Annotated Information
Function
DEP1 (Dense and Erect Panicle1) gene is identified to be an approximately 85 kb segment of the Nipponbare BAC AP005419 between newly developed markers S2 and S11-2, which locates the interval between the molecular marker RM3700 and RM7424 on rice chromosome 9, as showed in Figure 1[1,2].This gene encodes an unknown protein containing the PEBP (phosphatidylethanolamine-binding protein) domain which share some homology with the N terminus of GS3. In the case of the rice plant, more tillering equates to more grain-bearing branches. Rice branching determines the number of panicle and grain number per panicle ,and then control the grain yield.We can see the rice tillering at Figure 2. DEP1 is pleiotropically responsible for all three traits: dense panicle, high grain number per panicle and erect panicle.
Mutation
dep1 is the mutant DEP1 allele.The variant involves the replacement of a 637-bp stretch of the middle of exon 5 by 12-bp sequence,which has the effect of creatig a premature stop codon and consequently a loss of 230 residues from C termimus.As showed in Figure 1[2].
DEP1 acts as a dominant negative regulator of panicle architecture ad grain number.The near isogenic lines(NILs) carrying a mutated DEP1 (NIL-dep1) exhibit increased number of grain per panicle,shorter infloresence internodes, increased number of both primary and secondary panicle branches,which may result from the enhanced meristematic activity and cell proliferation through regulating OsCKX2[2](Fig 3. a).But they do not exhibit noticeable change in panical architecture. The experiments are taken as the following several aspects[2]. Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c). Close examination of the shoot apex meristem (SAM) showed that the SAM of NIL-dep1 plants was larger than that of NIL-DEP1 plants (Fig 3. 2d). Cells in the uppermost internode of the mature NIL-dep1 culm were shorter than those in NIL-DEP1 plants (Fig 3. 2e). At the same time, cell number across the longitudinal axis of NIL-dep1 plants was higher than in NIL-DEP1 plants (Fig 3. 2f). Taken together, these observations suggest that the dep1 allele enhances meristematic activity and promotes cell proliferation. So dep1 allele enhances meristematic activity and promotes cell proliferation.The activity of axillary meristem in the shoot apex is important for the determination of the extent of panicle branching and hence grain number[3,4,5]. In NIL-dep1 plants, the Gn1a was clearly downregulated.Gn1a, a major grain number QTL, encodes a cytokinin oxidase/ dehydrogenase, and has been implicated in the regulation of meristematic activity, panicle branching and grain number through its effect on the level of cytokinin. ANIL-Gn1a line had the same number of primary branches as the control line but developed more secondary branches[6,7]. This suggests that dep1 genetically controls the number of both primary branches and secondary branches on primary branches at the panicle top, whereas Gn1a regulates the number of secondary branches on primary branches at the panicle base.
Preparing the field performation of DEP1 and dep1, the grain number per mian panicle is higher in the presence of dep1 (Fig 4.c) and there are clear differences in panicle architecture, influorescence internode and panicle length (Fig.b,e), and the number of both primary (Fig 4.b,f)and secondary (Fig 4.g) branches per panicle.Furthermore,he grain-weight of NIL-dep1 plants was slightly less than that of NIL-DEP1 plants (Fig 4.h),but the overall grain yield per plant under field conditions was increased(+40.9%) (Fig 4.I). The evidence of grain-fillinf failure in the presence of dep1 is unclear. The vascular system of NIL-dep1 plants appeared rather better developed and their sclerenchyma cell walls were thicker at maturity than those in NIL-DEP1 plants. These traits are favorable for both water transport capacity and the mechanical strength of the stem, both of which are important factors for the breeding of high-yielding, lodging-resistant varieties.Through testing the effect of dep1 on grain yield in an indica background by backcrossing the dep1 segment present in the japonica variety Wuyunjing 7 into the indica variety Zhefu 802. This NIL, ZF 802 (dep1), produced more grains per panicle and out-yielded its recurrent parent. Thus, dep1 is a useful allele for increasing grain yield in rice.
Expression
During reproductive development, DEP1 was preferentially expressed on the adaxial side of the bract primordium, as well as in the bract primordia of primary and secondary rachis-branches. Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c).
Evolution
Pedigree records show that many high-yielding Chinese japonica varieties, including Shennong 265, were derived from the Italian land race Balilla13,15, which was extensively cultivated in Italy in the 1970s and introduced into China in 1958[8]. The allelic constitution at the DEP1 locus was explored by resequencing from a panel of widely cultivated Chinese varieties (69 japonica and 83 indica). This truncated mutation was present in Balilla and all 36 japonica types having an erect or semierect panicle, including super high-yielding cultivars Liaojing 5 and Qianchonglang, but it was absent from all the other varieties. Thus, this natural allelic variation in DEP1 has clearly been exploited by japonica breeding programs in China. Several sequence variants at the DEP1 C terminus were present in the sample of indica types. The variety 93-11 differed from the japonica variety Nipponbare by three amino acids, whereas that of the variety Teqing differed by two amino acids. The Nipponbare sequence differed from that of an accession of Oryza rufipogon by one nucleotide at position 663, but this did not produce a variant peptide. We investigated the structure of the homologs of DEP1 in other smallgrain cereals. Several truncated C-terminal deletions were observed in barley, and in bread wheat and its diploid wild progenitor Triticum urartu. To determine whether any novel gain-of-function was induced by the presence of these truncated genes, we generated a number of transgenic wheat plants carrying a pUbi:RNAi-TaDEP1 construct. The consequent downregulation of TaDEP1 resulted in an increase in the length of the ear, a less compact ear and a somewhat reduced number of spikelets. This suggests that a functionally equivalent mutation may have occurred early in the divergence of the wheat and barley lineages.
Reference
