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Molecular breeding of tomato: Advances and challenges.

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

Solanum lycopersicum↗

Genetic dissection for leaf correlative traits of rice (Oryza sativa L.) under drought stress.

Water is becoming a restricted factor of agricultural development owing to the global shortage of water resources. Screening and improving drought tolerant rice cultivars would be helpful for increasing and stabilizing yield, economizing water and reducing environmental pollution. In this study, 127 rice lines of DII population derived from an indica variety Zhaiyeqing 8 (ZYQ8) and a japonica variety Jingxi 17 (JX17) were used to locate QTLs for leaf rolling, relative water content and rate of electric conductivity under drought stress. The results showed that significant differences between the parents were detected for all measured traits. The tremendous transgressive segregations for these traits were observed in the population. The frequency of all traits in the population was approximately normally distributed with slight skew. A total of six QTLs for the three traits were detected with molecular linkage map of 234 markers, including three QTLs (qLR-1, qLR-5 and qLR-11) for leaf rolling, two QTLs (qRWC-1 and qRWC-6) for relative water content and one QTL (qREC-6) for rate of electric conductivity. Visual measurement for leaf rolling can be used to screen a large number of rice germplasm resources or varieties, which is of importance to screening and utilization of drought tolerant rice varieties.

Alleles↗

Landscape Genomics Reveals Divergent Adaptation Modes and Predicts Climate Vulnerability in Xinjiang Indigenous Sheep.

Climate change increasingly endangers precious indigenous sheep germplasm resources distributed across diverse Chinese landscapes, and systematically decoding their polygenic climate-adaptive genetic mechanisms is essential for targeted breed conservation and long-term sustainable pastoral production. Whole-genome resequencing data from 93 individuals covering six representative local sheep breeds were analyzed in this work. After filtering highly collinear climate variables, three mature landscape genomic approaches were jointly applied to identify environment-linked gene variants, while two predictive metrics across ten CMIP6 future climate scenarios quantified each breed's long-term adaptive risks. Six temperature- and water-related environmental factors jointly drove sheep population genetic differentiation, with temperature fluctuation indices showing markedly stronger explanatory power. Detected adaptive genes were significantly enriched in ion transport, energy metabolism and cellular stress response pathways. Future projections indicated western breeds (Bayinbuluke, Cele Black, Xiahe) face severe maladaptation risks under high-emission SSP370 scenarios by 2100, whereas central and eastern breeds possess much broader climate tolerance. This study systematically reveals the core genomic basis of ovine climate adaptation and quantifies distinct breed-specific climate vulnerability, providing solid reliable theoretical support for precision germplasm conservation and selective breeding of climate-resilient sheep varieties.

adaptive loci↗

A CRISPR/Cas9 mutant resource for OsSm RNA-binding genes in rice.

Pre-mRNA, produced by eukaryotic DNA transcription, undergoes splicing by the spliceosome, which removes introns and joins exons to form mRNA. The spliceosome is a large and highly dynamic molecular machine. Its core components include five small nuclear ribonucleoproteins (snRNPs) and the various spliceosome-related proteins. The conserved Smith (Sm) complex and the Sm-like proteins (LSm) serve as primary components of the snRNPs. Sm proteins are involved in processes such as pre-mRNA splicing and mRNA degradation, which can regulate gene expression, thereby influencing plant growth, development, and stress responses. While 25 Sm proteins have been identified in rice, their specific roles in regulating rice growth and development remain unclear. In this study, we employed the CRISPR/Cas9 system to edit 15 OsSm genes, and 13 mutants were obtained, with mutation rates ranging from 20.83 to 83.87%. In comparison to the wild type (WT), the mutants exhibited dwarfism, reduced tiller numbers, lower seed-setting rates or sterility, and increased susceptibility to diseases. One Sm mutant, ossmf-2, exhibited dwarfism, delayed flowering, and small grains. Through transcriptome analysis, three target genes, OsMRG702, OsRGG2, and OsLA1, were identified. Mutations of the OsSmF protein may lead to the abnormal splicing of these genes and finally lead to the inhibition of growth and development. Our study first edited the OsSm genes and generated a mutant library in rice. Most of the mutants exhibited abnormal growth and development, underscoring the essential roles of OsSm proteins in rice physiology. Furthermore, this work addresses a critical gap in the functional characterization of Sm proteins in rice. The resulting mutant collection offers valuable germplasm resources and lays a theoretical foundation for elucidating the molecular regulatory networks involving spliceosomal components and their target genes in the control of crop growth, development, and reproduction.

Oryza↗

Molecular and functional diversity of maize.

Over the past 10,000 years, man has used the rich genetic diversity of the maize genome as the raw material for domestication and subsequent crop improvement. Recent research efforts have made tremendous strides toward characterizing this diversity: structural diversity appears to be largely mediated by helitron transposable elements, patterns of diversity are yielding insights into the number and type of genes involved in maize domestication and improvement, and functional diversity experiments are leading to allele mining for future crop improvement. The development of genome sequence and germplasm resources are likely to further accelerate this progress.

Genetic Variation↗

Transcription factor NtELF3 promotes the polyphenol accumulation by targeting NtFLS-1 and NtCHIL-2 genes in tobacco.

Tobacco (Nicotiana tabacum L.) is an important economic crop, from which polyphenols are crucial for regulating its growth and development as well as shaping its quality. However, few genes associated with polyphenol accumulation have been cloned from tobacco, and the molecular mechanisms underlying this process remain poorly understood. Here, we found that the tobacco transcription factor EARLY FLOWERING 3 (NtELF3), which is highly expressed in tobacco leaves, positively regulates the accumulation of chlorogenic acid, neochlorogenic acid, cryptochlorogenic acid, rutin, scopoletin, and total polyphenols in tobacco middle leaves. The metabolomic and transcriptomic analyses of middle leaves showed that a total of 177 differentially accumulated metabolites and 7409 differentially expressed genes (DEGs) were identified in ntelf3-1 mutant versus wild type, respectively. Further investigation identified that 17 DEGs were involved in phenylpropanoid metabolic and flavonoid metabolic processes. Combined analysis indicated that the phenylpropanoid and flavonoid biosynthesis pathways were also co-enriched in kyoto encyclopedia of genes and genomes enrichment analysis. Molecular biology experiment demonstrated that NtELF3 directly binds to the promoters of NtFLS-1 and NtCHIL-2 that are both associated with phenylpropanoid and flavonoid biosynthesis, and promotes their expression. Taken together, our results not only provide new theoretical support for in-depth understanding of the regulatory mechanisms underlying polyphenol accumulation in tobacco, but also offer excellent genes and germplasm resources for tobacco quality breeding.

NtCHIL↗

Cryopreservation of flounder (Paralichthys olivaceus) embryos by vitrification.

Conventional cryopreservation of complex teleost embryos has been unsuccessful, possibly because their large size (1-7 mm diameter), multi-compartmental structure and low water permeability lead to intracellular ice formation and chilling injury. To overcome these obstacles, we have developed a vitrification procedure for cryopreservation of flounder (Paralichthys olivaceus) embryos. In initial toxicity tests, propylene glycol (PG) and methanol (MeOH) were less toxic to embryos than dimethylformamide (DMF) or dimethyl sulfoxide (Me2SO), whereas ethylene glycol (EG) and glycerol (Gly) were toxic to all tested embryos. Embryos between four-somite and tail bud stages were more tolerant to vitrifying solutions than embryos in other developmental stages. Four vitrifying solutions (FVS1-FVS4) were prepared by combining a basic saline solution (BS2) and cryoprotectants PG and MeOH in different proportions (FVS1: 67, 20 and 13%; FVS2: 60, 24 and 16%; FVS3: 55, 27 and 18%; FVS4: 50, 30 and 20% of BS2, PG and MeOH, respectively). Their impact on flounder embryos was then compared. FVS1 produced the highest survival rate; whereas deformation rate was highest for FVS4. Five-step equilibration of embryos in FVS2 resulted in higher survival rates than equilibration in 4, 3, 2 or 1 steps. Flounder embryos varying from the 14-somite to the pre-hatching stage were cryopreserved in the four vitrifying solutions in liquid nitrogen for 1-7 h. From eight experiments, 20 viable thawed embryos were recovered from 292 cryopreserved embryos. Fourteen larvae with normal morphology hatched successfully from the 20 surviving frozen-thawed embryos from five experiments. Embryos at the tail bud stage exhibited greater tolerance to vitrification than embryos at other stages. These results establish that cryopreservation of flounder embryos by vitrification is possible. The technology has many potential applications in teleost germplasm resource conservation.

Animals↗

High-quality chromosome-level genome of three Meretrix species using Nanopore and Hi-C technologies.

Meretrix is a commercially valuable bivalve genus in Asia, but only one reference genome has hindered comprehensive genetic studies and germplasm resource evaluation. In this study, we present three reference genomes of Meretrix species: Meretrix sp. MF1, Meretrix sp. MT1, and Meretrix lamarckii JML1. Meretrix sp. MF1 was assembled at the chromosome level using Nanopore sequencing and Hi-C technologies, whereas Meretrix sp. MT1 and Meretrix lamarckii were assembled as scaffold-level assemblies. The chromosome-level genome of Meretrix sp. MF1 consists of 36 contigs, including 19 chromosomes and 17 scaffolds, with a total length of 883.3 Mb and a scaffold N50 of 46.87 Mb. Notably, the genome of Meretrix sp. MF1, a putative novel species, exhibits an Average Nucleotide Identity (ANI) of 94.33% with its closest relative, Meretrix lamarckii. These genomic resources not only provide a crucial foundation for genetic research on Meretrix but also contribute to the development of effective conservation strategies for its sustainable management.

Animals↗

Genetic structure of the endangered plant Neolitsea sericea (Lauraceae) from the Zhoushan archipelago using RAPD markers.

BACKGROUND AND AIMS: The Zhoushan archipelago is the largest archipelago in China. It separated from the mainland about 9000 years ago due to rising sea levels and climate change. Because of the long-term influences of human activities, the original forest vegetation on the large islands has been badly damaged and its plant diversity reduced. METHODS: Levels and patterns of genetic diversity in 114 individuals from six natural populations and four cultivated populations of the insular endangered plant Neolitsea sericea (Lauraceae) on the Zhoushan archipelago were assessed using random amplified polymorphic DNA (RAPD) markers. KEY RESULTS: A total of 99 discernible loci were obtained for all populations using ten primers, 50.5 % of which were polymorphic [percentage of polymorphic bands (PPB)=50.5 %]. Despite being a woody, long-lived, perennial, outcrossing and insect-pollinated plant, N. sericea exhibited low levels of genetic variation. The cultivated populations (PPB=18.9 %, HE=0.060, S=0.092) were genetically less diverse than the natural populations (PPB=23.1 %, HE=0.082, S=0.123). Based on analysis of molecular variance, a high degree of among-population differentiation was revealed for both natural (0.387) and cultivated populations (0.598). CONCLUSIONS: Removal of plants from the wild for horticulture purposes has eroded the level of genetic variation of N. sericea. Low levels of genetic diversity and a high degree of population differentiation indicate that management strategies should include conservation of natural habitats occupied by all six wild populations, and sampling of germplasm resources from multiple seed sources.

China↗

Genetic divergence between North American ancestral soybean lines and introductions with resistance to soybean cyst nematode revealed by chloroplast haplotype.

Domesticated soybean [Glycine max (L.) Merr.] is a major crop with an established ancestral relationship to wild soybean (Glycine soja Sieb. & Zucc.) native to Asia. Soybean genetic diversity can be assessed at different levels by identification of polymorphic alleles at genetic loci, in either the plastid or nuclear genomes. The objective of this study was to evaluate genetic diversity based on chloroplast haplotypes for soybean genotypes present in the USDA germplasm resource collection. Shared chloroplast haplotypes represent broad groups of genetic relatedness. Previous work categorized three-quarters of the cultivated soybeans from Asia into a single haplotype group. Our results confirmed the close relationship of North American soybean ancestors and G. max plant introductions previously identified as representing potential sources of soybean genetic variation with the finding that these genotypes belonged to a single chloroplast haplotype group. Genetic diversity was identified in soybean genotypes determined to have a high density of single nucleotide polymorphisms and in a screen of accessions with resistance to soybean cyst nematode. Characterization of soybean plant introduction lines into chloroplast haplotype group may be an important initial step in evaluating the appropriate use of particular soybean genotypes.

Animals↗

Large-Scale Genomic Analysis of Stripe Rust Resistance in Chinese Wheat Germplasm Using Multi-Environment Trial Data.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a significant disease affecting global wheat crops and causing substantial economic losses. This study aimed to identify effective resistance genes by evaluating 120 common wheat accessions from diverse regions in China. These samples were tested with three Pst races at the seedling stage and with natural Pst inoculum at four field locations in three crop seasons. Genotypic data were collected through a Wheat55K iSelect single-nucleotide polymorphism array. The genome-wide association study identified 17 distinct loci linked to stripe rust response, accounting for 1.07 to 30.58% of the phenotypic variation across trials. These loci were distributed among three wheat genome groups: 2 in Group A, 10 in Group B, and 5 in Group D. Among these, eight loci overlapped with the reported stripe rust resistance genes or quantitative trait loci, while nine loci were novel and mainly distributed on chromosomes 2A, 6B, and 7D. This research enhances the understanding of genetic mechanisms underlying wheat stripe rust resistance and provides valuable germplasm resources for breeding new cultivars with enhanced disease resilience.

Puccinia striiformis f. sp. tritici↗

Grains of knowledge: genomics of model cereals.

The economic and scientific importance of the cereals has motivated a rich history of research into their genetics, development, and evolution. The nearly completed sequence of the rice genome is emblematic of a transition to high-throughput genomics and computational biology that has also pervaded study of many other cereals. The relatively close (ca. <50 million years old) relationships among morphologically diverse cereals native to environments that sample much of global geographic diversity make the cereals particularly attractive for comparative studies of plant genome evolution. Extensive germplasm resources, largely a byproduct of their economic importance, together with growing collections of defined mutants, provide foundations for a host of post-genomic studies to shed more light on the relationship between sequence and function in this important group. Using the rapidly growing capabilities of several informatics resources, genomic data from model cereals are likely to be leveraged tremendously in the study and improvement of a wide range of crop plants that sustain much of the world's population, including many which still lack primary genomic resources.

DNA, Plant↗

Characterization of the common wheat (Triticum aestivum L.) mutation line producing three pistils in a floret.

In a normal wheat (Triticum ssp.L.) spike, one floret carries only one pistil that will further develop into one grain after fertilization. The cultivated common wheat (T. aestivum L.) mutation line Three Pistils (TP) carried three pistils in a floret. Although one or two of the pistils died out before seed set in some florets, there were exist many florets that set three seeds. Normally, it was observed that there were one to three seeds in different florets of the same spike. Therefore, this mutation trait could raise considerably the number of grains per spike. The weight of 100 grains in three seeds set florets was lower than that of in one seed set florets. But three seeds set florets were significantly to surpass the one seed set florets in grain(s) weight per floret. Based on these results, the three pistils trait was suggested to be an interesting germplasm resource. Localisation of the gene controlling the three pistils trait was carried out by the method of crossing TP with the Chinese Spring disomic substitutions. F2 population segregation analysis revealed that only the 5B F2 population did not show homogeneity to control population. chi2-test analysis indicated that 5B F2 population, and only this population, was deviated from the Mendelian segregation ratio (3:1). As a conclusion, the gene for three pistils trait was located on chromosome 5B. According to the Recommended rules for gene symbolization in wheat, the name of the dominant gene for three pistils trait in the line TP was suggested as Pis1.

Genes, Plant↗

A robust biotechnology induces artificial genomic duplication via transient RNAi-mediated suppression of OSD1 in rice.

Ploidy manipulation is a crucial strategy for generating germplasm in crop breeding. However, artificial genomic duplication, often induced by colchicine treatment, is associated with toxicity and unpredictability. Although mutations in OSD1 have shown promise for inducing genomic duplication, the instability of ploidy across generations limits their practical application. In this study, we developed a Plant Polyploidization via Gene Interference (PPGI) system that utilizes transient RNAi-mediated suppression of OSD1 to efficiently induce artificial genomic duplication, demonstrating obvious potential for producing autotetraploids. We first validated this system by successfully generating PPGI-induced autotetraploid plants from the Taichung65 cultivar. These PPGI-induced plants exhibited notable differences from Taichung65 but resembled the existing Taichung65-4x line obtained through colchicine treatment. Haplotype analysis indicated that the OSD1 RNAi fragment is conserved across 2,908 rice cultivars. Consequently, we employed the same PPGI vector to develop autotetraploid lines from various germplasms, including another japonica cultivar, seven indica cultivars, and one Oryza rufipogon line. The probability of genomic duplication achieved by our PPGI method was higher than that obtained by colchicine treatment. Typically, autotetraploid lines exhibit severe sterility in the first generation following polyploidization. Leveraging fertile neo-tetraploid rice and the PPGI system, we designed and verified two strategies to directly induce fertile autotetraploid germplasms in the first generation, thereby substantially shortening the breeding cycle. Our method provides a universal, efficient, and non-toxic approach for inducing autotetraploid rice germplasms and contributes to enriching fertile autotetraploid rice germplasm resources.

OSD1↗

SUG2 controls grain size and weight by influencing GS2 transcription level in rice.

Grain size is a critical yield determinant and a complex quantitative trait in rice. The major quantitative trait locus GS2, which encodes the transcriptional regulator OsGRF4, has been characterized as a key controller of grain size and grain weight in rice. Building upon existing germplasm resources, exploring the upstream and downstream genes of known grain size regulators is an effective approach to gradually refine and expand the molecular regulatory network underlying grain size. Here, we report that a suppressor of the gain-of-function allele GS2AA, SUG2, which encodes an importin &#x3b2; nuclear transport protein. Phenotypic characterization reveals that the sug2 GS2AA mutant exhibits small grains by inhibiting cell expansion in the spikelet hull. Protein interaction analyses demonstrate that SUG2 physically interacts with GS2 both in vivo and in vitro, and the SUG2A mutation reduces SUG2 expression levels and inhibits GS2 transcriptional activation activity, resulting in decreased GS2 expression levels and GS2 protein abundance in sug2 GS2AA. Genetic analyses indicate that SUG2 and GS2 may be partially involved in a common pathway regulating grain size and weight in rice. These findings elucidate the grain size regulatory relationship between SUG2 and GS2 and provide novel insights into the precision breeding of yield optimization in rice.

Oryza↗

Seed banks and molecular maps: unlocking genetic potential from the wild.

Nearly a century has been spent collecting and preserving genetic diversity in plants. Germplasm banks-living seed collections that serve as repositories of genetic variation-have been established as a source of genes for improving agricultural crops. Genetic linkage maps have made it possible to study the chromosomal locations of genes for improving yield and other complex traits important to agriculture. The tools of genome research may finally unleash the genetic potential of our wild and cultivated germplasm resources for the benefit of society.

Chromosome Mapping↗

Freeze Tolerance of Seed-Producing Turf Bermudagrasses.

Bermudagrass, Cynodon dactylon (L.) Pers., suffers periodic severe winter-kill throughout much of its area of use in the contiguous USA. A research goal is to increase freeze tolerance in cultivars to lessen the risk of such damage. An identified research need is for Cynodon germplasm resources to be characterized for freeze tolerance and hybridization potential. Accordingly, the objective of this research was to characterize the relative freeze tolerance of selected fertile bermudagrass plants. Nine tetraploid (2n = 4x = 36) C. dactylon and two triploid (2n = 3x = 27) hybrid (C. dactylon x C. transvaalensis Burtt Davy) clonal plants (standards) were evaluated in two experiments. Plants were propagated clonally and established in Cone-tainers (Ray Leach Cone-tainer Nursery, Canby, OR) for about 10 wk. Acclimation took place for 4 wk in controlled environment chambers at 8/2 degrees C (day/night) temperatures with a 10-h photoperiod. Following acclimation, Cone-tainers were placed into a freeze chamber and cooled rapidly to -2 degrees C, induced to freeze with ice chips, then held overnight at -2 degrees C. The freeze chamber was then programmed to cool linearly at 1 degrees C per hour. For each cultivar, three Cone-tainers were removed at each test temperature. Following thawing, Cone-tainers were transferred to a greenhouse and regrowth was evaluated visually. Nonlinear regression was used to estimate T(mid), which corresponded to the midpoint of the sigmoidal response curve of survival vs temperature. Within experiment one, Tifgreen (T(mid) = -7.2 degrees C) was significantly less cold hardy than Quickstand (-9.0 degrees C), A-12204 (-9.2 degrees C), Midiron (-9.9 degrees C), and A-12195 (-10.5 degrees C). A-12195 was significantly hardier than all genotypes except Midiron. In the second experiment, Arizona Common (-6.6 degrees C), Tifgreen (-7.1 degrees C), and A-12205 (-7.1 degrees C) were less hardy than A-9959 (-8.7 degrees C), A-12156 (-8.9 degrees C), A-12198 (-9.5 degrees C), and Midiron (-10.0 degrees C). Midiron was hardier than all genotypes except A-12198. The range of test temperatures chosen did not allow estimate of a T(mid) value for Zebra, but nearly 50% of the plants were killed at -6.0 degrees C.

Journal Article↗

Development and validation of whole-genome SSR markers in sugar beet (Beta vulgaris L.).

Sugar beet (Beta vulgaris L.) is an important sugar and cash crop worldwide. To systematically characterize SSR (Simple Sequence Repeat) loci across sugar beet chromosomes and enable the precise identification of germplasm resources, this study conducted a genome-wide scan for SSR loci, analyzed their distribution patterns, and determined their genotypes using resequencing data from 123 sugar beet varieties. The results revealed an abundance of SSR loci in the sugar beet genome, with a total of 135, 379 identified, from which 135, 344 pairs of SSR primers were designed (135, 344 primer pairs successfully designed; 35 loci failed to meet design criteria). Specifically, 31, 748 primer pairs were designed based on SSRs located in unassigned scaffolds, and 103, 596 primer pairs from SSRs assigned to the nine chromosomes. Through bioinformatic analysis, we identified 28, 768 SSR primers located in multi-copy genes with PIC (Polymorphism Information Content) &#x2265; 0.5, and 2, 326 SSR markers located in single-copy genes residing in various genic regions (among which 543 had PIC &#x2265; 0.5, with the highest reaching 0.776). PCR (Polymerase Chain Reaction) validation confirmed 20 robust and polymorphic markers producing clear and reproducible bands. Among them, 10 SSR primers located in multi-copy genes exhibited three or more polymorphic types, and 10 markers located in single-copy genes displayed 2-3 polymorphic types. The most polymorphic marker, YCD-4-2, detected 11 polymorphic types across 48 varieties. Furthermore, to explore markers with potential functional significance, we annotated the genes harboring SSR markers located in single-copy genes. The results showed that 1, 264 SSRs located in single-copy genes were localized to 967 genes, which are significantly enriched in pathways related to carbohydrate metabolism, stress responses, and plant-pathogen interactions. The 20 validated markers and the 2, 326 SSRs located in single-copy genes provided in this study can be directly applied to fingerprinting of sugar beet varieties, seed purity testing, and marker-assisted selection, thus representing a practical resource for molecular breeding.

genome-wide↗