No abstract

Background Rice ( Oryza sativa L.) is a staple food crop worldwide. Its yield and quality are affected by its tillering pattern and spikelet development. Although many genes involved in the vegetative and reproductive development of rice have been characterized in previous studies, the genetic mechanisms that control axillary tillering, spikelet development, and panicle exsertion remain incompletely understood. Results Here, we characterized a novel rice recombinant inbred line (RIL), panicle exsertion defect and aberrant spikelet ( pds ). It was derived from a cross between two indica varieties, S142 and 430. Intriguingly, no abnormal phenotypes were observed in the parents of pds . This RIL exhibited sheathed panicles at heading stage. Still, a small number of tillers in pds plants were fully exserted from the flag leaves. Elongated sterile lemmas and rudimentary glumes (occurred occasionally) were observed in the spikelets of the exserted panicles and were transformed into palea/lemma-like structures. Furthermore, more interestingly, tillers occasionally grew from the axils of the elongated rudimentary glumes. Via genetic linkage analysis, we found that the abnormal phenotype of pds manifesting as genetic incompatibility or hybrid weakness was caused by genetic interaction between a recessive locus, pds1 , which was derived from S142 and mapped to chromosome 8, and a locus pds2 , which not yet mapped from 430. We fine-mapped pds1 to an approximately 55-kb interval delimited by the markers pds-4 and 8 M3.51 . Six RGAP-annotated ORFs were included in this genomic region. qPCR analysis revealed that Loc_Os080595 might be the target of pds1 locus, and G1 gene might be involved in the genetic mechanism underlying the pds phenotype. Conclusions In this study, histological and genetic analyses revealed that the pyramided pds loci resulted in genetic incompatibility or hybrid weakness in rice might be caused by a genetic interaction between pds loci derived from different rice varieties. Further isolation of pds1 and its interactor pds2 , would provide new insight into the molecular regulation of grass inflorescence development and exsertion, and the evolution history of the extant rice. Electronic supplementary material The online version of this article (10.1186/s12870-019-1805-z) contains supplementary material, which is available to authorized users.

Grain shape and size, which are characterized by grain length, grain width, grain thickness, and length to width ratio, are the key determinants of grain weight. In this study, a 188-individual F 2 population, which derived from a cross between large grain Indica cultivar Nangyangzhan and medium grain Indica cultivar Ce253, were used to analyze grain size related QTLs with 110 molecular markers. Inclusive Composite Interval Mapping (ICIM), was applied to genome-wide detection of QTLs underlying grain size related traits. For grain length, 4 QTLs were detected on chromosome 1, 3, 4, and 9, respectively. qGL-3, a major effect QTL, explained 27.60% phenotypic variation of grain length. Four QTLs for grain width were detected on chromosome 2, 3, and 5. Among them, qGW-5a was major QTL for grain width, which explained 21.30% of phenotypic variation. Five QTLs for length to width ratio, which were distributed on chromosome 2, 3, 5, and 12, were identified. The range of their phenotypic contribution varied from 8.60% to 16.86%. For TGW QTLs, only two were identified on chromosome 5 and 6, respectively, with which 13.26% and 9.04% phenotypic contribution. In our results, qGL-4 and qGL-9 for grain length were novel loci. They have not seen reported in literature previously. Our results shed new light on further fine mapping and understanding the molecular genetic mechanism of novel gra in size QTLs.