Comprehensive genetic analysis reveals seed germination activity-related QTL and meta-QTL in rice (Oryza sativa L.)

To get rice varieties with specific germination activity (GA) suitable for production and breeding, the genetic characteristics of GA were revealed by measuring the seed weight (SW), germination rate (GR), coleoptile length (CL) and radicle length (RL) of seeds at 5, 6 and 7 weeks after heading with the recombinant inbred line (RIL) as the material. A total of 10 unconditional QTLs were detected, and the phenotypic variation explained by a single QTL ranged from 3.97 to 14.16%. Among them, 10 unconditional QTLs were detected at three different developmental stages, and the phenotypic variation explained by a single QTL ranged from 3.97 to 14.16%. Among them, qGR-7, qSW7-1, qSW7-2, qCL7-1, and qRL3-1 played an important role in seed activity. In addition, a total of 295 epistatic QTLs were detected, of which 4 were located in the qRL3-1 and qGR-7 intervals. Three RIL lines (RIL18, RIL106, and RIL155) were further screened through genotype and phenotype identification. These three lines contain 3–6 additive QTLs, which can aggregate 6–8 excellent alleles, and have an important theoretical value of resistance to pre-harvest sprouting breeding. In addition, a total of 41 Mqtls was detected by meta-analysis, of which 15 Mqtls had physical intervals less than 1.0 Mb. And qSW2-2, qSW2-3, qSW2-1, qCL2-1, and qRL3-1 were located in the Mqtl2-2, Mqtl2-4, Mqtl3-3, and Mqtl4-2 intervals. A further prediction of candidate genes, expression level determination, and variation analysis showed that Os01g0813100 was a candidate gene affecting seed activity.