Genetic linkage between the training and selection sets impacts the predictive ability of SNP markers in a cloned population of Pinus taeda L.

2022 ◽  
Vol 18 (1) ◽  
Author(s):  
Mohammad Nasir Shalizi ◽  
Kitt G. Payn ◽  
Fikret Isik
Keyword(s):  
Pinus Taeda ◽  
Genetic Linkage ◽  
Predictive Ability ◽  
Snp Markers ◽  
Pinus Taeda L

Single-Step Genomic Analysis Increases the Accuracy of Within-Family Selection in a Clonally Replicated Population of Pinus taeda L.

2021 ◽  
Author(s):  
Trevor D Walker ◽  
W Patrick Cumbie ◽  
Fikret Isik
Keyword(s):  
Pinus Taeda ◽  
Predictive Ability ◽  
Single Step ◽  
Breeding Value ◽  
Family Selection ◽  
Breeding Values ◽  
Genomic Markers ◽  
Clonal Testing ◽  
Model Training ◽  
Pinus Taeda L

Abstract The use of genomic markers in forest tree breeding is expected to improve the response to selection, especially within family. To evaluate the potential improvements from genotyping, we analyzed a large Pinus taeda L. clonal population (1,831 cloned individuals) tested in multiple environments. Of the total, 723 clones from five full-sib families were genotyped using 10,337 single-nucleotide polymorphism markers. Single-step models with genomic and pedigree-based relationships produced similar heritability estimates. Breeding value predictions were greatly improved with inclusion of genomic relationships, even when clonal replication was abundant. The improvement was limited to genotyped individuals and attributable to accounting for the Mendelian sampling effect. Reducing clonal replication by omitting data indicated that genotyping improved breeding values similar to clonal replication. Genomic selection predictive ability (masking phenotypes) was greater for stem straightness (0.68) than for growth traits (0.41 to 0.44). Predictive ability for a new full-sibling family was poorer than when full-sibling relationships were present between model training and validation sets. Species that are difficult to propagate clonally can use genotyping to improve within-family selection. Clonal testing combined with genotyping can produce breeding value accuracies adequate to graft selections directly into deployment orchards without progeny testing. Study Implications Genomic markers can improve the reliability of breeding values, resulting in a more confident ranking of individuals within families. For genotyped individuals, the improvements were comparable to clonal testing. Breeding programs for species that are difficult to propagate clonally should consider genotyping to replace or supplement clonal testing as a means to improve within-family selection. For genomic prediction of breeding values without phenotypes (genomic selection), a robust genetic relationship between model training and validation sets is required. The single-step model allows genotyping a subset of the population and is a straightforward extension of well-established methods.

Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high-density genetic linkage map for loblolly pine (Pinus taeda L.)

2013 ◽  
Vol 9 (6) ◽  
pp. 1529-1535 ◽  
Author(s):  
Pedro J. Martínez-García ◽  
Kristian A. Stevens ◽  
Jill L. Wegrzyn ◽  
John Liechty ◽  
Marc Crepeau ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Linkage Map ◽  
Pinus Taeda ◽  
Loblolly Pine ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Mapping Algorithms ◽  
Regression Mapping ◽  
Pinus Taeda L

scholarly journals A Consensus Map for Loblolly Pine (Pinus taeda L.). I. Construction and Integration of Individual Linkage Maps From Two Outbred Three-Generation Pedigrees

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 321-330 ◽  
Author(s):  
Mitchell M Sewell ◽  
Bradley K Sherman ◽  
David B Neale
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Mapping Function ◽  
Genetic Maps ◽  
Linkage Data ◽  
Linkage Maps ◽  
Consensus Map ◽  
Pinus Taeda L

Abstract A consensus map for loblolly pine (Pinus taeda L.) was constructed from the integration of linkage data from two unrelated three-generation outbred pedigrees. The progeny segregation data from restriction fragment length polymorphism, random amplified polymorphic DNA, and isozyme genetic markers from each pedigree were recoded to reflect the two independent populations of parental meioses, and genetic maps were constructed to represent each parent. The rate of meiotic recombination was significantly greater for males than females, as was the average estimate of genome length for males {1983.7 cM [Kosambi mapping function (K)]} and females [1339.5 cM(K)]. The integration of individual maps allows for the synthesis of genetic information from independent sources onto a single consensus map and facilitates the consolidation of linkage groups to represent the chromosomes (n = 12) of loblolly pine. The resulting consensus map consists of 357 unique molecular markers and covers ∼1300 cM(K).

Long-term effects of stand density management and genotype on wood properties of loblolly pine (Pinus taeda L.) in the mid-South USA

2021 ◽  
Vol 491 ◽  
pp. 119176
Author(s):  
Michael A. Blazier ◽  
Thomas Hennessey ◽  
Laurence Schimleck ◽  
Scott Abbey ◽  
Ryan Holbrook ◽  
...  
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Stand Density ◽  
Wood Properties ◽  
Long Term Effects ◽  
Stand Density Management ◽  
Pinus Taeda L

scholarly journals Comparative Dynamics of Above-Ground Litter Production and Decomposition from Eucalyptus Grandis Hill ex Maiden and Pinus Taeda L., and Their Contribution to Soil Organic Carbon

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 349
Author(s):  
Andrés Baietto ◽  
Jorge Hernández ◽  
Amabelia del Pino
Keyword(s):  
Pinus Taeda ◽  
Decomposition Rate ◽  
Methodological Approach ◽  
Eucalyptus Grandis ◽  
Isotopic Analysis ◽  
Forest Litter ◽  
First Year ◽  
Litter Production ◽  
Forest Species ◽  
Pinus Taeda L

The replacement of native pasture by exotic commercial forest species is an infrequent situation worldwide. In these systems, a new component is introduced, forest litter, which constitutes one of the main ways of incorporating carbon into the soil–plant system. The present work seeks to establish a methodological approach to study the dynamics of litter production and decomposition in an integrated way. The general objective was to characterize and compare the litter production dynamics in 14-year-old Eucalyptus grandis Hill ex Maiden and Pinus taeda L. commercial plantations. During two years, seasonal evaluations of fall, decomposition and accumulation of litter were carried out in stands of both species. In turn, the contribution of carbon from forest species to the soil through isotopic analysis techniques was quantified. Litterfall in E. grandis showed maximums during the spring of the first year and in the spring and summer of the second. In P. taeda, the maximums occurred in summer of the first year and in autumn of the second. In relation to the decomposition rate, the results based on short periods of evaluation between 15 and 21 months did not show differences between species, nor for the different moments of beginning of the evaluation, obtaining average values of 0.0369 month−1 for E. grandis and 0.0357 month−1 for P. taeda. In turn, both the decomposition rate of the material as a whole and the estimates of accumulated biomass in equilibrium state did not show significant differences between the species. Additionally, there was a relevant incorporation of carbon into the soil by forest species, fundamentally in the first few centimeters, substituting an important proportion of the carbon inherited by the original cover of native pastures. Finally, it is necessary to specify that the scope of the findings obtained is greatly limited by the sample size used in this study.

scholarly journals Edaphic and Topographic Factors and their Relationship with Dendrometric Variation of Pinus Taeda L. in a High Altitude Subtropical Climate

2018 ◽  
Vol 42 (0) ◽  
Author(s):  
Taciara Zborowski Horst ◽  
Ricardo Simão Diniz Dalmolin ◽  
Alexandre ten Caten ◽  
Jean Michel Moura-Bueno ◽  
Luciano Campos Cancian ◽  
...  
Keyword(s):  
High Altitude ◽  
Pinus Taeda ◽  
Subtropical Climate ◽  
Topographic Factors ◽  
Pinus Taeda L

Comparison of container-grown Pinus taeda L. seedlings raised outdoors and in a growth chamber in sunlight

New Forests ◽  
1990 ◽  
Vol 4 (3) ◽  
pp. 223-230
Author(s):  
William A. Retzlaff ◽  
Ansel E. Miller ◽  
Robert M. Allen
Keyword(s):  
Pinus Taeda ◽  
Growth Chamber ◽  
Pinus Taeda L

scholarly journals Four Site-Preparation Techniques for Regenerating Pine-Hardwood Mixtures in the Piedmont

1997 ◽  
Vol 21 (3) ◽  
pp. 116-122 ◽  
Author(s):  
Thomas A. Waldrop
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Height Growth ◽  
Site Preparation ◽  
Site Conditions ◽  
Growing Seasons ◽  
Southern Appalachian ◽  
Medium Quality ◽  
Pinus Taeda L ◽  
Preparation Techniques

Abstract Four variations of the fell-and-burn technique, a system developed to produce mixed pine-hardwood stands in the Southern Appalachian Mountains, were compared in the Piedmont region. All variations of this technique successfully improved the commercial value of low-quality hardwood stands by introducing a pine component. After six growing seasons, loblolly pine (Pinus taeda L.) occupied the dominant crown position and oaks the codominant position in fell-and-burn treated stands on poor to medium quality sites. The precise timing of felling residual stems, as prescribed by the fell-and-burn technique, may be flexible because winter and spring felling produced similar results. Although summer site preparation burns reduced hardwood height growth by reducing the length of the first growing season, they did not improve pine survival or growth. Pines were as tall as hardwoods within four growing seasons in burned plots and within six growing seasons in unburned plots. Additional research is needed to determine the level or intensity of site preparation needed to establish pine-hardwood mixtures over a range of site conditions. South. J. Appl. For. 21(3):116-122.

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