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.