Phenotypic and molecular dissection of grain quality using the USDA rice mini-core collection

Genetic and molecular dissection of ginseng (Panax ginseng Mey.) germplasm using high-density genic SNP markers, secondary metabolites, and gene expressions

Genetic and molecular knowledge of a species is crucial to its gene discovery and enhanced breeding. Here, we report the genetic and molecular dissection of ginseng, an important herb for healthy food and medicine. A mini-core collection consisting of 344 cultivars and landraces was developed for ginseng that represents the genetic variation of ginseng existing in its origin and diversity center. We sequenced the transcriptomes of all 344 cultivars and landraces; identified over 1.5 million genic SNPs, thereby revealing the genic diversity of ginseng; and analyzed them with 26,600 high-quality genic SNPs or a selection of them. Ginseng had a wide molecular diversity and was clustered into three subpopulations. Analysis of 16 ginsenosides, the major bioactive components for healthy food and medicine, showed that ginseng had a wide variation in the contents of all 16 ginsenosides and an extensive correlation of their contents, suggesting that they are synthesized through a single or multiple correlated pathways. Furthermore, we pair-wisely examined the relationships between the cultivars and landraces, revealing their relationships in gene expression, gene variation, and ginsenoside biosynthesis. These results provide new knowledge and new genetic and genic resources for advanced research and breeding of ginseng and related species.

Metabolic Disturbance Induced by the Embryo Contributes to the Formation of Chalky Endosperm of a Notched-Belly Rice Mutant

Grain chalkiness is a key quality trait of the rice grain, whereas its underlying mechanism is still not thoroughly understood because of the complex genetic and environmental interactions. We identified a notched-belly (NB) mutant that has a notched-line on the belly of grains. The line dissects the endosperm into two distinct parts, the upper translucent part, and the bottom chalky part in the vicinity of the embryo. Using this mutant, our previous studies clued the negative influence of embryo on the biochemical makeup of the endosperm, suggesting the need for the in-depth study of the embryo effect on the metabolome of developing endosperm. This study continued to use the NB mutant to evolve a novel comparison method to clarify the role of embryo in the formation of a chalky endosperm. Grain samples of the wild-type (WT) and NB were harvested at 10, 20, and 30 days after fertilization (DAF), and then divided into subsamples of the embryo, the upper endosperm, and the bottom endosperm. Using non-targeted metabolomics and whole-genome RNA sequencing (RNA-seq), a nearly complete catalog of expressed metabolites and genes was generated. Results showed that the embryo impaired the storage of sucrose, amino acid, starch, and storage proteins in the bottom endosperm of NB by enhancing the expression of sugar, amino acids, and peptide transporters, and declining the expression of starch, prolamin, and glutelin synthesis-related genes. Importantly, the competitive advantage of the developing embryo in extracting the nutrients from the endosperm, transformed the bottom endosperm into an "exhaustive source" by diverting the carbon (C) and nitrogen (N) metabolism from synthetic storage to secondary pathways, resulting in impaired filling of the bottom endosperm and subsequently the formation of chalky tissue. In summary, this study reveals that embryo-induced metabolic shift in the endosperm is associated with the occurrence of grain chalkiness, which is of relevance to the development of high-quality rice by balancing the embryo-endosperm interaction.

Molecular and genetic dissection of the USDA rice mini-core collection using high-density SNP markers

Molecular tools and knowledge of crop germplasm are vital for their effective utilization. In this study, we developed 40,866 high-quality and well distributed SNPs for a rice mini-core collection (RMC) developed by the United States Department of Agriculture (USDA). The high-quality SNPs clustered the USDA-RMC into five subpopulations (Ind, indica; Aus, aus; Afr, African rice; TeJ, temperate japonica; TrJ, tropical japonica) and one admixture (Adm). This classification was further confirmed by phylogenetic and principal component analyses. The rice ARO (aromatic) subpopulation of previous studies was re-assigned with Adm and the WD (wild-type) subpopulation was re-defined to the Afr subpopulation because most of its accessions are African cultivated rice. The Aus and Ind subpopulations had a substantially wider genetic variation than the TrJ and TeJ subpopulations. The genetic diversities were much larger between the Ind or Aus subpopulation and the TrJ or TeJ subpopulation than between the Afr subpopulation and the Ind, Aus, TrJ or TeJ subpopulation. Comparative agronomic trait analysis between the subpopulations also supported the genetic structure and variation of the RMC, and suggested the existence of extensive variation in the genes controlling agronomic traits among them. Furthermore, analysis of ancestral membership of the RMC accessions revealed that reproductive barrier or wide incompatibility existed between the Indica and Japonica groups, while gene flow occurred between them. These results provide high-quality SNPs and knowledge of genetic structure and diversity of the USDA-RMC necessary for enhanced rice research and breeding.

Genetic diversity for starch quality and alkali spreading value in sorghum

Sorghum is an important food crop in many parts of Africa and Asia. Landraces of sorghum are known to exhibit variation in food quality traits including starch and protein content and composition. In this study, a panel of diverse sorghum breeding lines and 788 sorghum conversion (SC) lines representing the global germplasm diversity of the crop were evaluated for variation in starch quality based on alkali spreading value (ASV). A small number of genotypes with stable expression of the ASV+ phenotype across seasons were identified; mostly representing Nandyal types from India. Genetic studies showed the ASV+ phenotype was inherited as a recessive trait. Whole genome resequencing of ASV+ donor lines revealed SNPs in genes involved in starch biosynthesis. A genome wide association study (GWAS) identified a significant SNP associated with ASV near Sobic.010G273800, a starch branching enzyme I precursor, and Sobic.010G274800 and Sobic.010G275001, both annotated as glucosyltransferases. Physiochemical analyses of accessions with contrasting ASV phenotypes demonstrated an environment dependent lower starch gelatinization temperature (GT), amylose content of approximately 22%, and good gel consistency. The starch quality attributes of these lines could be valuable in food products that require good gel consistency and viscosity.

Genetic Diversity Relationship Between Grain Quality and Appearance in Rice

Grain quality is an important breeding objective in rice, and the appearance of the grain also affects its commercial value in the market. The aim of this study was to decode the rice grain qualities and appearances, such as gelatinization temperature (GT), amylose content (AC), grain protein content (GPC), pericarp color (PC), length/width ratio (LWR), and grain volume (GV) at phenotypic and genetic levels, as well as the relationships among them. A genome-wide association study (GWAS) was used to identify the quantitative trait locus (QTLs) associated with the target traits using mixed linear model (MLM) and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) methods. In general, AC was negatively correlated with GPC and GV, while it was positively correlated with LWR and PC. GPC was positively correlated with LWR. Using the rice diversity panel 1 (RDP1) population, we identified 11, 6, 2, 7, 11, and 6 QTLs associated with GT, AC, GPC, PC, LWR, and GV, respectively. Five germplasm lines, superior in grain qualities and appearances for basic breeding materials or improvement, were identified. Notably, an F-box gene OsFbox394 was located in the linkage disequilibrium (LD) block of qLWR7-2, which specifically expresses in endosperm and seed tissues, suggesting that this gene may regulate the seed development in rice grain. Besides, different haplotypes of OsHyPRP45 showed significant differences in AC, indicating that this gene may be related to AC in rice grain.

Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing

An accurate depiction of the genetic relationship, the development of core collection, and genome-wide association analysis (GWAS) are key for the effective exploitation and utilization of genetic resources. Here, genotyping-by-sequencing (GBS) was used to characterize 415 tea accessions mostly collected from the Guizhou region in China. A total of 30,282 high-quality SNPs was used to estimate the genetic relationships, develop core collections, and perform GWAS. We suggest 198 and 148 accessions to represent the core set and mini-core set, which consist of 47% and 37% of the whole collection, respectively, and contain 93–95% of the total SNPs. Furthermore, the frequencies of all alleles and genotypes in the whole set were very well retained in the core set and mini-core set. The 415 accessions were clustered into 14 groups and the core and the mini-core collections contain accessions from each group, species, cultivation status and growth habit. By analyzing the significant SNP markers associated with multiple traits, nine SNPs were found to be significantly associated with four leaf size traits, namely MLL, MLW, MLA and MLSI (P < 1.655E−06). This study characterized the genetic distance and relationship of tea collections, suggested the core collections, and established an efficient GWAS analysis of GBS result.