Silvae GeneticaPub Date : 2024-08-09DOI: 10.2478/sg-2024-0013
Abdul Bari Muneera Parveen, K. Jayabharathi, Muthusamy Muthupandi, Naveen Kumar, Shakti Singh Chauhan, D. Rajasugunasekar, Modhumita Ghosh Dasgupta
{"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":"55 1","pages":""},"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}
Silvae GeneticaPub Date : 2024-07-22DOI: 10.2478/sg-2024-0012
Jeremias Götz, Oliver Caré, Winston Beck, Oliver Gailing, Bernhard Hosius, Ludger Leinemann
{"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":"23 1","pages":""},"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}
Silvae GeneticaPub Date : 2024-07-06DOI: 10.2478/sg-2024-0010
Gye-Hong Cho, Ye-Ji Kim, Koeun Jeon, Hye-Jun Joo, Kyu-Suk Kang
{"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":"60 1","pages":""},"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}
Silvae GeneticaPub Date : 2024-07-06DOI: 10.2478/sg-2024-0009
Melina Krautwurst, Annika Eikhof, Sylke Winkler, Daniel Bross, Birgit Kersten, Niels A. Müller
{"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":"24 1","pages":""},"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}
{"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":"20 1","pages":""},"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}
Silvae GeneticaPub Date : 2024-05-31DOI: 10.2478/sg-2024-0006
Alison Paulo Bernardi, Miguel Busarello Lauterjung, Tiago Montagna, Adelar Mantovani, Maurício Sedrez dos Reis
{"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":"4 1","pages":""},"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}
Silvae GeneticaPub Date : 2024-04-13DOI: 10.2478/sg-2024-0005
Thomas Mørtvedt Solvin, Tore Skrøppa, Arne Steffenrem
{"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":"45 1","pages":""},"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}
Silvae GeneticaPub Date : 2024-04-04DOI: 10.2478/sg-2024-0004
Liliana López-Ramírez, Gerardo Hernández-Vera, Dulce María Galván-Hernández, Pablo Octavio Aguilar, Ahtziri Socorro Carranza-Aranda, José Antonio Vázquez-García, Arturo Sánchez-González
{"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":"45 1","pages":""},"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}
{"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":"41 1","pages":""},"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}
Silvae GeneticaPub Date : 2024-03-16DOI: 10.2478/sg-2024-0002
Andrew N. Callister, Jose P. Jiménez-Madrigal, Ross W. Whetten, Olman Murillo
{"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":"56 1","pages":""},"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}