Plant Genome最新文献_第7页

Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR. 通过测序对马铃薯进行定向基因分型，并利用 R/polyBreedR 进行数据分析。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-06-17 DOI: 10.1002/tpg2.20484

Jeffrey B Endelman, Moctar Kante, Hannele Lindqvist-Kreuze, Andrzej Kilian, Laura M Shannon, Maria V Caraza-Harter, Brieanne Vaillancourt, Kathrine Mailloux, John P Hamilton, C Robin Buell

{"title":"Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR.","authors":"Jeffrey B Endelman, Moctar Kante, Hannele Lindqvist-Kreuze, Andrzej Kilian, Laura M Shannon, Maria V Caraza-Harter, Brieanne Vaillancourt, Kathrine Mailloux, John P Hamilton, C Robin Buell","doi":"10.1002/tpg2.20484","DOIUrl":"10.1002/tpg2.20484","url":null,"abstract":"Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato (Solanum tuberosum L.) was developed using the DArTag technology and later expanded to 4K targets. Genomic markers were selected from the potato Infinium single nucleotide polymorphism (SNP) array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root mean squared error) <0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N = 85), which was significantly lower than the RMSE of 0.42 with the random forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20484"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141421506","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}

引用次数: 0

Integrating genomics, phenomics, and deep learning improves the predictive ability for Fusarium head blight-related traits in winter wheat. 整合基因组学、表型组学和深度学习，提高冬小麦镰刀菌头孢疫病相关性状的预测能力。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-06-09 DOI: 10.1002/tpg2.20470

Subash Thapa, Harsimardeep S Gill, Jyotirmoy Halder, Anshul Rana, Shaukat Ali, Maitiniyazi Maimaitijiang, Upinder Gill, Amy Bernardo, Paul St Amand, Guihua Bai, Sunish K Sehgal

{"title":"Integrating genomics, phenomics, and deep learning improves the predictive ability for Fusarium head blight-related traits in winter wheat.","authors":"Subash Thapa, Harsimardeep S Gill, Jyotirmoy Halder, Anshul Rana, Shaukat Ali, Maitiniyazi Maimaitijiang, Upinder Gill, Amy Bernardo, Paul St Amand, Guihua Bai, Sunish K Sehgal","doi":"10.1002/tpg2.20470","DOIUrl":"10.1002/tpg2.20470","url":null,"abstract":"Fusarium head blight (FHB) remains one of the most destructive diseases of wheat (Triticum aestivum L.), causing considerable losses in yield and end-use quality. Phenotyping of FHB resistance traits, Fusarium-damaged kernels (FDK), and deoxynivalenol (DON), is either prone to human biases or resource expensive, hindering the progress in breeding for FHB-resistant cultivars. Though genomic selection (GS) can be an effective way to select these traits, inaccurate phenotyping remains a hurdle in exploiting this approach. Here, we used an artificial intelligence (AI)-based precise FDK estimation that exhibits high heritability and correlation with DON. Further, GS using AI-based FDK (FDK_QVIS/FDK_QNIR) showed a two-fold increase in predictive ability (PA) compared to GS for traditionally estimated FDK (FDK_V). Next, the AI-based FDK was evaluated along with other traits in multi-trait (MT) GS models to predict DON. The inclusion of FDK_QNIR and FDK_QVIS with days to heading as covariates improved the PA for DON by 58% over the baseline single-trait GS model. We next used hyperspectral imaging of FHB-infected wheat kernels as a novel avenue to improve the MT GS for DON. The PA for DON using selected wavebands derived from hyperspectral imaging in MT GS models surpassed the single-trait GS model by around 40%. Finally, we evaluated phenomic prediction for DON by integrating hyperspectral imaging with deep learning to directly predict DON in FHB-infected wheat kernels and observed an accuracy (R2 = 0.45) comparable to best-performing MT GS models. This study demonstrates the potential application of AI and vision-based platforms to improve PA for FHB-related traits using genomic and phenomic selection.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20470"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141297021","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}

引用次数: 0

Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana. 转录组和表观遗传学反应揭示了大豆对 Phytophthora sansomeana 的抗性。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-07-12 DOI: 10.1002/tpg2.20487

Gwonjin Lee, Charlotte N DiBiase, Beibei Liu, Tong Li, Austin G McCoy, Martin I Chilvers, Lianjun Sun, Dechun Wang, Feng Lin, Meixia Zhao

{"title":"Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana.","authors":"Gwonjin Lee, Charlotte N DiBiase, Beibei Liu, Tong Li, Austin G McCoy, Martin I Chilvers, Lianjun Sun, Dechun Wang, Feng Lin, Meixia Zhao","doi":"10.1002/tpg2.20487","DOIUrl":"10.1002/tpg2.20487","url":null,"abstract":"Phytophthora root rot, caused by oomycete pathogens in the Phytophthora genus, poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied in soybean, the molecular basis underlying immune responses to Phytophthora sansomeana remains unclear. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 h post inoculation [hpi]) after P. sansomeana inoculation. Comparative transcriptomic analyses revealed a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in resistant lines, particularly at 8 and 16 hpi. These DEGs were predominantly associated with defense response, ethylene, and reactive oxygen species-mediated defense pathways. Moreover, DE transposons were predominantly upregulated after inoculation, and more of them were enriched near genes in Colfax than other soybean lines. Notably, we identified a long non-coding RNA (lncRNA) within the mapped region of the resistance gene that exhibited exclusive upregulation in the resistant lines after inoculation, potentially regulating two flanking LURP-one-related genes. Furthermore, DNA methylation analysis revealed increased CHH (where H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in Colfax compared to Williams 82. Overall, our results provide comprehensive insights into soybean responses to P. sansomeana, highlighting potential roles of lncRNAs and epigenetic regulation in plant defense.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20487"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141602026","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}

引用次数: 0

Erratum to: Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2. 勘误：全球部署的高粱蚜虫抗性基因 RMES1 易受生物型转变的影响，但 RMES2 可增强其抗性。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-07-29 DOI: 10.1002/tpg2.20499

Carl VanGessel, Brian Rice, Terry J Felderhoff, Jean Rigaud Charles, Gael Pressoir, Vamsi Nalam, Geoffrey P Morris

引用次数: 0

Genetic diversity and population structure in banana (Musa spp.) breeding germplasm. 香蕉（Musa spp.）育种种质的遗传多样性和种群结构。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-07-29 DOI: 10.1002/tpg2.20497

Violet Akech, Therése Bengtsson, Rodomiro Ortiz, Rony Swennen, Brigitte Uwimana, Claudia F Ferreira, Delphine Amah, Edson P Amorim, Elizabeth Blisset, Ines Van den Houwe, Ivan K Arinaitwe, Liana Nice, Priver Bwesigye, Steve Tanksley, Subbaraya Uma, Backiyarani Suthanthiram, Marimuthu S Saraswathi, Hassan Mduma, Allan Brown

{"title":"Genetic diversity and population structure in banana (Musa spp.) breeding germplasm.","authors":"Violet Akech, Therése Bengtsson, Rodomiro Ortiz, Rony Swennen, Brigitte Uwimana, Claudia F Ferreira, Delphine Amah, Edson P Amorim, Elizabeth Blisset, Ines Van den Houwe, Ivan K Arinaitwe, Liana Nice, Priver Bwesigye, Steve Tanksley, Subbaraya Uma, Backiyarani Suthanthiram, Marimuthu S Saraswathi, Hassan Mduma, Allan Brown","doi":"10.1002/tpg2.20497","DOIUrl":"10.1002/tpg2.20497","url":null,"abstract":"Bananas (Musa spp.) are one of the most highly consumed fruits globally, grown in the tropical and sub-tropical regions. We evaluated 856 Musa accessions from the breeding programs of the International Institute of Tropical Agriculture of Nigeria, Tanzania, and Uganda; the National Agricultural Research Organization of Uganda; the Brazilian Agricultural Research Corporation (Embrapa); and the National Research Centre for Banana of India. Accessions from the in vitro gene bank at the International Transit Centre in Belgium were included to provide a baseline of available global diversity. A total of 16,903 informative single nucleotide polymorphism markers were used to estimate and characterize the genetic diversity and population structure and identify overlaps and unique material among the breeding programs. Analysis of molecular variance displayed low genetic variation among accessions and diploids and a higher variation among tetraploids (p < 0.001). Structure analysis revealed two major clusters corresponding to genomic composition. The results indicate that there is potential for the banana breeding programs to increase the diversity in their breeding materials and should exploit this potential for parental improvement and to enhance genetic gains in future breeding efforts.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20497"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793854","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}

引用次数: 0

Integrated meta-QTL and in silico transcriptome assessment pinpoint major genomic regions responsible for spike length in wheat (Triticum aestivum L.). 综合元 QTL 和默观转录组评估确定了小麦（Triticum aestivum L.）穗长的主要基因组区域。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-07-31 DOI: 10.1002/tpg2.20492

Changgang Yang, Xueting Zhang, Shihong Wang, Na Liu

{"title":"Integrated meta-QTL and in silico transcriptome assessment pinpoint major genomic regions responsible for spike length in wheat (Triticum aestivum L.).","authors":"Changgang Yang, Xueting Zhang, Shihong Wang, Na Liu","doi":"10.1002/tpg2.20492","DOIUrl":"10.1002/tpg2.20492","url":null,"abstract":"Spike length (SL) is one of the major contributors to wheat yield. Uncovering major genetic regions affecting SL is an integral part of elucidating the genetic basis of wheat yield traits and goes further pivotal for marker-assisted selection breeding. A genome-wide meta-quantitative trait locus (MQTL) analysis of wheat SL resulted in the refinement of 48 MQTLs using 227 initial QTLs retrieved from previous studies published over the past decades. The average confidence interval (CI) of these MQTLs amounted to a 5.16-fold reduction compared to the mean CI of the initial QTLs. As many as 2240 putative candidate genes (CGs) were identified from the MQTL intervals using transcriptomics data in silico of wheat, of which 58 CGs were identified based on wheat-rice homology analysis. For the key CG affecting SL, a functional kompetitive allele-specific PCR (KASP) marker, TaPP2C-3B-KASP, was developed to distinguish TaPP2C-3B-Hap I and TaPP2C-3B-Hap II based on the single nucleotide polymorphism at the 272 bp (A/G). The frequency of the elite allelic variation TaPP2C-3B-Hap II with high SL remained relatively stable at about 49.62% from the 1960s to 1990s. Integration of MQTL analysis and in silico transcriptome data led to a significant increase in the reliability of CGs for the genetic regulation of wheat SL, and the haplotype analysis for key CGs TaPP2C-3B of SL provided insights into the biological function of the TaPP2C-3B gene.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20492"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141856913","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}

引用次数: 0

Multi-trait multi-environment genomic prediction of preliminary yield trial in pulse crop. 脉冲作物初步产量试验的多性状多环境基因组预测

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-08-04 DOI: 10.1002/tpg2.20496

Rica Amor Saludares, Sikiru Adeniyi Atanda, Lisa Piche, Hannah Worral, Francoise Dariva, Kevin McPhee, Nonoy Bandillo

{"title":"Multi-trait multi-environment genomic prediction of preliminary yield trial in pulse crop.","authors":"Rica Amor Saludares, Sikiru Adeniyi Atanda, Lisa Piche, Hannah Worral, Francoise Dariva, Kevin McPhee, Nonoy Bandillo","doi":"10.1002/tpg2.20496","DOIUrl":"10.1002/tpg2.20496","url":null,"abstract":"Phenotypic selection of complex traits such as seed yield and protein in the preliminary yield trial (PYT) is often constrained by limited seed availability, resulting in trials with few environments and minimal to no replications. Multi-trait multi-environment enabled genomic prediction (MTME-GP) offers a valuable alternative to predict missing phenotypes of selection candidates for multiple traits and diverse environments. In this study, we assessed the efficiency of MTME-GP for improving seed protein and seed yield in field pea, the top two breeding targets but highly antagonistic traits in pulse crop. We utilized a set of 300 selection candidates in the PYT that virtually represented all possible families of the North Dakota State University field pea breeding program. Selection candidates were evaluated in three diverse, contrasting environments, as indicated by a range of heritability. Using whole- and split-environment cross validation schemes, MTME-GP had higher predictive ability than a standard additive G-BLUP model. Integrating a range of overlapping genotypes in between environments showed improvement on the predictive ability of the MTME-GP model but tends to plateau at 50%-80% training set size. Regardless of the cross-validation scheme, accuracy was among the lowest in stressed environments, presumably due to low heritability for seed protein and yield. This study provided insights into the potential of MTME-GP in a public pulse crop breeding program. The MTME-GP framework can be further improved with more testing environments and integration of additional orthogonal information in the early stages of the breeding pipeline.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20496"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890646","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}

引用次数: 0

Genetic resources and genes/QTLs for gram pod borer (Helicoverpa armigera Hübner) resistance in chickpea from the Western Himalayas. 西喜马拉雅山鹰嘴豆抗禾本科豆荚螟（Helicoverpa armigera Hübner）的遗传资源和基因/QTLs。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-07-04 DOI: 10.1002/tpg2.20483

Sheikh Aafreen Rehman, Shaheen Gul, M Parthiban, Ishita Isha, M S Sai Reddy, Annapurna Chitikineni, Mahendar Thudi, R Varma Penmetsa, Rajeev Kumar Varshney, Reyazul Rouf Mir

{"title":"Genetic resources and genes/QTLs for gram pod borer (Helicoverpa armigera Hübner) resistance in chickpea from the Western Himalayas.","authors":"Sheikh Aafreen Rehman, Shaheen Gul, M Parthiban, Ishita Isha, M S Sai Reddy, Annapurna Chitikineni, Mahendar Thudi, R Varma Penmetsa, Rajeev Kumar Varshney, Reyazul Rouf Mir","doi":"10.1002/tpg2.20483","DOIUrl":"10.1002/tpg2.20483","url":null,"abstract":"Helicoverpa armigera (also known as gram pod borer) is a serious threat to chickpea production in the world. A set of 173 chickpea genotypes were evaluated for H. armigera resistance, including mean larval population (MLP), percentage pod damage (PPD), and pest resistance (PR) for 2 consecutive years (year 2020 and 2021). The same core set was also genotyped with 50K Axiom CicerSNP Array. The trait data and 50,000 single nucleotide polymorphism genotypic data were used together to work out marker-trait associations (MTAs) using different genome-wide association studies models. For MLP, a total of 53 MTAs were identified, including 25 MTAs in year 2020 and 28 MTAs in year 2021. A set of three MTAs was found common in both environments. For PPD, two MTAs in year 2020 and five MTAs in year 2021 were identified. A set of two MTAs were common in both environments. Similarly, for PR, only two MTAs common in both environments were identified. Interestingly, a common MTA (Affx_123255526) on chromosome 2 (Ca2) was found to be associated with all the three component traits (MLP, PPD, and PR) of pod borer resistance in chickpea. Further, we report key genes that encode SCAMPs (that facilitates the secretion of defense-related molecules), quinone oxidoreductase (enables the production of reactive oxygen species that promotes diapause of gram pod borer), and NB-LRR proteins that have been implicated in plant defense against H. armigera. The resistant chickpea genotypes, MTAs, and key genes reported in the present study may prove useful in the future for developing pod borer-resistant chickpea varieties.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20483"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141535684","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}

引用次数: 0

Comprehensive molecular evolutionary analysis of small heat shock proteins in five diploid Gossypium species. 五种二倍体格桑花小型热休克蛋白的全面分子进化分析。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-06-12 DOI: 10.1002/tpg2.20478

Kai Fan, Zhengyi Qian, Yuxi He, Jiayuan Chen, Fangting Ye, Xiaogang Zhu, Wenxiong Lin, Lili Cui, Tao Lan, Zhaowei Li

{"title":"Comprehensive molecular evolutionary analysis of small heat shock proteins in five diploid Gossypium species.","authors":"Kai Fan, Zhengyi Qian, Yuxi He, Jiayuan Chen, Fangting Ye, Xiaogang Zhu, Wenxiong Lin, Lili Cui, Tao Lan, Zhaowei Li","doi":"10.1002/tpg2.20478","DOIUrl":"10.1002/tpg2.20478","url":null,"abstract":"The small heat shock proteins (sHSPs) are important components in plant growth and development, and stress response. However, a systematical understanding of the sHSP family is yet to be reported in five diploid Gossypium species. In this study, 34 GlsHSPs, 36 GrsHSPs, 37 GtsHSPs, 37 GasHSPs, and 38 GhesHSPs were identified in Gossypium longicalyx, Gossypium raimondii, Gossypium turneri, Gossypium arboreum, and Gossypium herbaceum, respectively. These sHSP members can be clustered into 10 subfamilies. Different subfamilies had different member numbers, motif distributions, gene structures, gene duplication events, gene loss numbers, and cis-regulatory elements. Besides, the paleohexaploidization event in cotton ancestor led to expanding the sHSP members and it was also inherited by five diploid Gossypium species. After the cotton ancestor divergence, the sHSP members had the relatively conserved evolution in five diploid Gossypium species. The comprehensive evolutionary history of the sHSP family was revealed in five diploid Gossypium species. Furthermore, several GasHSPs and GhesHSPs were important candidates in plant growth and development, and stress response. These current findings can provide valuable information for the molecular evolution and further functional research of the sHSP family in cotton.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20478"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307151","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}

引用次数: 0

Leveraging genomics and temporal high-throughput phenotyping to enhance association mapping and yield prediction in sesame. 利用基因组学和时间高通量表型技术加强芝麻的关联图谱绘制和产量预测。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-06-26 DOI: 10.1002/tpg2.20481

Idan Sabag, Ye Bi, Maitreya Mohan Sahoo, Ittai Herrmann, Gota Morota, Zvi Peleg

{"title":"Leveraging genomics and temporal high-throughput phenotyping to enhance association mapping and yield prediction in sesame.","authors":"Idan Sabag, Ye Bi, Maitreya Mohan Sahoo, Ittai Herrmann, Gota Morota, Zvi Peleg","doi":"10.1002/tpg2.20481","DOIUrl":"10.1002/tpg2.20481","url":null,"abstract":"Sesame (Sesamum indicum) is an important oilseed crop with rising demand owing to its nutritional and health benefits. There is an urgent need to develop and integrate new genomic-based breeding strategies to meet these future demands. While genomic resources have advanced genetic research in sesame, the implementation of high-throughput phenotyping and genetic analysis of longitudinal traits remains limited. Here, we combined high-throughput phenotyping and random regression models to investigate the dynamics of plant height, leaf area index, and five spectral vegetation indices throughout the sesame growing seasons in a diversity panel. Modeling the temporal phenotypic and additive genetic trajectories revealed distinct patterns corresponding to the sesame growth cycle. We also conducted longitudinal genomic prediction and association mapping of plant height using various models and cross-validation schemes. Moderate prediction accuracy was obtained when predicting new genotypes at each time point, and moderate to high values were obtained when forecasting future phenotypes. Association mapping revealed three genomic regions in linkage groups 6, 8, and 11, conferring trait variation over time and growth rate. Furthermore, we leveraged correlations between the temporal trait and seed-yield and applied multi-trait genomic prediction. We obtained an improvement over single-trait analysis, especially when phenotypes from earlier time points were used, highlighting the potential of using a high-throughput phenotyping platform as a selection tool. Our results shed light on the genetic control of longitudinal traits in sesame and underscore the potential of high-throughput phenotyping to detect a wide range of traits and genotypes that can inform sesame breeding efforts to enhance yield.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20481"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460191","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}

引用次数: 0