Abdul Bari Muneera Parveen, K. Jayabharathi, Muthusamy Muthupandi, Naveen Kumar, Shakti Singh Chauhan, D. Rajasugunasekar, Modhumita Ghosh Dasgupta
Genotype × environment (G×E) interaction is a major challenge in selecting superior genotypes based on growth traits in Eucalyptus since phenotypic variability is significantly affected by environmental heterogeneity. The aim of the present investigation was to understand the relationship between wood property traits and fibre biometry in the bi-parental mapping population of E. camaldulensis × E. tereticornis across three locations and identify stable genotypes based on multiple traits to improve prediction accuracy in breeding programs. High broad-sense heritability was documented for fibre parameters indicating a good prospect of these traits for genotype selection in hybrid breeding programmes in Eucalyptus. Significant positive correlation of fibre parameters with cellulose, acoustic velocity, DMoE and negative correlation with lignin reiterate that the fibre traits can be improved by the selection of genotype for improved wood property traits. Multi-Trait Stability Index (MTSI) and weighted average of absolute scores of the genotype index (WAASB) short-listed four genotypes (C343, C327, C246 and C161) with improved wood property traits and the mean of selected genotypes for all traits was significantly higher than the grand mean of the overall genotypes. The identified superior and stable genotypes with improved wood properties and fibre biometry can be used in plantation programs or as genitors in breeding programs.
基因型 × 环境（G×E）交互作用是根据桉树生长性状选择优良基因型的一大挑战，因为表型变异受环境异质性的影响很大。本研究旨在了解三地 E. camaldulensis × E. tereticornis 双亲制图群体中木材性质性状与纤维生物测量之间的关系，并根据多个性状确定稳定的基因型，以提高育种计划中的预测准确性。纤维参数的广义遗传率较高，表明这些性状在桉树杂交育种计划中具有良好的基因型选择前景。纤维参数与纤维素、声速、DMoE 呈显著的正相关，而与木质素呈负相关，这说明纤维性状可以通过选择基因型来改善木材特性。多性状稳定指数（MTSI）和基因型指数绝对值加权平均值（WAASB）筛选出了四种具有改良木材特性的基因型（C343、C327、C246 和 C161），所选基因型的所有性状平均值均显著高于总体基因型的总平均值。鉴定出的具有改良木材特性和纤维生物测定的优良稳定基因型可用于种植计划或作为育种计划的基因型。
{"title":"Identification of superior hybrid clones for fibre biometry in Eucalyptus camaldulensis × E. tereticornis using multi trait stability index","authors":"Abdul Bari Muneera Parveen, K. Jayabharathi, Muthusamy Muthupandi, Naveen Kumar, Shakti Singh Chauhan, D. Rajasugunasekar, Modhumita Ghosh Dasgupta","doi":"10.2478/sg-2024-0013","DOIUrl":"https://doi.org/10.2478/sg-2024-0013","url":null,"abstract":"Genotype × environment (G×E) interaction is a major challenge in selecting superior genotypes based on growth traits in <jats:italic>Eucalyptus</jats:italic> since phenotypic variability is significantly affected by environmental heterogeneity. The aim of the present investigation was to understand the relationship between wood property traits and fibre biometry in the bi-parental mapping population of <jats:italic>E. camaldulensis × E. tereticornis</jats:italic> across three locations and identify stable genotypes based on multiple traits to improve prediction accuracy in breeding programs. High broad-sense heritability was documented for fibre parameters indicating a good prospect of these traits for genotype selection in hybrid breeding programmes in <jats:italic>Eucalyptus</jats:italic>. Significant positive correlation of fibre parameters with cellulose, acoustic velocity, DMoE and negative correlation with lignin reiterate that the fibre traits can be improved by the selection of genotype for improved wood property traits. Multi-Trait Stability Index (MTSI) and weighted average of absolute scores of the genotype index (WAASB) short-listed four genotypes (C343, C327, C246 and C161) with improved wood property traits and the mean of selected genotypes for all traits was significantly higher than the grand mean of the overall genotypes. The identified superior and stable genotypes with improved wood properties and fibre biometry can be used in plantation programs or as genitors in breeding programs.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141940244","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}
Jeremias Götz, Oliver Caré, Winston Beck, Oliver Gailing, Bernhard Hosius, Ludger Leinemann
Juglans is an economically important genus distributed all over the world. Due to its high value, there is a large interest in genetic markers for population genetic analyses and the certification of reproductive material. Using chloroplast genomes of different Juglans species, we developed a highly polymorphic and reliable chloroplast SSR marker set of eleven cpSSRs. It was successfully tested in five different Juglans species. Genetic differentiation among species and provenances within species was assessed. We were able to define a total of nine different chloroplast haplotypes using the novel cpSSR markers with up to four different haplotypes within a single Juglans species. Due to the cost and labor effective character of SSR markers, when compared to other available methods, such as whole chloroplast genome sequencing or SNP analyses, this novel cpSSR marker set will contribute to future population genetic studies in the Juglans genus.
胡桃属（Juglans）是分布于世界各地的重要经济树种。由于其价值很高，人们对用于种群遗传分析和繁殖材料认证的遗传标记很感兴趣。我们利用不同胡桃品种的叶绿体基因组，开发了一套由 11 个 cpSSR 组成的高多态性和可靠的叶绿体 SSR 标记。我们在五个不同的红豆杉物种中成功地进行了测试。评估了物种之间和物种内部产地之间的遗传差异。通过使用新型 cpSSR 标记，我们总共确定了九种不同的叶绿体单倍型，在一个胡颓子物种中最多可有四种不同的单倍型。与全叶绿体基因组测序或 SNP 分析等其他可用方法相比，SSR 标记具有成本低、省力的特点，因此这套新型 cpSSR 标记将有助于未来的胡桃属种群遗传研究。
{"title":"A Novel Set of Chloroplast SSR Markers for the Genus Juglans Reveals Within Species Differentiation","authors":"Jeremias Götz, Oliver Caré, Winston Beck, Oliver Gailing, Bernhard Hosius, Ludger Leinemann","doi":"10.2478/sg-2024-0012","DOIUrl":"https://doi.org/10.2478/sg-2024-0012","url":null,"abstract":"<jats:italic>Juglans</jats:italic> is an economically important genus distributed all over the world. Due to its high value, there is a large interest in genetic markers for population genetic analyses and the certification of reproductive material. Using chloroplast genomes of different <jats:italic>Juglans</jats:italic> species, we developed a highly polymorphic and reliable chloroplast SSR marker set of eleven cpSSRs. It was successfully tested in five different Juglans species. Genetic differentiation among species and provenances within species was assessed. We were able to define a total of nine different chloroplast haplotypes using the novel cpSSR markers with up to four different haplotypes within a single <jats:italic>Juglans</jats:italic> species. Due to the cost and labor effective character of SSR markers, when compared to other available methods, such as whole chloroplast genome sequencing or SNP analyses, this novel cpSSR marker set will contribute to future population genetic studies in the <jats:italic>Juglans</jats:italic> genus.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141754199","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}
Gye-Hong Cho, Ye-Ji Kim, Koeun Jeon, Hye-Jun Joo, Kyu-Suk Kang
This study aimed to test near-infrared spectroscopy to assess insect damage to oak acorns collected from a seed orchard of Quercus acuta in Jeju Island, Korea. A total of 550 acorns were sorted into 362 sound and 178 unsound (insect-damaged) acorns, followed by near-infrared spectroscopy. To minimize spectral data errors, preprocessing techniques such as first derivative, multiplicative scatter correction, standard normal variate, and Savitzky-Golay filter were applied, along with multivariate analysis methods like partial least squares. Then the model performance, including accuracy and precision, was evaluated using the Variable Importance in Projection. The near-infrared wavelength of the acorns showed strong absorption peaks at 660~720nm and a slight downward trend at 900~1000nm. The most effective model for distinguishing unsound acorns was Savitzky-Golay filtering treatment applied in the 400~1000nm range and used partial least squares, showing prediction accuracy of 86 % (p<0.05). The performance was significantly influenced by absorption points at 660~720nm and 960~1000nm, with the latter range believed to be affected by changes in moisture and carbohydrates due to insect damage. The former range showed lower classification capability due to chlorophyll and color variation but affected the model performance when used with near-infrared wavelength range. These findings can narrow down the scope of investigation for future research using wider wavelength ranges or multispectral analysis.
{"title":"Accuracy Evaluation of Visible-Near Infrared Spectroscopy for Detecting Insect Damage in Acorns of Quercus acuta","authors":"Gye-Hong Cho, Ye-Ji Kim, Koeun Jeon, Hye-Jun Joo, Kyu-Suk Kang","doi":"10.2478/sg-2024-0010","DOIUrl":"https://doi.org/10.2478/sg-2024-0010","url":null,"abstract":"This study aimed to test near-infrared spectroscopy to assess insect damage to oak acorns collected from a seed orchard of <jats:italic>Quercus acuta</jats:italic> in Jeju Island, Korea. A total of 550 acorns were sorted into 362 sound and 178 unsound (insect-damaged) acorns, followed by near-infrared spectroscopy. To minimize spectral data errors, preprocessing techniques such as first derivative, multiplicative scatter correction, standard normal variate, and Savitzky-Golay filter were applied, along with multivariate analysis methods like partial least squares. Then the model performance, including accuracy and precision, was evaluated using the Variable Importance in Projection. The near-infrared wavelength of the acorns showed strong absorption peaks at 660~720nm and a slight downward trend at 900~1000nm. The most effective model for distinguishing unsound acorns was Savitzky-Golay filtering treatment applied in the 400~1000nm range and used partial least squares, showing prediction accuracy of 86 % (p<0.05). The performance was significantly influenced by absorption points at 660~720nm and 960~1000nm, with the latter range believed to be affected by changes in moisture and carbohydrates due to insect damage. The former range showed lower classification capability due to chlorophyll and color variation but affected the model performance when used with near-infrared wavelength range. These findings can narrow down the scope of investigation for future research using wider wavelength ranges or multispectral analysis.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141566431","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}
Melina Krautwurst, Annika Eikhof, Sylke Winkler, Daniel Bross, Birgit Kersten, Niels A. Müller
Plant genome sequencing based on long reads has increasingly been applied also to tree species in recent years. A crucial step in these genome projects is the successful extraction of high-molecular-weight DNA in high quality and sufficient quantity, which is imperative for long-read sequencing. The extraction of high-molecular-weight DNA in trees has been limited and difficult to conduct. To achieve successful extraction, modification of the protocol for tree species is necessary. Here, we present a protocol for high-molecular-weight DNA extraction from the broadleaved tree species Fraxinus excelsior and from the conifer species Taxus baccata. The protocol is based on nuclei isolation and is divided into two main steps, i.e. nuclei separation based on the nuclei isolation buffer and DNA extraction using the Nanobind® plant nuclei kit by Pacific Biosciences (PacBio). The protocol can be applied to different tree species to obtain high-molecular-weight DNA in high quality, which can be used for Oxford Nanopore Technologies (ONT) and PacBio sequencing. ONT sequencing using four high-molecular-weight DNA preparations from Fraxinus excel-sior resulted in different read length N50 values (12.91-38.19 kb) and total base output (5.81-23.17 Gb), emphasizing the complex nature of the sequencing pipeline of high-molecular-weight DNA. PacBio HiFi sequencing of Taxus baccata produced circular consensus sequencing reads with an average length of 12.9 kb and an N50 of 13.59 kb. Altogether, this study presents a protocol to obtain high-molecular-weight DNA from different challenging tree species and discusses several important points that can be considered when adapting the protocol to additional species.
近年来，基于长读数的植物基因组测序也越来越多地应用于树种。这些基因组项目的一个关键步骤是成功提取高质量、足量的高分子量 DNA，这对于长读数测序至关重要。树木中高分子量DNA的提取一直受到限制且难以进行。要想成功提取，必须针对树种修改提取方案。在此，我们介绍一种从阔叶树种 Fraxinus excelsior 和针叶树种 Taxus baccata 提取高分子量 DNA 的方法。该方案以细胞核分离为基础，分为两个主要步骤，即使用细胞核分离缓冲液进行细胞核分离，以及使用太平洋生物科学公司（PacBio）的 Nanobind® 植物细胞核试剂盒进行 DNA 提取。该方案适用于不同树种，可获得高质量的高分子量 DNA，用于牛津纳米孔技术（ONT）和 PacBio 测序。利用四种来自Fraxinus excel-sior的高分子量DNA制备物进行ONT测序，结果出现了不同的读长N50值（12.91-38.19 kb）和总碱基输出（5.81-23.17 Gb），强调了高分子量DNA测序流水线的复杂性。PacBio HiFi测序产生的Taxus baccata环状共识测序读数平均长度为12.9 kb，N50为13.59 kb。总之，本研究提出了一种从不同挑战性树种中获取高分子量 DNA 的方案，并讨论了将该方案应用于其他树种时可以考虑的几个要点。
{"title":"High-molecular-weight DNA extraction for broadleaved and conifer tree species","authors":"Melina Krautwurst, Annika Eikhof, Sylke Winkler, Daniel Bross, Birgit Kersten, Niels A. Müller","doi":"10.2478/sg-2024-0009","DOIUrl":"https://doi.org/10.2478/sg-2024-0009","url":null,"abstract":"Plant genome sequencing based on long reads has increasingly been applied also to tree species in recent years. A crucial step in these genome projects is the successful extraction of high-molecular-weight DNA in high quality and sufficient quantity, which is imperative for long-read sequencing. The extraction of high-molecular-weight DNA in trees has been limited and difficult to conduct. To achieve successful extraction, modification of the protocol for tree species is necessary. Here, we present a protocol for high-molecular-weight DNA extraction from the broadleaved tree species <jats:italic>Fraxinus excelsior</jats:italic> and from the conifer species <jats:italic>Taxus baccata</jats:italic>. The protocol is based on nuclei isolation and is divided into two main steps, i.e. nuclei separation based on the nuclei isolation buffer and DNA extraction using the Nanobind® plant nuclei kit by Pacific Biosciences (PacBio). The protocol can be applied to different tree species to obtain high-molecular-weight DNA in high quality, which can be used for Oxford Nanopore Technologies (ONT) and PacBio sequencing. ONT sequencing using four high-molecular-weight DNA preparations from <jats:italic>Fraxinus excel-sior</jats:italic> resulted in different read length N50 values (12.91-38.19 kb) and total base output (5.81-23.17 Gb), emphasizing the complex nature of the sequencing pipeline of high-molecular-weight DNA. PacBio HiFi sequencing of <jats:italic>Taxus baccata</jats:italic> produced circular consensus sequencing reads with an average length of 12.9 kb and an N50 of 13.59 kb. Altogether, this study presents a protocol to obtain high-molecular-weight DNA from different challenging tree species and discusses several important points that can be considered when adapting the protocol to additional species.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141577085","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}
There are many challenges involved in obtaining high-quality DNA from tissues/cells, especially when using plants as the raw material. Three different DNA extraction protocols were employed in order to isolate high quality of genomic DNA from Pyracantha crenulata leaves. P. crenulata is a complex, versatile, and evergreen shrub species in Rosaceae family which is ecologically, economically and culturally important. This species produces valuable antioxidants like polyphenols, polysaccharides and secondary metabolites which interfere with DNA extraction thus making molecular marker based studies difficult in this species. This study aimed to develop a simple, rapid, cost-effective and highly efficient protocol for P. crenulata leaves rich in salts and phenols. The results demonstrated that modified CTAB (double buffer) protocol is very effective in overcoming the challenges that could impede next-generation sequencing analysis. The yield of the extracted DNA was excellent ranging from 368 to 410 ng/μL DNA with A260/280 ratio ranging from 1.80 to 1.84. The extracted DNA was amenable to PCR amplification making it suitable for DNA-based molecular marker studies. None procedures have been published for the purpose up this species, therefore, double buffer based extraction protocol is reported for the first time in P. crenulata and might prove useful in other species of family Rosa-ceae. This study describes an effective DNA isolation method that is appropriate for frequent population genetic screening. In conclusion, the double buffer protocol showed the most efficient and effective approach for extracting DNA from phenol rich, fresh, mature, and dry leaves.
从组织/细胞中获取高质量的 DNA 有许多挑战，尤其是使用植物作为原材料时。为了从Pyracantha crenulata叶片中分离出高质量的基因组DNA，我们采用了三种不同的DNA提取方案。Pyracantha crenulata 是蔷薇科常绿灌木，品种复杂，用途广泛，具有重要的生态、经济和文化价值。该物种会产生宝贵的抗氧化剂，如多酚、多糖和次生代谢物，这些物质会干扰 DNA 的提取，因此很难对该物种进行基于分子标记的研究。本研究旨在为富含盐类和酚类的 P. crenulata 树叶开发一种简单、快速、经济高效的提取方法。结果表明，改良的 CTAB（双缓冲液）方案能有效克服阻碍下一代测序分析的难题。提取 DNA 的产率非常高，从 368 到 410 ng/μL DNA 不等，A260/280 比值从 1.80 到 1.84 不等。提取的 DNA 可以进行 PCR 扩增，因此适用于基于 DNA 的分子标记研究。目前还没有针对该物种的提取方法，因此，本研究首次报道了基于双缓冲液的 P. crenulata 提取方法，该方法可能对蔷薇科的其他物种有用。本研究描述了一种有效的 DNA 分离方法，适合于频繁的种群遗传筛选。总之，双缓冲液方案是从富含酚的新鲜、成熟和干燥叶片中提取 DNA 的最有效方法。
{"title":"An improved and effective DNA extraction protocol for Pyracantha crenulata with optimal PCR reliability","authors":"Haripriya Kavidayal, Anita Rawat, Shanti Saroj, Harish Singh Ginwal","doi":"10.2478/sg-2024-0011","DOIUrl":"https://doi.org/10.2478/sg-2024-0011","url":null,"abstract":"There are many challenges involved in obtaining high-quality DNA from tissues/cells, especially when using plants as the raw material. Three different DNA extraction protocols were employed in order to isolate high quality of genomic DNA from <jats:italic>Pyracantha crenulata</jats:italic> leaves. <jats:italic>P. crenulata</jats:italic> is a complex, versatile, and evergreen shrub species in Rosaceae family which is ecologically, economically and culturally important. This species produces valuable antioxidants like polyphenols, polysaccharides and secondary metabolites which interfere with DNA extraction thus making molecular marker based studies difficult in this species. This study aimed to develop a simple, rapid, cost-effective and highly efficient protocol for <jats:italic>P. crenulata</jats:italic> leaves rich in salts and phenols. The results demonstrated that modified CTAB (double buffer) protocol is very effective in overcoming the challenges that could impede next-generation sequencing analysis. The yield of the extracted DNA was excellent ranging from 368 to 410 ng/μL DNA with A260/280 ratio ranging from 1.80 to 1.84. The extracted DNA was amenable to PCR amplification making it suitable for DNA-based molecular marker studies. None procedures have been published for the purpose up this species, therefore, double buffer based extraction protocol is reported for the first time in <jats:italic>P. crenulata</jats:italic> and might prove useful in other species of family Rosa-ceae. This study describes an effective DNA isolation method that is appropriate for frequent population genetic screening. In conclusion, the double buffer protocol showed the most efficient and effective approach for extracting DNA from phenol rich, fresh, mature, and dry leaves.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141566430","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}
Alison Paulo Bernardi, Miguel Busarello Lauterjung, Tiago Montagna, Adelar Mantovani, Maurício Sedrez dos Reis
Podocarpus lambertii (Podocarpaceae) is an endangered conifer, endemic to Brazil and occurring in continuous forest and forest-grassland landscapes from the Araucaria Forest. Aiming to support conservation efforts for P. lambertii populations and gain insights into the preservation of forest-grassland mosaics in southern Brazil, we assessed the spatial pattern, genetic diversity, and fine-scale genetic structure (FSGS) within a population situated in a forest-grassland mosaic. The study was conducted in a 9-ha plot in forest-grassland mosaic. All P. lambertii individuals with height ≥ 0.1 m were sampled and the population was stratified into four demographic categories (Seedling, Juvenile, Immature, and Reproductive). For each of these categories, we used 13 allozyme markers to evaluate the spatial pattern, genetic diversity and FSGS. All individuals occurred inside the forest-patches, presenting an aggregated pattern of distribution. Low genetic diversity was recorded for all categories and for the population (H⌢E=0.046{mathord{buildrel{lower3pthbox{$scriptscriptstylefrown$}}over H} _E} = ,0.046), as well as a high number of rare alleles (20). Positive and significant FSGS was estimated only for the Juveniles (θ⌢xy=0.012{mathord{buildrel{lower3pthbox{$scriptscriptstylefrown$}}over theta } _{xy}} = ,0.012) up to maximum distance of 7.1 m, and the minimum viable area for the long-term conservation of Reproductive genetic diversity was approximately 68 ha. The set of our findings suggests that conservation actions need to enhance connectivity among forest-patches to prevent the loss of rare alleles due to genetic drift. Additionally, we highlight the significance of preserving forest-patches as repositories of species diversity and as crucial connectors between populations.
Podocarpus lambertii（Podocarpaceae）是巴西特有的一种濒危针叶树，分布于阿劳卡里亚森林的连续森林和森林-草地景观中。为了支持对 P. lambertii 种群的保护工作，并深入了解巴西南部森林-草地镶嵌景观的保护情况，我们评估了森林-草地镶嵌景观中一个种群的空间模式、遗传多样性和精细尺度遗传结构（FSGS）。该研究在森林-草地镶嵌区的一块 9 公顷的土地上进行。我们对所有高度≥ 0.1 米的兰柏个体进行了采样，并将种群分为四个人口统计学类别（幼苗、幼年、未成熟和生殖）。我们对每个类别都使用了 13 个同源酶标记来评估空间模式、遗传多样性和 FSGS。所有个体都出现在林区内，呈现聚集分布模式。所有类别和种群的遗传多样性都很低（H ⌢ E = 0.046 {mathord{buildrel{lower3pthbox{$scriptscriptstylefrown$}}over H}_E} = ,0.046），以及大量稀有等位基因（20）。仅对幼鱼的 FSGS 进行了估计（θ ⌢ x y = 0.012 {mathord{buildrel{lower3pthbox{$scriptscriptstylefrown$}}over theta } _{xy}} = mathord{buildrel{lower3pthbox{$scriptscriptstylefrown$}}over theta }）。_{xy}}=,0.012），最大距离为 7.1 米，生殖遗传多样性长期保护的最小可行区域约为 68 公顷。我们的一系列研究结果表明，保护行动需要加强林片之间的连通性，以防止遗传漂变导致稀有等位基因的丢失。此外，我们还强调了保护作为物种多样性宝库和种群间重要连接点的林片的重要性。
{"title":"Genetic diversity and fine-scale genetic structure of the conifer Podocarpus lambertii in a forest-grassland mosaic from Southern Brazil","authors":"Alison Paulo Bernardi, Miguel Busarello Lauterjung, Tiago Montagna, Adelar Mantovani, Maurício Sedrez dos Reis","doi":"10.2478/sg-2024-0006","DOIUrl":"https://doi.org/10.2478/sg-2024-0006","url":null,"abstract":"<jats:italic>Podocarpus lambertii</jats:italic> (Podocarpaceae) is an endangered conifer, endemic to Brazil and occurring in continuous forest and forest-grassland landscapes from the Araucaria Forest. Aiming to support conservation efforts for <jats:italic>P. lambertii</jats:italic> populations and gain insights into the preservation of forest-grassland mosaics in southern Brazil, we assessed the spatial pattern, genetic diversity, and fine-scale genetic structure (FSGS) within a population situated in a forest-grassland mosaic. The study was conducted in a 9-ha plot in forest-grassland mosaic. All <jats:italic>P. lambertii</jats:italic> individuals with height ≥ 0.1 m were sampled and the population was stratified into four demographic categories (Seedling, Juvenile, Immature, and Reproductive). For each of these categories, we used 13 allozyme markers to evaluate the spatial pattern, genetic diversity and FSGS. All individuals occurred inside the forest-patches, presenting an aggregated pattern of distribution. Low genetic diversity was recorded for all categories and for the population (<jats:inline-formula> <jats:alternatives> <jats:inline-graphic xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"graphic/j_sg-2024-0006_eq_001.png\"/> <m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\"> <m:mrow> <m:msub> <m:mrow> <m:mover accent=\"true\"> <m:mi>H</m:mi> <m:mo>⌢</m:mo> </m:mover> </m:mrow> <m:mi>E</m:mi> </m:msub> <m:mo>=</m:mo> <m:mi> </m:mi> <m:mn>0.046</m:mn> </m:mrow> </m:math> <jats:tex-math>{mathord{buildrel{lower3pthbox{$scriptscriptstylefrown$}}over H} _E} = ,0.046</jats:tex-math> </jats:alternatives> </jats:inline-formula>), as well as a high number of rare alleles (20). Positive and significant FSGS was estimated only for the Juveniles (<jats:inline-formula> <jats:alternatives> <jats:inline-graphic xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"graphic/j_sg-2024-0006_eq_002.png\"/> <m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\"> <m:mrow> <m:msub> <m:mrow> <m:mover accent=\"true\"> <m:mi>θ</m:mi> <m:mo>⌢</m:mo> </m:mover> </m:mrow> <m:mrow> <m:mi>x</m:mi> <m:mi>y</m:mi> </m:mrow> </m:msub> <m:mo>=</m:mo> <m:mi> </m:mi> <m:mn>0.012</m:mn> </m:mrow> </m:math> <jats:tex-math>{mathord{buildrel{lower3pthbox{$scriptscriptstylefrown$}}over theta } _{xy}} = ,0.012</jats:tex-math> </jats:alternatives> </jats:inline-formula>) up to maximum distance of 7.1 m, and the minimum viable area for the long-term conservation of Reproductive genetic diversity was approximately 68 ha. The set of our findings suggests that conservation actions need to enhance connectivity among forest-patches to prevent the loss of rare alleles due to genetic drift. Additionally, we highlight the significance of preserving forest-patches as repositories of species diversity and as crucial connectors between populations.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141197873","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}
Thomas Mørtvedt Solvin, Tore Skrøppa, Arne Steffenrem
Genetic variation and performance of up to 40-year-old Norway spruce (Picea abies (L.) Karst.) families from half-diallel crosses made in natural populations where studied, and the results were compared with results from nursery test of seedlings (1-2 years from seed) and short-term farm-field tests at 6-10 years from seed. The diallel analyses revealed significant levels of additive genetic variance for growth and phenology traits. The non-additive genetic variance was generally small to moderate. Strong genetic correlations for growth performance were found between the short-term and long-term trials but not between the nursery and long-term trials. Similarly, genetic correlations for phenology traits were strong between short-term trials and long-term trials, whereas the nursery tests generally did not predict phenology at older age well. The findings indicate that early selection for growth and adaptive traits based on short-term trials is effective for improvement of long-term performance in field if the test site is not outside the normal range of deployment of the reproductive material.
{"title":"Diallel crosses in Picea abies V. Can early testing predict long-term performance?","authors":"Thomas Mørtvedt Solvin, Tore Skrøppa, Arne Steffenrem","doi":"10.2478/sg-2024-0005","DOIUrl":"https://doi.org/10.2478/sg-2024-0005","url":null,"abstract":"Genetic variation and performance of up to 40-year-old Norway spruce (<jats:italic>Picea abies</jats:italic> (L.) Karst.) families from half-diallel crosses made in natural populations where studied, and the results were compared with results from nursery test of seedlings (1-2 years from seed) and short-term farm-field tests at 6-10 years from seed. The diallel analyses revealed significant levels of additive genetic variance for growth and phenology traits. The non-additive genetic variance was generally small to moderate. Strong genetic correlations for growth performance were found between the short-term and long-term trials but not between the nursery and long-term trials. Similarly, genetic correlations for phenology traits were strong between short-term trials and long-term trials, whereas the nursery tests generally did not predict phenology at older age well. The findings indicate that early selection for growth and adaptive traits based on short-term trials is effective for improvement of long-term performance in field if the test site is not outside the normal range of deployment of the reproductive material.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140560437","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}
Liliana López-Ramírez, Gerardo Hernández-Vera, Dulce María Galván-Hernández, Pablo Octavio Aguilar, Ahtziri Socorro Carranza-Aranda, José Antonio Vázquez-García, Arturo Sánchez-González
In Mexico, Magnolia species of the section Macrophylla have been segregated based on phenotypic characteristics. However, the wide environmental variation throughout their distribution area in the eastern region of the country could be the main cause of the high degree of morphological variation among the taxa of this section. Therefore, it is necessary to carry out studies at the genetic level to confirm the taxonomic identity of these species. In the present study, the diversity and genetic structure of the populations of Magnolia rzedowskiana and M. zotictla were estimated using simple sequence repeat markers. We evaluated whether the taxonomic delimitation as independent species is consistent with their degree of genetic differentiation, comparing three regions of chloroplast DNA: trnH-psbA, ORF350, and rpl32-trnL. The DNA was obtained from four populations of the two species, which are distributed in the states of Hidalgo, Querétaro and San Luis Potosí. The populations presented intermediate–high genetic diversity (He = 0.52–0.60), limited gene flow (Nm = 0.62) and high genetic differentiation (Fst = 0.288), which may be related to their low density and strong geographic isolation, caused by the high degree of fragmentation of their habitat. The phylogenetic analysis and the genetic differentiation values indicate that each of the populations of the two Magnolia species analyzed behaves as an independent evolutionary unit, so the taxonomic delimitation of the three M. rzedowskiana populations must be reconsidered. The results obtained could be very useful for implementing management and conservation strategies for these populations in the short term.
在墨西哥，Macrophylla 科的木兰属植物已根据表型特征进行了分类。然而，在墨西哥东部地区的整个分布区，环境差异很大，这可能是造成该部分分类群形态差异很大的主要原因。因此，有必要在遗传水平上开展研究，以确认这些物种的分类学特征。本研究利用简单序列重复标记对 Magnolia rzedowskiana 和 M. zotictla 种群的多样性和遗传结构进行了估计。通过比较叶绿体 DNA 的三个区域：trnH-psbA、ORF350 和 rpl32-trnL，我们评估了作为独立物种的分类划分是否与它们的遗传分化程度一致。DNA 取自这两个物种的四个种群，它们分布在伊达尔戈州、克雷塔罗州和圣路易斯波托西州。这些种群呈现出中等程度的遗传多样性（He = 0.52-0.60）、有限的基因流（Nm = 0.62）和较高的遗传分化（Fst = 0.288），这可能与其栖息地高度破碎化导致的低密度和较强的地理隔离有关。系统进化分析和遗传分化值表明，所分析的两个木兰种的每个种群都是一个独立的进化单元，因此必须重新考虑对三个 M. rzedowskiana 种群的分类划分。这些结果对于在短期内对这些种群实施管理和保护战略非常有用。
{"title":"Structure, diversity, and genetic delimitation of two Magnolia species endemic to eastern Mexico","authors":"Liliana López-Ramírez, Gerardo Hernández-Vera, Dulce María Galván-Hernández, Pablo Octavio Aguilar, Ahtziri Socorro Carranza-Aranda, José Antonio Vázquez-García, Arturo Sánchez-González","doi":"10.2478/sg-2024-0004","DOIUrl":"https://doi.org/10.2478/sg-2024-0004","url":null,"abstract":"In Mexico, <jats:italic>Magnolia</jats:italic> species of the section <jats:italic>Macrophylla</jats:italic> have been segregated based on phenotypic characteristics. However, the wide environmental variation throughout their distribution area in the eastern region of the country could be the main cause of the high degree of morphological variation among the taxa of this section. Therefore, it is necessary to carry out studies at the genetic level to confirm the taxonomic identity of these species. In the present study, the diversity and genetic structure of the populations of <jats:italic>Magnolia rzedowskiana</jats:italic> and <jats:italic>M. zotictla</jats:italic> were estimated using simple sequence repeat markers. We evaluated whether the taxonomic delimitation as independent species is consistent with their degree of genetic differentiation, comparing three regions of chloroplast DNA: trnH-psbA, ORF350, and rpl32-trnL. The DNA was obtained from four populations of the two species, which are distributed in the states of Hidalgo, Querétaro and San Luis Potosí. The populations presented intermediate–high genetic diversity (He = 0.52–0.60), limited gene flow (Nm = 0.62) and high genetic differentiation (Fst = 0.288), which may be related to their low density and strong geographic isolation, caused by the high degree of fragmentation of their habitat. The phylogenetic analysis and the genetic differentiation values indicate that each of the populations of the two <jats:italic>Magnolia</jats:italic> species analyzed behaves as an independent evolutionary unit, so the taxonomic delimitation of the three <jats:italic>M. rzedowskiana</jats:italic> populations must be reconsidered. The results obtained could be very useful for implementing management and conservation strategies for these populations in the short term.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140560304","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}
The present study measured the growth traits of 98 open-pollinated half-sibling families from the second-generation clonal seed orchard of Chinese fir for 6 consecutive years from age 2 to 7, the change patterns of genetic variation in growth traits and genetic parameters were analyzed, and best linear unbiased prediction (BLUP) was used for early selection to determine the excellent families. The growth traits of Chinese fir revealed highly significant differences between families, indicating that there was significant genetic variation at the family level, which serves as the foundation for exceptional family selection. The heritabilities of family and individual for H (height) ranged from 0.61 to 0.65 and 0.41 to 0.46, respectively; for DGH (the diameter at ground height)/DBH (the diameter at breast height), they were 0.55 to 0.66 and 0.35 to 0.46, respectively; and for V (tree volume), they were 0.66 to 0.70 and 0.48 to 0.49, respectively. The growth traits of genetic control were at a greater level at age 5. The findings of the coefficient of variation analysis demonstrated that the phenotypic variation coefficient were larger than the genetic variation coefficient for three growth traits at various ages. The juvenile-mature genetic and phenotypic correlations revealed an increasing tendency with age, and mainly controlled by genetic factors. Compared to other age groups for growth traits, age 5 had greater phenotypic and genetic association coefficients, as well as greater efficiency of early selection. Based on the selection method of breeding value, nine families were selected with a 9.2 % selection rate.
{"title":"Age trends of genetic variation and early selection for growth traits in Cunninghamia lanceolata open-pollinated families","authors":"Sirui Li, Jiayi Li, Hanbo Yang, Changdong Yang, Yunjie Gu, Zhi Chen, Hongying Guo, Zhen Huang, Peng Zhu","doi":"10.2478/sg-2024-0003","DOIUrl":"https://doi.org/10.2478/sg-2024-0003","url":null,"abstract":"The present study measured the growth traits of 98 open-pollinated half-sibling families from the second-generation clonal seed orchard of Chinese fir for 6 consecutive years from age 2 to 7, the change patterns of genetic variation in growth traits and genetic parameters were analyzed, and best linear unbiased prediction (BLUP) was used for early selection to determine the excellent families. The growth traits of Chinese fir revealed highly significant differences between families, indicating that there was significant genetic variation at the family level, which serves as the foundation for exceptional family selection. The heritabilities of family and individual for H (height) ranged from 0.61 to 0.65 and 0.41 to 0.46, respectively; for DGH (the diameter at ground height)/DBH (the diameter at breast height), they were 0.55 to 0.66 and 0.35 to 0.46, respectively; and for V (tree volume), they were 0.66 to 0.70 and 0.48 to 0.49, respectively. The growth traits of genetic control were at a greater level at age 5. The findings of the coefficient of variation analysis demonstrated that the phenotypic variation coefficient were larger than the genetic variation coefficient for three growth traits at various ages. The juvenile-mature genetic and phenotypic correlations revealed an increasing tendency with age, and mainly controlled by genetic factors. Compared to other age groups for growth traits, age 5 had greater phenotypic and genetic association coefficients, as well as greater efficiency of early selection. Based on the selection method of breeding value, nine families were selected with a 9.2 % selection rate.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140560315","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}
Andrew N. Callister, Jose P. Jiménez-Madrigal, Ross W. Whetten, Olman Murillo
Teak (Tectona grandis) is a premier hardwood timber, extensively cultivated throughout the tropics. The study aimed to undertake the first genomic selection of teak clones using single nucleotide polymorphism (SNP) markers and evaluate the prospects for prediction of stem volume (VOL), diameter (DBH), form Quality Score (QS), Specific Gravity (SG), and Heartwood Percentage (HW). Thirty-three elite teak clones from a genetic test in northern Costa Rica were genotyped at 10812 SNP loci and aligned to the teak reference genome sequence. The genomic relationship matrix revealed 7 cryptic groups of more highly related clones and within-group kinship values were consistent with full-sib families. Clone values for each of the 5 traits were calculated from 5-year field data for 26 of the geno-typed clones. Genomic prediction models were fitted to clone values using Bayesian Ridge Regression, BayesA, BayesB, BayesC, and Bayes Lasso. Predictive ability (PA) was greatest for DBH (up to 0.66), VOL (up to 0.63), SG (0.58), with 0.42 and 0.40 as the best PA for QS and HW, respectively. GWAS resulted in the discovery of 7 unique SNP markers for volume, 7 for DBH, 4 for QS, and 8 for SG. The small experimental size resulted in relatively large false discovery rates. Teak breeders are well positioned to benefit from the genomic tools and approaches to genotyping teak breeding and deployment populations on a large scale. Significant advantages are expected from widespread integration of genomic technologies into teak breeding systems to allow shortening of the breeding cycle.
{"title":"Genomic predictions and candidate single nucleotide polymorphisms for growth, form, and wood properties of teak clones","authors":"Andrew N. Callister, Jose P. Jiménez-Madrigal, Ross W. Whetten, Olman Murillo","doi":"10.2478/sg-2024-0002","DOIUrl":"https://doi.org/10.2478/sg-2024-0002","url":null,"abstract":"Teak (<jats:italic>Tectona grandis</jats:italic>) is a premier hardwood timber, extensively cultivated throughout the tropics. The study aimed to undertake the first genomic selection of teak clones using single nucleotide polymorphism (SNP) markers and evaluate the prospects for prediction of stem volume (VOL), diameter (DBH), form Quality Score (QS), Specific Gravity (SG), and Heartwood Percentage (HW). Thirty-three elite teak clones from a genetic test in northern Costa Rica were genotyped at 10812 SNP loci and aligned to the teak reference genome sequence. The genomic relationship matrix revealed 7 cryptic groups of more highly related clones and within-group kinship values were consistent with full-sib families. Clone values for each of the 5 traits were calculated from 5-year field data for 26 of the geno-typed clones. Genomic prediction models were fitted to clone values using Bayesian Ridge Regression, BayesA, BayesB, BayesC, and Bayes Lasso. Predictive ability (PA) was greatest for DBH (up to 0.66), VOL (up to 0.63), SG (0.58), with 0.42 and 0.40 as the best PA for QS and HW, respectively. GWAS resulted in the discovery of 7 unique SNP markers for volume, 7 for DBH, 4 for QS, and 8 for SG. The small experimental size resulted in relatively large false discovery rates. Teak breeders are well positioned to benefit from the genomic tools and approaches to genotyping teak breeding and deployment populations on a large scale. Significant advantages are expected from widespread integration of genomic technologies into teak breeding systems to allow shortening of the breeding cycle.","PeriodicalId":21834,"journal":{"name":"Silvae Genetica","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140152528","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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