D. K. Kaviriri, Ling Yang, Chunli Zhao, Xiaona Pei, Zuoyi Fan, Jingyuan Wang, Liang Xu, M. Tigabu, Xiangling You, Yuhua Li, Huanzhen Liu, Xiyang Zhao
Abstract Korean pine (Pinus koraiensis) is an economically valuable species owing to its excellent timber quality and nuts useful for various purposes. But few studies have been made on growth performance, and aspects combining the genetic gain and classification method on phenotypic similarity in the selection process of superior families. Thus, the present study aimed at analyzing the genetic variation and highlight suitable morphological traits for family selection; establishing trait correlations and families’ ordination based on similarities in phenotypic characters, and selecting elite families and suitable parent trees. Full-sib families from 28 crosses established in randomized complete block design from Naozhi orchard in Northeast China were used, and 11 morphological traits were investigated. Significant differences were observed among families for all traits. The traits coefficients of variation ranged from 6.07 to 56.25 % and from 0.029 to 15.213 % in phenotype and genotypic variation, respectively. A moderate level of inherited genetic control was observed (broad sense heritability H2, varied from 0.155 to 0.438). Traits related to stem growth were highly positively correlated to each other whereas crown traits showed a weak correlation with stem traits (Pearson correlation r, ranged from -0.161 to 0.956). Based on multi-trait comprehensive analysis, we selected six elite families and six parents, which resulted in a genetic gain of 5.6 %, 16.9 %, and 36.4 % in tree height, diameter at breast height, and volume, respectively. These results make a theoretical basis for selecting excellent families and establish orchards of Korean pine from improved seeds.
{"title":"Morphological growth performance and genetic parameters on Korean pine in Northeastern China","authors":"D. K. Kaviriri, Ling Yang, Chunli Zhao, Xiaona Pei, Zuoyi Fan, Jingyuan Wang, Liang Xu, M. Tigabu, Xiangling You, Yuhua Li, Huanzhen Liu, Xiyang Zhao","doi":"10.2478/sg-2023-0004","DOIUrl":"https://doi.org/10.2478/sg-2023-0004","url":null,"abstract":"Abstract Korean pine (Pinus koraiensis) is an economically valuable species owing to its excellent timber quality and nuts useful for various purposes. But few studies have been made on growth performance, and aspects combining the genetic gain and classification method on phenotypic similarity in the selection process of superior families. Thus, the present study aimed at analyzing the genetic variation and highlight suitable morphological traits for family selection; establishing trait correlations and families’ ordination based on similarities in phenotypic characters, and selecting elite families and suitable parent trees. Full-sib families from 28 crosses established in randomized complete block design from Naozhi orchard in Northeast China were used, and 11 morphological traits were investigated. Significant differences were observed among families for all traits. The traits coefficients of variation ranged from 6.07 to 56.25 % and from 0.029 to 15.213 % in phenotype and genotypic variation, respectively. A moderate level of inherited genetic control was observed (broad sense heritability H2, varied from 0.155 to 0.438). Traits related to stem growth were highly positively correlated to each other whereas crown traits showed a weak correlation with stem traits (Pearson correlation r, ranged from -0.161 to 0.956). Based on multi-trait comprehensive analysis, we selected six elite families and six parents, which resulted in a genetic gain of 5.6 %, 16.9 %, and 36.4 % in tree height, diameter at breast height, and volume, respectively. These results make a theoretical basis for selecting excellent families and establish orchards of Korean pine from improved seeds.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89924039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract The breeding of a fast-growing tree species, Acacia mangium Willd. has entered the third-generation cycle in Indonesia. To fulfill timber industry needs, wood traits, as well as growth traits, should be improved by conducting appropriate tree breeding programs for this species. In the present study, growth and wood traits were measured for the 10-year-old third-generation A. mangium from 40 half-sib families originating from four sub-lines from two provenances. The mean values of ten families in each sub-line ranged from 17.7 to 21.8 cm for stem diameter, 14.3 to 16.2 m for tree height, 3.60 to 3.77 km/s for stress-wave velocity, and 19.9 to 20.9 mm for Pilodyn penetration, respectively. The broad-sense heritability values in each sub-line ranged from 0.014 to 0.444 for stem diameter, 0.000 to 0.208 for tree height, 0.261 to 0.715 for stress-wave velocity, and 0.171 to 0.484 for Pilodyn penetration, respectively. These results suggested that families with higher density and Young’s modulus of wood, suitable for solid wood production, can be selected from the third-generation A. mangium . Stem diameter significantly correlated with the other three measured traits, while phenotypic correlation coefficients between stem diameter and stress-wave velocity or Pilodyn penetration were very low. In addition, no significant phenotypic correlations were found between other measured traits. Furthermore, positive- or non-significant genetic correlations were found between growth and wood traits in all sub-lines. Thus, it is concluded that the selection of families with good growth characteristics will not always reduce the wood properties of this species.
{"title":"Variations of growth and wood traits in standing trees of the third-generation <i>Acacia mangium</i> families in Indonesia","authors":"None Masendra, Ikumi Nezu, Futoshi Ishiguri, Fanny Hidayati, Arif Nirsatmanto, Sri Sunarti, None Surip, Dwi Kartikaningtyas, Yuya Takashima, Yusuke Takahashi, Jyunichi Ohshima, Shinso Yokota","doi":"10.2478/sg-2023-0016","DOIUrl":"https://doi.org/10.2478/sg-2023-0016","url":null,"abstract":"Abstract The breeding of a fast-growing tree species, Acacia mangium Willd. has entered the third-generation cycle in Indonesia. To fulfill timber industry needs, wood traits, as well as growth traits, should be improved by conducting appropriate tree breeding programs for this species. In the present study, growth and wood traits were measured for the 10-year-old third-generation A. mangium from 40 half-sib families originating from four sub-lines from two provenances. The mean values of ten families in each sub-line ranged from 17.7 to 21.8 cm for stem diameter, 14.3 to 16.2 m for tree height, 3.60 to 3.77 km/s for stress-wave velocity, and 19.9 to 20.9 mm for Pilodyn penetration, respectively. The broad-sense heritability values in each sub-line ranged from 0.014 to 0.444 for stem diameter, 0.000 to 0.208 for tree height, 0.261 to 0.715 for stress-wave velocity, and 0.171 to 0.484 for Pilodyn penetration, respectively. These results suggested that families with higher density and Young’s modulus of wood, suitable for solid wood production, can be selected from the third-generation A. mangium . Stem diameter significantly correlated with the other three measured traits, while phenotypic correlation coefficients between stem diameter and stress-wave velocity or Pilodyn penetration were very low. In addition, no significant phenotypic correlations were found between other measured traits. Furthermore, positive- or non-significant genetic correlations were found between growth and wood traits in all sub-lines. Thus, it is concluded that the selection of families with good growth characteristics will not always reduce the wood properties of this species.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135009853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ei Sandi Sett, H. Lee, Yang-Gil Kim, Ye-Ji Kim, D. Lee, Sunjeong Kim, Yoon-Ji Hahn, Tae-Lim Yeo, K. Kang
Abstract This study was conducted to examine the variation and growth performance among eight and nine provinces at age 15 years in two trial sites in Myanmar. At the Ngalaik Reserved Forest (Ngalaik RF), the survival rates of provenances ranged from 62.4 % to 80.8 %. The Kanbalu followed by the Oaktwin and Nattalin provenances had the best survival rates at 80.8 %, 79.2 %, and 77.6 % respectively. Likewise, the survival rates ranged from 25.6 % to 74.4 % at the Yenwe Reserved Forest (Yenwe RF). The Nattalin followed by the Bago and Oaktwin provenances had the best survival rates at 74.4 %, 65.6 %, and 63.2 % respectively. The differences in stem form were found to be significant at both sites, whereas 36.24 % of teak in Ngalaik RF and 20.23 % in Yenwe RF were recorded in the class of straight tree. Based on the overall assessment of traits, teak trees in the provenances of Ngalaik RF had much better traits quality than that of Yenwe RF. According to analyses, the Bago provenance was outstanding among the provenances, followed by Phyu, Nattalin, and Paukkhaung provenances at both sites. The best-performing Bago provenance likely grew 10 % betterthan the average volume at Ngalaik RF, 1.4 % more than the average at the Yenwe RF. Among all provenances at both sites, the Thabeikkyin provenance was likely to separate as the poorest one. Based on the results, the selection of mother trees (plus trees) would make a great contribution to the application of future tree improvement programs in Myanmar.
{"title":"Assessing the performance on phenotypic traits of teak (Tectona grandis L.f.) provenances across two trial sites in Myanmar","authors":"Ei Sandi Sett, H. Lee, Yang-Gil Kim, Ye-Ji Kim, D. Lee, Sunjeong Kim, Yoon-Ji Hahn, Tae-Lim Yeo, K. Kang","doi":"10.2478/sg-2023-0009","DOIUrl":"https://doi.org/10.2478/sg-2023-0009","url":null,"abstract":"Abstract This study was conducted to examine the variation and growth performance among eight and nine provinces at age 15 years in two trial sites in Myanmar. At the Ngalaik Reserved Forest (Ngalaik RF), the survival rates of provenances ranged from 62.4 % to 80.8 %. The Kanbalu followed by the Oaktwin and Nattalin provenances had the best survival rates at 80.8 %, 79.2 %, and 77.6 % respectively. Likewise, the survival rates ranged from 25.6 % to 74.4 % at the Yenwe Reserved Forest (Yenwe RF). The Nattalin followed by the Bago and Oaktwin provenances had the best survival rates at 74.4 %, 65.6 %, and 63.2 % respectively. The differences in stem form were found to be significant at both sites, whereas 36.24 % of teak in Ngalaik RF and 20.23 % in Yenwe RF were recorded in the class of straight tree. Based on the overall assessment of traits, teak trees in the provenances of Ngalaik RF had much better traits quality than that of Yenwe RF. According to analyses, the Bago provenance was outstanding among the provenances, followed by Phyu, Nattalin, and Paukkhaung provenances at both sites. The best-performing Bago provenance likely grew 10 % betterthan the average volume at Ngalaik RF, 1.4 % more than the average at the Yenwe RF. Among all provenances at both sites, the Thabeikkyin provenance was likely to separate as the poorest one. Based on the results, the selection of mother trees (plus trees) would make a great contribution to the application of future tree improvement programs in Myanmar.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80451305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. M. Cunill-Flores, I. Salgado Escobar, D Guerra Ramírez, N. Jiménez-Juárez, A. Nettel-Hernanz, G. M. Horta-Valerdi, W. A. Matamoros, Y. Pacheco Hernández
Abstract Mangroves, unique tree and shrub species inhabiting coastal saline environments, exhibit distinctive ecological and morpho-physiological traits, including forming pure intertidal stands and possessing specialized mechanisms for salt excretion and aerial root respiration. These species produce valuable antioxidants, such as phenols and tannins, with significant pharmacological, ecological, and toxicological implications. This study aimed to develop a highly efficient DNA extraction protocol for mangrove leaves rich in salt and tannins. The commonly used CTAB extraction protocol and a commercial DNA extraction kit were modified to enhance DNA purity and yield. The antioxidant capacity of the samples was assessed using various protocols. The results demonstrated that the modified commercial kit outperformed other methods in extracting DNA from mangrove leaves, effectively overcoming challenges associated with high salt and phenolic compounds that could impede next-generation sequencing (NGS) analysis. Furthermore, the findings revealed an inverse relationship between tannin concentration and DNA extraction yield. This study offers a valuable resource for DNA extraction protocols from tannin-rich plant materials. In conclusion, the modified commercial kit represents the most efficient and effective approach for extracting DNA from tannin-rich mangrove leaves.
{"title":"Genomic DNA extraction and phenolic content of salty and tannic plant material of two mangrove tree species from the mexican pacific coast","authors":"J. M. Cunill-Flores, I. Salgado Escobar, D Guerra Ramírez, N. Jiménez-Juárez, A. Nettel-Hernanz, G. M. Horta-Valerdi, W. A. Matamoros, Y. Pacheco Hernández","doi":"10.2478/sg-2023-0015","DOIUrl":"https://doi.org/10.2478/sg-2023-0015","url":null,"abstract":"Abstract Mangroves, unique tree and shrub species inhabiting coastal saline environments, exhibit distinctive ecological and morpho-physiological traits, including forming pure intertidal stands and possessing specialized mechanisms for salt excretion and aerial root respiration. These species produce valuable antioxidants, such as phenols and tannins, with significant pharmacological, ecological, and toxicological implications. This study aimed to develop a highly efficient DNA extraction protocol for mangrove leaves rich in salt and tannins. The commonly used CTAB extraction protocol and a commercial DNA extraction kit were modified to enhance DNA purity and yield. The antioxidant capacity of the samples was assessed using various protocols. The results demonstrated that the modified commercial kit outperformed other methods in extracting DNA from mangrove leaves, effectively overcoming challenges associated with high salt and phenolic compounds that could impede next-generation sequencing (NGS) analysis. Furthermore, the findings revealed an inverse relationship between tannin concentration and DNA extraction yield. This study offers a valuable resource for DNA extraction protocols from tannin-rich plant materials. In conclusion, the modified commercial kit represents the most efficient and effective approach for extracting DNA from tannin-rich mangrove leaves.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135599781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Molecular responses to drought stress have been mainly studied in deciduous tree species although conifers dominate boreal forests. Here, we analysed the transcriptional response of Picea abies (L.) H. Karst. needles after exposure to severe drought by quantitative RNA-sequencing. In total, 2,402 differentially expressed genes (DEGs) were identified, of which 1,186 were up- and 1,216 downregulated. The upregulated DEGs are mainly involved in responses to stress, nitrogen compound, water deprivation, and abscisic acid as well as in channel activity. Although only one bZIP was identified among the DEGs, several other transcription factors involved in ABA-dependent pathways such as MYB, bHLH and WRKY showed differential expression. AP2/EREBP transcription factors related to ABA-independent pathways were also identified as DEGs. A functional interaction network of the 40 most connected Arabidopsis thaliana homologs of all Picea abies DEGs placed the two top-hubs P5CS1 and P5CS2 in the center. P5CS1 is the key enzyme in the biosynthesis of proline known to be accumulated in plants under abiotic stress. Lignin synthesis and DNA-related processes, among others, are overrepresented in this network. Our data highlight interesting gene targets for functional studies and natural genetic variation analyses to support the future identification and selection of potential drought tolerant trees.
{"title":"Drought stress-induced <i>Picea abies</i> transcriptome changes in the context of functional interactions","authors":"Malte Mader, Heike Liesebach, Birgit Kersten","doi":"10.2478/sg-2023-0017","DOIUrl":"https://doi.org/10.2478/sg-2023-0017","url":null,"abstract":"Abstract Molecular responses to drought stress have been mainly studied in deciduous tree species although conifers dominate boreal forests. Here, we analysed the transcriptional response of Picea abies (L.) H. Karst. needles after exposure to severe drought by quantitative RNA-sequencing. In total, 2,402 differentially expressed genes (DEGs) were identified, of which 1,186 were up- and 1,216 downregulated. The upregulated DEGs are mainly involved in responses to stress, nitrogen compound, water deprivation, and abscisic acid as well as in channel activity. Although only one bZIP was identified among the DEGs, several other transcription factors involved in ABA-dependent pathways such as MYB, bHLH and WRKY showed differential expression. AP2/EREBP transcription factors related to ABA-independent pathways were also identified as DEGs. A functional interaction network of the 40 most connected Arabidopsis thaliana homologs of all Picea abies DEGs placed the two top-hubs P5CS1 and P5CS2 in the center. P5CS1 is the key enzyme in the biosynthesis of proline known to be accumulated in plants under abiotic stress. Lignin synthesis and DNA-related processes, among others, are overrepresented in this network. Our data highlight interesting gene targets for functional studies and natural genetic variation analyses to support the future identification and selection of potential drought tolerant trees.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134884941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Poliana Perrut-Lima, A. M. Sebbenn, A. F. Francisconi, Doriane Picanço-Rodrigues, C. Clement
Abstract Euterpe precatoria is a Neotropical palm from South and Central America and is hyperdominant in Amazonia, where it is increasingly important in the Brazilian market for açaí. Genetic diversity, population structure and mating system of E. precatoria were characterized with 10 microsatellite markers in three localities (Codajás, Manacapuru, and Manaquiri) along the lower Solimões River, Amazonas, Brazil. Leaves of 63 mature palms were collected, as well as fruits from 30 of these to analyze 20 seedlings per progeny. Genetic differentiation across localities was substantial (GS′ = 0.304) for mature palms, suggesting that gene flow is restricted between localities due to isolation by distance. Inbreeding was significant in progenies from all populations (ranging from 0.059–0.076), but not for mature palms, suggesting selection for heterozygosity during maturation to the adult stage. The outcrossing rate was high (0.917–1.0), confirming that the species is predominantly allogamous. Matings were not random due to the occurrence of biparental inbreeding (0.021–0.079) and correlated matings (0.059–0.424), so open-pollinated progenies present mixtures of self-sibs, half-sibs, full-sibs, and self-half-sibs, resulting in mean effective population size within progenies (2.23–3.06) lower than expected for a random mating population. The mating system’s characteristics are those expected in a predominantly allogamous hyper-abundant palm and suggest that human management of these often-anthropogenic populations is unlikely to reduce genetic diversity in the short term if done in situ, as practiced by Indigenous Peoples and local communities. Intensification will require careful attention to maintain genetic diversity.
{"title":"Genetic diversity and mating system of Euterpe precatoria in three localities along the lower Solimões River in Central Amazonia","authors":"Poliana Perrut-Lima, A. M. Sebbenn, A. F. Francisconi, Doriane Picanço-Rodrigues, C. Clement","doi":"10.2478/sg-2023-0008","DOIUrl":"https://doi.org/10.2478/sg-2023-0008","url":null,"abstract":"Abstract Euterpe precatoria is a Neotropical palm from South and Central America and is hyperdominant in Amazonia, where it is increasingly important in the Brazilian market for açaí. Genetic diversity, population structure and mating system of E. precatoria were characterized with 10 microsatellite markers in three localities (Codajás, Manacapuru, and Manaquiri) along the lower Solimões River, Amazonas, Brazil. Leaves of 63 mature palms were collected, as well as fruits from 30 of these to analyze 20 seedlings per progeny. Genetic differentiation across localities was substantial (GS′ = 0.304) for mature palms, suggesting that gene flow is restricted between localities due to isolation by distance. Inbreeding was significant in progenies from all populations (ranging from 0.059–0.076), but not for mature palms, suggesting selection for heterozygosity during maturation to the adult stage. The outcrossing rate was high (0.917–1.0), confirming that the species is predominantly allogamous. Matings were not random due to the occurrence of biparental inbreeding (0.021–0.079) and correlated matings (0.059–0.424), so open-pollinated progenies present mixtures of self-sibs, half-sibs, full-sibs, and self-half-sibs, resulting in mean effective population size within progenies (2.23–3.06) lower than expected for a random mating population. The mating system’s characteristics are those expected in a predominantly allogamous hyper-abundant palm and suggest that human management of these often-anthropogenic populations is unlikely to reduce genetic diversity in the short term if done in situ, as practiced by Indigenous Peoples and local communities. Intensification will require careful attention to maintain genetic diversity.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81004211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sufang Zhang, Shanshan Yan, Pingyu Yan, Li Zhang, Hanguo Zhang, Lei Zhang
Abstract Suitable selection of endogenous controls is necessity for obtaining reliable qRT-PCR results. However, insufficient attention has been paid to the selection of endogenous controls for normalization in different stresses in plant, especially Larix olgensis . In this study, we screened candidate internal reference genes for miRNA expression normalization after subjecting Larix olgensis PEG-induced drought, NaHCO 3 , or NaCl stress. Needles samples were collected at 0, 12, 24, 48 and 96 h after treatment. Four common housekeeping genes and 11 mature miRNAs that were found to be stably expressed in small RNA sequencing data of Larix olgensis were selected as candidate internal reference genes. Their expression levels were assessed by qRT-PCR. GeNorm and NormFinder were used to analyse the stability of gene expression from the candidate internal reference genes. Finally, the expression of some miRNAs was analysed after stress. The results showed that miRNAs exhibited better expression stability compared to the analysed ncRNAs. Under PEG, NaHCO 3 , or NaCl stress, miR83321, miR43169, and miR74940 were identified as the most suitable internal reference genes, respectively. Under PEG stress, the expression of most miRNAs reached its highest level at 12 h, showing a trend of first increasing expression and then decreasing. Similarly, under NaHCO 3 and NaCl stress, the expression of most miRNAs reached its maximum levels at 48 h and 12 h, respectively. This indicates that most miRNAs more quickly respond to PEG and NaCl stress than NaHCO 3 stress.
{"title":"Selection of suitable reference genes for miRNA expression normalization by quantitative RTPCR under abiotic stress in <i>Larix olgensis</i>","authors":"Sufang Zhang, Shanshan Yan, Pingyu Yan, Li Zhang, Hanguo Zhang, Lei Zhang","doi":"10.2478/sg-2023-0018","DOIUrl":"https://doi.org/10.2478/sg-2023-0018","url":null,"abstract":"Abstract Suitable selection of endogenous controls is necessity for obtaining reliable qRT-PCR results. However, insufficient attention has been paid to the selection of endogenous controls for normalization in different stresses in plant, especially Larix olgensis . In this study, we screened candidate internal reference genes for miRNA expression normalization after subjecting Larix olgensis PEG-induced drought, NaHCO 3 , or NaCl stress. Needles samples were collected at 0, 12, 24, 48 and 96 h after treatment. Four common housekeeping genes and 11 mature miRNAs that were found to be stably expressed in small RNA sequencing data of Larix olgensis were selected as candidate internal reference genes. Their expression levels were assessed by qRT-PCR. GeNorm and NormFinder were used to analyse the stability of gene expression from the candidate internal reference genes. Finally, the expression of some miRNAs was analysed after stress. The results showed that miRNAs exhibited better expression stability compared to the analysed ncRNAs. Under PEG, NaHCO 3 , or NaCl stress, miR83321, miR43169, and miR74940 were identified as the most suitable internal reference genes, respectively. Under PEG stress, the expression of most miRNAs reached its highest level at 12 h, showing a trend of first increasing expression and then decreasing. Similarly, under NaHCO 3 and NaCl stress, the expression of most miRNAs reached its maximum levels at 48 h and 12 h, respectively. This indicates that most miRNAs more quickly respond to PEG and NaCl stress than NaHCO 3 stress.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135262015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract The complete diallel cross is the only mating design that provides estimates of variance components of general combining (GCA), specific combining ability (SCA), maternal and reciprocal effects, in addition to heritabilities and genetic correlations. To obtain such estimates, complete diallels were made among 10 trees in each of three natural Norway spruce populations from altitude 300 and 500 m in Norway. Nursery trials were performed with the families from these crosses and families from seeds collected from open pollination. Traits measured and analysed are seed weight, germination rate, germination percentage, terminal bud set, and seedling heights the first and second years. The seedlings from the population at origin 500 m had lower seed weight, lower heights and earlier bud set than those from the two populations from lower altitude. A considerable variation was present among families within each diallel, and the GCA variance components had the highest values and were significant for most traits. Variance components for SCA and maternal effects were also significant for some traits, but with inconsistent values in the three diallels. A strong relationship was present between the weight of the seed lots from the maternal parent and mean family height after one and two growing seasons. The highest estimate of heritability was observed for bud set, with similar values in all three diallels.
{"title":"Diallel crosses in Picea abies III. Variation and inheritance patterns in nursery trials","authors":"T. Skrøppa, T. Solvin, Arne Steffenrem","doi":"10.2478/sg-2023-0005","DOIUrl":"https://doi.org/10.2478/sg-2023-0005","url":null,"abstract":"Abstract The complete diallel cross is the only mating design that provides estimates of variance components of general combining (GCA), specific combining ability (SCA), maternal and reciprocal effects, in addition to heritabilities and genetic correlations. To obtain such estimates, complete diallels were made among 10 trees in each of three natural Norway spruce populations from altitude 300 and 500 m in Norway. Nursery trials were performed with the families from these crosses and families from seeds collected from open pollination. Traits measured and analysed are seed weight, germination rate, germination percentage, terminal bud set, and seedling heights the first and second years. The seedlings from the population at origin 500 m had lower seed weight, lower heights and earlier bud set than those from the two populations from lower altitude. A considerable variation was present among families within each diallel, and the GCA variance components had the highest values and were significant for most traits. Variance components for SCA and maternal effects were also significant for some traits, but with inconsistent values in the three diallels. A strong relationship was present between the weight of the seed lots from the maternal parent and mean family height after one and two growing seasons. The highest estimate of heritability was observed for bud set, with similar values in all three diallels.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73766958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marcio José de Araujo, Guilherme Nichele da Rocha, Regiane Abjaud Estopa, Javier Oberschelp, P. H. M. da Silva
Abstract The greatest challenge faced when breeding populations of forest species is to achieve the right equilibrium among genetic gain and no loss of the effective population size. Thus this study aims to define the best thinning strategy to compose a seed orchard of Eucalyptus benthamii to obtain genetic gain maintaining the effective population size. The population of E. benthamii studied consisted of 28 open-pollinated progenies. The diameter at breast height (DBH) and height (H) parameters were determined three years after planting. Measurement data were analyzed and compared using four different mathematical models (with and without competition effect and spatial variation). Strategies considering genetic gain and effective population size were simulated considering the number of families, the number of individuals between families, and the total number of individuals. The mathematical model accounting for the competition effect had the best fit for DBH whereas the model accounting for the environmental variation effect presented the best fit for H. The ranking of BLUPs grouped the families into three clusters (best, intermediate/average, worst/poor families). The strategy that maintains 40 % of the individuals, generates a genetic gain of 13 % in DBH and 8 % in total height while maintaining an effective population size greater than 92 for booth traits.
{"title":"Conservative or non-conservative strategy to advance breeding generation? A case study in Eucalyptus benthamii using spatial variation and competition model","authors":"Marcio José de Araujo, Guilherme Nichele da Rocha, Regiane Abjaud Estopa, Javier Oberschelp, P. H. M. da Silva","doi":"10.2478/sg-2023-0001","DOIUrl":"https://doi.org/10.2478/sg-2023-0001","url":null,"abstract":"Abstract The greatest challenge faced when breeding populations of forest species is to achieve the right equilibrium among genetic gain and no loss of the effective population size. Thus this study aims to define the best thinning strategy to compose a seed orchard of Eucalyptus benthamii to obtain genetic gain maintaining the effective population size. The population of E. benthamii studied consisted of 28 open-pollinated progenies. The diameter at breast height (DBH) and height (H) parameters were determined three years after planting. Measurement data were analyzed and compared using four different mathematical models (with and without competition effect and spatial variation). Strategies considering genetic gain and effective population size were simulated considering the number of families, the number of individuals between families, and the total number of individuals. The mathematical model accounting for the competition effect had the best fit for DBH whereas the model accounting for the environmental variation effect presented the best fit for H. The ranking of BLUPs grouped the families into three clusters (best, intermediate/average, worst/poor families). The strategy that maintains 40 % of the individuals, generates a genetic gain of 13 % in DBH and 8 % in total height while maintaining an effective population size greater than 92 for booth traits.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91236452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract SNPscan breeder is a software that enables the simulation of breeding programs using simulated individual whole genome data, different genetic architectures of a trait of interest, different mating designs and different selection criteria, i.e. pheno-types, breeding values from progeny tests, marker-assisted selection (MAS) and genomic selection (GS). The impact of breeding population size, mating design, selection intensity, genetic architecture, heritability and selection criteria on genetic gains, kinship, inbreeding and genetic diversity can be evaluated to optimize the breeding program. A special feature is the possibility for post-hoc analysis of different strategies to identify causal SNPs and allele effects within the frame of genome-wide association studies (GWAS). The proportion of true and false positive SNPs and the correlation of estimated and true allelic effects can be measured and the overall impact of their use for MAS on the success of the breeding program can be tested.
{"title":"SNPscan breeder – a computer program to test genomic tools in breeding programs","authors":"B. Degen, Niels A. Müller","doi":"10.2478/sg-2023-0013","DOIUrl":"https://doi.org/10.2478/sg-2023-0013","url":null,"abstract":"Abstract SNPscan breeder is a software that enables the simulation of breeding programs using simulated individual whole genome data, different genetic architectures of a trait of interest, different mating designs and different selection criteria, i.e. pheno-types, breeding values from progeny tests, marker-assisted selection (MAS) and genomic selection (GS). The impact of breeding population size, mating design, selection intensity, genetic architecture, heritability and selection criteria on genetic gains, kinship, inbreeding and genetic diversity can be evaluated to optimize the breeding program. A special feature is the possibility for post-hoc analysis of different strategies to identify causal SNPs and allele effects within the frame of genome-wide association studies (GWAS). The proportion of true and false positive SNPs and the correlation of estimated and true allelic effects can be measured and the overall impact of their use for MAS on the success of the breeding program can be tested.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83898227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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