| Functional research of the genes underlying heterosis and complex traits is the main objective of modern genetics, through new technology and method. With the development of biological technology, especially the development of genome project of human and other model organism, the research on the genetic basis of complex traits is more intensive. However, understanding the genetic basis of complex traits and heterosis is still a great challenge, which should be considered from the overall genetic systems. Each genetic system, including nuclear genome, mitochondrial genome and chloroplast genome, plays an important role in the genetic expression of complex traits and heterosis. Cytoplasm is the environment of gene expression, and mitochondrion provides the energy to support the biochemical reaction. It can be said that the realization of gene function is the result of cooperation between the nuclear gene and maternal cytoplasmic environment. Cytoplasmic effect exists widely in plants and animals. Researches on drosophila, mice and yeast also suggested that epistasis between nuclear and mitochondria affected significantly the phenotype of offspring. Furthermore, it was indicated that epistasis was the main genetic dynamics of speciation and adaption and the primary genetic component of heterosis and complex traits. However, because of the limitation of technology and the lack of flexible statistical method, epistasis, especially the cytonuclear epistasis was neglected too often in complex trait studies. Therefore, developing the proper methodology for dissecting the interaction between nuclear and cytoplasmic background was the core to understand the genetic basis of the cytonuclear epistasis. In this paper, we proposed a special genetic design to dissect cytonuclear epistasis. We called it cytonuclear interacting QTL mapping method, abbreviated to CNQM.Maize is one of the most important food crops in China. It plays a vital role in agricultural economy of China. The utilization of heterosis promotes the maize production greatly. So, understanding the genetic basis of heterosis and complex traits highlights the theoretical value and practical significance in maize. Based on the proposed genetic design, the maize inbreed lines JB and Y53, which are the parental lines of maize hybrid suyu 16 with strong heterosis, were used to create the mixed mapping population with two different cytoplasm backgrounds. The proposed method for mapping cytonuclear epistatic QTL were used to identify the cytonuclear QTL underlying maize agricultural and yield traits. The results are as follows.(1) Statictical model and method for dissecting cytonuclear epistasisThe mixed segregating population with the different cytoplasm backgrounds was created by using the reciprocal mating design. And the corresponding statistical method was proposed for dissecting cytonuclear epistatic interaction. The method can unbiasedly estimate positions and effects of cytonuclear epistatic QTL as well as simultaneously detect the important epistatic interaction between QTL and inherited cytoplasmic genomes. The validation of the statistical procedure was verified through two sets of simulation studies which are implemented via chromosome level and genome level, respectively.Simulation results showed that, higher QTL heritability and larger sample sizes tend to produce more accurate and precise estimates and higher statistical power, whereas lower heritability, especially with smaller sample sizes, produce less accurate estimates with large estimation errors and lower statistical power, which is in accordance with our general expectations. When the QTL heritability was above 15%, the statistical power of QTL can reach almost 100% when only 200 individuals were collected. Genome level simulation results suggested that, no matter which interaction model was adopted, the proposed method would perform very well.(2) The genetic dissection of maize hybrid Suyu 16 with strong heterosisBased on the proposed genetic design, JB and Y53, the parental lines of maize hybrid Suyu 16 with strong heterosis, were used to create reciprocal F2 and F2:3 populations. The genetic linkage map was constructed containing 105 SSR markers, which covered 1214.6cM of maize genome. The average distance of the flanking markers was 11.7cM. The phenotypic value of 12 traits were investigated in reciprocal F2 and F2:3 populations. The proposed method was used to identify the QTL with cytonuclear epistatic effect and to evaluate the contribution of QTL to the phenotypic variation. This will help us to understand the genetic components of maize hybrid Suyu 16, including cytoplasmic effect, nuclear gene effect, cytonuclear epistatic effect. For comparison, two QTL mapping softwares, QTL Network 2.0 and Windows QTL Cartographer 2.5, were used to verify the QTL mapping result without considering the cytoplasmic effect and cytonuclear epistasis.The results showed that 99 QTL controlling 12 traits were detected by CNQM method, and 53 of them were verified by different segregating populations or by different mapping methods. More than 10 QTL were detected in heading date, plant height, tassel branch number, tassel length, ear height and stem diameter, respectively. On average, half of them can be verified. The contribution of these QTL was over 10% of the phenotypic variation. Twenty four QTL were detected on Chromosome 7, in which eight of them had cytonuclear epistatic effects and eleven of them were verified by different mapping methods. However, only one QTL was detected on Chromosome 10. Thirty four of total 99 QTL showed significant cytonuclear epistatic effects. The size of cytonuclear epistasis had different altitudes in different traits. In addition, many QTL were found locating at the same marker interval. This implied the existence of pleiotropic QTL or tightly linked QTL. |
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