Search Results (358)

Fungal diseases such as soybean stem canker (SSC), frogeye leaf spot (FLS), and sudden death syndrome (SDS) cause substantial yield losses in soybean worldwide. This study aimed to pyramid major resistance genes and QTLs against these diseases through marker-assisted backcrossing (MABC). Diagnostic SSR markers, linked to Rdm4 (SSC), Rcs3 (FLS), and SDS resistance QTLs, were validated and successfully employed for foreground and background selection in crosses between the elite cultivar A8100RR and the resistant donor ‘Forrest’. Molecular analyses confirmed the effective introgression and fixation of multiple resistance loci in BC₂F₅ lines. Under artificial inoculation, lines R30-11 and R25-13 displayed high resistance levels to Diaporthe aspalathi, Cercospora sojina, Fusarium virguliforme, and F. tucumaniae. Genotype R30-11 exhibited the most consistent resistance across pathogens, while R25-13 combined multi-disease resistance with glyphosate tolerance and stable agronomic performance under field conditions comparable to commercial cultivars. These results represent, to our knowledge, the first report of successful pyramiding genes and QTLs against three distinct fungal diseases (SSC, FLS, and SDS) in soybean through MABC. The developed lines constitute valuable germplasm for breeding programs designed to achieve broad-spectrum, durable and sustainable disease management. Full article

Background: Genetic diversity and genetic differentiation between Gossypium hirsutum-Gossypium barbadense introgression lines (ILs) and early-maturing upland cotton lines are critical for resolving the core breeding contradiction in Xinjiang cotton region: narrow genetic basis of early-maturing cultivars and late maturity of ILs with superior fiber quality. Xinjiang is one of the major cotton-producing regions in China, and breeding high-quality early-maturing upland cotton adapted to local ecological conditions is essential for improving cotton yield and quality. However, the genetic relationship and differentiation between the two types of cotton germplasm remain unclear, which hinders the efficient utilization of germplasm resources in breeding. Therefore, this study aimed to clarify the genetic diversity and differentiation between the two germplasm types and identify key candidate loci related to early maturity and fiber quality, providing support for cotton breeding. Results: Here, we used a 40K Single Nucleotide Polymorphism chip to genotype core cotton germplasm in northern Xinjiang, and analyzed their population structure, genetic diversity and functional SNP loci associated with early maturity and fiber quality. The tested materials were clearly divided into two subgroups (ILs and early-maturing lines). Genetic diversity analysis revealed a significantly narrow genetic basis in the early-maturing subgroup, while the IL subgroup had higher genetic diversity. Specifically, the early-maturing subgroup showed lower nucleotide diversity and polymorphism information content compared with the IL subgroup, indicating that the genetic variation of early-maturing cotton germplasm in northern Xinjiang is relatively limited. A total of 25 non-synonymous SNPs were identified, among which the c.A613G:p.T205A mutation in GH_D09G1484 (mRNA-decapping enzyme 1, DCP1) was a characteristic variation of early-maturing cotton, and a possible non-synonymous mutation in GH_A09G2400 (Heat shock transcription factor A6b, HSFA6B) was associated with fiber development. These two candidate genes were annotated to be involved in plant growth and development, further supporting their potential roles in regulating cotton early maturity and fiber quality. Conclusions: This study clarified the genetic differentiation between the two types of germplasms and identified key candidate loci for early maturity and fiber quality, providing precise molecular markers and theoretical support for breeding high-quality early-maturing upland cotton adapted to Xinjiang’s ecological conditions. The results also highlight the value of Gossypium hirsutum–Gossypium barbadense introgression lines in enriching the genetic basis of early-maturing cotton, which can be further utilized to solve the core breeding contradiction in the Xinjiang cotton region. Full article

In recent years, plant genotyping has been shifting from the accumulation of whole-genome data toward their effective use in breeding programs This review examines key genotyping platforms, including single-nucleotide polymorphism (SNP) arrays, reduced-representation sequencing methods such as genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), targeted genotyping approaches, and whole-genome sequencing (WGS), analyzing their informativeness, cost, and computational limitations. The transition to pangenome-based genotyping and graph genomes is discussed, as these approaches reduce reference bias and increase sensitivity for detecting structural variants, introgressions, and rare alleles that are important for adaptation and breeding. The growing role of AI/ML is highlighted in modeling complex genotype–phenotype relationships, integrating genomic and phenotypic data, and improving the accuracy and interpretability of genomic predictions. Full article

The common bean (Phaseolus vulgaris L.) cultivar Jalo Vermelho carries the Co-12 gene, which confers resistance to both Andean and Mesoamerican races of Colletotrichum lindemuthianum. Despite its importance for breeding programs, the genomic location and candidate genes underlying this resistance remain poorly defined. The Co-12 locus was fine-mapped using a biparental population derived from the cross Jalo Vermelho × Crioulo 159. A total of 172 F₂ plants were used to generate 172 F_2:3 families, which were phenotyped after inoculation with race 1545 of C. lindemuthianum. Segregation analysis confirmed a 1:2:1 Mendelian ratio, consistent with a single dominant resistance gene. Genotyping of resistant and susceptible plants using the BARBean6K_3 Illumina BeadChip (5398 SNP markers) mapped Co-12 to chromosome Pv04, between 1695 bp (ss715649768) and 9,651,954 bp (ss715646644). Subsequent fine mapping with simple sequence repeat (SSR) markers delimited the locus to a 41 kb genomic interval flanked by BARCPVSSR04557 and BARCPVSSR04570. Within this region, three candidate genes were identified, including one encoding a gamma-glutamyl-GABA enzyme and two encoding lipid transfer proteins (LTP2). Lipid transfer proteins are widely recognized components of plant defense; however, their association with anthracnose resistance in the common bean has not been previously reported. The identification of LTP2 genes within the Co-12 interval suggests a previously unrecognized resistance mechanism and expands the current understanding of host defense pathways in Phaseolus vulgaris. The markers identified here provide valuable tools for marker-assisted selection and will facilitate efficient introgression of Co-12 into common bean cultivars. Full article

Honeybee (Apis mellifera L.) populations are a vital resource for pollination and honey production, yet their genetic diversity in Central Asia remains poorly understood. This study provides a comprehensive genetic assessment of 16 honeybee populations from Kazakhstan, with comparative samples from Russia, Georgia and Kyrgyzstan, utilizing mitochondrial COI–COII intergenic region and 12 highly polymorphic nuclear STR markers. Mitochondrial DNA analysis revealed the predominance of the Eastern European C lineage (A. m. carnica), while a few populations from East Kazakhstan and Russia attributed the M lineage (A. m. mellifera), indicating local introgression and the persistence of relict lineages. STR analyses showed high levels of polymorphism and genetic diversity, with variation in heterozygosity and inbreeding across populations. Analyses of population genetic structure delineated four principal genetic clusters shaped by regional differentiation, historical gene flow, and sporadic admixture. Concordance between mitochondrial and nuclear markers confirms the robustness of these findings. Overall, this study highlights the rich genetic diversity of honeybees from Kazakhstan and emphasizes the importance of conserving local populations and implementing selective breeding programs to sustain adaptive potential and long-term apiculture. Full article

Crossbreeding indigenous goats with exotic meat breeds is a common strategy to improve production performance, but its combined effects on growth and reproductive traits and the potential contribution of the gut microbiota have not been systematically evaluated in Chinese goat populations. This study used high-prolific Jining Grey (JJ) does mated with Nubian (N) bucks to establish three genetic groups: purebred Jining Grey (JJ), F1 Nubian × Jining Grey (NJ), and backcross offspring (Nubian × (Nubian × Jining Grey); NJJ). Body weight from birth to 12 months and average daily gain were recorded, reproductive traits (lambing rate, litter size, and kid survival) of primiparous and multiparous does were analyzed, and litter total birth weight and weaning weight per lambing were calculated. Fecal samples from JJ and NJJ goats were subjected to 16S rRNA gene sequencing to characterize gut bacterial communities. Body weight differed significantly among the three genetic groups at all ages (p < 0.01). Crossbred kids (NJ and NJJ) were about 30% heavier at birth and showed higher body weight and average daily gain during pre- and post-weaning periods than JJ kids (p < 0.05), representing a consistent growth advantage. In contrast, lambing rate, litter size and kid survival did not differ among genotypes (p > 0.05), whereas litter total birth weight and weaning weight were higher in crossbred than in purebred does (p < 0.05). Alpha-diversity indices were similar between JJ and NJJ goats (p > 0.05), but community structure was significantly distinct (PERMANOVA, p = 0.001), characterized by an increased Firmicutes-to-Bacteroidota ratio and shifts in several energy metabolism-related genera (p < 0.05). In conclusion, introgression of Nubian genetics into Jining Grey goats improves growth performance and litter weight while maintaining high prolificacy; these improvements are accompanied by a restructured gut microbiota that is associated with these growth patterns. Full article

Low temperature and drought are among the most pervasive abiotic stresses limiting crop productivity worldwide, and their frequent co-occurrence or alternation imposes compounded constraints on agricultural sustainability. Increasing evidence supports cross-tolerance, whereby exposure to one stress enhances resistance to another, as an emergent property of shared signaling networks and integrative regulatory layers. In this review, we summarize recent advances in understanding cold–drought cross-talk, from early stress perception and secondary messengers to hormonal coordination via abscisic acid, transcriptional reprogramming centered on dehydration responsive element binding protein/C repeat binding factor (DREB/CBF) modules, and longer-term regulatory memory mediated by chromatin remodeling and biomolecular condensates. Importantly, we further discuss how these mechanistic insights can be translated into precision breeding strategies, including genome editing, allele mining, and backcross-assisted introgression, to accelerate the development of crop varieties with stable multi-stress tolerance. Finally, we highlight future directions for integrating multi-omics, high-throughput phenotyping, and data-driven approaches to enable efficient molecular design breeding for complex stress environments. Full article

Anaerobic germination tolerance (AGT) is a critical adaptive trait for rice establishment in flood-prone environments and direct-seeded systems. Here, we identified and validated the quantitative trait locus qAG2.1 for AGT and introgressed it into the elite lowland rice variety CR Dhan 801 through marker-assisted backcross breeding. The introgressed lines exhibited significantly improved germination under anaerobic conditions, demonstrating the effectiveness of qAG2.1 in a high-yielding genetic background. While CR Dhan 801 showed a low anaerobic germination percentage (17.6%), the donor ARC10424 exhibited 82.6%, and the best-performing introgressed line (22009-3) achieved 49.2%. Importantly, the improved lines maintained agronomic performance comparable to CR Dhan 801 under non-stress conditions, indicating minimal yield penalty. To gain mechanistic insight, the qAG2.1 interval was dissected in silico to prioritise candidate genes putatively associated with AGT. This analysis highlighted genes linked to ethylene biosynthesis and signalling (e.g., OsACO3, OsERF109), abscisic acid biosynthesis (OsNCED1), gibberellin homeostasis (OsGA2ox9), trehalose metabolism (OsTPS5, OsTPP1), detoxification of anaerobic by-products (OsALDH2A), and water transport (OsPIP1;3). Collectively, these results validate qAG2.1 as a further deployable locus for improving anaerobic germination in elite rice backgrounds and provide a set of putative candidate genes for future functional characterisation. Full article

Domestic cattle represent one of the most significant evolutionary successes in the history of human–animal mutualism. This review synthesizes evidence from paleogenomics and modern population genetics, particularly recent pangenome analyses, to reconstruct a comprehensive evolutionary trajectory of cattle. We outline the two domestication events: the emergence of taurine cattle (Bos taurus) in the Fertile Crescent (~10,500 years ago) and zebu cattle (Bos indicus) in the Indus Valley (~8000 years ago). Following domestication, cattle dispersed globally alongside human migration, resulting in a complex genetic mosaic shaped by introgression with wild relatives and extensive admixture between lineages. By integrating data from mitochondrial DNA, Y-chromosome haplotypes, and whole-genome sequencing of modern, ancient, and wild samples, we reconstruct the detailed global dispersal of cattle. Furthermore, we dissect the molecular mechanisms underlying phenotypic diversity, emphasizing how natural selection has driven environmental adaptation, how artificial selection has optimized production traits, and how the emerging bovine pangenome is unveiling “hidden” genetic variations critical for climate resilience and disease resistance. Ultimately, this review summarizes the origin, dispersal, and genomic diversity of cattle, offering vital insights for the conservation of indigenous genetic resources and the advancement of molecular breeding strategies in the face of a changing global climate. Full article

Background: Bruchids (Acanthoscelides obtectus and Zabrotes subfasciatus) are responsible for severe post-harvest losses in common bean (Phaseolus vulgaris L.). Understanding the genetic mechanisms and molecular markers of resistance is critical for breeding durable cultivars, especially in Africa. Methods: This systematic review followed PRISMA guidelines. The protocol was registered on OSF before implementation. Ten databases and repositories were searched for peer-reviewed and gray literature evaluating cultivars, landraces, wild derivatives, or interspecific lines. Eligible studies reported genetic mechanisms, molecular markers, or breeding strategies for bruchid resistance. Results: Twenty-nine studies met inclusion criteria. Most identified resistance at the APA locus on chromosome Pv04, involving arcelins, phytohemagglutinin, and α-amylase inhibitors, which confer strong antibiosis. Additional loci on Pv03 and Pv07, together with seed-coat traits, contributed complementary non-APA resistance. Validated protein markers and SNPs linked to these loci were reported. Breeding approaches included backcrossing and interspecific introgression. Conclusions: Marker-assisted selection offers opportunities to pyramid multiple resistance genes into farmer-preferred germplasm. However, progress is constrained by limited germplasm diversity, inconsistent bioassays, and poor characterization of non-APA mechanisms. Greater emphasis on diverse African germplasm and standardized assays is needed to accelerate the breeding of resistant cultivars. Full article

This study developed a 60K single-nucleotide polymorphism (SNP) liquid-phase chip (‘Shenxin I’) based on genotyping by target sequencing (GBTS) technology. The chip was used to genotype 1451 individuals spanning five conserved local pig breeds: Fengjing (FJ), Meishan (MMS), Pudong White (PD), Shaowutou (SW), and Shanghai White (SHW), and newborn purebred Meishan offspring (MMS_New). The study assessed the genetic diversity, population structure, and genomic breed composition (GBC) of these breeds. The GBC analysis provided insights into genomic introgression within admixed individuals. Results indicate that PD and FJ breeds exhibited the higher fraction of the genome covered by runs of homozygosity (F_ROH) and slower linkage disequilibrium (LD) decay rate, suggesting higher genetic inbreeding level in these two breeds. The study conducted genetic distance of identity-by-state (IBS) analysis and molecular pedigree construction for the MMS population. Subsequently, purebred mating was implemented by selecting boars from different pedigrees to mate with sows and excluding individuals with high inbreeding coefficients from the breeding program. This resulted in a significant reduction in the overall inbreeding level of the born progeny and an increase in genetic diversity compared to the original population. Consequently, the study concludes that utilizing liquid-phase chip technology for genotyping, constructing molecular pedigrees, and optimizing mating combinations in small populations of locally conserved pig breeds contributes to enhancing the conservation effectiveness. Full article

Plant viruses cause substantial yield and quality losses worldwide, and their rapid evolution can erode deployed host resistance. This review synthesizes current knowledge of antiviral resistance and tolerance mechanisms, using barley yellow dwarf virus (BYDV) in cereals as an illustrative case study. We first summarize key layers of plant antiviral immunity, including pre-formed physical and chemical barriers, dominant and recessive resistance genes, RNA silencing, hormone-regulated defense signaling, and degradation pathways such as the ubiquitin–proteasome system and selective autophagy. We then discuss how these mechanisms are exploited in breeding and biotechnology, covering conventional introgression, marker-assisted selection, QTL mapping and pyramiding, induced variation (mutation breeding and TILLING/ecoTILLING), transgenic strategies (pathogen-derived resistance and plantibodies), RNA interference-based approaches, and CRISPR-enabled editing of susceptibility factors. Finally, we highlight emerging nano-enabled tools and propose integrated strategies that combine genetic resistance with surveillance and vector management to improve durability under climate change and ongoing viral diversification. Full article

Peanut (Arachis hypogaea L.) is a globally important oilseed and food legume, yet its productivity is persistently constrained by devastating diseases and insect pests that thrive under changing climates. This review aims to provide a comprehensive synthesis of advances in precision breeding and molecular approaches for enhancing disease and pest resistance in peanut. Traditional control measures ranging from crop rotation and cultural practices to chemical protection have delivered only partial and often unsustainable relief. The narrow genetic base of cultivated peanut and its complex allotetraploid genome further hinder the introgression of durable resistance. Recent advances in precision breeding are redefining the possibilities for resilient peanut improvement. Multi-omics platforms genomics, transcriptomics, proteomics, and metabolomics have accelerated the identification of resistance loci, effector-triggered immune components, and molecular cross-talk between pathogen, pest, and host responses. Genome editing tools such as CRISPR-Cas systems now enable the precise modification of susceptibility genes and defense regulators, overcoming barriers of conventional breeding. Integration of these molecular innovations with phenomics, machine learning, and remote sensing has transformed resistance screening from manual assessment to real-time, data-driven prediction. Such AI-assisted breeding pipelines promise enhanced selection accuracy and faster deployment of multi-stress-tolerant cultivars. This review outlines current progress, technological frontiers, and persisting gaps in leveraging precision breeding for disease and pest resistance in peanut, outlining a roadmap toward climate-resilient, sustainable production systems. Full article

Breeding for disease-resistant varieties is a sustainable solution to reduce substantial production losses caused by pathogenic infestations in Brassica vegetables, bypassing environmentally risky disease management practices. Host-resistant genetic mechanisms aid breeders to identify resistance loci and linked markers for the clubroot, Fusarium yellows, downy mildew, black rot, stem rot, soft rot, white rust, and turnip mosaic virus diseases in Brassica vegetables. Introgression of the resistance (R) genes by marker-assisted selection (MAS) breeding strategies allow the development of disease-resilient varieties. Brassica rapa clubroot-resistant genes (CRa, CRc, CRd, CRk, and Crr5) have been introgressed into Chinese cabbage, while CR genes (CRa, CRb, CRc, Crr1, Crr2, and Crr3) from B. rapa were also introgressed into B. oleracea. Beyond MAS, R genes can be precisely engineered by CRISPR-based technologies into precise and durable resistant varieties. The involvement of DNA methylation and histone modifications epigenetically regulate resistance mechanisms, often via ethylene/salicylic acid/jasmonic acid signaling pathways. DNA methylation mediates systemic acquired resistance by the differential expression of genes such as JAZ1, PR3, and NDR1. Future progress will depend on identifying epiQTLs and epi-markers linked to R genes. Epigenetic insights with genetic knowledge will facilitate breeding of biotic stress-resilient Brassica vegetables. This review synthesizes current molecular understanding of biotic stressors and provides future directions for disease resistance breeding of Brassica vegetable plants. Full article

Triticale, a man-made cereal, has been grown worldwide since the 1980s in order to replace established cereals in difficult areas, at least partially. The present cultivars are mostly hexaploid genotypes with 42 chromosomes, of genomic structure AA BB RR. Their agricultural performance does not meet all breeding requirements. In particular, some technological characteristics are inadequate compared to tetraploid (durum) and hexaploid (soft) wheats. Therefore, we aimed to find ways to improve modern triticale varieties by targeted introgression with genes and even chromosomes from wheat, in particular, from the D genome. Through appropriate bridge crossings and embryo culture technique and under cytogenetic control, a series of new stable hexaploid lines with reasonable agronomic stability were finally produced. All of them carried a complete D sub-genome, a complete R sub-genome, plus a mixed genome consisting of various combinations of chromosomes derived from the A and B genomes representing the seven homoeologous groups. It is clear that such mixed genomes can be of genetic and breeding significance. These large introgression lines demonstrate the flexibility of genome organization and offer the opportunity for further regulatory and genetic optimization. Full article