Natural variation in ARF18 gene simultaneously affects seed weight and silique length in polyploid rapeseed

Abstract

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...

Genetic and signalling pathways of dry fruit size: targets for genome editing‐based crop improvement

“…Recently, a major QTL for both silique length and seed weight has been cloned on the A9 chromosome of Brassica napus , which is resulted from a 55‐amino acid deletion in an orthologue of the Arabidopsis auxin response factor 18 (designated as BnaA9.ARF18 ). The BnaA9.ARF18 acts as a negative regulator of fruit and seed size by restricting cell elongation in the silique wall through its inhibitory activity on downstream auxin‐responsive genes (Liu et al , ). Overexpression of two auxin‐repressed protein genes BrARP1 and BrDRM1 in Brassica rapa reduced vegetative and reproductive growth, including the number and length of siliques, possibly from inhibition of either cell elongation or expansion (Lee et al , ).…”

“…Besides, many of these genes have similar functions in regulating fruit size in Arabidopsis and other crops. For example, ARF18 , ARP1 , BoMF2 , DRM1 , CYP78A9 , CLV1 , CLV3 and SMG7 can regulate silique length in Arabidopsis and rapeseed (Kang et al , ; Lee et al , ; Li et al , ; Liu et al , ; Shi et al , ; Xiao et al , ; Yang et al , ). More importantly, many of the fruit size regulatory genes have expression activity and additional effects on other organs, such as roots, stems, leaves, flowers and seeds, indicating a cooperative/synergistic regulation.…”

Normalized Seed Weight of Three Species of the Genus Peganum L. (Peganaceae Van Tieghem) in Mongolia

“…As stated by Liu et al (2015) that fruit wall may aff ect seed weight by regulating the accumulation of photosynthesis. Present results suggest that the accumulation of photosynthesis might aff ect seed weight of big populations, while cotyledon number and shape of embryo contribute to seed weight of small populations.…”

Structural basis for specific gene regulation by Auxin Response Factors

“…Furthermore, mutations impairing dimerization reduced DNA-binding affinity and rendered proteins non-functional in vivo. Interestingly, a natural variant of the Brassica napus ARF18 gene that deletes 55 amino acids from the dimerization domain within the DBD prevents dimerization and causes changes in seed size and seed pod length 173 . Brassica ARF18 is co-orthologous to Arabidopsis ARF11 and ARF18, which belong to the class B (repressor) ARFs.…”

“…Interestingly, a natural variant in the Brassica rapa that affects seed size was shown to be caused by a mutation that affected ARF18 DBD dimerization 173 , which suggests that this property may be generally important for ARF function.…”