A Unified DNA Sequence-based Effects And Non-DNA Sequence-Based Efects Mapping Model Construction For Outcrossing Species

There is increasing evidence that the inheritance of quantitative traits is affected by both DNA sequences and non-DNA sequence variations.A genome-wide association analysis of complex traits found that the genetic factors associated with the explained factors were lower than the expected heritable part.The discrepancy is known as "missing heritability",and its underlying factors and molecular mechanisms are not established.Non-DNA sequenced-based effects may account forasignificant fraction of the "missing heritability".However,there is currently no localization model that can simultaneously detect these genetic effects,preventing researchers from interpreting the genetic structure of complex traits.We developing a unified DNA sequence-based effects and non-DNA sequence-based effects mapping model based on the half-sib family.Through the two-level hierarchical data of the half-sib population,firstly,the linkage analysis and association analysis can be effectively combined.The complementation of two methods can achieve better results in the study of population evolution history and QTL mapping.Secondly,the EM algorithm can be used to estimate the genetic effects of QTLbased on DNA sequences and the genetic effects of non-DNAsequences,and systematically analyze the genetic mechanism of target traits.The main research results and conclusions are as follows:1.For the linkage-linkage disequilibrium analyss model of multiallelic,the meiotic gamete pairing process can be simulated by computer program,and any corresponding number of alleles can be intelligently generated corresponding to the iterative algorithm.The computer simulation experiment was used to evaluate the statistical power of the model,and compared with the traditional model,it was found that the amount of information that the model can use w hen processing the multiallelic data is much larger than the traditional model,and the estimated parameters are accurate or precise.This model was used to analyze 160 SSR marker loci in 146+146×5 samples of Populus euphratica population.The linkage map of 112 markers into 9 linkage groups was obtained,covering the total length of Populus euphratica genome 300.16cM,and the average marker spacing was 2.68.cM.The linkage-linkage disequilibrium map was drawn between the normalized LD and the genetic distance.It was found that the LD coefficient decreased sharply with the grenetic distance,which means that the Populus euphratica population has a long history in its growing region.2.The linkage-linkage disequilibrium analysis model for dominant markers can be applied to epigenetic markers such as methylation sensitive amplification polymorphism,and to develop the evolution history of populations and the genetic mechanism of complex traits from the perspective of epigenetics..Computer simulation results show that due to the lack of data in the dominant marker,the explicit marker analysis model will be slightly less interior to the codominant marker model in parameter estimation,but it can still accurately estimate the parameters.Using this model,233 SRAP markers of 50+50×20=1050 samples from the half-sib population of Torreya grandis were analyzed.The low-density linkage map of Torreya grandis,which divided 160 markers into 8 linkage groups,was mapped.The total length of the linkage map was 533.2 cM.The average distance between markers is 3.33 cM.A standardized linkage-linkage disequilibrium map was drawn between the standardized LD and the genetic distance.It is speculated that the Torreya grandis population has a long history,but some regions of its genome have recently experienced evolutionary forces.3.Combining the genetic effects of non-DNAsequences with traditional QTL mapping methods,can develop the QTL localization model of the half-sib family genetic imprint at the haplotype level,and quantify the contribution rate of traditional genetic effects and genetic imprinting to phenotype.The model is then further extended to analyze the maternal effects,imprinting effects,genetic and non-DNA sequences interatcions at the single marker level.The statistical power of the model was evaluated by computersimulation experiments.It was found that the analysis method can select the appropriate optimal model according to different data;has good applicability to the data containing arbitrary effects:and the false positive rate is low.The model was applied to the half-sib sibling data of Torreya grandis and 15 and 16 significant QTLs related to seedling height and ground diameter growth were detected.Among them,7 QTLs only contain traditional genetic effects,12 QTLs contain genetic effects and imprinting effects,and 11 QTLs contain genetic effects and multiple epigenetic effects.