Biology subjects

Dan, Z.

Publications and source records attributed to Dan, Z..

4 recordsLinked to original sources

bioRxiv2026

Additive genes contribute to yield heterosis in rice

The molecular mechanisms underlying heterosis remain unresolved, largely owing to the scarcity of accurately identified heterosis-associated genes. Here, we systematically investigate the inheritance patterns of three yield heterosis-related genes in rice, analyzing their effects in both homozygous and heterozygous genetic backgrounds. We find that heterozygosity at individual loci predominantly produces additive, rather than overdominant, effects. Nevertheless, heterozygous states of these genes generate yield heterosis in heterozygous genetic backgrounds, supporting the overdominance model. Our findings confirm that heterozygous additive genes are key contributors to yield heterosis in rice.

genetics↗

bioRxiv2024

The metabolic pathways underlying dynamic heterosis for plant height are robust biomarkers in rice

The development of robust biomarkers enables accurate prediction of complex phenotypes. However, the dynamic nature of biomarkers is often underestimated since their quantitative changes during development are directly connected to phenotypic transformations, influencing both crop agronomic traits and human diseases. Here, we performed network analysis of untargeted metabolite profiles to investigate height heterosis in rice, which is dynamic that varies during development and is a key determinant of yield heterosis. We found that the levels of pyruvaldehyde were predictive of height heterosis specific at the seedling stage, while 4-hydroxycinnamic acid positively correlated with height heterosis across four developmental stages. We identified metabolic pathways associated with height heterosis and found that metabolomic changes during the elongation stage had a greater impact than those in other stages. Finally, 11 heterosis-associated pathways were developed into metabolomic biomarkers through random forest analysis, successfully predicting height heterosis in an independent population under different growth conditions. This study elucidates the metabolomic landscape of dynamic height heterosis in rice and develops pathway biomarkers for complex phenotypes, demonstrating robustness across diverse populations, environments, and developmental stages.

systems biology↗

bioRxiv2024

Structural variations contribute to genetic diversity and heterosis in rice

Yield heterosis has been extensively exploited in hybrid breeding, with inter-subspecies hybrids often exhibiting the most pronounced effects. However, developing elite hybrids remains a laborious and time-consuming process. The genetic basis of heterosis has been debated for over a century, hindered largely by the lack of high-quality genomes. Here, we assembled genomes for 12 representative indica and japonica rice accessions. Using sequence variants of the Phr1 gene, we functionally validated two deletions responsible for phenol reaction variation between the subspecies. Comparative genomic analyses revealed extensive sequence variation among these inbred lines and highlighted the pivotal role of structural variants (SVs) in rice subspeciation. Importantly, the number of SVs between parental inbred lines significantly correlated with heterosis across 17 agronomic traits, with distinct correlation patterns for intra- and inter-subspecific F1 hybrids. We identified SVs associated with S5-ORF5 and OsBZR1 and validated their function to heterosis for seed setting rate and yield heterosis, respectively, underscoring the importance of SVs in breeding inter-subspecific hybrids. The genomic SVs altered gene expression and these transcriptional changes effectively explained the variances in heterosis. Furthermore, translocations outperformed other SVs and their heterozygous haplotypes exhibited heterosis over homozygous ones. Our findings establish SVs as pivotal drivers in subspeciation and highlight the overdominance model for harnessing rice heterosis.

plant biology↗

bioRxiv2024

Additive and partially dominant effects contribute to crop heterosis

Heterosis, or hybrid vigor, describes the superior performance of F1 hybrids relative to their parents. Despite its significant importance in crop breeding, the molecular mechanisms underlying heterosis remain debated, mainly attributable to discrepancies across genotypes, traits, tissues, populations, developmental stages, growth environments, and species. In this study, we systematically identified heterosis-associated genes and metabolites from parental molecular differences in rice and functionally validated three genes for heterosis of seedling length. We incorporated these heterosis-associated molecules into network modules and explained the variance of heterosis. The predominant inheritance patterns of these molecules were additive and partially dominant effects, namely at mid-parent levels or values between mid-parent and parental levels, respectively. These two genetic effects contributed to heterosis of 17 agronomic traits in rice, including grain yield and plant height across developmental stages. They also explained yield heterosis in diverse hybrid populations and distinct growth environments in both rice and maize, as well as biomass heterosis in Arabidopsis. Notably, additive and partially dominant effects were associated with parental genomic variants in rice, and the number of these variants correlated significantly with heterosis of agronomic traits. Furthermore, we demonstrated the significant impact of parental genomic, transcriptomic, and metabolomic variation in phenylpropanoid biosynthesis on heterosis for seedling length/plant height. Unlike classical heterosis models primarily focused on genomic sequence variation, our findings provide quantitative insights from genomic downstream information into the molecular mechanisms of plant heterosis, highlighting their potential for improving breeding efficiency of hybrid crops.

plant biology↗