Elucidating the evolutionary trajectories and genetic basis of critical agronomic traits in regional rice germplasm is paramount for discovering elite allelic variations for crop improvement. Here, we systematically characterized a panel of 109 rice accessions from Zhejiang Province through whole-genome resequencing (~10× coverage) coupled with two years of rigorous field phenotypic evaluations. A total of 4,753,071 high-quality genomic variants, including 4,147,316 SNPs, were identified across the genome. Population structure and evolutionary analyses revealed sharp genetic differentiation at the subspecies level, partitioning the panel into distinct indica and japonica clusters accompanied by intricate subpopulation stratification and historical gene flow. Through a joint scanning of the fixation index (Fst) and nucleotide diversity (Pi) ratios, three prominent selective sweep regions (qSS1, qSS10, and qSS12) driving subspecific differentiation were captured on chromosomes 1, 10, and 12. Notably, the qSS12 locus harbors the sucrose transporter gene OsSUT2, indicating that carbohydrate transport and energy metabolism served as core genomic targets driving the indica–japonica divergence. Furthermore, genome-wide association studies (GWAS) successfully mapped 9 significant loci modulating heading date, effective tiller number, and grain size. Subsequent gene-based haplotype analyses within these target intervals pinpointed elite allelic variations in core candidate genes, including OsSPX1 (phosphate homeostasis, 1000-grain weight), Chl9 (chlorophyll synthesis, grain width), and OsCER1 (wax biosynthesis, panicle length). Collectively, this study deciphers the genomic landscape and subspecies differentiation patterns of Zhejiang rice germplasm, providing pivotal molecular targets and invaluable genomic resources for germplasm conservation and precision molecular breeding.
The narrow genetic base of cultivated rice necessitates the identification of diverse germplasm accessions possessing superior agronomic performance and enhanced nutritional quality. The present study aimed to assess the phenotypic and genetic diversity among a subset of 300 rice germplasm accessions and identify elite accessions for rice biofortification and yield improvement programmes. The germplasms were evaluated during Kharif 2023 for nine quantitative traits using an alpha lattice design at Mandya and Gangavathi. Analysis of variance revealed significant differences among the accessions for all traits, indicating substantial phenotypic diversity. Principal Component Analysis identified the major contributors to phenotypic variation, with the first four principal components explaining 69% of the total variation. Based on phenotypic performance, 50 representative accessions were selected for K-means clustering and Multi-Trait Genotype–Ideotype Distance Index (MGIDI) analysis. The accessions were grouped into three distinct clusters with contrasting grain yield and grain zinc concentration. MGIDI identified IRGC 349 as the accession closest to the ideotype, combining high grain yield (6.10 t/ha) with favourable grain zinc concentration (24.59 ppm) and desirable agronomic traits. Based on mean performance across locations, IRGC 647 exhibited the highest grain zinc concentration (34.97 ppm) and was identified as a promising donor for rice biofortification programmes. Genetic diversity and population structure were assessed using 102,580 genome-wide single nucleotide polymorphism (SNP) markers. STRUCTURE analysis, SNP-based principal component analysis (PCA) and phylogenetic-based clustering consistently identified two major genetic subpopulations. The combined phenotypic and genotypic analyses revealed substantial genetic diversity and identified elite accessions for the development of high-yielding and zinc-biofortified rice cultivars.
Spoorthi Siddeswara Rekha, Deepak Chikkaballi Annegowda, Sanketh Ashok Umapathi et al.· Genetic Resources and Crop E...· 0 citations
Molecular characterization of wheat varieties is of high importance for wheat breeding. In the present study, 1883 Chinese wheat cultivars released between 1971 and 2025 were genotyped using a wheat 90K SNP array. Analysis of genetic diversity indicated a consistent A > B > D pattern, with the D subgenome showing the lowest genetic diversity and fastest LD decay (4.2 Mb), indicating diminished genetic diversity driven by breeding and selection. Population structure analysis revealed ten genetic clusters with clear ecological preferences, whereas genetic differentiation was weak (FST < 0.05) and gene flow extensive (Nem > 1), indicating the co-existence of strong ecological adaptation and frequent interregional germplasm exchange. Selective sweeps were identified on chromosome 5A (TaVRN1) and 2D (Rht8/RNHL-D1) regions controlling vernalization, plant height, and stress tolerance. Despite high gene flow, these loci for variety adaptiveness remained differentiated, highlighting the impact of artificial selection. Average pairwise genetic similarity was 0.56, but only a minority of cultivar pairs exceeded 0.98, especially in the Northeastern Spring Wheat and Middle-Lower Yangtze River Facultative Wheat regions, revealing severe genetic homogeneity from the excessive use of core parents. Nucleotide diversity increased to a peak in 2011–2015. These findings indicate that Chinese wheat cultivars still harbor significant potential for genetic improvement, highlighting the critical need to integrate exotic germplasm into core breeding parents to drive future advancements.
A new approach to identify environment-specific quantitative trait loci (QTL) using GWAS and the validated resistance gene Yr27 was identified as sole candidate gene for one QTL region of particular relevance for Central European wheat.
Jiao-Jiao Wang, Renate H. Schmidt, Guoliang Li et al.· Theoretical and Applied Gene...· 1 citation
This comprehensive review demonstrates that shifting from reactive field evaluation to marker-driven, genomics-assisted precision design provides the definitive molecular framework required to engineer high-yielding, climate-resilient, and disease-proof cacao cultivars, thereby permanently safeguarding the long-term economic sustainability of global cocoa supply chains.
Atharva Gangurde, Adesina Christiana, Franc Olivier Nzogang· International Journal of Inn...· 0 citations
Potato late blight, Phytophthora infestans, remains a major global threat to potato production due to the rapid genetic change, long-distance dispersal and fungicide resistance. To clarify the genetic structure and phenotypic characteristics of P. infestans populations in southwestern China during 2019–2025, this study analyzed 241 isolates collected from Sichuan, Chongqing, Guizhou, Yunnan and Hubei. The isolates were characterized using 14 SSR markers, together with mating-type determination, metalaxyl sensitivity assays, mitochondrial haplotype identification and virulence profiling. A total of 70 alleles and 118 multilocus genotypes were detected, with certain genotypes (SW-40, SW-48 and SW-81) broadly distributed across regions, while the simultaneous presence of numerous low-frequency genotypes reflected high overall genetic diversity. Population genetic analyses revealed weak regional differentiation and strong genetic connectivity, with most genetic variation occurring within regional populations, where self-fertile isolates, metalaxyl-resistant phenotypes and mitochondrial haplotype Ia were predominant. Cluster and principal component analyses separated the isolates into three major genetic groups, with the largest group containing most isolates and showing close genetic similarity to the Blue_13 reference genotype. These findings indicate that southwestern China harbors a highly diverse and admixed P. infestans population, likely driven by frequent pathogen movement among potato-growing regions.
Xiao-Feng Liu, Jun Chun, Hong Zhang et al.· Journal of Fungi· 1 citation
The swimming crab (Portunus trituberculatus) is a commercially important marine aquaculture species. After multiple generations of selective breeding, the third improved variety in China, “Huangxuan No 2” (HX2), was successfully developed in 2018. Compared to the original wild populations, HX2 exhibits enhanced resistance to low salinity stress and growth RATE. However, the genomic characteristics underlying these selected traits remain largely unexplored. To investigate the genetic variation associated with artificial selection, we genotyped 90 individuals from the HX2 strain and two wild populations (C and D) using a high-density SNP array. A total of 43,314 single nucleotide polymorphisms (SNPs) were identified, which were evenly distributed across the genome in 1 Mb windows. Genetic diversity analysis showed that HX2 and wild populations were similar but overall low in diversity levels. Population structure analysis and fixation index (Fst) values revealed low-to-moderate genetic differentiation between HX2 and the wild populations, whereas no differentiation was observed between the two wild populations. Using the wild populations as a reference, we identified 24 genomic regions under potential selection in HX2 based on the Fst between populations and the nucleotide diversity ratio (π-ratio), encompassing 425 candidate genes. Enrichment analysis indicated that these genes are primarily involved in pathways related to immune response, infection, signal transduction, and metabolism. Notably, genes associated with stress tolerance (e.g., GPX3, HMGCS1, Duox), immunity (e.g., LAMB1, HSPG2), and growth (e.g., Cht5) were identified. These findings provide valuable insights into the genomic signatures of artificial selection and offer fundamental resources for further genetic improvement of P. trituberculatus.
