Three-Dimension Genome Study In Maize And Identification Of Minor-Effect QTLs For Plant Architecture-Related Traits By GBS

Maize is the most important staple crop plant in the world as its largest planting areas and yields.Considering the versatile applications of maize as food,feed,fuel and fiber,it’s thus crucial to acknowledge more information to maize genome and genomics.This work consists of two parts,the first focused on the development and application of ChIA-PET on maize tissues in the 3D context,and the latter based on Genotyping-By-Sequencing to dissect the genotypes underlying the plant architecture-related traits of the ZD958 RILs.As for the 3D interaction with ChIA-PET,I used two histone modifications H3K4me3 and H3K27ac.Combined with multi-omics data,three types of chromatin interactions,Promoter-Promoter(P-P),Promoter-Enhancer(P-E)and Enhancer-Enhancer(E-E)were identified.Most of them are intra-chr,consistent with results in mammals.Both in immature ear and shoot,I identified about 26,500 peaks in H3K4me3 and 56,730 in H3K27ac.And when in H3K4me3-directed interactions,12,224 and 16,054 interactions were determined in immature ear and shoot respectively,while 18,995 and 17,578 in H3K27ac respectively.I improved traditional 4C-seq method and used it to validate the resulting interactions by ChIA-PET,and I found unreported novel regulatory elements despite of reported ones.Chromatin interactions were both common and tissue-specific.Most of P-E interactions were within 50 Kb,and the TAD in maize is about 1 Mb.I explored the interaction patterns for P-E in maize.Comparing my results with reported,especially genes related with agronomic traits,it indicated that I can obtain novel elements as well as those reported,for example,tb1.Collectively,the use of ChIA-PET on maize lay the foundation for us to probe newly regulatory elements and thus accelerating maize breeding.Meanwhile,by the use of GBS method,we genotyped the ZD958 RILs with the combinational adoption of large combination with more than 1,000 individuals and ultrahigh density markers.We deciphered six agronomic traits including silk color,ear height,plant height,EH/PH,tassel branching number and upper leaf number.We identified 51 QTLs related with maize genetic architecture,all of which were minor-effect QTLs.To validate our method,an introgression line was constructed and finally supported the reliability and precise of our method.Our results not only covered the QTLs reported,but also the covered intervals shorter than previously reported.Furthermore,we identified newly QTLs.It indicates that our method by combining a large population and high density markers are promising.