Objective Exploring excellent genes for low temperature germinability in rice and applying these genes to perform molecular breeding will be the key to make a breakthrough in rice breeding for low temperature germinability. After finding the functional gene, molecular markers linked to the target gene or within the target gene are used to carry out molecular marker-assisted selection, which will greatly improve the efficiency and accuracy of target trait selection in the breeding process.

Method qLTG3-1(Os03g0103300)is the first cloned QTL related to low te mperature germinability, which has abundant allelic variations. Designing appropriate molecular markers to type the gene and evaluating the relationship between its genotype and low temperature germinability in indica rice will facilitate the use of this gene in molecular breeding of low temperature germinability in rice regions of South China.

Result Based on the 18 bp variation widely existing in the qLTG3-1, an intragenic molecular marker Gltg3-1 was designed, which could specifically distinguish the 18 bp variation between the qLTG3-1 alleles. 111 indica rice of South China were genotyped by using this marker. The amplification results showed that 51 were of D-band type(with 18 bp deletion), 53 were of R-band type (without 18 bp deletion)and 7 were heterozygous. The rice varieties/lines were divided into 2 groups according to the band patterns, and there was no significant difference in low temperature germinability between the two groups. In indica rice, it is impossible to judge the strength and weakness of low temperature germinability according to the 18 bp variation of qLTG3- 1. Therefore, it is necessary to evaluate the effects of qLTG3-1 alleles from different sources in rice variety improvement. Through the identification of low temperature germinability of single segment substitution line, it was found that qLTG3-1 derived from Nanyangzhan could significantly improve the low temperature germinability of Huajingxian 74.

Conclusion There is no corresponding relationship between the 18 bp variation of qLTG3-1 and low temperature germinability. The qLTG3-1 derived from Nanyangzhan can be used to improve the low temperature germinability of rice. The molecular marker Gltg3-1 can accurately select the target gene in the offspring derived from the cross between two rice parents.