stringent filtering. Populations resolved into a bipartite genetic structure (K = 2) comprising two major sub-populations with an admixed group, with the help of high-polymorphism information content SNP panels. Genome-wide diversity analyses revealed the positive Tajima's D values, indicating extensive population structure and balancing selection, with localized signatures of directional selection. The allelic characterization explained the rich diversity at the functionally polymorphic loci linked to domestication, quality, and adaptive traits, particularly those associated with cold tolerance. The gene repository shall provide for development of better quality and climate resilient cultivars.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 3","pages":"e70289"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148799895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A high-quality haplotype-resolved genome of Pyrus calleryana provides insights into adaptive gene families.","authors":"Xiaogang Dai, Xiaoyue Yang, Changci Jiang, Lizhen Huang, Fangping Li, Zhuangwei Hou, Fenghou Shi, Zefu Wang, Wenjie Yang, Yongbao Shen","doi":"10.1002/tpg2.70286","DOIUrl":"10.1002/tpg2.70286","url":null,"abstract":"<p><p>Callery pear (Pyrus calleryana) is a deciduous species native to East Asia with notable ornamental and ecological value, but the genomic resources for this species remain limited. Here, we report the first haplotype-resolved, chromosome-scale genome of P. calleryana. The final genome assembly comprises two phased haplotypes measuring 506.97 and 504.62 Mb. These haplotypes contain 41,234 and 41,329 predicted protein-coding genes, respectively, with more than 97% of the genes receiving functional annotations. Comparative genomic analyses further identified 680 species-specific orthogroups enriched in hormone signaling, metabolic processes, and stress-responsive pathways, among which several LIK1-like genes may contribute to environmental adaptation. This high-quality genome assembly offers an essential foundation for subsequent studies on the ecological adaptability, invasiveness, and functional genomics of P. calleryana.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 3","pages":"e70286"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13431685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148609190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2026-09-01DOI: 10.1002/tpg2.70296
Jayanta Roy, Rian Lee, Caroline Osborne, Phillip N Miklas, Juan M Osorno, Phillip E McClean
{"title":"Genomic resources to advance seed coat color and patterning genetics and breeding in common bean (Phaseolus vulgaris L.).","authors":"Jayanta Roy, Rian Lee, Caroline Osborne, Phillip N Miklas, Juan M Osorno, Phillip E McClean","doi":"10.1002/tpg2.70296","DOIUrl":"10.1002/tpg2.70296","url":null,"abstract":"<p><p>Seed coat color and patterning are key quality traits in common bean (Phaseolus vulgaris L.) that define market classes and strongly influence consumer preference and market value. These traits are controlled by a complex network of major genes (sometimes with epistatic interactions), which complicates the recovery of desired market class phenotypes following inter-market class hybridization. Although many of the underlying loci have been genetically mapped, diagnostic, high-throughput molecular markers for efficient allele tracking across the Middle American and Andean gene pools remain limited. In this study, we developed and validated 24 gene-specific PCR Allele Competitive Extension (PACE) markers targeting seven major seed coat color genes (G, B, V, J, Rk, T, and Z) and two patterning genes (C<sup>Pi</sup> and C<sup>St</sup>), together with a previously reported marker associated with the postharvest seed coat darkening locus (P<sup>sd</sup>). An additional PACE marker targeting the Phaseolin (Phs) locus was developed to distinguish Middle American (S-type) and Andean (T-type) gene pools, providing a complementary tool for assessing genetic background alongside seed coat-specific loci. Marker performance was evaluated across three diverse panels, revealing high diagnostic accuracy for most loci (90%-100%). However, for loci such as J, V, Rk, T, and Z, allele-specific markers or marker combinations were required to capture full allelic diversity. Haplotype analysis further revealed substantial allelic diversity across market classes and identified background-specific interactions. Collectively, these results provide a comprehensive set of high-resolution, gene-anchored PACE markers for seed coat color, patterning, and gene pool classification in common bean. These markers enable rapid and precise allele tracking in breeding populations and germplasm collections, facilitating marker-assisted selection for market class-specific seed coat traits and accelerating genetic improvement.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 3","pages":"e70296"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13547584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148901355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Dissecting genetic architecture and improving machine learning‑based genomic prediction of flowering time in Osmanthus fragrans by integrating structural variants.","authors":"Hui Xia, Hongguo Chen, Yuanhang Wu, Ting Zhang, Guifu Zhang, Jingiing Zou, Yingting Zhang","doi":"10.1002/tpg2.70301","DOIUrl":"10.1002/tpg2.70301","url":null,"abstract":"<p><p>Sweet osmanthus (Osmanthus fragrans), a traditional ornamental plant in China, exhibits substantial variation in autumn flowering time, which significantly affects landscape application and cultivation efficiency. Here, we performed a genome-wide association study on 127 resequenced accessions classified into early, intermediate, and late flowering types, using a set of 2,325,410 single-nucleotide polymorphisms (SNPs) and 246,824 structural variants (SVs). By integrating SNP/insertion and deletion (Indel) and SV data with weighted gene co-expression network analysis, machine learning, and genomic prediction, we dissected the genetic architecture of flowering time. We identified 24 associated SNP/Indels and six SVs, mapping to 30 candidate genes, including known flowering regulators FLK, LOS1, Y14, MIF2, and GID1B. These genes showed tissue-specific expression, with some responding to low temperature. The two hub genes, GUX1 and LYG027904, were located within modules of the co-expression network associated with low-temperature treatment. Haplotype analysis revealed a specific three-SNP haplotype associated with late flowering and linked to LOS1, and epistatic interactions among combined genotypes contributed to phenotypic variation. Notably, integrating SVs with SNP/Indels improved genomic prediction accuracy; the gradient boosting decision tree model outperformed other machine learning algorithms, achieving a mean accuracy of 0.859 and an AUC > 0.8 (where AUC is area under receiver operating characteristic curve) for all flowering types. These findings provide insights into the genetic mechanisms underlying flowering time variation in O. fragrans, offer candidate genes and haplotypes for molecular breeding, and highlight the value of integrating SVs with machine learning for genomic prediction in woody ornamentals.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 3","pages":"e70301"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13550763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148907821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2026-09-01DOI: 10.1002/tpg2.70267
Ezekiel Ahn, Insuck Baek, Seunghyun Lim, Louis K Prom, Moon S Kim, Lyndel W Meinhardt, Clint Magill
{"title":"High-density mutation tracks are associated with proton-beam irradiation patterns in Sorghum bicolor.","authors":"Ezekiel Ahn, Insuck Baek, Seunghyun Lim, Louis K Prom, Moon S Kim, Lyndel W Meinhardt, Clint Magill","doi":"10.1002/tpg2.70267","DOIUrl":"10.1002/tpg2.70267","url":null,"abstract":"<p><p>Induced mutagenesis is a cornerstone of crop functional genomics, yet the extent to which distinct radiation sources reshape the spatial distribution of mutations remains difficult to evaluate in reduced-representation datasets. Here, we analyze a published genotyping-by-sequencing (GBS) panel (192,040 loci) to compare proton-beam and gamma-ray mutagenesis in Sorghum bicolor. Because GBS sampling is nonuniform, all analyses were conducted within an explicitly defined GBS-callable sequence space. Within this callable space, 96-channel trinucleotide spectra were broadly similar between radiation types, whereas spatial summaries differed. Macroscale analysis using the Gini coefficient indicated that proton-treated lines exhibit a highly unequal, spike-like distribution of mutations, whereas gamma-treated lines show a more diffuse window-level distribution. Microscale spatial statistics were consistent with clustering patterns that were more prominent in proton-treated lines, including an aggregation scale of ∼500 kb, with a substantial fraction of the mutational burden falling into high-density tracks. Within the callable locus set, coding- and promoter-proximal categories were not depleted of induced mutation events (single-nucleotide variants) across treatments. Furthermore, we did not detect a negative association between total mutational load and the coding-region mutation fraction in this dataset. These findings suggest that, within this dataset, proton mutagenesis is characterized not by unique chemical signatures but by a distinct spatial geometry that concentrates detectable mutation events. Because proton irradiation was represented by a single dose, whether proton treatment produces stronger clustering than gamma irradiation at equal mutational burden remains to be directly tested.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 3","pages":"e70267"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13315512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148354138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2026-09-01DOI: 10.1002/tpg2.70281
Prabhat Rana, Chanderkant Chaudhary, Rajat Pruthi, Mansi Sharma, Bhupinderjeet Singh, Ravi Kiran Reddy Kondi, Mallesham Bulle, Prasanta K Subudhi
{"title":"Molecular insights and translational opportunities to enhance heat tolerance in rice.","authors":"Prabhat Rana, Chanderkant Chaudhary, Rajat Pruthi, Mansi Sharma, Bhupinderjeet Singh, Ravi Kiran Reddy Kondi, Mallesham Bulle, Prasanta K Subudhi","doi":"10.1002/tpg2.70281","DOIUrl":"10.1002/tpg2.70281","url":null,"abstract":"<p><p>Heat stress is an increasingly serious threat to rice (Oryza sativa L.) productivity, yet the genetic and regulatory architecture underlying thermotolerance remain poorly resolved and fragmented across studies. Earlier research focused on individual pathways or specific developmental stages; however, recent advances now support an integrated understanding of heat stress adaptation in rice. This review synthesizes emerging insights into molecular physiology, regulatory signaling, epigenetic memory, and genome-scale variation associated with thermotolerance. We highlight the interconnected roles of calcium reactive oxygen species signaling, heat shock transcription factor networks, translational regulation, and chromatin-based stress memory in shaping reproductive-stage tolerance and maintaining grain quality under elevated temperatures. The review also emphasizes the value of pangenome analyses and structural variant discovery for identifying heat-responsive genes and regulatory elements absent from single-reference genomes. In addition, genome-wide association studies, haplotype-based breeding, genomic selection, and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based genome editing are discussed as promising approaches for functional validation and deployment of favorable alleles controlling polygenic heat resilience. Despite these advances, several challenges continue to hinder translation into breeding-ready outcomes, including limited field-based validation of candidate genes, poor integration of multi-omics datasets into predictive breeding frameworks, and insufficient understanding of reproductive-stage regulatory networks. Furthermore, genotype × environment interactions, together with trade-offs among yield, grain quality, and stress resilience, strongly influence the stability and transferability of thermotolerance traits across diverse agroecological environments. By integrating mechanistic insights with genome-scale diversity and predictive breeding tools, this review outlines a genomics-enabled roadmap for developing heat-resilient rice cultivars under intensifying global warming and supporting sustainable global rice production.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 3","pages":"e70281"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13377552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148473721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2026-06-01DOI: 10.1002/tpg2.70249
{"title":"Correction to \"The Big BIT maize experiment: A large multi-location, multi-year, multi-tester, multi-population predictive breeding validation study\".","authors":"","doi":"10.1002/tpg2.70249","DOIUrl":"10.1002/tpg2.70249","url":null,"abstract":"","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70249"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13176796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147943387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2026-06-01DOI: 10.1002/tpg2.70251
Pengshuo Shen, Qing Yang, Zheng Shi, Zhi Liu, Yan Feng, Sobhi F Lamlom, Honglei Ren, Fulong Liu, Jiahao Ma, Yuechen Zhang, Long Yan
{"title":"Genome-wide association studies reveal environment-dependent genetic associations for plant architecture in regional soybean germplasm.","authors":"Pengshuo Shen, Qing Yang, Zheng Shi, Zhi Liu, Yan Feng, Sobhi F Lamlom, Honglei Ren, Fulong Liu, Jiahao Ma, Yuechen Zhang, Long Yan","doi":"10.1002/tpg2.70251","DOIUrl":"10.1002/tpg2.70251","url":null,"abstract":"<p><p>Regional soybean (Glycine max (L.) Merr.) breeding has produced germplasm adapted to different growing seasons, but the transferability of genetic associations associated with plant architecture across populations remains unclear. We performed genome-wide association studies (GWASs) for plant height and main stem node number in 520 soybean accessions from two Chinese germplasm pools: a short-season, cool-climate Bashang population (260 accessions from the northeast region) and a long-season, warm-climate Baxia population (260 accessions from the Huang-Huai-Hai region). Each was evaluated in its environment over two seasons. Population analysis showed strong differentiation (fixation index [F<sub>ST</sub>]<sub> </sub>= 0.29) and less diversity in Bashang (H<sub>e </sub>= 0.0808) than Baxia (H<sub>e </sub>= 0.1538), reflecting different breeding histories. Phenotypically, Baxia plants were taller (+94.7%) and had more nodes (+88.2%) than Bashang, and the differences were highly heritable (H<sup>2</sup> = 0.77-0.97). GWAS using multiple methods identified non-overlapping loci: Bashang for height involved three loci on chromosomes 4, 7, and 12 (logarithm of the odds [LOD] = 7.44-9.88, effects +1.68 to +2.06 cm), with the chromosome 12 locus showing high differentiation (F<sub>ST </sub>= 0.498). Baxia loci included a major height locus on chromosome 4 (+6.65 cm, LOD = 7.90, 38 Mb from Bashang's Chr4 locus) and a stem node number locus on chromosome 19 (+1.30 nodes, LOD = 7.18), near maturity genes E3/Dt1 (where Dt1 is determinate 1 gene). Functional analysis revealed that Bashang genes are involved in DNA metabolism, whereas Baxia genes are associated with cell development and hormone regulation, indicating distinct developmental pathways. Differing differentiation metrics across loci suggest various evolutionary processes, such as selection and gene-environment interactions. These findings highlight that genetic links to plant structure are population-specific, impacting marker transferability and the need for tailored breeding strategies for regional environments.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70251"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147989802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2026-06-01DOI: 10.1002/tpg2.70244
Kyu-Chan Shim, Donghyun Jeon, Yun-A Jeon, Cheryl Adeva, Hyun-Sook Lee, Ju-Won Kang, Sa-Eun Park, Sang-Nag Ahn, Inkyu Park
{"title":"Genetic dissection and transcriptomic analysis of a novel high-tillering phenotype in rice derived from weedy rice (Hapcheonaengmi3) and Tongil-type Rice (Milyang23).","authors":"Kyu-Chan Shim, Donghyun Jeon, Yun-A Jeon, Cheryl Adeva, Hyun-Sook Lee, Ju-Won Kang, Sa-Eun Park, Sang-Nag Ahn, Inkyu Park","doi":"10.1002/tpg2.70244","DOIUrl":"10.1002/tpg2.70244","url":null,"abstract":"<p><p>Rice (Oryza sativa L.) tillering is a critical determinant of grain yield, yet the genetic mechanisms underlying non-productive tillers remain poorly understood. Here, we report a novel high-tillering (HT) phenotype derived from a cross between the elite cultivar Milyang23 and weedy rice Hapcheonaengmi3. The HT phenotype was absent in parental lines, suggesting it arises from unique allelic interactions. To elucidate the genetic basis of HT, we conducted quantitative trait locus sequencing and linkage analysis using recombinant inbred lines and an F<sub>2</sub> population. We identified and fine-mapped two major loci, qHT1 and qHT6, where alleles from Hapcheonaengmi3 induce the HT phenotype in the Milyang23 background. Advanced fine mapping facilitated by window-size adjustments further resolved qHT1 into two candidate intervals (qHT1.1 and qHT1.2). Candidate gene analysis highlighted a putative SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor within qHT6. Furthermore, transcriptomic profiling of HT plants uncovered extensive reprogramming of hormone signaling, specifically affecting the gibberellin, auxin, and cytokinin pathways. Notably, the miR156-SPL module, previously implicated in bushy tillering, exhibited significant expression changes, identifying it as a key regulatory candidate. These findings provide crucial insights into a novel polygenic mechanism controlling rice tillering and highlight the value of cryptic variation in weedy rice.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70244"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13096764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147730481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}