Maria G Rottersman, Wenjun Zhang, Junli Zhang, Gabriela Grigorean, German Burguener, Claudia Carter, Teng Vang, Joshua Hegarty, Xiaoqin Zhang, Sean Finnie, Jorge Dubcovsky
{"title":"Deletion of wheat alpha-gliadins from chromosome 6D improves gluten strength and reduces immunodominant celiac disease epitopes.","authors":"Maria G Rottersman, Wenjun Zhang, Junli Zhang, Gabriela Grigorean, German Burguener, Claudia Carter, Teng Vang, Joshua Hegarty, Xiaoqin Zhang, Sean Finnie, Jorge Dubcovsky","doi":"10.1007/s00122-025-04882-3","DOIUrl":"https://doi.org/10.1007/s00122-025-04882-3","url":null,"abstract":"<p><p>Wheat gliadins and glutenins confer valuable end-use characteristics but include amino acid sequences (epitopes) that can elicit celiac disease (CeD) in genetically predisposed individuals. The onset of CeD in these individuals is affected by the amount and duration of the exposure to immunogenic epitopes. Therefore, a reduction of epitopes that result in high immune responses in the majority of CeD patients (immunodominant epitopes) may reduce the incidence of CeD at a population level. We generated gamma radiation-induced deletions encompassing the α-gliadins in each of the three wheat genomes and characterized them using exome capture. These deletions, designated as Δgli-A2, Δgli-B2, and Δgli-D2, were deposited in GRIN-Global. The Δgli-A2 and Δgli-B2 deletions showed limited effects on breadmaking quality, but the Δgli-D2 deletion significantly increased gluten strength and improved breadmaking quality without compromising dough elasticity, protein content, or grain yield. The stronger effect of Δgli-D2 on gluten strength was associated with an increased proportion of glutenins and the deletion of α-gliadins with seven cysteines, which are absent in the GLI-A2 and GLI-B2 loci. We show that α-gliadins with seven cysteines are incorporated into the gluten polymer, where they likely function as chain terminators limiting the expansion of the gluten polymer and reducing its strength. In addition to its beneficial effects on breadmaking quality, the Δgli-D2 deletion eliminates major wheat immunodominant CeD epitopes. The deployment of this publicly available Δgli-D2 deletion can simultaneously improve wheat gluten strength and reduce the population-wide burden of CeD.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"94"},"PeriodicalIF":4.4,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143812459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Attiq Ur Rehman, Jahn Davik, Petteri Karisto, Janne Kaseva, Saila Karhu, Marja Rantanen, Ismo Strandén, Timo Hytönen, Alan H Schulman, Tuuli Haikonen
{"title":"A major QTL region associated with powdery mildew resistance in leaves and fruits of the reconstructed garden strawberry.","authors":"Attiq Ur Rehman, Jahn Davik, Petteri Karisto, Janne Kaseva, Saila Karhu, Marja Rantanen, Ismo Strandén, Timo Hytönen, Alan H Schulman, Tuuli Haikonen","doi":"10.1007/s00122-025-04871-6","DOIUrl":"10.1007/s00122-025-04871-6","url":null,"abstract":"<p><strong>Key message: </strong>Multiple QTLs for powdery mildew resistance were identified in a pre-breeding population derived from the octoploid progenitor species of garden strawberry, including a stable major novel factor on chromosome 3B. Powdery mildew (PM), caused by the biotrophic fungal pathogen Podosphaera aphanis, poses an increasing threat to garden strawberry (Fragaria × ananassa) production worldwide. While a few commercial cultivars exhibit partial resistance, fungicide application remains essential for managing PM outbreaks. However, breeding offers a more sustainable approach for controlling PM. A better understanding of the genetics of resistance is required for informed breeding strategies, e.g. through identifying novel resistance factors derived from the progenitor species of garden strawberry, F. chiloensis and F. virginiana. We conducted genome-wide association (GWA) and multivariate analyses in a reconstructed (ReC) strawberry population to investigate PM resistance under natural infection. Leveraging multi-year field trial data and 20,779 single-nucleotide polymorphism markers, we identified a novel major quantitative trait locus (QTL) on chromosome 3B, designated as q.LPM.Rec-3B.2, that was consistently associated with high PM resistance in both leaves and fruits. Greenhouse validation with a subset of the ReC population confirmed that this QTL region was stable across field and greenhouse environments. Promising candidate genes for resistance, including two for MLO and one for EXO70, were identified within this major QTL. In addition, multi-locus GWA models and non-additive GWA revealed additional resistance QTLs on multiple chromosomes. Despite previous challenges in breeding for robust PM resistance due to its quantitative nature and complex genetic control, our results provide valuable insights into resistance-contributing QTL regions already existing in strawberry, novel wild-derived resistance QTLs not previously known, candidate genes, and pre-breeding germplasm carrying resistance traits as resources for future genome-informed breeding efforts.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"93"},"PeriodicalIF":4.4,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Improving yield-related traits by editing the promoter and distal regulatory region of heading date genes Ghd7 and PRR37 in elite rice variety Mei Xiang Zhan 2.","authors":"Xiaotong Guo, Kangli Sun, Zeqiang Wu, Dongdong Xiao, Yingang Song, Shengting Li, Guangliang Wei, Weitao Li, Yu Hao, Bingqun Xu, Kai Zhang, Nan Liao, Dan Hu, Yao-Guang Liu, Wubei Zong, Jingxin Guo","doi":"10.1007/s00122-025-04880-5","DOIUrl":"https://doi.org/10.1007/s00122-025-04880-5","url":null,"abstract":"<p><strong>Key message: </strong>We revealed that editing the promoter and distal regulatory region of the pleiotropic genes Ghd7 and PRR37 reduces their ability to delay heading date while improving their capacity to boost crop yield, offering valuable resources for rice breeding. Heading date is a crucial agronomic characteristic in rice that governs the adaptability to different latitudes and the yield of various varieties. Optimizing the heading date of superior cultivars in breeding practice can significantly broaden their potential planting areas. Ghd7 and PRR37 are pivotal genes that control heading date and enhance agronomic traits. In the elite indica rice variety Mei Xiang Zhan 2 (MXZ2), we used CRISPR/Cas9 technology to effectively generate homozygous mutant lines with a gradient change in heading date by multi-target editing the promoter and distal regulatory region of Ghd7 and PRR37. Various degrees of down-regulation of Ghd7 or PRR37 expression, impaired gene functions, and advancement of the heading date were observed in the mutant lines. Certain mutant lines exhibited an early heading date and increased yield while preserving the exceptional quality of MXZ2. Our study revealed that editing the promoter and distal regulatory region of the pleiotropic genes Ghd7 and PRR37 reduces their ability to delay heading date while improving their capacity to boost crop yield, offering valuable resources for rice breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"92"},"PeriodicalIF":4.4,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gözde Yildiz, Silvia F Zanini, Sven Weber, Venkataramana Kopalli, Tobias Kox, Amine Abbadi, Rod J Snowdon, Agnieszka A Golicz
{"title":"Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus.","authors":"Gözde Yildiz, Silvia F Zanini, Sven Weber, Venkataramana Kopalli, Tobias Kox, Amine Abbadi, Rod J Snowdon, Agnieszka A Golicz","doi":"10.1007/s00122-025-04867-2","DOIUrl":"10.1007/s00122-025-04867-2","url":null,"abstract":"<p><strong>Key message: </strong>Pangenome graphs enable population-scale genotyping and improve expression analysis, revealing that structural variations (SVs), particularly transposable elements (TEs), significantly contribute to gene expression variation in winter oilseed rape. Structural variations (SVs) impact important traits, from yield to flowering behaviour and stress responses. Pangenome graphs capture population-level diversity, including SVs, within a single data structure and provide a robust framework for downstream applications. They have the potential to serve as unbiased references for SV genotyping, pan-transcriptomic analyses, and association studies, offering significant advantages over single reference genomes. However, their full potential for expression quantitative trait locus (eQTL) analysis is yet to be explored. We combined long and short-read whole genome sequencing data with expression profiling of Brassica napus (oilseed rape) to assess the impact of SVs on gene expression regulation and explored the utility of pangenome graphs for eQTL analysis. Over 90,000 SVs were discovered from 57 long-read datasets. Pangenome graph as reference was evaluated and used for SV genotyping with short reads and transcript expression quantification. Using SVs genotyped from the graph and 100 expression datasets, we identified 267 gene proximal (cis) SV-eQTLs. Over 70% of eQTL-SVs had similarity to transposable elements (TEs), especially Helitrons. The highest proportion of cis-eQTL-SVs were found in promoter regions. About a third of transcripts whose expression was associated with SVs, had no associated SNPs, suggesting that including SVs allows capturing of relationship which would be missed in SNP-only analyses. This study demonstrated that pangenome graphs provide a unifying framework for eQTL analysis by allowing population-scale SV genotyping and gene expression quantification. We also showed that SVs make an appreciable contribution to gene expression variation in winter oilseed rape.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"91"},"PeriodicalIF":4.4,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143773275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Integrative mapping in large inbred and hybrid association panels along with an F<sub>2</sub> population advanced a novel understanding of general combining ability for plant height in maize.","authors":"Jie Luo, Yangjing Li, Yulin Jiang, Xiaoxiang Zhang, Guangxiao Bai, Zhonghua Peng, Qiang Yi, Xianbin Hou","doi":"10.1007/s00122-025-04883-2","DOIUrl":"https://doi.org/10.1007/s00122-025-04883-2","url":null,"abstract":"<p><strong>Key message: </strong>We identified 44 QTL for PH-related traits evaluated for inbreds per se and GCA effects in large inbred and hybrid association panels and seven QTL for EH/PH in an F<sub>2</sub> population coupled with BSA-seq. Among four co-localized QTL, seven novel potential candidate genes were significantly associated with PH-related traits, shedding new light on understanding the genetics of GCA for PH. Breeding optimal plant height (PH) is essential for improving maize (Zea mays L.) plant architecture, yield, lodging resistance, and density tolerance, yet there is limited genetic loci available regarding the general combining ability (GCA) for PH-related traits. In the current study, an inbred association panel of 312 inbred lines (IAP) along with a hybrid association panel (HAP) of 764 hybrid combinations were utilized to dissect the genetics of PH-related traits and their GCA effects across three environments. We found 44 quantitative trait loci (QTL) with 76 significant single-nucleotide polymorphisms (SNPs) for PH-related traits evaluated for inbreds per se and GCA effects; however, no overlapping loci were identified across inbreds per se and GCA effects, indicating conspicuous discrepancies in their genetics. In addition, GCA effects with complex genetic basis differed for diverse testers, which highlighted the specificity and complexity among heterotic groups. Correspondingly, we evaluated an F<sub>2</sub> population derived from two parental lines LY-02 and LH513 with the contrasting EH/PH coupled with bulked segregant analysis by sequencing (BSA-seq) and found seven QTL for EH/PH. Among four co-localized loci across the association and QTL mapping, seven novel candidate genes were found to differently express among LY-02, LH513, and their F<sub>1</sub> and were potentially associated with PH-related traits. The current study with combined mapping in diverse mapping populations provided a novel understanding of GCA for PH-related traits in maize.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"90"},"PeriodicalIF":4.4,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shuqing Guo, Fei Han, Minxuan Liu, Huibing Han, Kongjun Dong, Junxue Yang, Liyuan Zhang, Xiaoli Gao, Baili Feng, Pu Yang
{"title":"A genome-wide association study reveals the genetic architecture of 19 agronomic traits in broomcorn millet (Panicum miliaceum L.).","authors":"Shuqing Guo, Fei Han, Minxuan Liu, Huibing Han, Kongjun Dong, Junxue Yang, Liyuan Zhang, Xiaoli Gao, Baili Feng, Pu Yang","doi":"10.1007/s00122-025-04870-7","DOIUrl":"https://doi.org/10.1007/s00122-025-04870-7","url":null,"abstract":"<p><strong>Key message: </strong>The genetic architecture of 19 growth and development and yield-related traits was dissected by a GWAS in multi-environment of a diverse population consisting of 301 broomcorn millet accessions. Broomcorn millet (Panicum miliaceum L.) is an ideal replant crop due to its advantages of drought resistance, short growth period, and strong adaptability. Understanding the genetic basis of agronomic traits is crucial for improving the efficiency of molecular breeding in broomcorn millet. In this study, a natural population consisting of 301 worldwide broomcorn millet accessions was genotyped using 208,169 high-quality single-nucleotide polymorphisms (SNPs). Nineteen agronomic traits, including growth period, plant architecture, and yield-related traits, were investigated across ten environments. Based on genomic and phenotypic data, a genome-wide association study (GWAS) was performed to identify significant marker-trait associations (MTAs) affecting these traits. Using the linear mixed model, 662 significant MTAs were identified for 19 traits, with 56 stable MTAs repeatedly identified over two environments. Among these stable SNPs, 40 were located in genomic regions where no relevant loci had been reported previously. Notably, superior alleles of four significant SNPs chr1_2925777, chr7_157147, chr4_3971792, and chr5_2126999 associated with panicle length (PL) and the whole growth period (GP) exhibited significantly higher phenotypic levels. Ultimately, 174 genes within the flanking regions of these four significant SNPs were annotated. Among these, six genes were identified as candidate genes associated with PL and GP. Further haplotype analysis identified seven haplotypes for longmi011379 and longmi011388. Phenotypic assessment of major haplotypes revealed significant differences between Hap1 and Hap2. These results provide a valuable resource for understanding the genetic mechanisms of growth and development and yield-related traits and developing marker-assisted selection breeding in broomcorn millet.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"89"},"PeriodicalIF":4.4,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143754187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bin Feng, Yu Wang, Xiaolong Zhang, Tingting Mu, Biaoming Zhang, Yan Li, Haitao Zhang, Wei Hua, Wenya Yuan, Haitao Li
{"title":"Targeted mutagenesis and functional marker development of two Bna.TAC1s conferring novel rapeseed germplasm with compact architecture.","authors":"Bin Feng, Yu Wang, Xiaolong Zhang, Tingting Mu, Biaoming Zhang, Yan Li, Haitao Zhang, Wei Hua, Wenya Yuan, Haitao Li","doi":"10.1007/s00122-025-04876-1","DOIUrl":"https://doi.org/10.1007/s00122-025-04876-1","url":null,"abstract":"<p><strong>Key message: </strong>Simultaneous disruption of two Bna.TAC1s, redundantly controlling the branch angle, generates a compact architecture in rapeseed, and two functional markers are developed to facilitate breeding rapeseed cultivars with compact architecture. Shoot branch angle is a key factor in determining the aerial plant architecture. A narrow branch angle can increase yields by facilitating mechanized harvest and high-density planting in rapeseed, a globally important oil crop. However, the available rapeseed varieties with narrow branch angle are very limited. In this study, two Bna.TAC1 members named BnaA5.TAC1 and BnaC4.TAC1 were found to have the four canonical domains of TAC1-like members, including domains I, II, III and IV in rapeseed. Each Bna.TAC1 exhibits dominant expression in the lateral branch with gradual dynamic response to light and encodes a protein localized in the plasma membrane. CRISPR/Cas9-mediated editing system was used to simultaneously knock out the two Bna.TAC1s to obtain two different Bna.tac1 double mutants, designed as CR-Bna.tac1-1 and CR-Bna.tac1-2. These two mutants displayed different degrees of compact architecture without affecting plant height and yield-related traits. The two Bna.TAC1s were also shown to play a redundant role in controlling branch angle by regulating the gravitropic response. In addition, we developed two specific gel-based functional markers in each Bna.TAC1 for the transgene-free mutant CR-Bna.tac1-1, which co-segregate with narrower branch angle and could help to identify the mutant alleles in a segregating population. We also found that the genomic variation of the two Bna.TAC1s is not associated with branch angle variation in the natural rapeseed population. Overall, these results reveal the key roles of Bna.TAC1s in regulation of rapeseed branch angle and provide a novel germplasm and functional markers for breeding superior varieties with compact architecture in rapeseed.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"86"},"PeriodicalIF":4.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"In vitro- and in vivo-based approaches for doubled haploid production in Zea mays L.: challenges and opportunities.","authors":"Behzad Ahmadi","doi":"10.1007/s00122-025-04873-4","DOIUrl":"https://doi.org/10.1007/s00122-025-04873-4","url":null,"abstract":"<p><p>Maize (Zea mays L.) is a cereal species of significant importance for global food security, animal nutrition, and agricultural economies. The enhancement of maize yield through hybrid breeding and the selection of desirable traits-such as increased vigor, resilience to biotic and abiotic stressors, and improved adaptability to diverse environmental conditions-represents a significant milestone in the field of agricultural biotechnology. Production of parental inbred lines, which is a prerequisite for hybrid breeding, can be accomplished through conventional breeding or doubled haploid (DH) techniques, the latter provides accelerated homozygosity and genetic uniformity. This review focuses on the various in vitro- and in vivo-based methods for the production of DH lines in maize, discussing their respective challenges and opportunities. Furthermore, it explores recent advancements in chromosome doubling techniques necessary for restoring fertility to haploids, which are essential for their effective integration into breeding programs. This review also aims to delineate current knowledge and future directions in maize DH technology, ultimately contributing to optimized breeding strategies for enhanced maize production.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"87"},"PeriodicalIF":4.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qingfeng Dong, Hao Ren, Xuefen Cai, Yujie Zhang, Shan Lu, Dezheng Liu, Muhammad Ateeq, Liang Chen, Yin-Gang Hu
{"title":"Deciphering the regulatory network of lignocellulose biosynthesis in bread wheat through genome-wide association studies.","authors":"Qingfeng Dong, Hao Ren, Xuefen Cai, Yujie Zhang, Shan Lu, Dezheng Liu, Muhammad Ateeq, Liang Chen, Yin-Gang Hu","doi":"10.1007/s00122-025-04868-1","DOIUrl":"https://doi.org/10.1007/s00122-025-04868-1","url":null,"abstract":"<p><strong>Key message: </strong>This study identified 46 key QTL and 17 candidate genes and developed a KASP marker, providing valuable molecular tools for enhancing lignocellulose traits, lodging resistance, and bioenergy potential in wheat. Wheat lignocellulose, composed of lignin, cellulose, and hemicellulose, plays a crucial role in strengthening plant cell walls, enhancing lodging resistance, and contributing to bioenergy production. However, the genetic basis underlying the variation in lignocellulose content in wheat remains poorly understood. The stem lignin, cellulose, and hemicellulos contents in the second stem internode of a panel of 166 wheat accessions grown in three environments were measured, combined with the genotyping data with 660 K wheat SNP chip; a genome-wide association studies (GWAS) were conducted to identify loci associated with the lignocellulose content in wheat. Significant variations in lignin, cellulose, and hemicellulose contents were observed among the wheat accessions. GWAS identified 1146 significant SNPs associated with lignin, cellulose, and hemicellulose contents, distributed across the A, B, and D sub-genomes of wheat. Joint analysis of haplotype blocks refined these associations, identifying 46 significant quantitative trait loci (QTL) regions and 17 candidate genes, primarily linked to vascular development, hemicellulose synthesis, internode elongation regulation, and lignin biosynthesis. A KASP marker (NW_CC5951) for lignocellulose was developed. These findings provide valuable molecular markers for marker-assisted selection, supporting wheat breeding for improved stem quality and lodging resistance, and offer insights into balancing grain yield with lodging resistance and lignocellulosic energy production.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"85"},"PeriodicalIF":4.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143731712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vahe Avagyan, Martin P Boer, Junita Solin, Aalt D J van Dijk, Daniela Bustos-Korts, Bart-Jan van Rossum, Jip J C Ramakers, Fred van Eeuwijk, Willem Kruijer
{"title":"Penalized factorial regression as a flexible and computationally attractive reaction norm model for prediction in the presence of GxE.","authors":"Vahe Avagyan, Martin P Boer, Junita Solin, Aalt D J van Dijk, Daniela Bustos-Korts, Bart-Jan van Rossum, Jip J C Ramakers, Fred van Eeuwijk, Willem Kruijer","doi":"10.1007/s00122-025-04865-4","DOIUrl":"https://doi.org/10.1007/s00122-025-04865-4","url":null,"abstract":"<p><strong>Key message: </strong>Penalized factorial regression offers a computationally attractive alternative to kernel and deep learning methods for prediction of genotype by environment interactions. For two representative data sets on wheat and maize, prediction accuracies were comparable, while computing requirements and time were clearly lower. A longstanding challenge in plant breeding and genetics is the prediction of yield for new environments in the presence of genotype by environment interaction ( <math><mrow><mi>G</mi> <mo>×</mo> <mi>E</mi></mrow> </math> ). The genotypes in this case are promising candidate varieties at an advanced stage of breeding programs or are part of statutory variety trials or post registration trials. The genotypes have been tested in a limited set of trials and the question is how these genotypes will perform in future growing conditions. A reaction norm approach seems adequate to address this challenge. Reaction norms are functions with genotype-specific parameters that express the phenotype as a function of environmental inputs. <math><mrow><mi>G</mi> <mo>×</mo> <mi>E</mi></mrow> </math> follows from differences in genotype-specific slope or rate parameters. Prediction of yield for new environments requires the identification of suitable reaction norm functions and the estimation of genotype-specific parameters together with knowledge about the environmental conditions. Here, we present penalized factorial regression with simple linear reaction norms for individual genotypes whose slopes are regularized by imposing a penalty upon them. Different types of penalization provide shrinkage, automatic selection of environmental covariates (EC's) and protection against overfitting for prediction of yield with medium to large numbers of EC's. Illustrations of our approach are given for a maize and a wheat data set. For these data, our approach compares well to alternative methods based on Bayesian regression and deep learning with respect to prediction accuracy, while computational demands are clearly lower.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"88"},"PeriodicalIF":4.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11953130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}