Seed weight (SW), which is one of the three major factors influencing grain yield, has been widely accepted as a complex trait that is controlled by polygenes, particularly in polyploid crops. Brassica napus L., which is the second leading crop source for vegetable oil around the world, is a tetraploid (4×) species. In the present study, we identified a major quantitative trait locus (QTL) on chromosome A9 of rapeseed in which the genes for SW and silique length (SL) were colocated. By fine mapping and association analysis, we uncovered a 165-bp deletion in the auxin-response factor 18 (ARF18) gene associated with increased SW and SL. ARF18 encodes an auxinresponse factor and shows inhibitory activity on downstream auxin genes. This 55-aa deletion prevents ARF18 from forming homodimers, in turn resulting in the loss of binding activity. Furthermore, reciprocal crossing has shown that this QTL affects SW by maternal effects. Transcription analysis has shown that ARF18 regulates cell growth in the silique wall by acting via an auxin-response pathway. Together, our results suggest that ARF18 regulates silique wall development and determines SW via maternal regulation. In addition, our study reveals the first (to our knowledge) QTL in rapeseed and may provide insights into gene cloning involving polyploid crops.seed weight | silique length | ARF18 | cell growth | maternal effect T he rapid growth of the world population has increased the global requirement for food, which in turn warrants significant improvement in crop grain yield. As one of the three direct factors influencing crop grain yield, seed weight (SW) has been widely accepted as a complex trait that is controlled by polygenes. Therefore understanding the genetic and molecular basis of SW is extremely important for crop-improvement programs.The size of seeds is influenced by a variety of cellular processes (1). In Arabidopsis, some mutants such as ap2, arf2, da1, eod3, ttg2, and klu control seed size mainly by regulating cell elongation in the integument surrounding the seed (1-5). In mini3, iku1, iku2, and shb1 mutants, premature cellularization or proliferation of the endosperm in the early phase of seed development affects seed mass (6-10). The met1 gene has been determined to have parent-of-origin effects on seed size because of the loss of methylation in cytosine residues in CG islands (11). In rice, a total of 47 quantitative trait loci (QTLs) for grain length and 48 for grain width have been identified (12). Recent studies have shown that certain genes such as GW2, GIF1, qSW5, GS3, GS5, GW8, and qGL3 regulate grain size (13)(14)(15)(16)(17)(18)(19)(20). Among these, GW2 and qSW5 were determined to regulate grain weight by increasing cell number in the outer glume, whereas the others affected grain weight by directly regulating cell division and/or cell expansion of grain. Despite this progress, no genes responsible for SW have been identified in polyploid crops.Polyploidy is produced by the multiplication of a single genome (autopolyploid) or the c...

Cytoplasmic effects (CEs) have been discovered to influence a diverse array of agronomic traits in crops, and understanding the underlying mechanisms can help accelerate breeding programs. Seed oil content (SOC) is of great agricultural, nutritional, and economic importance. However, the genetic basis of CEs on SOC (CE-SOC) remains enigmatic. In this study, we use an optimized approach to sequence the cytoplasmic (plastid and mitochondrial) genomes of allotetraploid oilseed rape (Brassica napus) cultivars, 51218 and 56366, that bear contrasting CE-SOC. By combining comparative genomics and genome-wide transcriptome analysis, we identify mitochondria-encoded orf188 as a potential CE-SOC determinant gene. Functional analyses in the model system Arabidopsis thaliana and rapeseed demonstrated that orf188 governs CE-SOC and could significantly increase SOC, strikingly, through promoting the yield of ATP. Consistent with this finding, transcriptional profiling with microarray and RNA sequencing revealed that orf188 affects transcriptional reprogramming of mitochondrial energy metabolism to facilitate ATP production. Intriguingly, orf188 is a previously uncharacterized chimeric gene, and the presence of this genetic novelty endows rapeseed with positive CE-SOC. Our results shed light on the molecular basis of CEs on a key quantitative trait in polyploid crops and enrich the theory of maternal control of oil content, providing new scientific guidance for breeding high-oil rapeseed germplasms.