Effects of GS3 Gene Haplotypes on Japonica Rice Panicle and Grain Traits under Different Alkaline Conditions

DUAN Kairong; DONG Yue; WANG Jingwen; LIU Chang; LIU Songrui; NIAN Hua; TIAN Lei

doi:10.15933/j.cnki.1004-3268.2025.12.003

Abstract：Thirty japonica rice germplasm resources were used as experimental materials and planted in normal paddy soil(control,CK)and soils with different alkalization degrees[alkalized saline soil(T1,alkalization degree of 39.7%)and alkaline soil(T2,alkalization degree of 57.3%)].The full-length sequence of the GS3 gene was obtained by Sanger sequencing.Combined with panicle and grain phenotypic traits such as 1 000-grain weight,grain length and panicle length,as well as the change rates of panicle and grain traits under different treatments,haplotype analysis was carried out to explore the regulatory effects of different haplotypes of the GS3 gene on panicle and grain traits of japonica rice under alkaline stress condition.Comparative analysis of the full-length GS3 gene in 30 japonica rice germplasm resources was studied,and a total of 27 effective variation sites,including 13 missense mutation sites and 14 Indel sites,were detected.A correlation analysis between these sites and the change rate of 1 000-grain weight revealed that two Indel sites,SDP(significant differences are present in all)and SOA(significant differences are only under higher alkaline stress),which were located at positions 16730526 and 16732228 on chromosome 3,respectively,were significantly correlated with the change rate of 1 000-grain weight,and together formed four main haplotypes,SDP1,SDP2,SOA1 and SOA2.A frameshift mutation in the coding region of SDP2 haplotype led to the premature termination of the protein domain,which weakened the sensitivity of GS3 to changes of alkalinity,mainly reflecting in the non-significant difference in 1 000-grain weight,grain length,panicle length and their change rates between T1 and T2 treatments.The SOA2 haplotype had a 2 bp insertion mutation in the intron region,which reduced the response ability of GS3 to alkaline stress and weakened its functional effect,mainly manifesting in that the 1 000-grain weight under T2 treatment was extremely significantly higher than that of SOA1,and the change rate of 1 000-grain weight under T2 treatment was extremely significantly different from SOA1,but there were no significant difference in grain length,panicle length and their change rates compared with SOA1.In summary,this study is the first to reveal the functional trade-off mechanism of the GS3 gene between alkali tolerance and grain weight trait regulation,and clarify the specific regulatory effects of the SDP2 and SOA2 haplotypes on panicle and grain traits under alkaline environments.