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Source leaf/sink capacity (SS) traits are important determinants of grain yield (GY) of rice. To understand the genetic basis of the SS relationship in rice, five SS and GY traits of rice were genetically dissected using two reciprocal introgression populations. Seventy-three QTL affecting the SS and GY traits were identified, most of which were detected in one of the parental genetic backgrounds (GBs). Two major QTL at bins 4.7 ( SS1 ) and 3.12 ( SS2 ) were associated consistently with all measured SS and yield traits in both GBs across two contrasting environments. Strong interactions between  SS1 / SS2  and the detected QTL led us to the discovery of genetic networks affecting the SS and GY traits. The  SS1  acted as a regulator controlling two groups of downstream QTL affecting the source leaf width and grain number per panicle (GNP).  SS2  functioned as a regulator positively regulating different groups of downstream QTL affecting the source leaf length, GNP, grain weight, and GY. Map-based cloning of  SS1  indicates that  SS1  is  NAL1  involved in polar auxin/IAA transport. Different alleles at  NAL1  were apparently able to qualitatively and/or quantitatively control the IAA transport from the apical meristem to different plant tissues and thus regulate those downstream loci/pathways controlling different SS traits of rice. There was a functional allele and a non-functional mutation in the parents at each of the QTL downstream of  SS1  or  SS2 , which were detectable only in the presence of the functional allele of  SS1  or  SS2 . Our results provided direct evidence that SS and yield traits in rice are controlled by complex signaling pathways and suggest further improvement of rice yield potential with enhanced and balanced SS relationships can be achieved by accurately manipulating allelic combinations at loci in the  SS1  and  SS2  mediated pathways.

SS1 (NAL1)- and SS2-Mediated Genetic Networks Underlying Source-Sink and Yield Traits in Rice (Oryza sativa L.)