A minor QTL,SG3, encoding an R2R3-MYB protein, negatively controls grain length in rice

摘要

Key message SG3, an R2R3 MYB protein coding gene that tightly linked to a major QTLGS3, negatively regulates grain length while dependent on the status ofGS3in rice. It is often very difficult to isolate a minor QTL that is closely linked to a major QTL in rice. In this study, we focused on the isolation of a minor grain length QTL,small grain 3(SG3), which is closely linked to the major QTLgrain size 3(GS3). The genetic effect ofSG3on grain length was dependent onGS3status. Its genetic effect was larger in the presence of nonfunctionalsg3than functionalSG3. A large number of near-isogenic F2 plants in whichGS3was fixed with nonfunctional alleles were developed to cloneSG3. A gene encoding an R2R3 MYB domain transcriptional regulator was identified as the candidate gene forSG3.SG3overexpression and knockdown plants showed shortened and elongated grains, respectively, which demonstrated thatSG3acts as a negative regulator of grain length.SG3was preferentially expressed in panicles after flowering, andSG3acted as a transcription activator. Comparative sequencing analysis identified a 12-bp insertion in the third exon of NYZ that led to a frameshift and resulted in a premature stop codon. The insertion/deletion was associated with grain length in the presence of functionalGS3in theindicasubspecies.SG3andGS3were frequently in coupling phase inindicarice, making them good targets for the breeding of cultivars with short or long grains. The isolation of theSG3MYB gene provides new gene resource and contributes to the regulatory network of grain length in rice.