Fine mapping of QTL for grain size in rice 
Peng Qi, Jun-Xiang Shan, Ji-Ping Gao, Hong-Xuan Lin*

National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032.
*Corresponding Author: Tel: (+8621)54924129; Fax: (+8621)54924015; E-mail: hxlin@sibs.ac.cn

Abstract
Fengaizhan-1 (FAZ1) is a small grain indica variety while Waiyin-3 (WY3) is a larger grain japonica variety. They were chosen as parents for mapping the QTL controlling grain size. WY3 was crossed with FAZ1 to produce F1 plants, and then F1 plants were backcrossed with FAZ1 as the recurrent parent to generate BC1F1. Repetitive backcrossing and marker-assisted selection produced some plants where the region around GL was heterozygous but almost all other regions were FAZ1 homozygous. We used segregating populations for the fine mapping and high-resolution mapping of GL. To further determine the location of GL, we developed markers based on the sequence of the PAC clone. Then, a total of 5542 BC3F2 plants were used to further fine-map GL. We narrowed GL to about 20-kb region. From the BC4F2 generations, we developed a nearly isogenic line (NIL) for GL, which contains a 30-kb region from the WY3 chromosomal region including the GL locus in the FAZ1 genetic background. NIL(GL) had a longer grain length (+16.1%) than FAZ1 but there were only slight changes in grain width or thickness, plant height or tiller number. NIL(GL) had a significantly greater 1000-grain weight than FAZ1 (+43.5%) and reduced grain number per main panicle (21.3%). Our results showed that NIL(GL) has an increased milk filling rate, which led to a significant increase in plot grain yield; however, grain quality was not significantly affected. These findings indicated that GL has the potential to increase grain yield.