Plant Genome最新文献_第2页

Identification of resistance sources and genomic regions regulating Septoria tritici blotch resistance in South Asian bread wheat germplasm. 鉴定南亚面包小麦种质的抗性来源和调控七叶蓟马斑点病抗性的基因组区域。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-11-27 DOI: 10.1002/tpg2.20531

Manjeet Kumar, Xinyao He, Sudhir Navathe, Umesh Kamble, Madhu Patial, Pawan Kumar Singh

{"title":"Identification of resistance sources and genomic regions regulating Septoria tritici blotch resistance in South Asian bread wheat germplasm.","authors":"Manjeet Kumar, Xinyao He, Sudhir Navathe, Umesh Kamble, Madhu Patial, Pawan Kumar Singh","doi":"10.1002/tpg2.20531","DOIUrl":"10.1002/tpg2.20531","url":null,"abstract":"The Septoria tritici blotch (STB) [Zymoseptoria tritici (Desm.)] of wheat (Triticum aestivum L.) is characterized by its polycyclic and hemibiotrophic nature. It is one of the most dangerous diseases affecting wheat production worldwide. Durable resistance is largely decided by the combined effect of several quantitative trait loci (QTLs) having a minor effect. Currently, STB is not important in South Asia. However, STB expanding and wider adaptability, changing climatic conditions, and agronomic practices can create a situation of concern. Therefore, dissection of the genetic architecture of adult-plant resistance with genome-wide association mapping and selection of resistant sources for adult plant STB resistance were carried out on a panel of South Asian germplasm. We discovered the 91 quantitative trait nucleotides (QTNs) associated with STB resistance; 23 QTNs were repetitive across the different years and models. Many of these QTNs could differentiate the mapping panel into resistant versus susceptible groups and were linked to candidate genes related to disease resistance functions within linkage disequilibrium blocks. The repetitive QTNs, namely, Q.CIM.stb.2DL.2, Q.CIM.stb_dh.2DL.3, Q.CIM.stb.2AL.5, and Q.CIM.stb.7BL.1, may be novel due to the absence of co-localization of previously reported QTLs, meta-quantitative trait loci, and STB genes. There was a perfect negative correlation between the stacking of favorable alleles and STB susceptibility, and STB resistance response was improved by ∼50% with the stacking of ≥60% favorable alleles. The genotypes, namely, CIM20, CIM56, CIM57, CIM18, CIM44, WK2395, and K1317, could be used as resistant sources in wheat breeding programs. Therefore, this study could aid in designing the breeding programs for STB resistance before the onset of the alarming situation of STB in South Asia.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20531"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142733655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide association studies on resistance to powdery mildew in cultivated emmer wheat. 关于栽培小麦白粉病抗性的全基因组关联研究。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-07-28 DOI: 10.1002/tpg2.20493

Dhondup Lhamo, Genqiao Li, George Song, Xuehui Li, Taner Z Sen, Yong-Qiang Gu, Xiangyang Xu, Steven S Xu

{"title":"Genome-wide association studies on resistance to powdery mildew in cultivated emmer wheat.","authors":"Dhondup Lhamo, Genqiao Li, George Song, Xuehui Li, Taner Z Sen, Yong-Qiang Gu, Xiangyang Xu, Steven S Xu","doi":"10.1002/tpg2.20493","DOIUrl":"10.1002/tpg2.20493","url":null,"abstract":"Powdery mildew, caused by the fungal pathogen Blumeria graminis (DC.) E. O. Speer f. sp. tritici Em. Marchal (Bgt), is a constant threat to global wheat (Triticum aestivum L.) production. Although ∼100 powdery mildew (Pm) resistance genes and alleles have been identified in wheat and its relatives, more is needed to minimize Bgt's fast evolving virulence. In tetraploid wheat (Triticum turgidum L.), wild emmer wheat [T. turgidum ssp. dicoccoides (Körn. ex Asch. & Graebn.) Thell.] accessions from Israel have contributed many Pm resistance genes. However, the diverse genetic reservoirs of cultivated emmer wheat [T. turgidum ssp. dicoccum (Schrank ex Schübl.) Thell.] have not been fully exploited. In the present study, we evaluated a diverse panel of 174 cultivated emmer accessions for their reaction to Bgt isolate OKS(14)-B-3-1 and found that 66% of accessions, particularly those of Ethiopian (30.5%) and Indian (6.3%) origins, exhibited high resistance. To determine the genetic basis of Bgt resistance in the panel, genome-wide association studies were performed using 46,383 single nucleotide polymorphisms (SNPs) from genotype-by-sequencing and 4331 SNPs from the 9K SNP Infinium array. Twenty-five significant SNP markers were identified to be associated with Bgt resistance, of which 21 SNPs are likely novel loci, whereas four possibly represent emmer derived Pm4a, Pm5a, PmG16, and Pm64. Most novel loci exhibited minor effects, whereas three novel loci on chromosome arms 2AS, 3BS, and 5AL had major effect on the phenotypic variance. This study demonstrates cultivated emmer as a rich source of powdery mildew resistance, and the resistant accessions and novel loci found herein can be utilized in wheat breeding programs to enhance Bgt resistance in wheat.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20493"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11733656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141789607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A 24-nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis.

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-03-01 DOI: 10.1002/tpg2.70013

Yongsheng Bai, Xiaoting Wang, Shahid Ali, Yang Liu, Jiannan Zhou, Meiting Liu, Shuai Liu, Yulin Tang

{"title":"A 24-nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis.","authors":"Yongsheng Bai, Xiaoting Wang, Shahid Ali, Yang Liu, Jiannan Zhou, Meiting Liu, Shuai Liu, Yulin Tang","doi":"10.1002/tpg2.70013","DOIUrl":"10.1002/tpg2.70013","url":null,"abstract":"MicroRNAs (miRNAs) control gene expression in plant through transcript cleavage and translation inhibition. Recently, 24-nt miRNAs have been shown to direct DNA methylation at target sites, regulating the neighboring gene expression. Our study focused on miR9560, a 24-nt miRNA induced by cadmium (Cd) stress in Brassica rapa ssp. parachinensis (B. parachinensis). Phylogenetic analysis revealed miR9560 predominantly emerged in the Rosanae superorder and was conserved in Brassicaceae, with potential target sites adjacent to transporter family genes HMAs. RNA gel blotting showed that mature miR9560 was only detected in various Brassica crops roots after Cd stress. In B. parachinensis, miR9560's putative target site is upstream of BrpHMA2, an afflux-type Cd transporter. In a transient expression system of B. parachinensis protoplasts, the expression of miR9560 increased the DNA methylation upstream of BrpHMA2, reducing the transcription of BrpHMA2. This regulation was also observed in Arabidopsis wild-type protoplasts but not in the mutants dcl234 and ago4 with impairments in the RNA-dependent DNA methylation (RdDM) pathway. We deduced that miR9560 modulates BrpHMA2 expression via the RdDM pathway, potentially regulating Cd uptake and movement in B. parachinensis. Furthermore, this regulatory mechanism may extend to other Brassica plants. This study enhances our comprehension of 24-nt miRNAs role in regulating Cd accumulation within Brassica plants.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70013"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665100","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

Introducing CHiDO-A No Code Genomic Prediction software implementation for the characterization and integration of driven omics. 介绍 CHiDO--无代码基因组预测软件实现，用于表征和整合驱动的全息图学。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-10-24 DOI: 10.1002/tpg2.20519

Francisco González, Julián García-Abadillo, Diego Jarquín

{"title":"Introducing CHiDO-A No Code Genomic Prediction software implementation for the characterization and integration of driven omics.","authors":"Francisco González, Julián García-Abadillo, Diego Jarquín","doi":"10.1002/tpg2.20519","DOIUrl":"10.1002/tpg2.20519","url":null,"abstract":"Climate change represents a significant challenge to global food security by altering environmental conditions critical to crop growth. Plant breeders can play a key role in mitigating these challenges by developing more resilient crop varieties; however, these efforts require significant investments in resources and time. In response, it is imperative to use current technologies that assimilate large biological and environmental datasets into predictive models to accelerate the research, development, and release of new improved varieties that can be more resilient to the increasingly variable climatic conditions. Leveraging large and diverse datasets can improve the characterization of phenotypic responses due to environmental stimuli and genomic pulses. A better characterization of these signals holds the potential to enhance our ability to predict trait performance under changes in weather and/or soil conditions with high precision. This paper introduces characterization and integration of driven omics (CHiDO), an easy-to-use, no-code platform designed to integrate diverse omics datasets and effectively model their interactions. With its flexibility to integrate and process datasets, CHiDO's intuitive interface allows users to explore historical data, formulate hypotheses, and optimize data collection strategies for future scenarios. The platform's mission emphasizes global accessibility, democratizing statistical solutions for situations where professional ability in data processing and data analysis is not available.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20519"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142511131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Association mapping and genomic prediction for processing and end-use quality traits in wheat (Triticum aestivum L.). 小麦（Triticum aestivum L.）加工和最终用途品质性状的关联图谱和基因组预测。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-11-13 DOI: 10.1002/tpg2.20529

Harsimardeep S Gill, Emily Conley, Charlotte Brault, Linda Dykes, Jochum C Wiersma, Katherine Frels, James A Anderson

{"title":"Association mapping and genomic prediction for processing and end-use quality traits in wheat (Triticum aestivum L.).","authors":"Harsimardeep S Gill, Emily Conley, Charlotte Brault, Linda Dykes, Jochum C Wiersma, Katherine Frels, James A Anderson","doi":"10.1002/tpg2.20529","DOIUrl":"10.1002/tpg2.20529","url":null,"abstract":"End-use and processing traits in wheat (Triticum aestivum L.) are crucial for varietal development but are often evaluated only in the advanced stages of the breeding program due to the amount of grain needed and the labor-intensive phenotyping assays. Advances in genomic resources have provided new tools to address the selection for these complex traits earlier in the breeding process. We used association mapping to identify key variants underlying various end-use quality traits and evaluate the usefulness of genomic prediction for these traits in hard red spring wheat from the Northern United States. A panel of 383 advanced breeding lines and cultivars representing the diversity of the University of Minnesota wheat breeding program was genotyped using the Illumina 90K single nucleotide polymorphism array and evaluated in multilocation trials using standard assessments of end-use quality. Sixty-three associations for grain or flour characteristics, mixograph, farinograph, and baking traits were identified. The majority of these associations were mapped in the vicinity of glutenin/gliadin or other known loci. In addition, a putative novel multi-trait association was identified on chromosome 6AL, and candidate gene analysis revealed eight genes of interest. Further, genomic prediction had a high predictive ability (PA) for mixograph and farinograph traits, with PA up to 0.62 and 0.50 in cross-validation and forward prediction, respectively. The deployment of 46 markers from GWAS to predict dough-rheology traits yielded low to moderate PA for various traits. The results of this study suggest that genomic prediction for end-use traits in early generations can be effective for mixograph and farinograph assays but not baking assays.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20529"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726427/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142630996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimization of high-throughput marker systems for genomic prediction in alfalfa family bulks. 苜蓿科群体基因组预测的高通量标记系统优化。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-12-05 DOI: 10.1002/tpg2.20526

Pablo Sipowicz, Mario Henrique Murad Leite Andrade, Claudio Carlos Fernandes Filho, Juliana Benevenuto, Patricio Muñoz, L Felipe V Ferrão, Marcio F R Resende, C Messina, Esteban F Rios

{"title":"Optimization of high-throughput marker systems for genomic prediction in alfalfa family bulks.","authors":"Pablo Sipowicz, Mario Henrique Murad Leite Andrade, Claudio Carlos Fernandes Filho, Juliana Benevenuto, Patricio Muñoz, L Felipe V Ferrão, Marcio F R Resende, C Messina, Esteban F Rios","doi":"10.1002/tpg2.20526","DOIUrl":"10.1002/tpg2.20526","url":null,"abstract":"Alfalfa (Medicago sativa L.) is a perennial forage legume esteemed for its exceptional quality and dry matter yield (DMY); however, alfalfa has historically exhibited low genetic gain for DMY. Advances in genotyping platforms paved the way for a cost-effective application of genomic prediction in alfalfa family bulks. In this context, the optimization of marker density holds potential to reallocate resources within genomic prediction pipelines. This study aimed to (i) test two genotyping platforms for population structure discrimination and predictive ability (PA) of genomic prediction models (G-BLUP) for DMY, and (ii) explore optimal levels of marker density to predict DMY in family bulks. For this, 160 nondormant alfalfa families were phenotyped for DMY across 11 harvests and genotyped via targeted sequencing using Capture-seq with 17K probes and the DArTag 3K panel. Both platforms discriminated similarly against the population structure and resulted in comparable PA for DMY. For genotyping optimization, different levels of marker density were randomly extracted from each platform. In both cases, a plateau was achieved around 500 markers, yielding similar PA as the full set of markers. For phenotyping optimization, models with 500 markers built with data from five harvests resulted in similar PA compared to the full set of 11 harvests and full set of markers. Altogether, genotyping and phenotyping efforts were optimized in terms of number of markers and harvests. Capture-seq and DArTag yielded similar results and have the flexibility to adjust their panels to meet breeders' needs in terms of marker density.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20526"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Variation for QTL alleles associated with total dissolved solids among crop types in a GWAS of a Beta vulgaris diversity panel.

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-03-01 DOI: 10.1002/tpg2.70014

Audrey Pelikan, Irwin L Goldman

{"title":"Variation for QTL alleles associated with total dissolved solids among crop types in a GWAS of a Beta vulgaris diversity panel.","authors":"Audrey Pelikan, Irwin L Goldman","doi":"10.1002/tpg2.70014","DOIUrl":"10.1002/tpg2.70014","url":null,"abstract":"Sweetness is a main component of the table beet (Beta vulgaris L.) flavor profile and a key determinant of its market success for fresh consumption. Total dissolved solids (TDS) is a proxy for sugar content in produce and are easily measured through a refractometer, making TDS valuable in breeding programs focused on increasing sweetness. A diversity panel of 238 accessions from the Beta vulgaris crop complex and wild relatives was assembled and genotyped using genotyping-by-sequencing, yielding 10,237 single nucleotide polymorphisms (SNPs) from 226 full panel accessions and 9,847 SNPs from table beet only accessions after filtering. The panel was phenotyped in field trials over 2 years and mean values were adjusted using best linear unbiased estimates. TDS levels varied among crop types and a broad-sense heritability of 0.90 indicated that phenotypic differences can be attributed in large part to genetic variation. A genome-wide association study (GWAS) uncovered four quantitative trait loci (QTLs) identified across multiple models to significantly associate with TDS. A QTL on chromosome 2 was consistently identified among GWAS models, explaining 12.1%-62.6% of the phenotypic variation in the full panel. Bevul.2G176300, a gene directly involved in the sucrose biosynthesis pathway, was located downstream the significant marker. A second QTL identified on chromosome 7 revealed QTL alleles that may differentiate between table beet accessions, explaining nearly half the phenotypic variation, and is the first QTL reported in association with TDS unique to table beet. The QTL described can be used to efficiently breed for higher TDS levels in Beta vulgaris, avoiding intercrop type crosses and linkage drag.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70014"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A linkage map of Aegilops biuncialis reveals significant genomic rearrangements compared to bread wheat.

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-03-01 DOI: 10.1002/tpg2.70009

Adam Lampar, András Farkas, László Ivanizs, Kitti Szőke-Pázsi, Eszter Gaál, Mahmoud Said, Jan Bartoš, Jaroslav Doležel, Abraham Korol, Miroslav Valárik, István Molnár

{"title":"A linkage map of Aegilops biuncialis reveals significant genomic rearrangements compared to bread wheat.","authors":"Adam Lampar, András Farkas, László Ivanizs, Kitti Szőke-Pázsi, Eszter Gaál, Mahmoud Said, Jan Bartoš, Jaroslav Doležel, Abraham Korol, Miroslav Valárik, István Molnár","doi":"10.1002/tpg2.70009","DOIUrl":"10.1002/tpg2.70009","url":null,"abstract":"Goatgrasses with U- and M-genomes are important sources of new alleles for wheat breeding to maintain yield and quality under extreme conditions. However, the introgression of beneficial traits from wild Aegilops species into wheat has been limited by poor knowledge of their genomes and scarcity of molecular tools. Here, we present the first linkage map of allotetraploid Aegilops biuncialis Vis., developed using 224 F2 individuals derived from a cross between MvGB382 and MvGB642 accessions. The map comprises 5663 DArTseq markers assigned to 15 linkage groups corresponding to 13 chromosomes. Chromosome 1Mb could not be constructed due to a lack of recombination caused by rearrangements in the MvGB382 accession. The genetic map spans 2518 cM with an average marker density of 2.79 cM. The skeleton map contains 920 segregating markers, divided between the Mb sub-genome (425 markers) and the Ub sub-genome (495 markers). Chromosomes of the Mb sub-genome, originating from Aegilops comosa Sm. in Sibth. et Sm., show well-preserved collinearity with Triticum aestivum L. chromosomes. In contrast, chromosomes of the Ub sub-genome, originating from Aegilops umbellulata Zhuk., exhibit a varying degree of collinearity, with 1Ub, 3Ub, and 5Ub retaining a substantial level of collinearity with Triticum aestivum, while 2Ub, 4Ub, 6Ub, and 7Ub show significant rearrangements. A quantitative trait locus affecting fertility was identified near the centromere on the long arm of chromosome 3Mb, explaining 23.5% of the variance. The genome structure of Aegilops biuncialis, highlighted by the genetic map, provides insights into the speciation within the species and will support alien gene transfer into wheat.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70009"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11863542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143505095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium.

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-03-01 DOI: 10.1002/tpg2.70010

Kate E Jaggi, Karol Krak, Helena Štorchová, Bohumil Mandák, Ashley Marcheschi, Alexander Belyayev, Eric N Jellen, John Sproul, David Jarvis, Peter J Maughan

{"title":"A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium.","authors":"Kate E Jaggi, Karol Krak, Helena Štorchová, Bohumil Mandák, Ashley Marcheschi, Alexander Belyayev, Eric N Jellen, John Sproul, David Jarvis, Peter J Maughan","doi":"10.1002/tpg2.70010","DOIUrl":"10.1002/tpg2.70010","url":null,"abstract":"The genus Chenopodium L. is characterized by its wide geographic distribution and ecological adaptability. Species such as quinoa (Chenopodium quinoa Willd.) have served as domesticated staple crops for centuries. Wild Chenopodium species exhibit diverse niche adaptations and are important genetic reservoirs for beneficial agronomic traits, including disease resistance and climate hardiness. To harness the potential of the wild taxa for crop improvement, we developed a Chenopodium pangenome through the assembly and comparative analyses of 12 Chenopodium species that encompass the eight known genome types (A-H). Six of the species are new chromosome-scale assemblies, and many are polyploids; thus, a total of 20 genomes were included in the pangenome analyses. We show that the genomes vary dramatically in size with the D genome being the smallest (∼370 Mb) and the B genome being the largest (∼700 Mb) and that genome size was correlated with independent expansions of the Copia and Gypsy LTR retrotransposon families, suggesting that transposable elements have played a critical role in the evolution of the Chenopodium genomes. We annotated a total of 33,457 pan-Chenopodium gene families, of which ∼65% were classified as shell (2% private). Phylogenetic analysis clarified the evolutionary relationships among the genome lineages, notably resolving the taxonomic placement of the F genome while highlighting the uniqueness of the A genome in the Western Hemisphere. These genomic resources are particularly important for understanding the secondary and tertiary gene pools available for the improvement of the domesticated chenopods while furthering our understanding of the evolution and complexity within the genus.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70010"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11869160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143525018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gene mapping and candidate gene analysis of a sorghum sheathed panicle-I mutant.

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-03-01 DOI: 10.1002/tpg2.70007

Jianling Ao, Ruoruo Wang, Wenzeng Li, Yanqing Ding, Jianxia Xu, Ning Cao, Xu Gao, Bin Cheng, Degang Zhao, Liyi Zhang

{"title":"Gene mapping and candidate gene analysis of a sorghum sheathed panicle-I mutant.","authors":"Jianling Ao, Ruoruo Wang, Wenzeng Li, Yanqing Ding, Jianxia Xu, Ning Cao, Xu Gao, Bin Cheng, Degang Zhao, Liyi Zhang","doi":"10.1002/tpg2.70007","DOIUrl":"10.1002/tpg2.70007","url":null,"abstract":"Panicle exsertion is essential for crop yield and quality, and understanding its molecular mechanisms is crucial for optimizing plant architecture. In this study, the sheathed panicle-I (shp-I) mutant was identified from the ethyl methane sulfonate mutant population of the sorghum [Sorghum bicolor (L.) Moench] variety Hongyingzi (HYZ). While phenotypically similar to the wild type during the seedling stage, shp-I exhibits a significantly shorter peduncle internode at the heading stage. Cytomorphological analysis revealed reduced parenchyma cell size within the mutant's peduncle internode. Phytohormonal profiling showed lower levels of indole-3-acetic acid and higher concentrations of brassinosteroid in the mutant compared to the wild type at the peduncle internode. Genetic analysis confirmed that the mutant phenotype was caused by a recessive single-gene mutation. Through bulked segregant analysis sequencing (BSA-seq) genetic mapping, the causative locus for the mutant phenotype was localized to a 59.65-59.92 Mb interval on chromosome 10, which contains 28 putative genes. Additionally, the gene SbiHYZ.10G230700, which encodes a BTB/POZ and MATH (BPM) domain protein, was identified as a candidate gene. Further analysis revealed that the non-synonymous mutations in the candidate gene were located within the MATH domain, affecting the 3D structure of the protein. In summary, this study provides a new genetic material and candidate genes for future research into the molecular regulation of sorghum peduncle length.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70007"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0