Cloning qAG-9-2, a Major QTL for Anaerobic Germination Tolerance in Rice

Tolerance to flooding during germination conditions or anaerobic germination (AG) is an important trait for direct-seeded rice (DSR), especially in the tropical regions. This trait allows rice seeds to germinate and survive under flooding stress due to heavy rains right after sowing. Weed invasion, a major problem for DSR, can also be significantly controlled by rice varieties having AG tolerance. Here we reported further investigation of a major QTL for AG tolerance in rice, qAG-9-2, derived from Khao Hlan On, a landrace from Myanmar.  Near isogenic lines (NILs) carrying the QTL were developed and subsequent fine mapping delineated the region to a 50kb-DNA fragment.  Through over expression and loss-of-function mutant studies, a trehalose-6-phosphate phosphatase gene, OsTPP7, was confirmed as the causal gene underlying qAG-9-2. This gene is involved in trehalose-6-phosphate (T6P) metabolism, central to an energy sensor that determines anabolism or catabolism depending on local sugar availability. Under AG stress, OsTPP7 escalates sugars and amino acid pools, promotes anaerobic metabolism and increases transcripts associated with elongation growth. It is expressed in germinating embryos, coleoptiles and young roots, all sink tissues that depend on reserve carbohydrates for proliferation. OsTPP7 activity may increase sink strength in proliferating heterotrophic tissues by indicating low sugar availability through increase T6P turnover, thus enhancing starch mobilization to drive growth kinetics of the germinating embryo and elongating coleoptile, which consequently enhances AG tolerance. Marker-assisted breeding to introgress this gene into several Sub1 and non-Sub1 lines has been conducted.