Genetic Architecture Of Ear And Kernel Heterosis Based On Genome-wide Association Study In Maize

Maize（Zea mays L.）is one of the most important cereals in China with early and extensively heterosis application.Analyze the genetic basis of maize yield-related traits,their combining ability,and the mid-parent heterosis can guide the maize genetic improvement and molecular breeding.In this study,using Zheng58,Chang7-2,SCML103,18-599,and SN8-1-1 as testers and the 362 inbred lines as the crossers,we developed about 808 F₁.Using 19 yield-related traits in three environments and 56,110 SNPs,we identified the QTN related to the 19 traits and the GCA（general combining ability）,SCA（special combining ability）,and MPH（mid-parent heterosis）of the 19 traits.By combining the phenotype and genotype from all inbred lines and hybrids,GWAS for phenotype,combining ability and heterosis were performed with candidate genes selected,making it possible to complete GWAS for hybrids.The main results of this study are as follows:1.The 19 traits measured in this study had a high h_B²（heritability in the broadsense）in the FM population,which were all above 85%;the h_N²（heritability in the narrow sense）of the ear length,cob weight,cob diameter,and ear row number,which related to maize cob,were also high,all above 56%.Indicating that cob-related traits are mainly controlled by additive effector genes.The heterosis of maize yield per plant,ear weight,and row number was very obvious.There was almost no heterosis in starch content,protein content,lysine content,and glutamic content.Kernal thickness oil content showed significant negative heterosis.Therefore,different breeding strategies should be adopted for different traits in maize breeding,traits with high h_N²would be more efficient in the slection and breeding of inbred lines,while traits with strong heterosis need selective breeding during the hybridization process to improve selection efficiency.2.The yield per plant（Y）of FM and ABT hybrid populations was significantly positively correlated with genomic heterozygosity.It was more reasonable to divide the associated groups of inbred lines into three subgroups（A,B,and C）,and the genetic structure was clearer.The GCA of Y were higher in A sub-population.The GCA of ED（ear diameter）and RN（row number）were higher in B sub-population.The GCA of EL were higher in T sub-population.The heterosis pattern A×T was recommended to be as the core pattern in the process of the“three sub-population pattern”evolved into the“two sub-population pattern”in southwestern of China.And the B sub-population shall gradually infiltrated into the A sub-population or the T sub-population germplasm,as the role of excellent features.3.In the FM and ABT populations,GWAS analysis was performed on the phenotypic traits,GCA,SCA and MPH of the ear by using the mr MLM analysis method.A total of 10,808 QTN were detected to be significantly associated with them,and 28candidate genes were screened.Zm00001d030034,one of the candidate gene,was annotated as glucose-inhibitory division family A protein.It is speculated that this gene affects the Y by regulating the sugar metabolism to affect the kernel number and the kernel size.A QTN hotspot region associated with the enrichment of ear diameter,cob diameter,and ear row number was detected in the FM and ABT populations.The hotspot region was located in the region 210 Mb～232 Mb on chromosome 3.Five important candidate genes were screened in this region.4.3170 QTN were significantly correlated with kernel size in the FM population.Four candidate genes were screened,the most important of which were the genes Zm00001d029784and Zm00001d007937,which contain the DUF241 domain protein and amino acid transferase protein 8,respectively.Participate in the regulation of amino acid metabolism pathways,regulate maize kernel development,and affect kernel size.5.The 4268 QTNs in the FM population were significantly correlated with grain quality traits,and 7 candidate genes were screened.These genes are closely related to corn sugar metabolism,amino acid metabolism,and fatty acid metabolism.The gene（Zm00001d040901）encodes a plant basic leucine zipper（b ZIP）protein that interacts directly with the promoter of the Opaque2 gene to regulate the transcription of the zein gene,ultimately altering the starch type of the grain and increasing the alcohol solubility protein and lysine content.