G3: Genes|Genomes|Genetics最新文献_第2页

De novo whole genome assembly of the critically endangered southern muriqui (Brachyteles arachnoides).

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-02-17 DOI: 10.1093/g3journal/jkaf034

Christopher Faulk, Carrie Walls, Brandie Nelson, Paloma R Arakaki, Irys H L Gonzalez, Nancy Banevicius, Rodrigo H F Teixeira, Marina A Medeiros, Gessiane P Silva, Mauricio Talebi, Wilson C J Chung, Rafaela S C Takeshita

{"title":"De novo whole genome assembly of the critically endangered southern muriqui (Brachyteles arachnoides).","authors":"Christopher Faulk, Carrie Walls, Brandie Nelson, Paloma R Arakaki, Irys H L Gonzalez, Nancy Banevicius, Rodrigo H F Teixeira, Marina A Medeiros, Gessiane P Silva, Mauricio Talebi, Wilson C J Chung, Rafaela S C Takeshita","doi":"10.1093/g3journal/jkaf034","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf034","url":null,"abstract":"The southern muriqui (Brachyteles arachnoides) is one of the two species of muriquis (genus Brachyteles), the largest body sized nonhuman primate from the Neotropics. Deforestation and illegal hunting have led to a continuing decline in the muriqui population, leading to their current classification as critically endangered. The lack of a reference genome for the genus Brachyteles prevents scientists from taking full advantage of genomic tools to improve their conservation status. This study reports the first whole-genome assemblies of the genus Brachyteles, using DNA from two zoo-housed southern muriqui females. We performed sequencing with Oxford Nanopore Technologies' PromethION 2 Solo using a native DNA library preparation to preserve DNA modifications. We used Flye to assemble genomes for each individual. The best final assembly was 2.6 Gb, in 319 contigs, with an N50 of 58.8 Mb and L50 of 17. BUSCO completeness score for this assembly was 99.5%. The assembly of the second individual had similar quality, with length of 2.6 Gb, 759 contigs, N50 of 47.9 Mb, L50 of 18, and BUSCO completeness score of 99.04%. Both assemblies had <1% duplicates, missing, or fragments. Gene model mapper detected 24,353 protein coding genes, and repetitive elements accounted for 46% of the genome. We also reported the mitogenome, which had 16,562 bp over 37 genes, and global methylation of CpG sites, which revealed a mean of 80% methylation. Our study provides a high-quality reference genome assembly for the southern muriqui, expanding the tools that can be used to aid in their conservation efforts.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

VPS13D mutations affect mitochondrial homeostasis and locomotion in Caenorhabditis elegans.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-02-17 DOI: 10.1093/g3journal/jkaf023

Xiaomeng Yin, Ruoxi Wang, Andrea Thackeray, Eric H Baehrecke, Mark J Alkema

{"title":"VPS13D mutations affect mitochondrial homeostasis and locomotion in Caenorhabditis elegans.","authors":"Xiaomeng Yin, Ruoxi Wang, Andrea Thackeray, Eric H Baehrecke, Mark J Alkema","doi":"10.1093/g3journal/jkaf023","DOIUrl":"10.1093/g3journal/jkaf023","url":null,"abstract":"Mitochondria control cellular metabolism, serve as hubs for signaling and organelle communication, and are important for the health and survival of cells. VPS13D encodes a cytoplasmic lipid transfer protein that regulates mitochondrial morphology, mitochondria and endoplasmic reticulum (ER) contact, quality control of mitochondria. VPS13D mutations have been reported in patients displaying ataxic and spastic gait disorders with variable age of onset. Here we used CRISPR/Cas9 gene editing to create VPS13D related-spinocerebellar ataxia-4 (SCAR4) missense mutations and C-terminal deletion in VPS13D's orthologue vps-13D in C. elegans. Consistent with SCAR4 patient movement disorders and mitochondrial dysfunction, vps-13D mutant worms exhibit locomotion defects and abnormal mitochondrial morphology. Importantly, animals with a vps-13D deletion or a N3017I missense mutation exhibited an increase in mitochondrial unfolded protein response (UPRmt). The cellular and behavioral changes caused by VPS13D mutations in C. elegans advance the development of animal models that are needed to study SCAR4 pathogenesis.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143432658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

The Histone Chaperone Spn1 Preserves Chromatin Protections at Promoters and Nucleosome Positioning in Open Reading Frames.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-02-17 DOI: 10.1093/g3journal/jkaf032

Andrew J Tonsager, Alexis Zukowski, Catherine A Radebaugh, Abigail Weirich, Laurie A Stargell, Srinivas Ramachandran

{"title":"The Histone Chaperone Spn1 Preserves Chromatin Protections at Promoters and Nucleosome Positioning in Open Reading Frames.","authors":"Andrew J Tonsager, Alexis Zukowski, Catherine A Radebaugh, Abigail Weirich, Laurie A Stargell, Srinivas Ramachandran","doi":"10.1093/g3journal/jkaf032","DOIUrl":"10.1093/g3journal/jkaf032","url":null,"abstract":"Spn1 is a multifunctional histone chaperone that associates with RNA polymerase II during elongation and is essential for life in eukaryotes. While previous work has elucidated regions of the protein important for its many interactions, it is unknown how these domains contribute to the maintenance of chromatin structure. Here, we employ digestion by micrococcal nuclease followed by single-stranded library preparation and sequencing (MNase-SSP) to characterize chromatin structure in Saccharomyces cerevisiae expressing wild-type or mutants of Spn1 (spn1K192N or spn1141-305). We mapped protections of all sizes genome-wide. Surprisingly, we observed a widespread loss of short fragments over nucleosome-depleted regions (NDRs) at promoters in the spn1K192N-containing strain, indicating critical functions of Spn1 in maintaining normal chromatin architecture outside open reading frames. Additionally, there are shifts in DNA protections in both Spn1 mutant expressing strains over open reading frames, which indicate changes in nucleosome and subnucleosome positioning. This was observed in markedly different Spn1 mutant strains, demonstrating that multiple functions of Spn1 are required to maintain proper chromatin structure in open reading frames. Changes in chromatin structure correlate positively with changes in gene expression as shown by RNA-seq analysis in the Spn1 mutant strains. Taken together, our results reveal a previously unknown role of Spn1 in the maintenance of NDR architecture and deepen our understanding of Spn1-dependent chromatin maintenance over transcribed regions.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Improving genomic selection in hexaploid wheat with sub-genome additive and epistatic models.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-02-15 DOI: 10.1093/g3journal/jkaf031

Augusto Tessele, David O González-Diéguez, José Crossa, Blaine E Johnson, Geoffrey P Morris, Allan K Fritz

{"title":"Improving genomic selection in hexaploid wheat with sub-genome additive and epistatic models.","authors":"Augusto Tessele, David O González-Diéguez, José Crossa, Blaine E Johnson, Geoffrey P Morris, Allan K Fritz","doi":"10.1093/g3journal/jkaf031","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf031","url":null,"abstract":"The goal of wheat breeding is the development of superior cultivars tailored to specific environments, and the identification of promising crosses is crucial for the success of breeding programs. Although genomic estimated breeding values were developed to estimate additive effects of genotypes before testing as parents, application has focused on predicting performance of candidate lines, ignoring non-additive genetic effects. However, non-additive genetic effects are hypothesized to be especially important in allopolyploid species due to the interaction between homeologous genes. The objectives of this study were to model additive and additive-by-additive epistatic effects to better delineate the genetic architecture of grain yield in wheat and to improve the accuracy of genomewide predictions. The dataset utilized consisted of 3740 F5:6 experimental lines tested in the K-State wheat breeding program across the years 2016 and 2018. Covariance matrices were calculated based on whole and sub-genome marker data and the natural and orthogonal interaction approach (NOIA) was used to estimate variance components for additive and additive-by-additive epistatic effects. Incorporating epistatic effects in additive models resulted in non-orthogonal partitioning of genetic effects but increased total genetic variance and reduced deviance information criteria. Estimation of sub-genome effects indicated that genotypes with the greatest whole genome effects often combine sub-genomes with intermediate to high effects, suggesting potential for crossing parental lines which have complementary sub-genome effects. Modeling epistasis in either whole-genome or sub-genome models led to a marginal (3%) improvement in genomic prediction accuracy, which could result in significant genetic gains across multiple cycles of breeding.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143425212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 semidominant point mutation of Mediator tail subunit MED5b in Arabidopsis leads to altered enrichment of H3K27me3 and reduced expression of targets of MYC2.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-02-14 DOI: 10.1093/g3journal/jkae301

Jiaxin Long, Shelby Sliger, Zhi-Wei Luo, Pete E Pascuzzi, Clint Chapple, Joe Ogas

{"title":"A semidominant point mutation of Mediator tail subunit MED5b in Arabidopsis leads to altered enrichment of H3K27me3 and reduced expression of targets of MYC2.","authors":"Jiaxin Long, Shelby Sliger, Zhi-Wei Luo, Pete E Pascuzzi, Clint Chapple, Joe Ogas","doi":"10.1093/g3journal/jkae301","DOIUrl":"https://doi.org/10.1093/g3journal/jkae301","url":null,"abstract":"The Mediator complex coordinates regulatory input for transcription driven by RNA polymerase II in eukaryotes. reduced epidermal fluorescence4-3 (ref4-3) is a semidominant mutation that results in a single amino acid substitution in the Mediator tail subunit Med5b. Previous characterization of ref4-3 revealed altered expression of a variety of loci in Arabidopsis, including those contributing to phenylpropanoid biosynthesis. Examination of existing RNA-seq data indicated that loci enriched for the transcriptionally repressive chromatin modification H3K27me3 are overrepresented among genes that are misregulated in ref4-3. We used ChIP-seq and RNA-seq to examine the possibility that perturbation of H3K27me3 homeostasis in ref4-3 plants contributed to altered transcript levels. We observed that ref4-3 results in a modest global reduction of H3K27me3 at enriched loci and that this reduction is not dependent on gene expression; however, altered H3K27me3 was not strongly predictive of altered expression in ref4-3 plants. Instead, our analyses revealed a substantial enrichment of targets of the MYC2 transcriptional regulator among genes that exhibit decreased expression in ref4-3. Consistent with previous characterization of ref4-3, we observed that ref4-3-dependent decreased expression of MYC2 targets can be suppressed by loss of another Mediator tail subunit, MED25. This observation is consistent with previous biochemical characterization of MYC2. Our data highlight the diverse and distinct impacts that a single amino acid change in the tail subunit of Mediator can have on transcriptional circuits and raise the prospect that Mediator directly contributes to H3K27me3 homeostasis in plants.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143413852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Conservation of imprinted expression across genotypes is correlated with consistency of imprinting across endosperm development in maize.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-02-14 DOI: 10.1093/g3journal/jkaf028

Kaitlin Higgins, Vital Nyabashi, Sarah Anderson

{"title":"Conservation of imprinted expression across genotypes is correlated with consistency of imprinting across endosperm development in maize.","authors":"Kaitlin Higgins, Vital Nyabashi, Sarah Anderson","doi":"10.1093/g3journal/jkaf028","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf028","url":null,"abstract":"Imprinted expression is an essential process for seed viability affecting hundreds of genes in Zea mays endosperm, however most studies have examined just one time point for analysis. The focus on single time points can limit our ability to identify imprinted genes, and our ability to draw conclusions for the role of imprinting in endosperm. In this study we examine imprinted expression across four time points ranging from the transition to endoreduplication from mitotic division through the beginning of programmed cell death. Additionally, we assessed imprinting variation across eight diverse maize lines, six of which have never before been assessed for imprinting. Through this analysis we identify over 700 imprinted genes with varying consistency across time points including 255 genes imprinted at every time point and 105 genes displaying transient imprinting. We find a correlation between high consistency of imprinting across time and high conservation of parental bias across eight diverse maize lines reciprocally crossed with B73. Additionally, we identify evidence of imprinting for three zein genes that are critical for nutrient accumulation in the endosperm, suggesting that imprinting may play a more important role in seed composition than previously thought. Taken together, this study provides a more holistic view of imprinting variation across time and across genotypes in maize and enables us to more thoroughly investigate the complex imprinting landscape.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143413919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

The Nuclear and Mitochondrial Genomes of Amoebophrya sp. ex Karlodinium veneficum.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-02-14 DOI: 10.1093/g3journal/jkaf030

Wesley DeMontigny, Tsvetan Bachvaroff

{"title":"The Nuclear and Mitochondrial Genomes of Amoebophrya sp. ex Karlodinium veneficum.","authors":"Wesley DeMontigny, Tsvetan Bachvaroff","doi":"10.1093/g3journal/jkaf030","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf030","url":null,"abstract":"Dinoflagellates are a diverse group of microplankton that include free-living, symbiotic, and parasitic species. Amoebophrya, a basal lineage of parasitic dinoflagellates, infects a variety of marine microorganisms, including harmful-bloom-forming algae. Although there are currently three published Amoebophrya genomes, this genus has considerable genomic diversity. We add to the growing genomic data for Amoebophrya with an annotated genome assembly for Amoebophrya sp. ex Karlodinium veneficum. This species appears to translate all three canonical stop codons contextually. Stop codons are present in the open reading frames of about half of the predicted gene models, including genes essential for cellular function. The in-frame stop codons are likely translated by suppressor tRNAs that were identified in the assembly. We also assembled the mitochondrial genome, which has remained elusive in the previous Amoebophrya genome assemblies. The mitochondrial genome assembly consists of many fragments with high sequence identity in the genes but low sequence identity in intergenic regions. Nuclear and mitochondrially-encoded proteins indicate that Amoebophrya sp. ex K. veneficum does not have a bipartite electron transport chain, unlike previously analyzed Amoebophrya species. This study highlights the importance of analyzing multiple genomes from highly diverse genera such as Amoebophrya.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143413927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Assessing genotype adaptability and stability in perennial forage breeding trials using random regression models for longitudinal dry matter yield data.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-02-14 DOI: 10.1093/g3journal/jkae306

Claudio Carlos Fernandes Filho, Sanzio Carvalho Lima Barrios, Mateus Figueiredo Santos, Jose Airton Rodrigues Nunes, Cacilda Borges do Valle, Liana Jank, Esteban Fernando Rios

{"title":"Assessing genotype adaptability and stability in perennial forage breeding trials using random regression models for longitudinal dry matter yield data.","authors":"Claudio Carlos Fernandes Filho, Sanzio Carvalho Lima Barrios, Mateus Figueiredo Santos, Jose Airton Rodrigues Nunes, Cacilda Borges do Valle, Liana Jank, Esteban Fernando Rios","doi":"10.1093/g3journal/jkae306","DOIUrl":"https://doi.org/10.1093/g3journal/jkae306","url":null,"abstract":"Genotype selection for dry matter yield (DMY) in perennial forage species is based on repeated measurements over time, referred to as longitudinal data. These datasets capture temporal trends and variability, which are critical for identifying genotypes with desirable performance across seasons. In this study, we have presented a random regression model (RRM) approach for selecting genotypes based on longitudinal DMY data generated from 10 breeding trials and three perennial species, alfalfa (Medicago sativa L.), guineagrass (Megathyrsus maximus), and brachiaria (Urochloa spp.). We also proposed the estimation of adaptability based on the area under the curve and stability based on the curve coefficient of variation. Our results showed that RRM always approximated the (co)variance structure into an autoregressive pattern. Furthermore, RRM can offer useful information about longitudinal data in forage breeding trials, where the breeder can select genotypes based on their seasonality by interpreting reaction norms. Therefore, we recommend using RRM for longitudinal traits in breeding trials for perennial species.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143413912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Disruption of recombination machinery alters the mutational landscape in plant organellar genomes.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-02-13 DOI: 10.1093/g3journal/jkaf029

Gus Waneka, Amanda K Broz, Forrest Wold-McGimsey, Yi Zou, Zhiqiang Wu, Daniel B Sloan

{"title":"Disruption of recombination machinery alters the mutational landscape in plant organellar genomes.","authors":"Gus Waneka, Amanda K Broz, Forrest Wold-McGimsey, Yi Zou, Zhiqiang Wu, Daniel B Sloan","doi":"10.1093/g3journal/jkaf029","DOIUrl":"10.1093/g3journal/jkaf029","url":null,"abstract":"Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the molecular machinery responsible for these patterns is critical for understanding the evolution of these genomes. While much progress has been made towards understanding recombination activity in land plant organellar genomes, the relationship between recombination pathways and point mutation rates remains uncertain. The organellar targeted mutS homolog MSH1 has previously been shown to suppress point mutations as well as non-allelic recombination between short repeats in Arabidopsis thaliana. We therefore implemented high-fidelity Duplex Sequencing to test if other genes that function in recombination and maintenance of genome stability also affect point mutation rates. We found small to moderate increases in the frequency of single nucleotide variants (SNVs) and indels in mitochondrial and/or plastid genomes of A. thaliana mutant lines lacking radA, recA1, or recA3. In contrast, osb2 and why2 mutants did not exhibit an increase in point mutations compared to wild type (WT) controls. In addition, we analyzed the distribution of SNVs in previously generated Duplex Sequencing data from A. thaliana organellar genomes and found unexpected strand asymmetries and large effects of flanking nucleotides on mutation rates in WT plants and msh1 mutants. Finally, using long-read Oxford Nanopore sequencing, we characterized structural variants in organellar genomes of the mutant lines and show that different short repeat sequences become recombinationally active in different mutant backgrounds. Together, these complementary sequencing approaches shed light on how recombination may impact the extraordinarily low point mutation rates in plant organellar genomes.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143413925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Genome-wide association studies dissect the genetic architecture of seed and yield component traits in cowpea (Vigna unguiculata L. Walp).

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-02-07 DOI: 10.1093/g3journal/jkaf024

Habib Akinmade, Rebecca Caroline Ulbricht Ferreira, Mario Henrique Murad Leite Andrade, Claudio Fernandes, Pablo Sipowicz, María Muñoz-Amatriaín, Esteban Rios

{"title":"Genome-wide association studies dissect the genetic architecture of seed and yield component traits in cowpea (Vigna unguiculata L. Walp).","authors":"Habib Akinmade, Rebecca Caroline Ulbricht Ferreira, Mario Henrique Murad Leite Andrade, Claudio Fernandes, Pablo Sipowicz, María Muñoz-Amatriaín, Esteban Rios","doi":"10.1093/g3journal/jkaf024","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf024","url":null,"abstract":"The identification of loci related to seed and yield component traits in cowpea constitutes a key step for improvement through marker-assisted selection (MAS). Furthermore, seed morphology has an impact on industrial processing and influences consumer and farmer preferences. In this study, we performed genome-wide association studies (GWAS) on a mini-core collection of cowpea to dissect the genetic architecture and detect genomic regions associated with seed morphological traits and yield components. Phenotypic data were measured both manually and by high-throughput image-based approaches to test associations with 41,533 single-nucleotide polymorphism markers using the FarmCPU model. From genome-associated regions, we also investigated putative candidate genes involved in the variation of the phenotypic traits. We detected 42 marker-trait associations for pod length and hundred seed weight, length, width, perimeter, and area of the seed. Candidate genes encoding leucine-rich repeat-containing (LRR) and F-box proteins, known to be associated with seed size, were identified; in addition, we identified candidate genes encoding PPR (Pentatricopeptide repeat) proteins, recognized to have an important role in seed development in several crops. Our findings provide insights into natural variation in cowpea for yield-related traits and valuable information for MAS breeding strategies in this and other closely related crops.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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