Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice

Comprehensive characterization and diversity analysis of the HIS1 gene family in rice subpopulations for herbicide resistance

BACKGROUND

Understanding the genetic diversity and functional roles of key resistance genes is crucial for developing sustainable weed management strategies in rice cultivation. HIS1 (HPPD INHIBITOR SENSITIVE 1) confers broad-spectrum resistance to β-triketone herbicides in rice. However, despite its importance, the family of HIS1-like genes (HSLs) in rice remains largely uncharacterized.

RESULTS

Here, we identified 25 HIS1 gene family members across four rice subpopulations, including 13 in Nipponbare, 4 in Minghui 63, 6 in Zhenshan 97, and 4 in Nagina-22. Phylogenetic analysis grouped these members into seven distinct subfamilies (HIS1, HSL1 ~ HSL6). While HIS1, HSL2, and HSL3 were present across all subpopulations, others exhibited subpopulation-specific presence/absence, underscoring the influence of evolutionary pressures on the HIS1 gene family. Haplotype analysis of family genes within a collection of 475 rice accessions revealed natural genetic variation for only three genes: HIS1, HSL2, and HSL3, with japonica accessions exhibiting high conservation across all genes, while indica accessions displayed diversity, forming 25 haplotypes for HSL3 and four for HSL2. However, these haplotypes did not strongly correlate with Benzobicyclon (BBC) resistance, suggesting that natural variations of these genes are not primary determinants of herbicide response. Expression profiling under BBC treatment revealed ecotype-specific regulation, with notable upregulation of HSL5 in BBC-resistant accessions.

CONCLUSIONS

Our analysis identified tandem duplication as a major driver for the expansion and diversification of HIS1 family members on chromosome 6 in japonica rice. The upregulation of HSL5 in herbicide response points to its potential role in mediating BBC resistance in indica ecotypes. Employing an ecotype-specific reference genome could further enhance insights into herbicide resistance mechanisms. This comprehensive analysis enhances understanding of the evolutionary patterns and functions of HIS1 family genes in rice, offering valuable knowledge for future herbicide resistance breeding programs.

CLINICAL TRIAL NUMBER

Not applicable.

Integrative transcriptogenomic analyses reveal the regulatory network underlying rice eating and cooking quality and identify a role for alpha-globulin in modulating starch and sucrose metabolism

Rice eating and cooking quality (ECQ) is significantly influenced by the physicochemical properties of rice starch. This study integrates whole-genome resequencing, transcriptomic data, and phenotypic analysis to identify the genetic factors that regulate transcript expression levels and contribute to phenotypic variation in rice ECQ traits. A TWAS (transcriptome-wide association study) identified 285 transcripts linked to 6 ECQ traits. Genome-wide mapping of these transcripts revealed 21 747 local eQTLs (expression quantitative trait loci) and 45 158 distal eQTLs. TWAS and eQTL analysis detected several known and novel genes, including starch synthesis-related genes, heat shock proteins, transcription factors, genes related to ATP accumulation, and UDP-glucosyltransferases, showcasing the complex genetic regulation of rice ECQ. WGCNA (weighted gene co-expression network analysis) uncovered key co-expression networks, including a module that links alpha-globulin1 (GLB1) to starch and sucrose metabolism. Genetic diversity analysis of the GLB1 gene across a Korean rice collection identified 26 haplotypes, with indica and aus forming 7 and 3 haplotypes, respectively, which showed significant phenotypic effects on ECQ traits. CRISPR-Cas9-created knockout lines validated these findings, demonstrating that loss of GLB1 function caused significant changes in seed storage proteins, reduced amylose content, altered starch granules, and modified pasting properties without affecting plant phenotypes. By integrating TWAS, eQTL mapping, haplotype analysis, gene expression networks, and CRISPR validation, this study establishes GLB1 as a regulator of ECQ, linking starch biosynthesis and protein accumulation pathways. This transcriptogenomic convergence approach provides novel insights into the genetic regulation of ECQ in rice, demonstrating its effectiveness for characterizing complex traits and enabling precision breeding.

Advances in seed hypoxia research

Seeds represent essential stages of the plant life cycle: embryogenesis, the intermittent quiescence phase, and germination. Each stage has its own physiological requirements, genetic program, and environmental challenges. Consequently, the effects of developmental and environmental hypoxia can vary from detrimental to beneficial. Past and recent evidence shows how low-oxygen signaling and metabolic adaptations to hypoxia affect seed development and germination. Here, we review the recent literature on seed biology in relation to hypoxia research and present our perspective on key challenges and opportunities for future investigations.

OsRAV1 Regulates Seed Vigor and Salt Tolerance During Germination in Rice

Seed vigor is a complex trait encompassing seed germination, seedling emergence, growth, seed longevity, and stress tolerance, all are crucial for direct seeding in rice. Here, we report that the AP2/ERF transcription factor OsRAV1 (RELATED TO ABI3 AND VP1) positively regulates seed germination, vigor, and salt tolerance. Additionally, OsRAV1 was differently expressed in embryo and endosperm, with the OsRAV1 localized in the nucleus. Transcriptomic analysis revealed that OsRAV1 modulates seed vigor through plant hormone signal transduction and phenylpropanoid biosynthesis during germination. Haplotype analysis showed that rice varieties carrying Hap3 displayed enhanced salt tolerance during seed germination. These findings suggest that OsRAV1 is a potential target in breeding rice varieties with high seed vigor suitable for direct seeding cultivation.

Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.