Epistasis between cytoplasmic and nuclear genes is the primary genetic component of complex quantitative traits.Genetic dissection of cytonuclear epistasis is fundamentally important to understand the genetic architec...Epistasis between cytoplasmic and nuclear genes is the primary genetic component of complex quantitative traits.Genetic dissection of cytonuclear epistasis is fundamentally important to understand the genetic architecture of complex traits.In this study,a two-dimensional genome scan strategy was employed to evaluate the contribution of cytoplasm,quantitative trait loci (QTL),QTL×QTL interactions and QTL×QTL×cytoplasm interactions to the phenotypic variation.The p-value and parameter value for each genetic effect were calculated by multiple regression analysis.A stepwise approach was suggested to build confidence in candidate QTL on the basis of q-value estimation,false discovery rate calculation and Bonferroni adjustment.A fine-scale grid scan strategy was proposed for further analysis of peaks of interest.Plant height in maize was used as an example to illustrate the efficiency of the two-dimensional genome scan strategy.展开更多
A single small population of chasmophytic plants is described as Mojiangia oreophila,a monotypic genus in the subtribe Crepidinae,characterised by a unique combination of morphological features,in particular densely l...A single small population of chasmophytic plants is described as Mojiangia oreophila,a monotypic genus in the subtribe Crepidinae,characterised by a unique combination of morphological features,in particular densely long-papillose homomorphic achenes with five main ribs each accompanied by two secondary ribs,coarse brownish pappus bristles,moderately many-flowered capitula,a small involucre with numerous outer phyllaries,perennial rosette herb growth and brown-woolly caudex and leaf axils.Molecular phylogenetic analysis detected that in the nrlTS phylogeny M.oreophila forms a clade of its own in the Crepidinae;in the plastid DNA phylogeny it is nested in the clade formed by the hybrid-ogenous genus Faberia,the maternal ancestor of which comes from the Crepidinae and the paternal ancestor from the Lactucinae,where Faberia is placed in nrlTS phylogenies.M.oreophila shares several morphological features with Faberia and also shares the expected chromosome number of 2n=16 with its hitherto unknown maternal ancestor.M.oreophila may therefore be a successor of the maternal ancestor of Faberia.Alternatively,cytonuclear discordance is to be assumed in Mojiangia,caused by chloroplast capture as a result of hybridisation and introgression with Faberia.展开更多
The complex interactions of historical,geological and climatic events on plant evolution have been an important research focus for many years.However,the role of desert formation and expansion in shaping the genetic s...The complex interactions of historical,geological and climatic events on plant evolution have been an important research focus for many years.However,the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well explored.In the present study,we investigated the phylogeography of Arnebia szechenyi,a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest China.We measured genetic diversity of populations using three maternally inherited chloroplast DNA(cpDNA)fragments and seven bi-paternally inherited nuclear DNA(nDNA)loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the species.Our data indicated a considerably high level of genetic variation within A.szechenyi and noteworthy asymmetry in historical migration from the east to the west.Moreover,two nuclear genetic groups of populations were revealed,corresponding to the two geographic regions separated by the Tengger Desert.However,analysis of cpDNA data did not show significant geographic structure.The most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that A.szechenyi populations experienced long periods of geographic isolation followed by range expansion,which would have promoted generalized recombination of the nuclear genome.Our findings further highlight the important role that the Tengger Desert,together with the Helan Mountains,has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.展开更多
基金supported by the National Basic Research Program of China(2011CB100106)the National Natural Science Foundation of China(30971846and31171187)+1 种基金the Vital Project of Natural Science of Universities in Jiangsu Province(09KJA210002) to C.Xufrom the National Natural Science Foundation of China(31100882) to Z.Tang
文摘Epistasis between cytoplasmic and nuclear genes is the primary genetic component of complex quantitative traits.Genetic dissection of cytonuclear epistasis is fundamentally important to understand the genetic architecture of complex traits.In this study,a two-dimensional genome scan strategy was employed to evaluate the contribution of cytoplasm,quantitative trait loci (QTL),QTL×QTL interactions and QTL×QTL×cytoplasm interactions to the phenotypic variation.The p-value and parameter value for each genetic effect were calculated by multiple regression analysis.A stepwise approach was suggested to build confidence in candidate QTL on the basis of q-value estimation,false discovery rate calculation and Bonferroni adjustment.A fine-scale grid scan strategy was proposed for further analysis of peaks of interest.Plant height in maize was used as an example to illustrate the efficiency of the two-dimensional genome scan strategy.
文摘A single small population of chasmophytic plants is described as Mojiangia oreophila,a monotypic genus in the subtribe Crepidinae,characterised by a unique combination of morphological features,in particular densely long-papillose homomorphic achenes with five main ribs each accompanied by two secondary ribs,coarse brownish pappus bristles,moderately many-flowered capitula,a small involucre with numerous outer phyllaries,perennial rosette herb growth and brown-woolly caudex and leaf axils.Molecular phylogenetic analysis detected that in the nrlTS phylogeny M.oreophila forms a clade of its own in the Crepidinae;in the plastid DNA phylogeny it is nested in the clade formed by the hybrid-ogenous genus Faberia,the maternal ancestor of which comes from the Crepidinae and the paternal ancestor from the Lactucinae,where Faberia is placed in nrlTS phylogenies.M.oreophila shares several morphological features with Faberia and also shares the expected chromosome number of 2n=16 with its hitherto unknown maternal ancestor.M.oreophila may therefore be a successor of the maternal ancestor of Faberia.Alternatively,cytonuclear discordance is to be assumed in Mojiangia,caused by chloroplast capture as a result of hybridisation and introgression with Faberia.
基金supported by the National Natural Science Foundation of China(41861008)Science Foundation of Yunnan Education Department(2018JS347)the Ten-thousand Talents Program of Yunnan Province(YNWR-QNBJ-2020).
文摘The complex interactions of historical,geological and climatic events on plant evolution have been an important research focus for many years.However,the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well explored.In the present study,we investigated the phylogeography of Arnebia szechenyi,a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest China.We measured genetic diversity of populations using three maternally inherited chloroplast DNA(cpDNA)fragments and seven bi-paternally inherited nuclear DNA(nDNA)loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the species.Our data indicated a considerably high level of genetic variation within A.szechenyi and noteworthy asymmetry in historical migration from the east to the west.Moreover,two nuclear genetic groups of populations were revealed,corresponding to the two geographic regions separated by the Tengger Desert.However,analysis of cpDNA data did not show significant geographic structure.The most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that A.szechenyi populations experienced long periods of geographic isolation followed by range expansion,which would have promoted generalized recombination of the nuclear genome.Our findings further highlight the important role that the Tengger Desert,together with the Helan Mountains,has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.
