Theoretical and Applied Genetics最新文献

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Creating a gene-indexed EMS mutation library of Zheng58 for improving maize genetics research. 建立玉米郑58基因索引EMS突变文库,提高玉米遗传研究水平。
IF 4.4 1区 农林科学
Theoretical and Applied Genetics Pub Date : 2025-03-27 DOI: 10.1007/s00122-025-04878-z
Leelyn Chong, Huihui Su, Yingpeng Liu, Lingling Zheng, Lianying Tao, Hai Bie, Di Xiao, Yang Yang, Wanjun Zhang, Jing Zhang, Jifei Ren, Huafeng Liu, Zhenzhen Ren, Yanhui Chen, Zhangying Xi, Chengwei Li, Lixia Ku
{"title":"Creating a gene-indexed EMS mutation library of Zheng58 for improving maize genetics research.","authors":"Leelyn Chong, Huihui Su, Yingpeng Liu, Lingling Zheng, Lianying Tao, Hai Bie, Di Xiao, Yang Yang, Wanjun Zhang, Jing Zhang, Jifei Ren, Huafeng Liu, Zhenzhen Ren, Yanhui Chen, Zhangying Xi, Chengwei Li, Lixia Ku","doi":"10.1007/s00122-025-04878-z","DOIUrl":"10.1007/s00122-025-04878-z","url":null,"abstract":"<p><strong>Key message: </strong>We created the Zheng58 EMS Mutation Library, which provides a valuable resource for future investigations into the functions and roles of specific genes in maize physiology and development. Understanding the genetic variations present within maize is fundamental to improving maize breeding programs and developing crops with desirable traits. In this work, the Gene-Indexed Ethyl Methanesulfonate (EMS) Mutation Library of Zheng58 in maize was created to accelerate maize genetics research. By chemically inducing mutations in the Zheng58 maize inbred line using (EMS), 426 M<sub>2</sub> EMS lines were generated, of which 185 exhibited heritable phenotypic changes. Coupling with high throughput sequencing techniques, over two million mutations, encompassing single nucleotide polymorphisms (SNPs) and small insertions and deletions (InDels), were subsequently identified. Functional annotation of mutation sites further indicated that a significant number of mutations influences important cellular processes, including translation termination (8,279), splice site disruption leading to mis-splicing (9,504), and missense mutations affecting protein-coding sequences (52,494). Therefore, the Gene-Indexed EMS Mutation Library of maize Zheng58 provides a valuable resource for future investigations into the functions and roles of specific genes in maize physiology and development.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"83"},"PeriodicalIF":4.4,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721498","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}
引用次数: 0
A genome-wide association study prioritizes VRN1-2 as a candidate gene associated with plant height in soybean. 一项全基因组关联研究优先考虑VRN1-2作为大豆植株高度相关的候选基因。
IF 4.4 1区 农林科学
Theoretical and Applied Genetics Pub Date : 2025-03-27 DOI: 10.1007/s00122-025-04875-2
Le Wang, Hong Xue, Zhenbin Hu, Yang Li, Tuya Siqin, Hengyou Zhang
{"title":"A genome-wide association study prioritizes VRN1-2 as a candidate gene associated with plant height in soybean.","authors":"Le Wang, Hong Xue, Zhenbin Hu, Yang Li, Tuya Siqin, Hengyou Zhang","doi":"10.1007/s00122-025-04875-2","DOIUrl":"10.1007/s00122-025-04875-2","url":null,"abstract":"<p><p>Plant height is an important architectural trait that affects crop growth, yield, and stress resistance. Tremendous efforts have been dedicated to revealing the genetic basis or regulatory mechanism; however, the underlying molecular mechanism remains largely unknown primarily due to the lack of controlling genes. In this study, we conducted a single-nucleotide resolution genome-wide association study (GWAS) of plant height using a diverse soybean panel collected worldwide with 6.7 million genome-wide variants (SNPs and Indels). The GWAS of plant height identified three QTLs on chromosomes 10, 18, and 19, of which the one on chromosome 19 precisely co-localized with Dt1, known as a major stem growth habit-controlling gene. Other loci without reported genes for plant height were regarded to be new. A close investigation within QTL intervals proposed nine genes that were likely involved in the regulation of plant height according to the expression specificity in developing shoot tip meristems. VRN1-2 underlies the significant QTL on chromosome 10 was prioritized as the most promising candidate gene. VRN1-2 shows higher expression in Williams 82 with indeterminate growth habit than Dongnong50 with semi-determinate growth habit across vegetative (V2, V3) and reproductive (R1) growth stages. VRN1-2 carries non-synonymous variants in the coding region that were significantly associated with plant height variation. The GT allele conferring short plant height was likely subjected to artificial selection during domestication. These results provide a source of new loci and genes for further elaborating the regulatory mechanism of plant height and the key variants would facilitate soybean molecular breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"84"},"PeriodicalIF":4.4,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721386","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}
引用次数: 0
Regreening mechanisms in cucumber: insights from a CsSIG2 mutation affecting chloroplast development. 黄瓜变绿机制:来自影响叶绿体发育的CsSIG2突变的见解。
IF 4.4 1区 农林科学
Theoretical and Applied Genetics Pub Date : 2025-03-23 DOI: 10.1007/s00122-025-04854-7
Hanqiang Liu, Zeqiang Huang, Xinyue Wang, Kaihong Hu, Qinqin Jiang, Feifan Chen, Yuxuan Ma, Zhihui Cheng, Yupeng Pan, Yiqun Weng
{"title":"Regreening mechanisms in cucumber: insights from a CsSIG2 mutation affecting chloroplast development.","authors":"Hanqiang Liu, Zeqiang Huang, Xinyue Wang, Kaihong Hu, Qinqin Jiang, Feifan Chen, Yuxuan Ma, Zhihui Cheng, Yupeng Pan, Yiqun Weng","doi":"10.1007/s00122-025-04854-7","DOIUrl":"https://doi.org/10.1007/s00122-025-04854-7","url":null,"abstract":"<p><strong>Key message: </strong>CsSIG2 is essential for cucumber chloroplast development, and mutations in CsSIG2 reveal mechanisms that restore chloroplast functionality and drive the regreening phenotype in the mutant. Chloroplast development and leaf color are essential traits that significantly influence plant photosynthesis and overall vigor. This study investigates a natural mutation in the cucumber that leads to a virescent leaf-color (Csvl-6) phenotype characterized by an initial yellow color in cotyledons and young leaves, which gradually transition to green as the plant matures. We utilized bulked segregant analysis and genetic linkage mapping to locate the best candidate gene sigma factor 2 (CsSIG2) on chromosome 6, identifying a single nonsynonymous SNP resulting in an arginine to glycine substitution in the CsSIG2 protein. Comparative transcriptome analysis highlighted that this mutation disrupts early chloroplast biogenesis and delays chlorophyll accumulation, but the chloroplasts can recover, leading to greening during later stages of leaf development. Our findings reveal that the recovery phenomenon involves upregulation of chloroplast-encoded genes responsible for thylakoid membrane formation and photosystem function, alongside altered expression of transcription factors linked to chlorophyll metabolism. This study elucidates the genetic and molecular basis of chloroplast development in cucumber, providing valuable insights into the mechanisms underlying leaf greening, which could inform future breeding efforts focused on manipulating leaf color traits for enhanced crop performance.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"82"},"PeriodicalIF":4.4,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143693346","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}
引用次数: 0
Melatonin enhances salt tolerance by promoting CcCAD10-mediated lignin biosynthesis in pigeon pea. 褪黑素通过促进cccad10介导的木素生物合成增强木豆的耐盐性。
IF 4.4 1区 农林科学
Theoretical and Applied Genetics Pub Date : 2025-03-22 DOI: 10.1007/s00122-025-04846-7
Feng Pan, Hongquan Li, Ming Qu, Xiaoli An, Jie Yang, Yujie Fu
{"title":"Melatonin enhances salt tolerance by promoting CcCAD10-mediated lignin biosynthesis in pigeon pea.","authors":"Feng Pan, Hongquan Li, Ming Qu, Xiaoli An, Jie Yang, Yujie Fu","doi":"10.1007/s00122-025-04846-7","DOIUrl":"https://doi.org/10.1007/s00122-025-04846-7","url":null,"abstract":"<p><p>Melatonin plays a crucial role in enhancing plant resistance to salt stress by regulating biosynthesis of specialized metabolites. Phenylpropanoids, especially lignin, contribute to all aspects of plant responses toward biotic and abiotic stresses. However, the crosstalk between melatonin and lignin is largely unknown in pigeon pea under salt stress. In this study, the cinnamyl alcohol dehydrogenase CcCAD10 was identified to be involved in melatonin treatment and salt stress. The content of lignin was significantly increased in CcCAD10 over-expression (OE) lines, the enhanced antioxidant enzyme activities, indicating enhanced salt resistance. As a parallel branch of the lignin synthesis pathway, the content of flavonoids was further determined. The accumulations of luteolin, genistin, genistein, biochain A, apigenin and isovitexin were down-regulated in CcCAD10-OE hairy root. The results indicate that CcCAD10-OE mediated carbon flow from the phenylalanine pathway is redirected to the lignin pathway at the expense of less carbon flow in the flavonoid pathway, enhancing the salt-tolerance. Furthermore, we found the exogenous melatonin stimulated endogenous melatonin production mainly by upregulating the expression of CcASMT2 gene. This study reveals a novel mechanism by which melatonin enhances salt tolerance in pigeon pea, which laid a foundation for exploring the molecular mechanism of melatonin in salt stress response.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"81"},"PeriodicalIF":4.4,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143693344","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}
引用次数: 0
Genome-wide association study reveals genetic loci for seed density per silique in rapeseed (Brassica napus L.). 油菜(Brassica napus L.)单株种子密度遗传位点的全基因组关联研究。
IF 4.4 1区 农林科学
Theoretical and Applied Genetics Pub Date : 2025-03-20 DOI: 10.1007/s00122-025-04857-4
Youjuan Quan, Haidong Liu, Kaixiang Li, Liang Xu, Zhigang Zhao, Lu Xiao, Yanmei Yao, Dezhi Du
{"title":"Genome-wide association study reveals genetic loci for seed density per silique in rapeseed (Brassica napus L.).","authors":"Youjuan Quan, Haidong Liu, Kaixiang Li, Liang Xu, Zhigang Zhao, Lu Xiao, Yanmei Yao, Dezhi Du","doi":"10.1007/s00122-025-04857-4","DOIUrl":"https://doi.org/10.1007/s00122-025-04857-4","url":null,"abstract":"<p><strong>Key message: </strong>Two stable QTLs controlling seed density per silique were detected on chromosomes A09 and C05 in rapeseed via GWAS, and ARF18 was the only causal gene of QTL qSDPS-A09. Seed density per silique (SDPS) is a key agronomic trait that directly or indirectly affects seed yield in rapeseed (Brassica napus L.). Exploring the genetic control of SDPS is beneficial for increasing rapeseed production. In this study, we evaluated the SDPS phenotypes of 413 rapeseed cultivars (lines) across five natural environments and genotyped them by resequencing. A GWAS analysis was performed using 5,277,554 high-quality variants with the MLM_PCA + K and FarmCPU models. A total of 51 loci were identified to be significantly (p < - log<sub>10</sub>(1.88 × 10<sup>-6</sup>)) associated with SDPS, of which 5 were detected in all environments (except for SNP-2095656) by both GWAS models. Among the five loci, three were located on chromosome A09, whereas the other two loci were located on chromosome C05. The three loci on chromosome A09 and the two loci on chromosome C05 were physically close to each other. Therefore, only the two common candidate QTLs were integrated and named QTL qSDPS-A09 (320 kb) and qSDPS-C05 (331.48 kb), respectively. Sixty-seven and forty-eight candidate genes were initially identified on A09 and C05 and then narrowed down to 17 and 13 candidate genes, respectively, via LD block analyses. Gene-based association studies, haplotype analyses and expression analyses confirmed that three homologs of Arabidopsis auxin-response factor 18 (BnaA09G0559300ZS) was the most likely candidate genes underlying the QTL qSDPS-A09. ARF18<sup>Hap4</sup> was identified as a favorable haplotype for high SDPS. These findings will aid in elucidating the genetic and molecular mechanisms of SDPS and promoting genetic modifications in rapeseed breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"80"},"PeriodicalIF":4.4,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143670773","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}
引用次数: 0
The speed breeding technology of five generations per year in cotton. 棉花年5代速成育种技术。
IF 4.4 1区 农林科学
Theoretical and Applied Genetics Pub Date : 2025-03-19 DOI: 10.1007/s00122-025-04837-8
Guoning Wang, Zhengwen Sun, Jun Yang, Qingming Ma, Xingyi Wang, Huifeng Ke, Xiao Huang, Li Zhang, Gengyao Wang, Qishen Gu, Dongmei Zhang, Jinhua Wu, Yan Zhang, Liqiang Wu, Guiyin Zhang, Zhiying Ma, Xingfen Wang
{"title":"The speed breeding technology of five generations per year in cotton.","authors":"Guoning Wang, Zhengwen Sun, Jun Yang, Qingming Ma, Xingyi Wang, Huifeng Ke, Xiao Huang, Li Zhang, Gengyao Wang, Qishen Gu, Dongmei Zhang, Jinhua Wu, Yan Zhang, Liqiang Wu, Guiyin Zhang, Zhiying Ma, Xingfen Wang","doi":"10.1007/s00122-025-04837-8","DOIUrl":"https://doi.org/10.1007/s00122-025-04837-8","url":null,"abstract":"<p><strong>Key message: </strong>Developed a speed breeding technique for cotton that enables up to five generations per year using optimized spectral conditions and immature embryo culture, and created new materials with iaaM gene. Shortening the breeding cycle is an effective way to accelerate crop genetic improvement. Previously we developed an integrated breeding technology for cotton that enabled three to four breeding cycles per year. Here, to further shorten the breeding time, we optimized the light spectrum conditions for cotton development and culture conditions for immature embryo developing into seedling. Under optimized spectrum conditions, JSh929 and ND601 plants exhibited the visible flower buds at 19 and 21 days after emergence (DAE), and the first flower bloomed at around 45 and 46 DAE. Using the optimized immature embryo culture technique, immature embryos of 25-30 days after pollination could develop into fertile plants with cotyledon unfolding at 6 days after culture in vitro. The improved speed breeding technique shortened cotton breeding cycle from about 130 days to a range from 71 to 85 days, an average of 79.5 days, achieving up to around five generations per year. Using this optimized system, we transferred iaaM gene into the high-yield and disease-resistant cultivar JND24, and BC<sub>4</sub>F<sub>3</sub> progenies were obtained within 1.5 years. In addition, the JND24-i3 line was selected with increased lint percentage and improved Micronaire value. These results demonstrate that the optimized speed breeding system offers a rapid and effective way to improve traits of cotton.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"79"},"PeriodicalIF":4.4,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664246","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}
引用次数: 0
Genetic architecture and genomic prediction for yield, winter damage, and digestibility traits in timothy (Phleum pratense L.) using genotyping-by-sequencing data. 利用基因分型测序数据对蒂莫西(Phleum pratense L.)产量、冬季损害和消化特性的遗传结构和基因组预测。
IF 4.4 1区 农林科学
Theoretical and Applied Genetics Pub Date : 2025-03-18 DOI: 10.1007/s00122-025-04860-9
N Vargas Jurado, H Kärkkäinen, D Fischer, O Bitz, O Manninen, P Pärssinen, M Isolahti, I Strandén, E A Mäntysaari
{"title":"Genetic architecture and genomic prediction for yield, winter damage, and digestibility traits in timothy (Phleum pratense L.) using genotyping-by-sequencing data.","authors":"N Vargas Jurado, H Kärkkäinen, D Fischer, O Bitz, O Manninen, P Pärssinen, M Isolahti, I Strandén, E A Mäntysaari","doi":"10.1007/s00122-025-04860-9","DOIUrl":"10.1007/s00122-025-04860-9","url":null,"abstract":"<p><strong>Key message: </strong>Accurate prediction of genomic breeding values for Timothy was possible using genomic best linear unbiased prediction. Timothy (Phleum pratense L.) is a grass species of great importance for Finnish agricultural production systems. Genotyping-by-sequencing along with genomic prediction methods offer the possibility to develop breeding materials efficiently. In addition, knowledge about the relationships among traits may be used to increase rates of genetic gain. Still, the quality of the genotypes and the validation population may affect the accuracy of predictions. The objectives of the study were (i) to estimate variance components for yield, winter damage and digestibility traits, and (ii) to assess the accuracy of genomic predictions. Variance components were estimated using genomic residual maximum likelihood where the genomic relationship matrix was scaled using a novel approach. Genomic breeding values were estimated using genomic best linear unbiased prediction in single- and multiple-trait settings, and for different marker filtering criteria. Estimates of heritability ranged from 0.13 ± 0.03 to 0.86 ± 0.05 for yield at first cut and organic matter digestibility at second cut, respectively. Genetic correlations ranged from -0.72 ± 0.12 to 0.59 ± 0.04 between yield at first cut and winter damage, and between digestibility at first and second cuts, respectively. Accuracy of prediction was not severely affected by the quality of genotyping. Using family cross-validation and single-trait models, predictive ability ranged from 0.18 to 0.62 for winter damage and digestibility at second cut, respectively. In addition, validation using forward prediction showed that estimated genomic breeding values were moderately accurate with little dispersion. Thus, genomic prediction constitutes a valuable tool for improving Timothy in Finland.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"77"},"PeriodicalIF":4.4,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11920354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658668","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}
引用次数: 0
Maximizing the accuracy of genetic variance estimation and using a novel generalized effective sample size to improve simulations. 最大限度地提高遗传方差估计的准确性,并使用一种新的广义有效样本量来改进模拟。
IF 4.4 1区 农林科学
Theoretical and Applied Genetics Pub Date : 2025-03-18 DOI: 10.1007/s00122-025-04861-8
Javier Fernández-González, Julio Isidro Y Sánchez
{"title":"Maximizing the accuracy of genetic variance estimation and using a novel generalized effective sample size to improve simulations.","authors":"Javier Fernández-González, Julio Isidro Y Sánchez","doi":"10.1007/s00122-025-04861-8","DOIUrl":"10.1007/s00122-025-04861-8","url":null,"abstract":"<p><strong>Key message: </strong>We developed an improved variance estimation that incorporates prediction error variance as a correction factor, alongside a novel generalized effective sample size to enhance simulations. This approach enables precise control of variance components, accommodating for more flexible and accurate simulations. Phenotypic variation in field trials results from genetic and environmental factors, and understanding this variation is critical for breeding program simulations. Additive genetic variance, a key component, is often estimated using linear mixed models (LMM), but can be biased due to improper scaling of the genomic relationship matrix. Here, we show that this bias can be minimized by incorporating prediction error variance (PEV) as a correction factor. Our results demonstrate that the PEV-based estimation of additive variance significantly improves accuracy, with root mean square errors orders of magnitude lower than traditional methods. This improved accuracy enables more realistic simulations, and we introduce a novel generalized effective sample size (ESS) to further refine simulations by accounting for sampling variation. Our method outperforms standard simulation approaches, allowing flexibility to include complex interactions such as genotype by environment effects. These findings provide a robust framework for variance estimation and simulation in genetic studies, with broad applicability to breeding programs.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"78"},"PeriodicalIF":4.4,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919955/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658670","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}
引用次数: 0
Fine mapping and candidate gene analysis of the major QTL qSW-A03 for seed weight in Brassica napus. 甘蓝型油菜种子重量主要 QTL qSW-A03 的精细作图和候选基因分析。
IF 4.4 1区 农林科学
Theoretical and Applied Genetics Pub Date : 2025-03-17 DOI: 10.1007/s00122-025-04866-3
Jiangyu Meng, Dingxue Hu, Bin Wang, Yuelin Zhu, Chunyan Lu, Yan Deng, Huiying Cai, Baohua Wang, Yajun He, Wei Qian
{"title":"Fine mapping and candidate gene analysis of the major QTL qSW-A03 for seed weight in Brassica napus.","authors":"Jiangyu Meng, Dingxue Hu, Bin Wang, Yuelin Zhu, Chunyan Lu, Yan Deng, Huiying Cai, Baohua Wang, Yajun He, Wei Qian","doi":"10.1007/s00122-025-04866-3","DOIUrl":"https://doi.org/10.1007/s00122-025-04866-3","url":null,"abstract":"<p><p>Seed weight is a determining factor for improving rapeseed productivity. In the present study, a high-density genetic map was constructed via genome resequencing in an RIL population derived from a cross of two rapeseed varieties, ZS11 and DL704, with great differences in thousand-seed weight (TSW). A total of 1,306 bins involving 1,261,526 markers were used to construct the bin map. On the basis of the genetic map, QTL mapping for seed weight was performed. In total, 15 QTLs associated with TSW were detected. A major and stable QTL, qSW-A03, was mapped to a 2.8 cM interval on chromosome A03. Fine mapping delimited the qSW-A03 locus into a 59-kb region, and 11 genes within this region were predicted. By employing a combination of gene variation, gene expression difference and gene coexpression network analysis of seed weight, BnaDUF1666 was identified as a promising candidate gene. This study provides useful information for the genetic dissection of seed weight and promotes the molecular breeding of high-yield rapeseed.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"76"},"PeriodicalIF":4.4,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143650898","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}
引用次数: 0
Rapid cycling genomic selection in maize landraces. 玉米地方品种的快速循环基因组选择。
IF 4.4 1区 农林科学
Theoretical and Applied Genetics Pub Date : 2025-03-17 DOI: 10.1007/s00122-025-04855-6
Clara Polzer, Hans-Jürgen Auinger, Michelle Terán-Pineda, Armin C Hölker, Manfred Mayer, Thomas Presterl, Carolina Rivera-Poulsen, Sofia da Silva, Milena Ouzunova, Albrecht E Melchinger, Chris-Carolin Schön
{"title":"Rapid cycling genomic selection in maize landraces.","authors":"Clara Polzer, Hans-Jürgen Auinger, Michelle Terán-Pineda, Armin C Hölker, Manfred Mayer, Thomas Presterl, Carolina Rivera-Poulsen, Sofia da Silva, Milena Ouzunova, Albrecht E Melchinger, Chris-Carolin Schön","doi":"10.1007/s00122-025-04855-6","DOIUrl":"10.1007/s00122-025-04855-6","url":null,"abstract":"<p><strong>Key message: </strong>A replicated experiment on genomic selection in a maize landrace provides valuable insights on the design of rapid cycling recurrent pre-breeding schemes and the factors contributing to their success. The genetic diversity of landraces is currently underutilized for elite germplasm improvement. In this study, we investigated the potential of rapid cycling genomic selection for pre-breeding of a maize (Zea mays L.) landrace population in replicated experiments. We trained the prediction model on a dataset (N = 899) composed of three landrace-derived doubled-haploid (DH) populations characterized for agronomic traits in 11 environments across Europe. All DH lines were genotyped with a 600 k SNP array. In two replications, three cycles of genomic selection and recombination were performed for line per se performance of early plant development, a major sustainability factor in maize production. From each cycle and replication, 100 DH lines were extracted. To evaluate selection response, the DH lines of all cycles and both replications (N = 688) were evaluated for per se performance of selected and unselected traits in seven environments. Selection was highly successful with an increase of about two standard deviations for traits under directional selection. Realized selection response was highest in the first cycle and diminished in following cycles. Selection gains predicted from genomic breeding values were only partially corroborated by realized gains estimated from adjusted means. Prediction accuracies declined sharply across cycles, but only for traits under directional selection. Retraining the prediction model with data from previous cycles improved prediction accuracies in cycles 2 and 3. Replications differed in selection response and particularly in accuracies. The experiment gives valuable insights with respect to the design of rapid cycling genomic selection schemes and the factors contributing to their success.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"75"},"PeriodicalIF":4.4,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11913984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143650900","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}
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