G3: Genes|Genomes|Genetics最新文献_第4页

The N terminus-only (trans) function of the adhesion G protein-coupled receptor latrophilin-1 controls multiple processes in reproduction of Caenorhabditis elegans. 粘附 GPCR Latrophilin-1 的纯 N 端（反式）功能控制着秀丽隐杆线虫繁殖的多个过程。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae206

Daniel Matúš, Willem Berend Post, Victoria Elisabeth Groß, Alexander Bernd Knierim, Christina Katharina Kuhn, Franziska Fiedler, Darian Benno Tietgen, Johanna Lena Schön, Torsten Schöneberg, Simone Prömel

{"title":"The N terminus-only (trans) function of the adhesion G protein-coupled receptor latrophilin-1 controls multiple processes in reproduction of Caenorhabditis elegans.","authors":"Daniel Matúš, Willem Berend Post, Victoria Elisabeth Groß, Alexander Bernd Knierim, Christina Katharina Kuhn, Franziska Fiedler, Darian Benno Tietgen, Johanna Lena Schön, Torsten Schöneberg, Simone Prömel","doi":"10.1093/g3journal/jkae206","DOIUrl":"10.1093/g3journal/jkae206","url":null,"abstract":"Adhesion G protein-coupled receptors are unique molecules. They are able to transmit classical signals via G protein activation as well as mediate functions solely through their extracellular N termini, completely independently of the seven transmembrane helices domain and the C terminus. This dual mode of action is highly unusual for G protein-coupled receptors and allows for a plethora of possible cellular consequences. However, the physiological implications and molecular details of this N terminus-mediated signaling are poorly understood. Here, we show that several distinct seven transmembrane helices domain-independent/trans functions of the adhesion G protein-coupled receptor latrophilin homolog latrophilin-1 in the nematode Caenorhabditis elegans together regulate reproduction: sperm guidance, ovulation, and germ cell apoptosis. In these contexts, the receptor elicits its functions in a noncell autonomous manner. The functions might be realized through alternative splicing of the receptor specifically generating N terminus-only variants. Thus, our findings shed light on the versatility of seven transmembrane helices domain-independent/N terminus-only/trans functions of adhesion G protein-coupled receptor and discuss possible molecular details.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

myh9b is a critical non-muscle myosin II encoding gene that interacts with myh9a and myh10 during zebrafish development in both compensatory and redundant pathways. myh9b 是一个重要的非肌球蛋白 II 编码基因，在斑马鱼的发育过程中，它与 myh9a 和 myh10 在补偿和冗余途径中相互作用。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae260

Laura A Rolfs, Elizabeth J Falat, Jennifer H Gutzman

{"title":"myh9b is a critical non-muscle myosin II encoding gene that interacts with myh9a and myh10 during zebrafish development in both compensatory and redundant pathways.","authors":"Laura A Rolfs, Elizabeth J Falat, Jennifer H Gutzman","doi":"10.1093/g3journal/jkae260","DOIUrl":"10.1093/g3journal/jkae260","url":null,"abstract":"Non-muscle myosin (NMII) motor proteins have diverse developmental functions due to their roles in cell shape changes, cell migration, and cell adhesion. Zebrafish are an ideal vertebrate model system to study the NMII encoding myh genes and proteins due to high sequence homology, established gene editing tools, and rapid ex utero development. In humans, mutations in the NMII encoding MYH genes can lead to abnormal developmental processes and disease. This study utilized zebrafish myh9a, myh9b, and myh10 null mutants to examine potential genetic interactions and roles for each gene in development. It was determined that the myh9b gene is the most critical NMII encoding gene, as myh9b mutants develop pericardial edema and have a partially penetrant lethal phenotype, which was not observed in the other myh mutants. This study also established that genetic interactions occur between the zebrafish myh9a, myh9b, and myh10 genes where myh9b is required for the expression of both myh9a and myh10, and myh10 is required for the expression of myh9b. Additionally, protein analyses suggested that enhanced NMII protein stability in some mutant backgrounds may play a role in compensation. Finally, double mutant studies revealed different and more severe phenotypes at earlier timepoints than single mutants, suggesting roles for tissue specific genetic redundancy, and in some genotypes, haploinsufficiency. These mutants are the first in vivo models allowing for the study of complete loss of the NMIIA and NMIIB proteins, establishing them as valuable tools to elucidate the role of NMII encoding myh genes in development and disease.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582682","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

Chromosome-level reference genome for the Jonah crab, Cancer borealis. 约拿蟹染色体级参考基因组。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae254

Jennifer M Polinski, Timothy P O'Donnell, Andrea G Bodnar

{"title":"Chromosome-level reference genome for the Jonah crab, Cancer borealis.","authors":"Jennifer M Polinski, Timothy P O'Donnell, Andrea G Bodnar","doi":"10.1093/g3journal/jkae254","DOIUrl":"https://doi.org/10.1093/g3journal/jkae254","url":null,"abstract":"The Jonah crab, Cancer borealis, is integral to marine ecosystems and supports a rapidly growing commercial fishery in the northwest Atlantic Ocean. This species also has a long history as a model for neuroscience that has expanded our understanding of central pattern generators, neuromodulation, synaptic plasticity, and the connectivity of neural circuits. Here we present a highly contiguous reference genome for the Jonah crab that will provide an essential resource to advance fisheries, conservation, and biomedical research. Using a combination of PacBio long-read sequencing and Omni-C scaffolding, we generated a final genome assembly spanning 691 Mb covering 51 chromosome-length scaffolds and 106 additional contigs. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis indicated a high-quality assembly with a completeness score of 90.8%. Repeat annotation identified 1,649 repeat families making up 48.27% of the Jonah crab genome. Gene model predictions annotated 24,830 protein coding genes with a 92.3% BUSCO score. Gene family evolution analysis revealed the expansion of gene families associated with nervous system function, and targeted analysis revealed an extensive repertoire of neural genes. The Jonah crab genome will not only provide a resource for neuroscience research but will also serve as a foundation to investigate adaptation to stress and population structure to support sustainable fisheries management during this time of rapidly changing environmental conditions in the northwest Atlantic Ocean.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580802","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

Genetic characterization of candidate ecdysteroid kinases in Drosophila melanogaster. 黑腹果蝇候选蜕皮激素激酶的遗传特征。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae204

Jack L Scanlan, Charles Robin

{"title":"Genetic characterization of candidate ecdysteroid kinases in Drosophila melanogaster.","authors":"Jack L Scanlan, Charles Robin","doi":"10.1093/g3journal/jkae204","DOIUrl":"10.1093/g3journal/jkae204","url":null,"abstract":"Ecdysteroids are major hormones in insects and control molting, growth, reproduction, physiology, and behavior. The biosynthesis of ecdysteroids such as 20-hydroxyecdysone (20E) from dietary sterols is well characterized, but ecdysteroid catabolism is poorly understood. Ecdysteroid kinases (EcKs) mediate the reversible phosphorylation of ecdysteroids, which has been implicated in ecdysteroid recycling during embryogenesis and reproduction in various insects. However, to date, only 2 EcK-encoding genes have been identified, in the silkworm Bombyx mori and the mosquito Anopheles gambiae. Previously, we identified 2 ecdysteroid kinase-like (EcKL) genes-Wallflower (Wall) and Pinkman (pkm)-in the model fruit fly Drosophila melanogaster that are orthologs of the ecdysteroid 22-kinase gene BmEc22K. Here, using gene knockdown, knockout, and misexpression, we explore Wall and pkm's possible functions and genetically test the hypothesis that they encode EcKs. Wall and pkm null mutants are viable and fertile, suggesting that they are not essential for development or reproduction, whereas phenotypes arising from RNAi and somatic CRISPR appear to derive from off-target effects or other artifacts. However, misexpression of Wall results in dramatic phenotypes, including developmental arrest, and defects in trachea, cuticle, and pigmentation. Wall misexpression fails to phenocopy irreversible ecdysteroid catabolism through misexpression of Cyp18a1, suggesting that Wall does not directly inactivate 20E. Additionally, Wall misexpression phenotypes are not attenuated in Cyp18a1 mutants, strongly suggesting that Wall is not an ecdysteroid 26-kinase. We hypothesize that the substrate of Wall in this misexpression experiment and possibly generally is an unknown, atypical ecdysteroid that plays essential roles in Drosophila development, and may highlight aspects of insect endocrinology that are as-yet uncharacterized. We also provide preliminary evidence that CG5644 encodes an ecdysteroid 22-kinase conserved across Diptera.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106126","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

Genomic factors shaping codon usage across the Saccharomycotina subphylum. 影响酵母菌亚门密码子使用的基因组因素。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae207

Bryan Zavala, Lauren Dineen, Kaitlin J Fisher, Dana A Opulente, Marie-Claire Harrison, John F Wolters, Xing-Xing Shen, Xiaofan Zhou, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas, Abigail Leavitt LaBella

{"title":"Genomic factors shaping codon usage across the Saccharomycotina subphylum.","authors":"Bryan Zavala, Lauren Dineen, Kaitlin J Fisher, Dana A Opulente, Marie-Claire Harrison, John F Wolters, Xing-Xing Shen, Xiaofan Zhou, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas, Abigail Leavitt LaBella","doi":"10.1093/g3journal/jkae207","DOIUrl":"10.1093/g3journal/jkae207","url":null,"abstract":"Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. It has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. We characterized codon usage across 1,154 strains from 1,051 species from the fungal subphylum Saccharomycotina to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns. We found a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is distinct between the 12 orders to such a degree that yeasts can be classified with an accuracy >90% using a machine learning algorithm. We also characterized the degree to which codon usage bias is impacted by translational selection. We found it was influenced by a combination of features, including the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that avoidance of the CGN codons is associated with a decline in arginine tRNA function. Consistent with previous findings, codon usage bias within the Saccharomycotina is shaped by genomic features and GC bias. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar. 干旱适应性花生栽培品种基因组中保留的种间杂交遗迹。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae208

Paul P Grabowski, Phat Dang, Jerry J Jenkins, Avinash Sreedasyam, Jenell Webber, Marshall Lamb, Qiong Zhang, Alvaro Sanz-Saez, Yucheng Feng, Victoria Bunting, Jayson Talag, Josh Clevenger, Peggy Ozias-Akins, C Corley Holbrook, Ye Chu, Jane Grimwood, Jeremy Schmutz, Charles Chen, John T Lovell

{"title":"Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar.","authors":"Paul P Grabowski, Phat Dang, Jerry J Jenkins, Avinash Sreedasyam, Jenell Webber, Marshall Lamb, Qiong Zhang, Alvaro Sanz-Saez, Yucheng Feng, Victoria Bunting, Jayson Talag, Josh Clevenger, Peggy Ozias-Akins, C Corley Holbrook, Ye Chu, Jane Grimwood, Jeremy Schmutz, Charles Chen, John T Lovell","doi":"10.1093/g3journal/jkae208","DOIUrl":"10.1093/g3journal/jkae208","url":null,"abstract":"Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here, we present the genome assembly and gene model annotation for \"Line8,\" a peanut genotype bred from drought-tolerant cultivars. Our assembly and annotation are the most contiguous and complete peanut genome resources currently available. The high contiguity of the Line8 assembly allowed us to explore structural variation both between peanut genotypes and subgenomes. We detect several large inversions between Line8 and other peanut genome assemblies, and there is a trend for the inversions between more genetically diverged genotypes to have higher gene content. We also relate patterns of subgenome exchange to structural variation between Line8 homeologous chromosomes. Unexpectedly, we discover that Line8 harbors an introgression from A.cardenasii, a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both haplotypes in this introgression provide the first in situ characterization of A.cardenasii candidate alleles that can be leveraged for future targeted improvement efforts. The completeness of our genome will support peanut biotechnology and broader research into the evolution of hybridization and polyploidy.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Disentangling cobionts and contamination in long-read genomic data using sequence composition. 利用序列组成在长读基因组数据中区分同源物和污染

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae187

Claudia C Weber

{"title":"Disentangling cobionts and contamination in long-read genomic data using sequence composition.","authors":"Claudia C Weber","doi":"10.1093/g3journal/jkae187","DOIUrl":"10.1093/g3journal/jkae187","url":null,"abstract":"The recent acceleration in genome sequencing targeting previously unexplored parts of the tree of life presents computational challenges. Samples collected from the wild often contain sequences from several organisms, including the target, its cobionts, and contaminants. Effective methods are therefore needed to separate sequences. Though advances in sequencing technology make this task easier, it remains difficult to taxonomically assign sequences from eukaryotic taxa that are not well represented in databases. Therefore, reference-based methods alone are insufficient. Here, I examine how we can take advantage of differences in sequence composition between organisms to identify symbionts, parasites, and contaminants in samples, with minimal reliance on reference data. To this end, I explore data from the Darwin Tree of Life project, including hundreds of high-quality HiFi read sets from insects. Visualizing two-dimensional representations of read tetranucleotide composition learned by a variational autoencoder can reveal distinct components of a sample. Annotating the embeddings with additional information, such as coding density, estimated coverage, or taxonomic labels allows rapid assessment of the contents of a dataset. The approach scales to millions of sequences, making it possible to explore unassembled read sets, even for large genomes. Combined with interactive visualization tools, it allows a large fraction of cobionts reported by reference-based screening to be identified. Crucially, it also facilitates retrieving genomes for which suitable reference data are absent.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Remote sensing for estimating genetic parameters of biomass accumulation and modeling stability of growth curves in alfalfa. 利用遥感技术估算紫花苜蓿生物量积累的遗传参数并模拟生长曲线的稳定性。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae200

Ranjita Thapa, Karl H Kunze, Julie Hansen, Christopher Pierce, Virginia Moore, Ian Ray, Liam Wickes-Do, Nicolas Morales, Felipe Sabadin, Nicholas Santantonio, Michael A Gore, Kelly Robbins

{"title":"Remote sensing for estimating genetic parameters of biomass accumulation and modeling stability of growth curves in alfalfa.","authors":"Ranjita Thapa, Karl H Kunze, Julie Hansen, Christopher Pierce, Virginia Moore, Ian Ray, Liam Wickes-Do, Nicolas Morales, Felipe Sabadin, Nicholas Santantonio, Michael A Gore, Kelly Robbins","doi":"10.1093/g3journal/jkae200","DOIUrl":"10.1093/g3journal/jkae200","url":null,"abstract":"Multispectral imaging by unoccupied aerial vehicles provides a nondestructive, high-throughput approach to measure biomass accumulation over successive alfalfa (Medicago sativa L. subsp. sativa) harvests. Information from estimated growth curves can be used to infer harvest biomass and to gain insights into the relationship between growth dynamics and forage biomass stability across cuttings and years. In this study, multispectral imaging and several common vegetation indices were used to estimate genetic parameters and model growth of alfalfa cultivars to determine the longitudinal relationship between vegetation indices and forage biomass. Results showed moderate heritability for vegetation indices, with median plot level heritability ranging from 0.11 to 0.64, across multiple cuttings in three trials planted in Ithaca, NY, and Las Cruces, NM. Genetic correlations between the normalized difference vegetation index and forage biomass were moderate to high across trials, cuttings, and the timing of multispectral image capture. To evaluate the relationship between growth parameters and forage biomass stability across cuttings and environmental conditions, random regression modeling approaches were used to estimate the growth parameters of cultivars for each cutting and the variance in growth was compared to the variance in genetic estimates of forage biomass yield across cuttings. These analyses revealed high correspondence between stability in growth parameters and stability of forage yield. The results of this study indicate that vegetation indices are effective at modeling genetic components of biomass accumulation, presenting opportunities for more efficient screening of cultivars and new longitudinal modeling approaches that can provide insights into temporal factors influencing cultivar stability.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540325/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142020131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Cross potential selection: a proposal for optimizing crossing combinations in recurrent selection using the usefulness criterion of future inbred lines. 杂交潜力选择：利用未来近交系的有用性标准优化循环选择中的杂交组合的建议。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae224

Kengo Sakurai, Kosuke Hamazaki, Minoru Inamori, Akito Kaga, Hiroyoshi Iwata

{"title":"Cross potential selection: a proposal for optimizing crossing combinations in recurrent selection using the usefulness criterion of future inbred lines.","authors":"Kengo Sakurai, Kosuke Hamazaki, Minoru Inamori, Akito Kaga, Hiroyoshi Iwata","doi":"10.1093/g3journal/jkae224","DOIUrl":"10.1093/g3journal/jkae224","url":null,"abstract":"In plant breeding programs, rapid production of novel varieties is highly desirable. Genomic selection allows the selection of superior individuals based on genomic estimated breeding values. However, it is worth noting that superior individuals may not always be superior parents. The choice of the crossing pair significantly influences the genotypic value of the resulting progeny. This study has introduced a new crossing strategy, termed cross potential selection, designed to expedite the production of novel varieties of inbred crops. Cross potential selection integrates fast recurrent selection and usefulness criterion to generate novel varieties. It considers the segregation of each crossing pair and computes the expected genotypic values of the top-performing individuals, assuming that the progeny distribution of genotypic values follows a normal distribution. It does not consider genetic diversity and focuses only on producing a novel variety as soon as possible. We simulated a 30-year breeding program in 2 scenarios, low heritability (h2=0.3) and high heritability (h2=0.6), to compare cross potential selection with 2 other selection strategies. Cross potential selection consistently demonstrated the highest genetic gains among the 3 strategies in early cycles. In the 3rd year of the breeding program with a high heritability (h2=0.6), cross potential selection exhibited the highest genetic gains, 138 times that of 300 independent breeding simulations. Regarding long-term improvement, the other selection strategies outperformed cross potential selection. Nevertheless, compared with the other 2 strategies, cross potential selection achieved significant short-term genetic improvements. Cross potential selection is a suitable breeding strategy for the rapid production of varieties within limited time and cost.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Correction to: Linkage mapping of root shape traits in two carrot populations. 更正：两个胡萝卜种群根形性状的连锁图谱。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae227

引用次数: 0