Optimization of crossing strategy based on the usefulness criterion in interpopulation crosses considering different marker effects among populations.

Herein, a method has been proposed for selecting optimal cross pairs based on the genetic potential of progeny in interpopulation crosses, considering different genetic effects among populations. In the breeding programs for self-pollinating plants, genetic improvements in multiple traits can be challenging when relying solely on a single biparental population, and interpopulation crosses are employed to integrate favorable alleles from multiple biparental populations to overcome this limitation. In this context, it is crucial to consider distinct genetic effects in different populations.

Powering Up Plant Genetic Research with Genomic Data 2.0.

Historically, plant genomic research has lagged behind mammalian studies, primarily due to the complexity of plant genomes and limited research resources [...

Genome-specific association study (GSAS) for exploration of variability in hemp (Cannabis sativa).

Hemp (Cannabis sativa L.) is a versatile crop with substantial potential for creating productive, sustainable, and resilient agricultural systems. However, in contrast to other crops such as cereals, hemp is highly heterozygous, resulting in both challenges and opportunities for agriculture, breeding, and research.

The homologous gene regulates inflorescence phenotypes in .

Most species have inflorescences composed of two types of flowers: decorative flowers with showy sepals and plain nondecorative flowers. In wild plants of , the decorative flowers are located at the periphery of the corymb, resulting in the lacecap phenotype. However, after the discovery of the mophead phenotype, in which decorative flowers are borne not only at the periphery but also on the entire inflorescence, it developed remarkably as a garden plant.

Whole-genome resequencing of Japanese large-sized tomato cultivars provides insights into the history of modern breeding.

Tomatoes have the highest agricultural production among vegetables in Japan and worldwide. Japanese large-sized fresh-market tomatoes have a unique breeding history that differs from that of other countries, represented by pink-colored and juicy fruits with a good taste and flavor. We performed whole-genome resequencing of 150 Japanese large-sized fresh-market tomato cultivars released from the 1940s to the 2000s to unveil how breeding selection has changed the genome of Japanese tomato cultivars and provide a genomic basis for future Japanese tomato breeding.

Hayai-Annotation: A functional gene prediction tool that integrates orthologs and gene ontology for network analysis in plant species.

Hayai-Annotation, an annotation tool powered by the R-shinydashboard browser interface, implements a workflow that integrates sequence alignment using DIAMOND against UniProtKB Plants and ortholog inference using OrthoLoger. We here propose a pipeline to explore genome evolution and adaptation from a different perspective, by creating a network considering orthologs and gene ontology as nodes, with edges based on the annotation for each gene. This approach aims to improve the visualization of conserved biological processes and functions, highlight species-specific adaptations, and enhance the ability to infer the functions of uncharacterized genes by comparing edge patterns across species.

Near-complete telomere-to-telomere de novo genome assembly in Egyptian clover (Trifolium alexandrinum).

Egyptian clover (Trifolium alexandrinum L.), also known as berseem clover, is an important forage crop to semi-arid conditions that was domesticated in ancient Egypt in 5,5000 BCE and introduced and well adapted to numerous countries including India, Pakistan, Turkey, and Mediterranean region. Despite its agricultural importance, genomic research on Egyptian clover has been limited to developing efficient modern breeding programs.

Establishing a comprehensive web-based analysis platform for Nicotiana benthamiana genome and transcriptome.

Nicotiana benthamiana has long served as a crucial plant material extensively used in plant physiology research, particularly in the field of plant pathology, because of its high susceptibility to plant viruses. Additionally, it serves as a production platform to test vaccines and other valuable substances. Among its approximately 3.

Structural variation in the pangenome of wild and domesticated barley.

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes.

Propagation path of a flowering cherry (Cerasus × yedoensis) cultivar 'Somei-Yoshino' traced by somatic mutations.

In the long history of human relations with flowering cherry trees in Japan, 'Somei-Yoshino' occupies an exceptional position among a variety of flowering trees: it is a self-incompatible interspecific hybrid but has been enthusiastically planted by grafting throughout Japan, due most likely to its flamboyant appearance upon full bloom. Thus, 'Somei-Yoshino' gives us a rare opportunity to trace and investigate the occurrence and distribution of somatic mutations within a single plant species through analysis of the genomes of the clonally propagated trees grown under a variety of geographical and artificial environments. In the studies presented here, a total of 46 samples of 'Somei-Yoshino' trees were collected and their genomes were analysed.

Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum).

Micro-Tom is a cultivar of tomato (Solanum lycopersicum), which is known as a major crop and model plant in Solanaceae. Micro-Tom has phenotypic traits such as dwarfism, and substantial EMS-mutagenized lines have been reported. After Micro-Tom was generated in Florida, USA, it was distributed to research institutes worldwide and used as a genetic resource.

Different control of resistance to two Colletotrichum orbiculare pathogenic races 0 and 1 in cucumber (Cucumis sativus L.).

Quantitative trait locus analysis identified independent novel loci in cucumbers responsible for resistance to races 0 and 1 of the anthracnose fungal pathogen Colletotrichum orbiculare. Cucumbers have been reported to be vulnerable to Colletotrichum orbiculare, causing anthracnose disease with significant yield loss under favorable conditions. The deployment of a single recessive Cssgr gene in cucumber breeding for anthracnose resistance was effective until a recent report on high-virulent strains infecting cucumbers in Japan conquering the resistance.

Transcriptome analysis of tomato plants following salicylic acid-induced immunity against ssp. .

Salicylic acid (SA) is known to be involved in the immunity against ssp. () that causes bacterial canker in tomato. To identify the candidate genes associated with SA-inducible resistance, transcriptome analysis was conducted via RNA sequencing in tomato plants treated with SA.

Assessing the Potential for Genome-Assisted Breeding in Red Perilla Using Quantitative Trait Locus Analysis and Genomic Prediction.

Red perilla is an important medicinal plant used in Kampo medicine. The development of elite varieties of this species is urgently required. Medicinal compounds are generally considered target traits in medicinal plant breeding; however, selection based on compound phenotypes (i.

Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon.

Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E.

Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species.

Background: Plant genome information is fundamental to plant research and development. Along with the increase in the number of published plant genomes, there is a need for an efficient system to retrieve various kinds of genome-related information from many plant species across plant kingdoms. Various plant databases have been developed, but no public database covers both genomic and genetic resources over a wide range of plant species.

Polyploid GWAS reveals the basis of molecular marker development for complex breeding traits including starch content in the storage roots of sweet potato.

Given the importance of prioritizing genome-based breeding of sweet potato to enable the promotion of food and nutritional security for future human societies, here, we aimed to dissect the genetic basis of storage root starch content (SC) when associated with a complex set of breeding traits including dry matter (DM) rate, storage root fresh weight (SRFW), and anthocyanin (AN) content in a mapping population containing purple-fleshed sweet potato. A polyploid genome-wide association study (GWAS) was extensively exploited using 90,222 single-nucleotide polymorphisms (SNPs) obtained from a bi-parental 204 F population between 'Konaishin' (having high SC but no AN) and 'Akemurasaki' (having high AN content but moderate SC). Through the comparison of polyploid GWAS on the whole set of the 204 F, 93 high-AN-containing F, and 111 low-AN-containing F populations, a total of two (consists of six SNPs), two (14 SNPs), four (eight SNPs), and nine (214 SNPs) significantly associated signals were identified for the variations of SC, DM, SRFW, and the relative AN content, respectively.

Identification of novel sex determination loci in Japanese weedy melon.

Japanese weedy melon exhibits unique sex expression with interactions between previously reported sex determination genes and two novel loci. Sex expression contributes to fruit quality and yield in the Cucurbitaceae. In melon, orchestrated regulation by sex determination genes explains the mechanism of sex expression, resulting in a great variety of sexual morphologies.

Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake).

Here, we report the first telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake), which consists of 13 sequences (spanning 161.0 Mb) and a 76 kb circular mitochondrial genome. All the 13 sequences were supported with telomeric repeats at the ends.

Power Up Plant Genetic Research with Genomic Data.

The official debut of the reference genome of in 2000 [...