The level of genetic variation within a breeding population affects the effectiveness of selection strategies for genetic improvement.The relationship between genetic variation level within Pinus tabuliformis breeding...The level of genetic variation within a breeding population affects the effectiveness of selection strategies for genetic improvement.The relationship between genetic variation level within Pinus tabuliformis breeding populations and selection strategies or selection effectiveness is not fully investigated.Here,we compared the selection effectiveness of combined and individual direct selection strategies using half-and full-sib families produced from advanced-generation P.tabuliformis seed orchard as our test populations.Our results revealed that,within half-sib families,average diameter at breast height(DBH),tree height,and volume growth of superior individuals selected by the direct selection strategy were higher by 7.72%,18.56%,and 31.01%,respectively,than those selected by the combined selection strategy.Furthermore,significant differences(P<0.01)were observed between the two strategies in terms of the expected genetic gains for average tree height and volume.In contrast,within full-sib families,the differences in tree average DBH,height,and volume between the two selection strategies were relatively minor with increase of 0.17%,2.73%,and 2.21%,respectively,and no significant differences were found in the average expected genetic gains for the studied traits.Half-sib families exhibited greater phenotypic and genetic variation,resulting in improved selection efficiency with the direct selection strategy but also introduced a level of inbreeding risk.Based on genetic distance estimates using molecular markers,our comparative seed orchard design analysis showed that the Improved Adaptive Genetic Programming Algorithm(IAPGA)reduced the average inbreeding coefficient by 14.36% and 14.73% compared to sequential and random designs,respectively.In conclusion,the combination of the direct selection strategy with IAPGA seed orchard design aimed at minimizing inbreeding offered an efficient approach for establishing advanced-generation P.tabuliformis seed orchards.展开更多
As global warming persistently alters and rapidly reshapes landscapes and habitats, conventional species distribution models relying solely on maintaining static conditions within the current climate are likely to fal...As global warming persistently alters and rapidly reshapes landscapes and habitats, conventional species distribution models relying solely on maintaining static conditions within the current climate are likely to falter, particularly at the genus level. Hence, we hypothesize that climate change will differentially affect ecological niches of the same genus species with various latitudinal positioning and local topography, and the high-latitude species may experience greater niche contraction than low-latitude species, and that mountainous regions with high elevational variability may serve as critical climate refugia. Herein, we simulate niche alterations and integrate an ensemble model(EM) strategy, taking into account species dispersal limitations factors(topography, soil, and ultraviolet), to construct a comprehensive habitat suitability(CHS) model for assessing the future vulnerability of the Betula genus, most of which are timber species in China. Our findings reveal that the niche spatial(geographic distribution) of most species(62%) within the Betula genus will undergo a gradual decline under climate change, supporting our hypothesis of latitudinal differentiation in climate vulnerability. Intriguingly, the projected high-latitude niche reduction within the genus cannot be counterbalanced by the anticipated niche expansion of closely related species in low-latitude regions, even considering the evident latitudinal gradient distribution of species. Nonetheless, the niche spatial of six Betula species in southwestern China remains stable or expands under warming scenarios, strongly supporting our secondary hypothesis about topographic buffering effects, which probably means the unique topography(i.e., the largest elevation difference) of this region may serve as a sanctuary for preserving Betula genetic diversity. Our results underscore the uncertain nature of pre-existing niche systems at the genus level under climate change, emphasizing the need for diligent resource management and conservation planning for vulnerable timber species.展开更多
We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate(Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis(WGCNA) to...We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate(Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis(WGCNA) to describe the functionality and complexity of the physiological and morphogenetic processes as well as gene expression and metabolic differences during seed germination stages. In total, 489 metabolites were detected, including 40 differentially accumulated metabolites. The transcriptomic analysis showed the expression of 6 984 genes changed significantly throughout the whole germination process. Using WGCNA, we identified modules related to the various seed germination stages and hub genes. In the initial imbibition stage(stage 1), the pivotal genes involved in RNA transduction and the glycolytic pathway were most active, while in the sprouting stage(stage 4), the pivotal genes were involved in multiple metabolic pathways. In terms of secondary metabolic pathways, we found flavonoid 4-reductase genes of anthocyanin biosynthesis pathway are most significantly affected during pomegranate seed germination, while the flavonol synthase gene was mainly involved in the regulation of isoflavonoid biosynthesis.展开更多
In angiosperms, low red (R)/far-red (FR) ratio light increases gibberellin (GA) levels. GA signaling in conifer seedlings requires FR to promote shoot elongation and reduce the inhibition of shoot elongation induced b...In angiosperms, low red (R)/far-red (FR) ratio light increases gibberellin (GA) levels. GA signaling in conifer seedlings requires FR to promote shoot elongation and reduce the inhibition of shoot elongation induced by paclobutrazol (PAC), yet the effects of far-red light in inducing shoot elongation in the presence or absence of PAC is poorly understood. In this study, transcriptomic and proteomic analyses was used to examine the molecular mechanism of FR regulation of shoot elongation in Chinese pine (Pinus tabuliformis Carr.) seedlings in the presence of PAC. Four treatments were compared: white light + water (WW), FR + water (RW), white light + PAC (WP), and FR + PAC (RP), and 1436 differentially expressed genes (DEGs) and 450 differentially expressed proteins (DEPs) were identified in RW_WW (RW contrast WW), and 1862 DEGs and 481 DEPs in RP_WP (RP contrast WP). Metabolic and signal transduction pathway analyses of DEGs and DEPs in RW_WW and RP_WP, indicated that the former required more energy than the latter. Moreover, gibberellic acid, auxin, and brassinolide are equally important in RW_WW and RP_WP for shoot elongation, except for the ethylene pathway. Amino acid metabolism and cell wall organization were significantly enriched in RW_WW and RP_WP, respectively. In summary, RW_WW and RP_WP had different effects in secondary metabolism, energy metabolism, amino acid metabolism, cell wall organization, and hormone response. These results provide an important theoretical and reference basis for studying the regulatory effect of low R/FR and PAC in conifer shoot elongation.展开更多
基金financially supported by the Biological BreedingNational Science and Technology Major Project(2023ZD0405806)the National Key R&D Program for the 14th Five-Year Plan in China(2022YFD2200304).
文摘The level of genetic variation within a breeding population affects the effectiveness of selection strategies for genetic improvement.The relationship between genetic variation level within Pinus tabuliformis breeding populations and selection strategies or selection effectiveness is not fully investigated.Here,we compared the selection effectiveness of combined and individual direct selection strategies using half-and full-sib families produced from advanced-generation P.tabuliformis seed orchard as our test populations.Our results revealed that,within half-sib families,average diameter at breast height(DBH),tree height,and volume growth of superior individuals selected by the direct selection strategy were higher by 7.72%,18.56%,and 31.01%,respectively,than those selected by the combined selection strategy.Furthermore,significant differences(P<0.01)were observed between the two strategies in terms of the expected genetic gains for average tree height and volume.In contrast,within full-sib families,the differences in tree average DBH,height,and volume between the two selection strategies were relatively minor with increase of 0.17%,2.73%,and 2.21%,respectively,and no significant differences were found in the average expected genetic gains for the studied traits.Half-sib families exhibited greater phenotypic and genetic variation,resulting in improved selection efficiency with the direct selection strategy but also introduced a level of inbreeding risk.Based on genetic distance estimates using molecular markers,our comparative seed orchard design analysis showed that the Improved Adaptive Genetic Programming Algorithm(IAPGA)reduced the average inbreeding coefficient by 14.36% and 14.73% compared to sequential and random designs,respectively.In conclusion,the combination of the direct selection strategy with IAPGA seed orchard design aimed at minimizing inbreeding offered an efficient approach for establishing advanced-generation P.tabuliformis seed orchards.
基金funded by the National Science Foundation for Young Scientists of China(No.32001327)the National Key Research and Development Program of China(No.2021YFD2200304-2).
文摘As global warming persistently alters and rapidly reshapes landscapes and habitats, conventional species distribution models relying solely on maintaining static conditions within the current climate are likely to falter, particularly at the genus level. Hence, we hypothesize that climate change will differentially affect ecological niches of the same genus species with various latitudinal positioning and local topography, and the high-latitude species may experience greater niche contraction than low-latitude species, and that mountainous regions with high elevational variability may serve as critical climate refugia. Herein, we simulate niche alterations and integrate an ensemble model(EM) strategy, taking into account species dispersal limitations factors(topography, soil, and ultraviolet), to construct a comprehensive habitat suitability(CHS) model for assessing the future vulnerability of the Betula genus, most of which are timber species in China. Our findings reveal that the niche spatial(geographic distribution) of most species(62%) within the Betula genus will undergo a gradual decline under climate change, supporting our hypothesis of latitudinal differentiation in climate vulnerability. Intriguingly, the projected high-latitude niche reduction within the genus cannot be counterbalanced by the anticipated niche expansion of closely related species in low-latitude regions, even considering the evident latitudinal gradient distribution of species. Nonetheless, the niche spatial of six Betula species in southwestern China remains stable or expands under warming scenarios, strongly supporting our secondary hypothesis about topographic buffering effects, which probably means the unique topography(i.e., the largest elevation difference) of this region may serve as a sanctuary for preserving Betula genetic diversity. Our results underscore the uncertain nature of pre-existing niche systems at the genus level under climate change, emphasizing the need for diligent resource management and conservation planning for vulnerable timber species.
基金supported by the Doctorate Fellowship Foundation of Nanjing Forestry University, China (163010550)the Priority Academic Program Development of Jiangsu High Education Institutions, China (PAPD)。
文摘We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate(Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis(WGCNA) to describe the functionality and complexity of the physiological and morphogenetic processes as well as gene expression and metabolic differences during seed germination stages. In total, 489 metabolites were detected, including 40 differentially accumulated metabolites. The transcriptomic analysis showed the expression of 6 984 genes changed significantly throughout the whole germination process. Using WGCNA, we identified modules related to the various seed germination stages and hub genes. In the initial imbibition stage(stage 1), the pivotal genes involved in RNA transduction and the glycolytic pathway were most active, while in the sprouting stage(stage 4), the pivotal genes were involved in multiple metabolic pathways. In terms of secondary metabolic pathways, we found flavonoid 4-reductase genes of anthocyanin biosynthesis pathway are most significantly affected during pomegranate seed germination, while the flavonol synthase gene was mainly involved in the regulation of isoflavonoid biosynthesis.
基金This work was supported by the National Natural Science Foundation of China(31770713)Biosafety and Genetic Resources Management Project of State Forestry and Grassland Administration(KJZXSA202030).
文摘In angiosperms, low red (R)/far-red (FR) ratio light increases gibberellin (GA) levels. GA signaling in conifer seedlings requires FR to promote shoot elongation and reduce the inhibition of shoot elongation induced by paclobutrazol (PAC), yet the effects of far-red light in inducing shoot elongation in the presence or absence of PAC is poorly understood. In this study, transcriptomic and proteomic analyses was used to examine the molecular mechanism of FR regulation of shoot elongation in Chinese pine (Pinus tabuliformis Carr.) seedlings in the presence of PAC. Four treatments were compared: white light + water (WW), FR + water (RW), white light + PAC (WP), and FR + PAC (RP), and 1436 differentially expressed genes (DEGs) and 450 differentially expressed proteins (DEPs) were identified in RW_WW (RW contrast WW), and 1862 DEGs and 481 DEPs in RP_WP (RP contrast WP). Metabolic and signal transduction pathway analyses of DEGs and DEPs in RW_WW and RP_WP, indicated that the former required more energy than the latter. Moreover, gibberellic acid, auxin, and brassinolide are equally important in RW_WW and RP_WP for shoot elongation, except for the ethylene pathway. Amino acid metabolism and cell wall organization were significantly enriched in RW_WW and RP_WP, respectively. In summary, RW_WW and RP_WP had different effects in secondary metabolism, energy metabolism, amino acid metabolism, cell wall organization, and hormone response. These results provide an important theoretical and reference basis for studying the regulatory effect of low R/FR and PAC in conifer shoot elongation.
