Dissecting The Genetic Architecture Of Vegetative Transition During Maize Domestication

All plants undergo a series of developmental transitions during their life cycles,and each of these phases is characterized by unique morphological and physiological attributes.In maize,the vegetative transition from juvenile to adult vegetative development occurs in a coordinated manner and is marked by the production of leaves that differ in a suite of morphological and physiological traits,many of which contribute to fitness and crop productivity.Maize(Zea mays ssp.mays)was domesticated from the wild ancestor teosinte(Zea mays ssp.parviglumis)9000 years ago.Maize has adapted to geographically widespread environments,accompanied by dramatic changes in its morphological structure and flowering time.Several studies have been conducted to identify the genetic factors that control the difference in morphological structure and flowering time between maize and teosinte,and a few key genes have been cloned.In contrast to the significant advances in understanding the reproductive transition,much less is known about the changes in the vegetative transition that have occurred during maize domestication and the underlying molecular mechanism.In our research,we used 50 diverse maize inbreds and 13 teosintes to examine the differences in the vegetative transition between maize and teosinte.We conducted quantitative trait locus(QTL)mapping for the timing of the juvenile-to-adult vegetative phase change using a large maize-teosint BC2S3 recombinant inbred lines(RILs),and identified the candidate gene underlying the large-effect QTL via fine mapping.At last we conducted an association analysis by sequencing candidate gene to identify potential functional variants and revealed the molecuar adaptative mechanism of the vegetative transition.The major conclusions are as follows:1.Cultivated maize has experienced a significant divergence in vegetative transition during its domestication from the wild ancestor teosinte.Maize evolved an early vegetative transition from its wild ancestor,teosinte.The maize exhibited an ealier vegetative transition about 2.5 leaves compared to teosinte.2.We conducted quantitative trait locus(QTL)mapping for the LLEW(Last Leaf with Epicuticular Wax),which represents the timing of the juvenile-to-adult vegetative phase change,using a large maize-teosint BC2S3 recombinant inbred lines(RILs).The results indicated the vegetative transition is controlled by a single large-effect QTL and 11 minor QTLs.The maize allele at 10 loci acted in the same direction for promoting the vegetative transition.This result indicated a strong directional selection for the early vegetative phase change during maize domestication.3.The relative low phenotypic correlation between flowering time and vegetative transition and the low genetic overlapping between them(only 2 overlapping QTL),suggested that the vegetative transition and reproductive transition might be under relatively independent genetic control.4.The single large-effect QTL on chromosome 9(qVT9-1)can explain 13.6%of phenotypic variation in vegetative transition.We conducted fine mapping to identify the candidate gene underlying qVT9-1 using near-isogenic lines(NILs).qVT9-1 was finally delimited to a 263-kb region that included one intact gene,Glossy15(G115),which has been identified as a qualitative mutation and found to play a primary role in the maintenance of the juvenile phase.5.Comparison of the differences in the production of macrohairs across leaf stages in NILs indicated the NIL_Maize entered into the adult vegetative development by one leaf.Despite the significant difference in the vegetative transition,NIL_Maize and NIL_Teosinte exhibited the same number of leaves at maturity and flowered a similar number of days after sowing,indicating that qVT9-1 has no effect on the onset of reproductive development.We next measured Gl15 mRNA expression in the shoot apices of NIL_Maize and NIL_Teosinte during early shoot development.At 8DAS(Days After Sowing),Gl15 was expressed at similarly high levels in NIL_Maize and NIL_Teosinte.While at 13-16DAS,the Gl15 mRNA level in NIL_Teosinte remained significantly higher than in NIL_Maize(P<0.05)when the Gl15 mRNA level were falling down.This differential Gl15 expression pattern might finally lead to the difference in the vegetative phase transition between NIL_Maize and NIL_Teosinte.6.To identify potential functional variants in the Gl15 region,we conducted an association analysis by sequencing Gl15 and its upstream and downstream regions in a panel of 517 diverse maize lines.A total of 32 sequence variants showed significant associations with vegetative transition.One of the most significant variants,SNP2154,which corresponded to a stop codon polymorphism is very likely the causal regulatory variant of Gl15.Molecular population genetic analysis indicated strong domestication selection on the SNP2154.