Abstract:

Dry direct seeding is an important future direction of rice production with a large area in South Asia and Southeast Asia of Indica rice growing regions. However, Japonica rice planting in tropical and subtropical areas mostly adopts traditional transplanting method. Mesocotyl length (ML) is an important factor affecting the emergence and vigor of rice seedlings in dry direct seeding. Breeding long mesocotyl germplasm based on molecular marker assisted selection (MAS) is the most economical and efficient way to promote the popularization of rice direct seeding. So far, four rice mesocotyl elongation genes have been cloned and reported, namely OsGSK2, GY1, OsPAO5 and OsSMAX1, respectively. In this study, we selected the TROP and TEMP Japonica rice subpopulations originated from the 3K re-sequencing project for analysis, determined the length of mesocotyl and identified superior haplotypes of OsGSK2, GY1, OsPAO5 and OsSMAX1. The results showed that the ML of TROP and TEMP populations presented a typical continuous normal distribution. OsGSK2, GY1, OsPAO5 and OsSMAX1 include 3, 3, 3 and 6 haplotypes, respectively. The frequency of haplotype distribution was different in TROP and TEMP panels for the same gene. OsGSK2-Hap1, GY1-Hap2, OsPAO5-Hap3, OsSMAx1-Hap2 and OsSMAx-Hap3 were identified as superior genes in TROP panel; whereas superior haplotypes OsGSK2-Hap1, OsPAO5-Hap2 and OsSMAX1-Hap2 were identified in TEMP panel. In addition, the seedling height for superior haplotype accessions was higher than that of un-superior haplotype accessions in the TROP and TEMP panels, which was easy to form a growth advantage in growth. The superior haplotypes identified showed significant additive effects in TROP and TEMP panels, which could be used in MAS breeding. This study provides reference for the breeding of direct seeding Japonica rice in different regions, and promotes the rapid popularization of dry direct seeding technology.

Key words: haplotypes, mesocotyl length, rice, superior haplotypes