Cloning and Functional Analysis of GS5 Controlling Grain Size/Weight and Yield, and Chalk5 Controlling Grain Chalkiness and Head Rice Yield in Rice

Increasing grain yield and improving grain quality of crops have been among the most important goals of plant basic and applied science research. Rice grain size is a highly important yield and quality trait, and a target trait of domestication. Grain chalkiness in rice, a chalky texture of endosperm, is a highly undesirable trait of the grain for human food that deteriorates milling, cooking, eating and appearance quality, and thus represents a major problem in many rice-producing areas of the world. Here we cloned two tightly linked QTL genes, GS5 that has a minor effect on grain size and yield by regulating grain width, filling and weight, and Chalk5 that has a major effect on grain chalkiness which also affects head rice yield and many other quality traits. GS5 functions as a positive regulator of grain size by increasing cell number. Natural variations in GS5 promoter are the cause of the QTL and have contributed greatly to grain size diversity. Chalk5 functions as a positive regulator of grain chalkiness rate. Elevated expression of Chalk5 increases chalkiness by affecting the biogenesis of protein bodies coupled with a great increase in small vesicle-like structures in developing seeds, thus forms air spaces among endosperm storage substances, resulting in chalky grain. Two consensus nucleotide polymorphisms among rice varieties in Chalk5 promoter may partly account for the difference in Chalk5 mRNA levels causing natural variation of grain chalkiness. The tight linkage of Chalk5, and GS5 and qSW5/GW5 for grain size/weight and yield, points to the genetic evidence for the inconsistency between grain quality and yield during modern breeding.