Objective Tolerance to hypoxia germination is one of the key traits for direct-seeding adaptability of rice. The temperate direct-seeding japonica rice variety Francis and multi-panicle indica restorer line R998 were used for QTL mapping of hypoxia germination related traits, aiming to provide new valuable gene resources for developing direct-seeding rice varieties and the promotion of direct-seeding rice production methods.

Method The coleoptile length, shoot length and maximum root length of rice seedlings submerged in 10-cm-depth water in the dark for 7 days at 28℃ were recorded as indicators of hypoxia germination tolerance capacity. A high-density genetic map containing 3 106 bin markers was constructed by low-coverage genome re-sequencing, and QTL scanning was performed with WinQTL Cart 2.5.

Result Under the condition of hypoxia germination, the coleoptile length and root length of Francis are significantly higher than those of R998, but there is no significant difference in shoot length between them. The total genetic distance of the constructed genetic map is 3 646.2 cM, in which the number of markers on chromosome 12 is the least, and that on chromosome 1 is the most, with 174 and 389, respectively. The average marker distance in the genetic map is 1.21 cM, the marker distance of each chromosomes is 0.68 -1.84 cM, and the gaps above 5 cM account for 0.36%. By using composite interval mapping (CIM), six QTLs related to hypoxia germination tolerance are detected on 5 chromosomes. Among them, the number of QTLs controlling coleoptile length, shoot length and root length are 3, 1 and 2, respectively. The coleoptile locus qCL9 and the shoot length locus qSL5 had a phenotypic variance explained (PVE) over 10%, which are 13.39% and 10.78%, respectively. The beneficial allele of qCL9 and the root length locus qRL2-1 come from the parent Francis, while the other four beneficial alleles are provided by the parent R998. Three of the six QTLs have not been reported previously, therefore, they may be novel QTLs.

Conclusion In summary, there is significant difference between Francis and R998 in hypoxia germination, and both parents have beneficial alleles for hypoxia germination tolerance. qCL9 and qSL5 are major effect QTLs controlling hypoxia germination tolerance and have practical value in the molecular breeding of direct-seeding rice.