Introduction Commercial spring maize germplasm in northern China has been shaped by five decades of intensive breeding and the continual incorporation of elite domestic and introduced germplasm, but its genetic diversity, pedigree structure, and genomic signatures of selection remain incompletely characterized. Methods We re-sequenced 108 representative inbred lines from China’s commercial spring maize germplasm and combined them with 14 previously published key inbred lines. Population structure, genetic diversity, identity-by-descent, selective sweeps, and haplotype-trait associations were analyzed across seven heterotic groups. Results The 122 inbred lines represented nearly five decades of elite maize germplasm in northern China. Modern breeding materials showed reduced nucleotide diversity, with π decreasing from 1.58 × 10−3 to 1.34 × 10−3, and an increased deleterious mutation burden. We identified 275 Mb of high-impact IBD regions shared among elite germplasm, containing genes associated with flowering, plant architecture, photosynthesis, and grain quality. Selective sweep analyses detected genomic regions associated with agronomic traits including grain quality and floral organ development. Haplotype analyses further revealed natural alleles related to tassel structure, with differential allele frequencies between the SS and TSPT heterotic groups. Discussion These findings provide a genomic resource for northern Chinese commercial maize germplasm and support future heterotic group optimization, marker-assisted breeding, and genomic selection.
Potato germplasm developed under tropical conditions may contain diversity for breeding, but the Brazilian materials remain poorly characterized. We evaluated 449 tetraploid potato clones, most from Brazilian breeding programs, with 12,595 SNPs. Dosage-aware analyses and STRUCTURE supported four breeding-related clusters. Genetic differentiation between Brazilian and foreign populations was low (Φ
ST
= 0.04), indicating extensive use of external germplasm in Brazilian breeding. In contrast, differentiation among the genetic clusters was moderate (Φ
ST
= 0.22), suggesting preferable restricted parental use in their pipelines. Heterozygosity and inbreeding estimates depended strongly on genotype encoding. Tajima’s D was positive (4.46), and suggested selection favoring increased heterozygosity. Three genome scans identified 92 shared candidate outlier SNPs within broad LD-based windows. The functional annotations generated hypotheses related to stress responses for further studies to be functionally validated. The results provide insights at a panel-level baseline for germplasm management and candidate prioritization in Brazilian potato breeding.
Givanildo Rodrigues da Silva, Gustavo Nandi, Marcio F. R. Resende et al.· Scientific Reports· 0 citations
The resources of rice germplasm are diverse in genetics and can provide the basis for new varieties. Systematically study the genetic diversity of yield, growth period and plant architecture traits in this paper to determine how distributed the phenotypic coefficient of variation, genetic diversity index and heritability are among various germplasm types and areas. Landraces have a relatively large number of different flag leaves and are generally taller than modern varieties, but they have fewer varieties of growth period and effective panicles. The coefficient of variation of empty grains is 89.75%, and the genetic diversity index for heading date is 2.069; thus, it is highly selected. More than 45% of the excellent haplotypes come from landraces, so traditional varieties need to be preserved and developed. There are three kinds of breeding and utilisation paths, in addition to direct application, parent selection and gene mining; in conjunction with pan-genomics and GWAS, a new model for precise characterisation and intelligent design breeding is being explored. This paper hopes to offer some references for the use and improvement of germplasm resources.
Hong Tan, Wen-Hua Xia, F. Ding et al.· World Journal of Agriculture...· 0 citations
Barley (Hordeum vulgare L.) is a major cereal in Kazakhstan, where diverse breeding material supports crop improvement. We characterized 86 two-row spring barley accessions from six breeding organizations using the Illumina Infinium 50K Barley SNP Array. Analysis of 29,920 high-quality SNPs revealed moderate diversity (He = 0.346, PIC = 0.278, Shannon = 0.752), with 80.84% of molecular variation occurring within and 19.16% among breeding organizations. A minor allele frequency-free (MAF-free) analysis showed that 95.61% of marker–allele combinations at polymorphic loci were shared by at least two organizations. Although PCA, kinship, and neighbor-joining analyses indicated extensive overlap, discriminant analysis of principal components (DAPC) cluster membership was significantly associated with breeding origin (χ2 = 106.38, Monte Carlo p = 1 × 10–5; bias-corrected Cramér’s V = 0.513), demonstrating substantial but incomplete differentiation among breeding programs. Phenotypic differentiation was evaluated using environment-adjusted genotype BLUPs. All seven traits differed significantly among five DAPC clusters. In a reduced six-trait linear discriminant analysis (LDA) excluding vegetation period, LD1 was associated most strongly with number of kernels per spike, followed by heading time, spike length, and heading-to-maturity time. Leave-one-out cross-validation (LOOCV) accuracy was 36.47%, exceeding the permutation mean of 19.83% but indicating considerable phenotypic overlap. The examined materials therefore constitute a diverse, interconnected breeding panel that may support germplasm management and parent selection and provide a genomic and phenotypic framework for future GWAS, genomic selection, and targeted validation of molecular markers within the represented collections.
Y. Genievskaya, V. Chudinov, G. Sereda et al.· International Journal of Mol...· 0 citations
Introduction Single-cross hybrids are the predominant type of cultivar planted by maize growers worldwide. The clear understanding of both the inheritance of target traits and the heterotic patterns of breeding germplasm is essential for the development of heterotic and high-yielding single-cross hybrids in maize breeding programs. Therefore, our objectives were to determine the inheritance of agronomic traits in improved tropical maize germplasm; estimate the general and specific combine abilities (GCA and SCA) effects for these traits among 15 selected inbred lines; group these lines into heterotic groups using two approaches; and identify high-yielding hybrids derived from these lines. Methods We evaluated 105 F1 single-cross hybrids derived from crossing among the 15 selected inbred lines using diallel mating design, along with five checks commercial hybrids, for a wide range of agronomic traits over three summer seasons in southeastern Brazil. A mixed model approach was used to estimate the variance components of GCA and SCA, to predict the GCA and SCA effects, and also to obtain adjusted means of the hybrids. Results and discussion We found that the inheritance of most traits is predominantly governed by additive gene action, whereas grain yield is largely modulated by non-additive gene action in our set of selected inbred lines of tropical maize. The lines VML016, VML062, VML081, VML083 and VML131 are promising for simultaneously improving GY and reducing cycle and plant stature, whereas the VML105 and VML157 should be used to reduce cycle and increase grain yield, respectively, in our maize breeding program. Both the genetic distance among lines and the SCA effects for GY are effective for grouping the improved breeding lines into genetically distinct groups. Also, molecular makers should be employed to support the allocation of inbred lines into heterotic groups and aid in the selection of the best parental combinations for the development of breeding populations and hybrids in improved tropical maize germplasm. Finally, we identified 13 outstanding experimental hybrids that must be evaluated to confirm the consistence and stability of their yield performance across a wider range of environments and management conditions in southeastern Brazil for future release and commercialization.
Gabriel dos Santos Pereira, Victória Manhago Salvador, Yuri Mike Pontes Belo Lança et al.· Frontiers in Plant Science· 0 citations
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.
Yang Lv, Hao Wu, M. Asad et al.· Plants· 0 citations
Genomic mapping has yielded extensive catalogs of quantitative trait loci underlying agronomic traits, yet translating these discoveries into breeding gains remains inefficient. Here, we introduce Flywheel Genomics, a framework that integrates trait discovery directly within rapid cycling breeding populations. Using empirical data from a smallholder-oriented sorghum breeding program, we demonstrate that recurrent intermating and selection maintain genetic diversity, effective population size, and recombination while reducing confounding from plant height and maturity. Within this population, we resolve loci underlying simple adaptive and complex environmentally responsive traits and generate large segregating populations for mapping and near-isogenic lines for locus validation. We further demonstrate applicability in a public wheat breeding program, where known agronomic loci were readily detected. Simulations show that rapid cycling better preserves the population genetic properties required for Flywheel Genomics than conventional pure line development. By integrating discovery with improvement, Flywheel Genomics reframes breeding programs as engines of both crop improvement and genetic insight.
Brian R. Rice, Ebenezer Ogoe, Jean Rigaud Charles et al.· bioRxiv· 0 citations
We use cookies to run the site and, with your consent, for analytics and to show ads.
See our Cookie Policy.
