Mariana de M. Queiroz, Daniele A.A. Arriel, Sidney F. Caldeira, Antônio R. Higa, Stefânia P. Araújo, Alexandre M. Sebbenn, Dario Grattapaglia
Abstract Forest trees cultivars developed by breeders have been increasingly deployed as clones, following long generations of breeding and testing. An established protocol for distinctiveness, uniformity and stability (DUS) testing becomes an essential element for protecting the intellectual property rights associated with these clones. DUS testing with morphological descriptors has, however, shown limitations in categorically distinguishing cultivars, especially with narrow genetic base. DNA fingerprinting based on microsatellite markers has been a powerful tool to discriminate clones. Teak ( Tectona grandis ) is an economically valuable exotic timber species planted in Brazil. We assessed the individual and combined performance of a selected set of 21 teak microsatellites for identity analysis and parentage testing in a sample of 50 clones planted in Brazil. The clones displayed high genetic diversity attributable to their wide provenance origin. The 21 microsatellites combined provide high power of individual identification with a combined probability of identity of 1.84E-23 for unrelated individuals, and 4.82E-09 for full-sibs, and a power of paternity exclusion higher than 99.99999 % in all testing scenarios. Variable subsets of these 21 markers still provide abundant power of discrimination, although a recommended set should include a minimum of 12 markers with higher information content and reliable genotyping performance. Relatedness and genetic distance analyses revealed unexpected identities or significant recent shared ancestry among otherwise considered unique clones. These results advocate for the importance of including DNA markers, at least as discretionary complementary descriptors to the 22 morphological traits currently adopted for plant variety protection of teak cultivars in Brazil.
{"title":"Microssatellite markers for plant variety protection of clonally propagated forest trees: a case study in teak (<i>Tectona grandis</i> L.f.)","authors":"Mariana de M. Queiroz, Daniele A.A. Arriel, Sidney F. Caldeira, Antônio R. Higa, Stefânia P. Araújo, Alexandre M. Sebbenn, Dario Grattapaglia","doi":"10.2478/sg-2023-0019","DOIUrl":"https://doi.org/10.2478/sg-2023-0019","url":null,"abstract":"Abstract Forest trees cultivars developed by breeders have been increasingly deployed as clones, following long generations of breeding and testing. An established protocol for distinctiveness, uniformity and stability (DUS) testing becomes an essential element for protecting the intellectual property rights associated with these clones. DUS testing with morphological descriptors has, however, shown limitations in categorically distinguishing cultivars, especially with narrow genetic base. DNA fingerprinting based on microsatellite markers has been a powerful tool to discriminate clones. Teak ( Tectona grandis ) is an economically valuable exotic timber species planted in Brazil. We assessed the individual and combined performance of a selected set of 21 teak microsatellites for identity analysis and parentage testing in a sample of 50 clones planted in Brazil. The clones displayed high genetic diversity attributable to their wide provenance origin. The 21 microsatellites combined provide high power of individual identification with a combined probability of identity of 1.84E-23 for unrelated individuals, and 4.82E-09 for full-sibs, and a power of paternity exclusion higher than 99.99999 % in all testing scenarios. Variable subsets of these 21 markers still provide abundant power of discrimination, although a recommended set should include a minimum of 12 markers with higher information content and reliable genotyping performance. Relatedness and genetic distance analyses revealed unexpected identities or significant recent shared ancestry among otherwise considered unique clones. These results advocate for the importance of including DNA markers, at least as discretionary complementary descriptors to the 22 morphological traits currently adopted for plant variety protection of teak cultivars in Brazil.","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":"135318646","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}
Isabela Pires Barros, Leonardo Oliveira Silva da Costa, P. H. M. da Silva, Marcio J. Araujo, E. Novaes
Abstract Eucalyptus urophylla S.T. Blake is a species of great commercial importance, especially in tropical regions, and it is the main eucalypts species cultivated in Brazil. This study evaluated the genetic diversity among and within seven populations of E. urophylla and estimated the genetic distance between individuals to draw inferences about the genetic structure between and within the sampled populations. For that, 19 microsatellite markers were genotyped in 254 individuals originating from four wild populations, introduced in Brazil, two breeding populations, and one population consisting of commercial clones. The wild populations of E. urophylla introduced in Brazil have high genetic similarity and the few generations of breeding have already generated significant differences in population structure between improved and wild populations. As expected, breeding populations are closer to commercial clones than wild populations. However, compared to wild populations, breeding populations exhibit greater genetic diversity as they originated from a mixture of provenances. The population formed by clones was the only one that showed a negative Wright fixation index, that is, heterozygosity was higher than expected for a population in Hardy-Weinberg equilibrium.
{"title":"Genetic structure and diversity in wild and breeding populations of Eucalyptus urophylla","authors":"Isabela Pires Barros, Leonardo Oliveira Silva da Costa, P. H. M. da Silva, Marcio J. Araujo, E. Novaes","doi":"10.2478/sg-2022-0015","DOIUrl":"https://doi.org/10.2478/sg-2022-0015","url":null,"abstract":"Abstract Eucalyptus urophylla S.T. Blake is a species of great commercial importance, especially in tropical regions, and it is the main eucalypts species cultivated in Brazil. This study evaluated the genetic diversity among and within seven populations of E. urophylla and estimated the genetic distance between individuals to draw inferences about the genetic structure between and within the sampled populations. For that, 19 microsatellite markers were genotyped in 254 individuals originating from four wild populations, introduced in Brazil, two breeding populations, and one population consisting of commercial clones. The wild populations of E. urophylla introduced in Brazil have high genetic similarity and the few generations of breeding have already generated significant differences in population structure between improved and wild populations. As expected, breeding populations are closer to commercial clones than wild populations. However, compared to wild populations, breeding populations exhibit greater genetic diversity as they originated from a mixture of provenances. The population formed by clones was the only one that showed a negative Wright fixation index, that is, heterozygosity was higher than expected for a population in Hardy-Weinberg equilibrium.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87171322","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 It is not known when the polyploid coast redwood (Sequoia sempervirens) evolved from its diploid ancestors, and what is its type of polyploidy. Whether close relatives of Sequoia, giant sequoia (Sequoiadendron giganteum) and dawn redwood (Metasequoia glyptostroboides), have possibly contributed to the ancestry of hexaploid of Sequoia remains an open question. The nature of hexaploidy in Sequoia has baffled biologists for more than a century. Based on the chromosome configurations in Sequoia, G. Ledyard Stebbins was the first geneticists who postulated in 1948 that Sequoia is an autoallohexaploid (AAAABB), and an ancient species of Metasequoia might have been one of the putative ancestors of Sequoia. After its chromosome number (2n=6x=66) was confirmed in hexaploid Sequoia, the type of polyploidy in Sequoia has been further investigated for the past 70 years by a number of investigators, using cytogenetic and genetic data. Although an autoallohexaploid (AAAABB) origin of Sequoia has remained one of the dominant hypotheses until recently, an alternative hypothesis, amongst other possible origins, was also put forth by Ahuja and Neale (2002), that Sequoia may be partially diploidized autohexaploid (AAAAAA), derived from some ancestral species of Sequoia, thus carrying a single ancestral genome. Cytogenetic, molecular genetics, and genome sequence data now support the hypothesis that Sequoia originated as an autohexaploid.
{"title":"Origin and genetic nature of polyploidy in paleoendemic coast redwood (Sequoia sempervirens (D. Don) Endl.)","authors":"M. R. Ahuja","doi":"10.2478/sg-2022-0007","DOIUrl":"https://doi.org/10.2478/sg-2022-0007","url":null,"abstract":"Abstract It is not known when the polyploid coast redwood (Sequoia sempervirens) evolved from its diploid ancestors, and what is its type of polyploidy. Whether close relatives of Sequoia, giant sequoia (Sequoiadendron giganteum) and dawn redwood (Metasequoia glyptostroboides), have possibly contributed to the ancestry of hexaploid of Sequoia remains an open question. The nature of hexaploidy in Sequoia has baffled biologists for more than a century. Based on the chromosome configurations in Sequoia, G. Ledyard Stebbins was the first geneticists who postulated in 1948 that Sequoia is an autoallohexaploid (AAAABB), and an ancient species of Metasequoia might have been one of the putative ancestors of Sequoia. After its chromosome number (2n=6x=66) was confirmed in hexaploid Sequoia, the type of polyploidy in Sequoia has been further investigated for the past 70 years by a number of investigators, using cytogenetic and genetic data. Although an autoallohexaploid (AAAABB) origin of Sequoia has remained one of the dominant hypotheses until recently, an alternative hypothesis, amongst other possible origins, was also put forth by Ahuja and Neale (2002), that Sequoia may be partially diploidized autohexaploid (AAAAAA), derived from some ancestral species of Sequoia, thus carrying a single ancestral genome. Cytogenetic, molecular genetics, and genome sequence data now support the hypothesis that Sequoia originated as an autohexaploid.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76842898","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}
Jorge Manuel Revilla-Chávez, M. A. de Moraes, Mack Henry Pinchi-Ramirez, A. Sebbenn
Abstract Guazuma crinita is a fast-growing tree with potential for use in agroforestry systems, due to its rapid wood production, which can contribute significantly to the livelihoods of small-scale farmers in the Peruvian Amazon. However, indiscriminate logging due to high demand is leading to the disappearance of natural forests. As such, the International Council for Research in Agroforestry (ICRAF) began a domestication program to reduce pressure on natural populations of the species. The objective of the present study was to use analyses of genetic parameters, adaptability (PRVG), productivity (MHPRVG), and stability (MHVG), to select G. crinita genotypes from a three-year-old progeny test established in the Aguaytía River Basin, in Ucayali, Peru. The test was established in three different sites, with three blocks, 200 progeny per block, and two individuals per plot. The measured traits were diameter at breast height (DBH), total height (H), and total aerial biomass (B). Significant differences in traits between progenies were detected, but with no genotype x environment interaction (GxE). However, the genotypic correlation among sites was important (> 0.702), suggesting that genetic improvement is possible by selecting the same progeny across sites. The mean heritability among progenies was moderate for all traits (0.34–0.369) and selective precision through combined site analysis was relatively high (0.583–0.608). Based on selection for DBH through combined analysis, MHVG, PRVG, and MHPRVG, 50 superior progenies (25.9 %) were identified for all environments. These should be prioritized in breeding programs as they can offer stable genetic variability for future selection cycles.
{"title":"Productivity, adaptability, and stability in Guazuma crinita progeny tests across three environments in the Aguaytia River Basin, Ucayali, Perú","authors":"Jorge Manuel Revilla-Chávez, M. A. de Moraes, Mack Henry Pinchi-Ramirez, A. Sebbenn","doi":"10.2478/sg-2022-0009","DOIUrl":"https://doi.org/10.2478/sg-2022-0009","url":null,"abstract":"Abstract Guazuma crinita is a fast-growing tree with potential for use in agroforestry systems, due to its rapid wood production, which can contribute significantly to the livelihoods of small-scale farmers in the Peruvian Amazon. However, indiscriminate logging due to high demand is leading to the disappearance of natural forests. As such, the International Council for Research in Agroforestry (ICRAF) began a domestication program to reduce pressure on natural populations of the species. The objective of the present study was to use analyses of genetic parameters, adaptability (PRVG), productivity (MHPRVG), and stability (MHVG), to select G. crinita genotypes from a three-year-old progeny test established in the Aguaytía River Basin, in Ucayali, Peru. The test was established in three different sites, with three blocks, 200 progeny per block, and two individuals per plot. The measured traits were diameter at breast height (DBH), total height (H), and total aerial biomass (B). Significant differences in traits between progenies were detected, but with no genotype x environment interaction (GxE). However, the genotypic correlation among sites was important (> 0.702), suggesting that genetic improvement is possible by selecting the same progeny across sites. The mean heritability among progenies was moderate for all traits (0.34–0.369) and selective precision through combined site analysis was relatively high (0.583–0.608). Based on selection for DBH through combined analysis, MHVG, PRVG, and MHPRVG, 50 superior progenies (25.9 %) were identified for all environments. These should be prioritized in breeding programs as they can offer stable genetic variability for future selection cycles.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73423664","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 A maritime pine (Pinus pinaster Ait.) breeding program was initiated in Türkiye by selecting plus trees from plantations across the country. Quantifying genetic variation in growth traits is essential for this program. Four-year old trees from 140 open-pollinated maritime pine families were assessed for height (HT), root collar diameter (D) and number of shoots in the fourth growing season (S) in three progeny test plantations (Kefken, Gebze and Çatalca) in northwest Türkiye. Growth was greater in Kefken, followed by Gebze and Çatalca. Both individual tree (hi2) and family mean (hf2) heritability estimates were greatest for HT (hi2=0.22 and hf2 =0.77) followed by D (0.16 and 0.59) and S (0.08 and 0.45). While genetic correlation between HT and D was strong (rA=0.72), S was correlated moderately with HT (0.56) and weakly with D (0.11). Genotype × environment interaction was significant only for D. While modest genetic gains (up to 15.20 % over the average of family means) from selections at age four seem possible for growth, changes in patterns of genetic variation and interrelationships among the traits as the trees age remains to be explored in the future.
{"title":"Genetic variation in height, diameter and second flushing in four-year old maritime pine progeny tests in Türkiye","authors":"Cihan Atmaca, F. Temel, Yusuf Taştan, B. Eken","doi":"10.2478/sg-2022-0012","DOIUrl":"https://doi.org/10.2478/sg-2022-0012","url":null,"abstract":"Abstract A maritime pine (Pinus pinaster Ait.) breeding program was initiated in Türkiye by selecting plus trees from plantations across the country. Quantifying genetic variation in growth traits is essential for this program. Four-year old trees from 140 open-pollinated maritime pine families were assessed for height (HT), root collar diameter (D) and number of shoots in the fourth growing season (S) in three progeny test plantations (Kefken, Gebze and Çatalca) in northwest Türkiye. Growth was greater in Kefken, followed by Gebze and Çatalca. Both individual tree (hi2) and family mean (hf2) heritability estimates were greatest for HT (hi2=0.22 and hf2 =0.77) followed by D (0.16 and 0.59) and S (0.08 and 0.45). While genetic correlation between HT and D was strong (rA=0.72), S was correlated moderately with HT (0.56) and weakly with D (0.11). Genotype × environment interaction was significant only for D. While modest genetic gains (up to 15.20 % over the average of family means) from selections at age four seem possible for growth, changes in patterns of genetic variation and interrelationships among the traits as the trees age remains to be explored in the future.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85870214","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}
Milena Stanković Neđić, M. Župunski, S. Orlović, B. Kovačević, M. Kebert, E. Vaštag, D. Miljković, M. Gutalj, Anđelina Gavranović Markić, S. Stojnić
Abstract Wild cherry (Prunus avium L.) is a multi-purpose tree species with great ecological and economic importance for European forestry. Evaluating this species phenotypic diversity and quantitative traits characterization is of great importance to define its genetic resources conservation and breeding strategies. In this work, variations of physiological, biochemical, anatomical and morphological traits of one-year-old wild cherry seedlings were evaluated within and among populations to distinguish and characterize their phenotypic portfolio. We observed significant differences at the intra- and inter-population levels considering both biochemical and physiological leaf traits, whereas differences in morphological and anatomical traits were found to be significant only among half-sib lines within populations (i.e. intra-population level). With a multivariate approach, we explored the inter-population specificity and found out that the tiered approach spanning from organ morphology, across physiological scale, to the biochemical level gave out enough power to discriminate between different populations, and their acquisition and resource-use strategies. Moreover, stepwise discriminative analysis showed that radical scavenger capacity against 2,2’-azino-bis(3-ethylbenzothiazoline- 6-sulfonic acid) (ABTS•+) and water-use efficiency contributed to discrimination of studied populations to the largest extend. Lastly, our study highlights the robustness of certain functional traits, such as ABTS•+, water-use efficiency, net photosynthesis, total flavonoid content, width of stomata guard cell, and stomatal aperture length, which could be considered as a proxy to discriminate between wild cherry populations and assess phenotypic diversity.
{"title":"Assessment of the phenotypic diversity of wild cherry (Prunus avium L.) populations and halfsib lines by multivariate statistical analyses","authors":"Milena Stanković Neđić, M. Župunski, S. Orlović, B. Kovačević, M. Kebert, E. Vaštag, D. Miljković, M. Gutalj, Anđelina Gavranović Markić, S. Stojnić","doi":"10.2478/sg-2022-0014","DOIUrl":"https://doi.org/10.2478/sg-2022-0014","url":null,"abstract":"Abstract Wild cherry (Prunus avium L.) is a multi-purpose tree species with great ecological and economic importance for European forestry. Evaluating this species phenotypic diversity and quantitative traits characterization is of great importance to define its genetic resources conservation and breeding strategies. In this work, variations of physiological, biochemical, anatomical and morphological traits of one-year-old wild cherry seedlings were evaluated within and among populations to distinguish and characterize their phenotypic portfolio. We observed significant differences at the intra- and inter-population levels considering both biochemical and physiological leaf traits, whereas differences in morphological and anatomical traits were found to be significant only among half-sib lines within populations (i.e. intra-population level). With a multivariate approach, we explored the inter-population specificity and found out that the tiered approach spanning from organ morphology, across physiological scale, to the biochemical level gave out enough power to discriminate between different populations, and their acquisition and resource-use strategies. Moreover, stepwise discriminative analysis showed that radical scavenger capacity against 2,2’-azino-bis(3-ethylbenzothiazoline- 6-sulfonic acid) (ABTS•+) and water-use efficiency contributed to discrimination of studied populations to the largest extend. Lastly, our study highlights the robustness of certain functional traits, such as ABTS•+, water-use efficiency, net photosynthesis, total flavonoid content, width of stomata guard cell, and stomatal aperture length, which could be considered as a proxy to discriminate between wild cherry populations and assess phenotypic diversity.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89795740","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}
K. Rajarajan, Muthamilarasan Mehanathan, Sakshi Sahu, Ashajyothi Mushineni, Sureshkannan Sundaram, Alka Bharti, H. Anuragi, A. Handa, Ayyanadar Arunachalam, D. Nayak, S. Dhyani, Hendre Prasad Suresh, J. Rizvi
Abstract Trees hold the lifeline of the earth’s biodiversity and serve as a commercial entity delivering broad applications to human-kind. In addition to being used as wood and timber, trees are a source of secondary metabolites, medicinal compounds, and other derivatives with high commercial value. Thus, the scope for improvement of these traits and quality traits (insect/pest resistance, wood quality, etc.) has always been demanding; however, limited progress has been made compared to other crop species. Trait improvement has always been challenging in trees owing to several practical difficulties, but genomics has enabled the precise identification of genetic determinants of these traits and provided tools and approaches to tweak them for enhancing the traits of interest. Next-generation sequencing (NGS) has expedited genomics and transcriptomics research by facilitating the sequencing of genomes and transcriptomes, identifying genes, profiling the regulation of their expression, and constructing gene regulatory networks. Also, NGS has enabled the development of large-scale genome-wide molecular markers for high-throughput genotyping applications, which are useful in breeding for desirable traits. As it allows improved understanding of the gene function and its network at different developmental stages of trees with reference to an environmental stimulus can further help the breeder to enhance the knowledge on spanning genotype and phenotype. Thus, the potential of genomics in expediting trait improvement has been well realized; however, its application in tree species, particularly in commercially important ones including Tectona grandis, Azadirachta indica, Casuarina spp., and Salix spp, requires further research. Given this, the present review enumerates the progress made in genomics research on these four species and provides the roadmap for their trait improvement toward enhancing productivity and ecosystem services.
{"title":"Genomics studies for trait improvement in four important tree species: Current status and future prospects","authors":"K. Rajarajan, Muthamilarasan Mehanathan, Sakshi Sahu, Ashajyothi Mushineni, Sureshkannan Sundaram, Alka Bharti, H. Anuragi, A. Handa, Ayyanadar Arunachalam, D. Nayak, S. Dhyani, Hendre Prasad Suresh, J. Rizvi","doi":"10.2478/sg-2022-0011","DOIUrl":"https://doi.org/10.2478/sg-2022-0011","url":null,"abstract":"Abstract Trees hold the lifeline of the earth’s biodiversity and serve as a commercial entity delivering broad applications to human-kind. In addition to being used as wood and timber, trees are a source of secondary metabolites, medicinal compounds, and other derivatives with high commercial value. Thus, the scope for improvement of these traits and quality traits (insect/pest resistance, wood quality, etc.) has always been demanding; however, limited progress has been made compared to other crop species. Trait improvement has always been challenging in trees owing to several practical difficulties, but genomics has enabled the precise identification of genetic determinants of these traits and provided tools and approaches to tweak them for enhancing the traits of interest. Next-generation sequencing (NGS) has expedited genomics and transcriptomics research by facilitating the sequencing of genomes and transcriptomes, identifying genes, profiling the regulation of their expression, and constructing gene regulatory networks. Also, NGS has enabled the development of large-scale genome-wide molecular markers for high-throughput genotyping applications, which are useful in breeding for desirable traits. As it allows improved understanding of the gene function and its network at different developmental stages of trees with reference to an environmental stimulus can further help the breeder to enhance the knowledge on spanning genotype and phenotype. Thus, the potential of genomics in expediting trait improvement has been well realized; however, its application in tree species, particularly in commercially important ones including Tectona grandis, Azadirachta indica, Casuarina spp., and Salix spp, requires further research. Given this, the present review enumerates the progress made in genomics research on these four species and provides the roadmap for their trait improvement toward enhancing productivity and ecosystem services.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90205331","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}
Yaping Ma, M. J. Devi, Lihua Song, Handong Gao, B. Cao
Abstract Ailanthus altissima is a deciduous tree native to China and introduced to other parts of the world as an ornamental plant. It exhibits resistance to both abiotic and biotic stress factors and has various pharmacological effects and strong allelopathy, generating significant research interests. However, the genome sequence of this species has not been reported, limiting its research development. The purpose of the study was to determine the genome size and characteristics of A. altissima to conduct its genomic survey. Next-generation sequencing and K-mer analysis were employed to measure the genome size of A. altissima. Overall, a total of 61.93 Gb high-quality clean data were acquired, representing approximately 64.09× coverage of the A. altissima genome. The genomic characteristics of A. altissima include a genome size of 966.38 Mbp, a heterozygosis rate of 0.78 %, and a repeat rate of 41.22 %. A total of 735,179 genomic SSRs markers were identified based on genome survey sequences. Alignment analysis showed that A. altissima was closely related to Citrus sinensis and Leitneria florida-na. This study provides basic information for future whole-genomic sequencing of A. altissima. This will facilitate a knowledge of the population structure, genetic diversity, long distance-gene transfer, and pollen-based gene flow analyses of A. altissima populations from its known distribution ranges in China, focusing on planted and natural forest stands.
{"title":"Genome survey sequencing of Ailanthus altissima and identification of simple sequence repeat (SSR) markers","authors":"Yaping Ma, M. J. Devi, Lihua Song, Handong Gao, B. Cao","doi":"10.2478/sg-2022-0006","DOIUrl":"https://doi.org/10.2478/sg-2022-0006","url":null,"abstract":"Abstract Ailanthus altissima is a deciduous tree native to China and introduced to other parts of the world as an ornamental plant. It exhibits resistance to both abiotic and biotic stress factors and has various pharmacological effects and strong allelopathy, generating significant research interests. However, the genome sequence of this species has not been reported, limiting its research development. The purpose of the study was to determine the genome size and characteristics of A. altissima to conduct its genomic survey. Next-generation sequencing and K-mer analysis were employed to measure the genome size of A. altissima. Overall, a total of 61.93 Gb high-quality clean data were acquired, representing approximately 64.09× coverage of the A. altissima genome. The genomic characteristics of A. altissima include a genome size of 966.38 Mbp, a heterozygosis rate of 0.78 %, and a repeat rate of 41.22 %. A total of 735,179 genomic SSRs markers were identified based on genome survey sequences. Alignment analysis showed that A. altissima was closely related to Citrus sinensis and Leitneria florida-na. This study provides basic information for future whole-genomic sequencing of A. altissima. This will facilitate a knowledge of the population structure, genetic diversity, long distance-gene transfer, and pollen-based gene flow analyses of A. altissima populations from its known distribution ranges in China, focusing on planted and natural forest stands.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82180739","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 Early selection is an imperative in ongoing forest tree breeding. This study estimated the optimal timing of early selection in Abies sachalinensis (F. Schmidt) Mast. based on time trends of genetic parameters obtained from two test sites. Tree height (Ht) at 5, 10 (11), 15, 20, 30, and 40 years of age and diameter at breast height (DBH) at 20, 30, and 40 years of age were analyzed. The efficiency of early selection per year (E) for performing early indirect selection relative to performing direct selection at the earliest rotation age (40 years of age) was estimated based on narrow-sense heritability (h2) and age–age genetic correlation (r). The h2 of Ht peaked at 10 or 15 years of age (0.52–0.71), and that of DBH was the highest at 20 years of age (0.19 or 0.22). The age–age genetic correlation between tree heights or between tree height and DBH at different ages decreased with increasing differences between ages (regression coefficients were −0.011 and −0.007, respectively). The E values were highest at 10 or 15 years of age (0.84-1.74 and 1.42-2.24 for Ht and Ht-DBH, respectively), indicating the optimum selection timing. In Japapnese forestry, the initial growth rate is considered important for reducing weeding costs. Selection at 10 or 15 years of age had more than in >65 % indirect genetic gain relative to the direct genetic gain at 5 years of age; thus, selection at 10-15 years of age is appropriate considering the initial and mature phases of tree growth.
{"title":"Estimation of optimal timing of early selection based on time trends of genetic parameters in Abies sachalinensis","authors":"S. Hanaoka, Kazutaka Kato","doi":"10.2478/sg-2022-0004","DOIUrl":"https://doi.org/10.2478/sg-2022-0004","url":null,"abstract":"Abstract Early selection is an imperative in ongoing forest tree breeding. This study estimated the optimal timing of early selection in Abies sachalinensis (F. Schmidt) Mast. based on time trends of genetic parameters obtained from two test sites. Tree height (Ht) at 5, 10 (11), 15, 20, 30, and 40 years of age and diameter at breast height (DBH) at 20, 30, and 40 years of age were analyzed. The efficiency of early selection per year (E) for performing early indirect selection relative to performing direct selection at the earliest rotation age (40 years of age) was estimated based on narrow-sense heritability (h2) and age–age genetic correlation (r). The h2 of Ht peaked at 10 or 15 years of age (0.52–0.71), and that of DBH was the highest at 20 years of age (0.19 or 0.22). The age–age genetic correlation between tree heights or between tree height and DBH at different ages decreased with increasing differences between ages (regression coefficients were −0.011 and −0.007, respectively). The E values were highest at 10 or 15 years of age (0.84-1.74 and 1.42-2.24 for Ht and Ht-DBH, respectively), indicating the optimum selection timing. In Japapnese forestry, the initial growth rate is considered important for reducing weeding costs. Selection at 10 or 15 years of age had more than in >65 % indirect genetic gain relative to the direct genetic gain at 5 years of age; thus, selection at 10-15 years of age is appropriate considering the initial and mature phases of tree growth.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73579214","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}
K. Chatti, S. Choulak, S. Rhouma, K. Guenni, A. Salhi-Hannachi, N. Chatti
Abstract Retrotransposon movements are considered to be an important factor in evolutionary processes and speciation as well as a source of genetic variation. In order to analyze genetic diversity and population structure in Tunisian pistachio species, nine inter-retrotransposon amplified polymorphism (IRAP) markers were used. As a result, eighty-six amplicons were produced among which 98.15 % were polymorphic. Mean numbers of the effective number of alleles (Ne), Shannon’s information index (I) and Nei’s genetic diversity (H) were respectively 1.529, 0.478, and 0.310. The average within-population genetic diversity (Hs) was 0.24 and the total diversity (Ht) was 0.3. The Tunisian pistachio populations exhibited high genetic differentiation (Gst =0.275) and gene flow (Nm = 1.888). The Analysis of Molecular Variance (AMOVA) indicated that variation was very high within populations (83 %). Phylogenetic tree using neighbor- joining (NJ) method and Principal Coordinates Analysis (PCoA) depicted that groupings of Tunisian varieties were made independently of the sex of the trees, but depending on their geographical origin and their breeding status. The modelbased Bayesian clustering (STRUCTURE) confirmed these observations. The inter-retrotransposons amplification polymorphism markers were significantly informative at the interspecific level. Findings reported in our study will be essential toward breeding for new pistachio genotypes with developed chemical and horticultural features.
{"title":"Retrotransposon-based markers revealed a repartition depending on geographical origin and breeding status of Tunisian pistachio species","authors":"K. Chatti, S. Choulak, S. Rhouma, K. Guenni, A. Salhi-Hannachi, N. Chatti","doi":"10.2478/sg-2022-0001","DOIUrl":"https://doi.org/10.2478/sg-2022-0001","url":null,"abstract":"Abstract Retrotransposon movements are considered to be an important factor in evolutionary processes and speciation as well as a source of genetic variation. In order to analyze genetic diversity and population structure in Tunisian pistachio species, nine inter-retrotransposon amplified polymorphism (IRAP) markers were used. As a result, eighty-six amplicons were produced among which 98.15 % were polymorphic. Mean numbers of the effective number of alleles (Ne), Shannon’s information index (I) and Nei’s genetic diversity (H) were respectively 1.529, 0.478, and 0.310. The average within-population genetic diversity (Hs) was 0.24 and the total diversity (Ht) was 0.3. The Tunisian pistachio populations exhibited high genetic differentiation (Gst =0.275) and gene flow (Nm = 1.888). The Analysis of Molecular Variance (AMOVA) indicated that variation was very high within populations (83 %). Phylogenetic tree using neighbor- joining (NJ) method and Principal Coordinates Analysis (PCoA) depicted that groupings of Tunisian varieties were made independently of the sex of the trees, but depending on their geographical origin and their breeding status. The modelbased Bayesian clustering (STRUCTURE) confirmed these observations. The inter-retrotransposons amplification polymorphism markers were significantly informative at the interspecific level. Findings reported in our study will be essential toward breeding for new pistachio genotypes with developed chemical and horticultural features.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90121094","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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