Plant Genome最新文献_第10页

Identification of the sweet orange (Citrus sinensis) bHLH gene family and the role of CsbHLH55 and CsbHLH87 in regulating salt stress. 甜橙（Citrus sinensis）bHLH 基因家族的鉴定以及 CsbHLH55 和 CsbHLH87 在调节盐胁迫中的作用。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-08-31 DOI: 10.1002/tpg2.20502

Yinqiang Zi, Mengjie Zhang, Xiuyao Yang, Ke Zhao, Tuo Yin, Ke Wen, Xulin Li, Xiaozhen Liu, Hanyao Zhang

{"title":"Identification of the sweet orange (Citrus sinensis) bHLH gene family and the role of CsbHLH55 and CsbHLH87 in regulating salt stress.","authors":"Yinqiang Zi, Mengjie Zhang, Xiuyao Yang, Ke Zhao, Tuo Yin, Ke Wen, Xulin Li, Xiaozhen Liu, Hanyao Zhang","doi":"10.1002/tpg2.20502","DOIUrl":"10.1002/tpg2.20502","url":null,"abstract":"Salt stress is one of the primary environmental stresses limiting plant growth and production and adversely affecting the growth, development, yield, and fruit quality of Citrus sinensis. bHLH (basic helix-loop-helix) genes are involved in many bioregulatory processes in plants, including growth and development, phytohormone signaling, defense responses, and biosynthesis of specific metabolites. In this study, by bioinformatics methods, 120 CsbHLHgenes were identified, and phylogenetic analysis classified them into 18 subfamilies that were unevenly distributed on nine chromosomes. The cis-acting elements of the CsbHLH genes were mainly hormone-related cis-acting elements. Seventeen CsbHLH genes exhibited significant differences in expression under salt stress. Six CsbHLH genes with significant differences in expression were randomly selected for quantitative real-time polymerase chain reaction (qRT-PCR) validation. The qRT-PCR results showed a strong correlation with the transcriptome data. Phytohormones such as jasmonic acid (JA) are essential for biotic and abiotic stress responses in plants, and CsbHLH55 and CsbHLH87 are considered candidate target genes for sweet orange MYC2 transcription factors involved in the JA signaling pathway. These genes are the main downstream effectors in the JA signaling pathway and can be activated to participate in the JA signaling pathway. Activation of the JA signaling pathway inhibits the production of reactive oxygen species and improves the salt tolerance of sweet orange plants. The CsbHLH55 and CsbHLH87 genes could be candidate genes for breeding new transgenic salt-resistant varieties of sweet orange.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20502"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113851","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

A first de novo transcriptome assembly of feijoa (Acca sellowiana [Berg] Burret) reveals key genes involved in flavonoid biosynthesis. 飞燕草（Acca sellowiana [Berg] Burret）的首个全新转录组汇编揭示了参与类黄酮生物合成的关键基因。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-08-20 DOI: 10.1002/tpg2.20501

Hector Oberti, Juan Gutierrez-Gonzalez, Clara Pritsch

{"title":"A first de novo transcriptome assembly of feijoa (Acca sellowiana [Berg] Burret) reveals key genes involved in flavonoid biosynthesis.","authors":"Hector Oberti, Juan Gutierrez-Gonzalez, Clara Pritsch","doi":"10.1002/tpg2.20501","DOIUrl":"10.1002/tpg2.20501","url":null,"abstract":"Acca sellowiana [Berg] Burret, a cultivated fruit tree originating from South America, is gaining the attention of the nutraceutical and pharmaceutical industries due to their high content of flavonoids and other phenolic compounds in fruits, leaves, and flowers. Flavonoids are a diverse group of secondary metabolites with antioxidant, anti-inflammatory, and antimicrobial properties. They also play a crucial role in plant immune response. Despite their importance, the lack of research on A. sellowiana genomics and transcriptomics hinders a deeper understanding of the molecular mechanisms behind flavonoid biosynthesis and its regulation. Here, we de novo assembled and benchmarked 11 A. sellowiana transcriptomes from leaves and floral tissues at three developmental stages using high-throughput sequencing. We selected and annotated the best assembly according to commonly used metrics and databases. This reference transcriptome consisted of 221,649 nonredundant transcripts, of which 107,612 were functionally annotated. We then used this reference transcriptome to explore the expression profiling of key secondary metabolite genes. Transcripts from genes involved in the flavonoid and anthocyanin biosynthesis pathways were identified. We also identified 4068 putative transcription factors, with the most abundant families being bHLH, C2H2, NAC, MYB, and MYB-related. Transcript expression profiling revealed distinct patterns of gene expression during flower development. Particularly, we found 71 differentially expressed transcripts representing 14 enzymes of the flavonoid pathway, suggesting major changes in flavonoid accumulation across floral stages. Our findings will contribute to understanding the genetic basis of flavonoids and provide a foundation for further research and exploitation of the economic potential of this species.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20501"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142005616","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

Chromosome-scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression. 染色体规模的丹参基因组组装揭示了丹参种间引种的猖獗。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-08-27 DOI: 10.1002/tpg2.20494

Julia Brose, John P Hamilton, Nicholas Schlecht, Dongyan Zhao, Paulina M Mejía-Ponce, Arely Cruz-Pérez, Brieanne Vaillancourt, Joshua C Wood, Patrick P Edger, Salvador Montes-Hernandez, Guillermo Orozco de Rosas, Björn Hamberger, Angélica Cibrian-Jaramillo, C Robin Buell

{"title":"Chromosome-scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression.","authors":"Julia Brose, John P Hamilton, Nicholas Schlecht, Dongyan Zhao, Paulina M Mejía-Ponce, Arely Cruz-Pérez, Brieanne Vaillancourt, Joshua C Wood, Patrick P Edger, Salvador Montes-Hernandez, Guillermo Orozco de Rosas, Björn Hamberger, Angélica Cibrian-Jaramillo, C Robin Buell","doi":"10.1002/tpg2.20494","DOIUrl":"10.1002/tpg2.20494","url":null,"abstract":"Salvia hispanica L. (Chia), a member of the Lamiaceae, is an economically important crop in Mesoamerica, with health benefits associated with its seed fatty acid composition. Chia varieties are distinguished based on seed color including mixed white and black (Chia pinta) and black (Chia negra). To facilitate research on Chia and expand on comparative analyses within the Lamiaceae, we generated a chromosome-scale assembly of a Chia pinta accession and performed comparative genome analyses with a previously published Chia negra genome assembly. The Chia pinta and Chia negra genome sequences were highly similar as shown by a limited number of single nucleotide polymorphisms and extensive shared orthologous gene membership. However, there is an enrichment of terpene synthases in the Chia pinta genome relative to the Chia negra genome. We sequenced and analyzed the genomes of 20 Chia accessions with differing seed color and geographic origin revealing population structure within S. hispanica and interspecific introgressions of Salvia species. As the genus Salvia is polyphyletic, its evolutionary history remains unclear. Using large-scale synteny analysis within the Lamiaceae and orthologous group membership, we resolved the phylogeny of Salvia species. This study and its collective resources further our understanding of genomic diversity in this food crop and the extent of interspecies hybridizations in Salvia.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20494"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142082333","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

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