| Maize is the world’s largest food crop,plant type is an important factor in determining maize yield.The increase in maize yield per unit area occurring over the past century has mainly been due to increased planting density,rather than an improvement in yield potential per plant.However,increasing planting density may prevent individual maize plants from obtaining light or other resources,possibly leading to the development of thin stems,limited root expansion,and often a tendency toward lodging during storms,all of which may decrease maize productivity.Hence,maize hybrids have been adapted for high-density planting.Plant height is one of the major factors that affect maize plant architecture,which in turn directly determine yield production.Therefore,excavating key regulatory genes related to plant height can lay an important foundation for genetic regulatory network.However,up to date,far less plant height related gene have been identified and molecular mechanisms for regulation of plant height remain elusive.In this study,genome-wide association study,gene co-expression network analysis and comparative genomics were used to identify plant height related genes.The main research contents and results were as follows:(1)A maize F1 population containing 573 hybrids was initially constructed through incomplete diallel crosses using 87 maize inbred lines with high density SNPs.Both mixed linear model and a newly developed mapping software of QTXNetwork based on GPU parallel computation were used to dissect the genetic architecture of four traits(plant height,leaf angle,leaf length and leaf width).The results showed that a total of 41 significant associated quantitative trait SNPs(QTSs)were identified,which could explain 51.86%～79.92%of the phenotypic variation.Among them,65.71%phenotypic variation was explained by plant height.Among the four traits,genotype of LA(h_GE^2=46.48%)and LL(h_GE^2=46.89%)showed more significantly interacted with environment,while leaf width(15.66%)and plant height(13.75%)were relatively stable.(2)The genetic effects of different genotypes and the superior lines were predicted in common(G)and different environments(GE).Additionally,the maize F1 population provides an opportunity to predict the superior hybrid,which can be used to estimate the highest genetic effects in the improvement of the four traits.For PH and LW,all of the predicted genetic effects were negative for homozygote QQ,but negative for homozygote qq.For LA,the genotypic effects of major-allele homozygote QQ were negative in the common environment and in environment 1,but positive in environments 2 and 3.For LL,the positive genotypic effects of major-allele homozygote QQ were detected only in environment 3.These results indicated that these traits could be further modified by selecting the homozygote genotype.(3)Genes contained or located near QTSs with highly significant genetic effects of the four traits were identified according to the B73 reference genome.A total of 108 associated candidate genes were identified.We also annotated these candidate genes,and found that these genes were closely related to development of plant height and leaf type.And a total of 10 PH candidate genes and 30 reported genes were contained in the final co-expression network.(4)Three hybrid combinations from F1 population were selected,which exhibiting extremely different plant height(low,middle and high),were subjected to high-throughput RNA-Seq with stems at jointing stage,big flare period and tasseling stage,respectively.Weighted Gene Co-expression Network Analysis was used to cluster the transcriptome data.We obtained some modules which showed high correlation to plant height,indicating that genes in specific module may regulate plant height in specific developmental stages.(5)Taking advantage of previously characterized genes,we constructed a co-expression network of plant height and obtained some critical hub genes,which also participated in various hormone pathways.These results repeatedly illustrated that plant hormone played an important role in regulation of plant height.These hub genes were mainly from three types:TFs,cell wall related and plant hormone related.These three types may play an important roles in plant height regulation.(6)Comparative genomics analysis was performed to excavate homologous genes from maize genome,a total of 82 newfound homologous genes were identified,then,all candidates from GWAS results,WGCNA analysis were located in co-expression network,and a genetic regulation network for plant height development were constructed,211 candidates genes were identified,and all candidates were closely related.Candidates from GWAS results,WGCNA analysis and Comparative genomics analysis can provide a solid basis for illustration of the genetic regulatory network of plant height in maize,and simultaneously could facilitate breeding new varieties with both ideal plant architecture and high yield production. |
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