Fikret Isik

• Professor
• Co-Director of Cooperative Tree Improvement Program at North Carolina State University

High-precision estimation of genetic parameters of growth traits is a fundamental requisite for effective selection of individuals to advance breeding cycles and support continued genetic gain in tree improvement. Due to the lack of efficient large-scale cloning techniques of adult trees, plantation forestry of Pinus taeda relies mostly on genetica...

Strawberry ( Fragaria × ananassa ) is an important crop in the United States. In this study, we analysed strawberry trials established across 7 years and two locations. Our objective was to estimate genetic parameters and predict breeding values for yield. Linear mixed models were used for unbalanced data across years and locations and study the ge...

Twenty Pinus taeda L. families from both the Coastal Plain and Piedmont provenances in the southeastern United States were planted on an upper Piedmont site that experienced a severe ice storm at age 3 years. Storm damage and defect rates through age 11 years were compared with the seed transfer distance and the seed parents’ breeding values to dev...

A newly developed software, AgMate, was used to perform optimized mating for monoecious Pinus taeda L. breeding. Using a computational optimization procedure called differential evolution, AgMate was applied under different breeding population sizes scenarios (50, 100, 150, 200, and 250) and candidate contribution scenarios (maximum use of each can...

Genotyping platforms for breeding programs should be repeatable, reliable, high-throughput, and cost-effective. In this study, we compared the efficiency of an Affymetrix genotyping array (Pita50K) and a targeted genotyping-by-sequencing (tGBS) panel for estimating genomic relationships and detecting potential pedigree errors in a Pinus taeda L. po...

Estimation of genetic parameters from progeny testing is essential for many important decisions in forest tree breeding. In this study, we estimated heritabilities, trait-trait genetic correlations, and genotype by environment (GxE) interactions using a large multi-environmental data set of Pinus taeda L. in the southern United States. In the study...

To facilitate the utility of genetic improvement in loblolly pine, individual-tree volume (productivity) scores estimated from single-tree plot or row-plot progeny test designs were compared with stand-level volume per unit area from block plots. A large number of families representing a wide range of progeny test scores for volume were established...

Loblolly pine (Pinus taeda L.) is the most widely planted forest tree species in the United States. Most of the seedlings used to establish these plantations come from seed collected in open-pollinated seed orchards, but an increasing number are coming from controlled crosses, about 15%–20% of the loblolly pine seedling crops in the last five years...

Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravates the deforestation and forest degradation. Forest genomics has great p...

Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great po...

Long-term response of two intra- and two inter-provenance populations of loblolly pine (Pinus taeda L.) were evaluated in the Piedmont region of the southeastern United States. In total, 82 polycross families of the Atlantic Coastal (C) and Piedmont (P) provenances (CxC, PxP) and their hybrids (CxP, PxC) were field tested for growth, sawtimber pote...

A newly developed software, AgMate, was used to perform optimized mating for monoecious Pinus taeda L. breeding. Using a computational optimization procedure called differential evolution (DE), AgMate was applied under different breeding population sizes scenarios (50, 100, 150, 200, 250) and candidate contribution scenarios (max use of each candid...

Breeding objectives aim to optimize two crucial but contrasting goals of maximizing genetic gain while managing genetic diversity. In advanced generations, this becomes a challenge in monoecious conifer tree species breeding programs because they suffer from inbreeding. Developing an algorithm that maximizes genetic gain while maintaining genetic d...

This chapter provides an overview of the genomic selection progress in long-lived forest tree species. Factors affecting the prediction accuracy in genomic prediction are assessed with examples from empirical studies. Infrastructure and resources required for the implementation of genomic selection are evaluated. Some general guidelines are provide...

We investigated the efficiency of genomic selection in a large clonal population (N = 2023) of Pinus taeda L. The study population comprised 58 families that were tested across eight locations in the southern USA. The clones were genotyped with the Pita50K SNP array. Whole-genome regression models were used to obtain genomic estimated breeding valu...

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 w...

Genomic prediction has the potential to significantly increase the rate of genetic gain in tree breeding programs. In this study, a clonally replicated population (n = 2063) was used to train a genomic prediction model. The model was validated both within the training population and in a separate population (n = 451). The prediction abilities from...

Genetic variation in frost tolerance, resistance to the rust fungus Uromycladium acaciae, growth, stem form, and gummosis were evaluated in 110 open-pollinated families of black wattle (Acacia mearnsii De Wild). Families were tested at six frost-prone sites in northern KwaZulu-Natal and southeastern Mpumalanga, South Africa. Frost-hardy provenances...

The effect of silvicultural treatments (herbicide, fertilization, herbicide + fertilization) and the interactions with genetic effects were investigated for wood quality traits in a 16-year-old loblolly pine (Pinus taeda L.) genetic test established in southwest Georgia, USA. Fertilizer and herbicide treatment combinations were applied multiple tim...

We performed gene and genome targeted SNP discovery towards the development of a genome‐wide, multi‐species genotyping array for tropical pines. Pooled RNA‐seq data from shoots of seedlings from five tropical pine species was used to identify transcript‐based SNPs resulting in 1.3 million candidate Affymetrix SNP probe sets. In addition, we used a...

In this study, 723 Pinus taeda L. (loblolly pine) clonal varieties genotyped with 16920 SNP markers were used to evaluate genomic selection for fusiform rust disease caused by the fungus Cronartium quercuum f. sp. fusiforme. The 723 clonal varieties were from five full-sib families. They were a subset of a larger population (1831 clonal varieties),...

This manuscript explains the methods for SNP discovery and the design of Pinus taeda SNP array (Pita50K) using the Axiom technology. The array was part of the Conifer SNP Consortium (established in 2018) to develop 6 arrays for different species: CSC-Pita50K (Pinus taeda), – Lead PI: Fikret Isik, USA CSC-Pira50K (Pinus radiata) – Lead PI: Natal...

Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. Unlike the major epidemics of agricultural crops, the coevolved pine-rust pathosystem is characterized by steady-state dynamics and high levels of geneti...

• Key message In this study, genetic variation in polycyclic growth was investigated in a young Pinus brutia Ten. study in Turkey. The number of flushes was partially under additive genetic control and was moderately correlated with the tree height at age 4. • Context Pinus brutia is the most economically important tree species in Turkey. Previous...

Considerable genetic differences in loblolly pine (Pinus taeda L.) exist for growth, stem form, and wood quality traits that influence biomass/biofuel production. By planting genetically superior trees with desirable biomass/biofuel traits, it is possible to substantially increase the amount of biomass and potential sawtimber trees produced from pl...

•Key message: Pronounced additive genetic variation and high narrow-sense heritability for lesion length caused by Neonectria neomacrospora were found in a Nordmann fir progeny test. Significant inbreeding depression was detected in traits important for Christmas tree production. Recurrent selection for multiple traits would be successful for Chris...

Eucalyptus grandis is one of the most important species for hardwood plantation forestry around the world. At present, its commercial deployment is in decline because of pests and pathogens such as Leptocybe invasa gall wasp (Lepto), and often co-occurring fungal stem diseases such as Botryosphaeria dothidea and Teratosphaeria zuluensis (BotryoTera...

Shiitake (Lentinula edodes) is an edible mushroom-producing fungus. ‘‘Natural log-grown’’ shiitake mushrooms are favored by consumers and are often produced by small farmers and hobbyists in the United States. The tree species most often recommended as a substrate for shiitake is white oak (Quercus alba), which has many other economic uses. We test...

Genetic parameters were estimated using a five-series multienvironment trial of Pinus taeda L. in the southern USA. There were 324 half-sib families planted in five test series across 37 locations. A set of six variance/covariance matrices for the genotype-by-environment (G × E) effect for tree height and diameter were compared on the basis of mode...

Background Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that w...

The correspondence between breeding values of 65 loblolly pine (Pinus taeda L.) genotypes from clonal genetic tests and half-sib seedling progeny tests was studied in the southern United States. The two experiments were established separately, 10 years apart. Additive genetic variance estimates from clonal tests were larger compared with the estima...

Genomic selection (GS) can substantially reduce breeding cycle times in forest trees compared to traditional breeding cycles. Practical implementation of GS in tree breeding requires an assessment of significant drivers of genetic gains over time, which may differ among species and breeding objectives. We present results of a GS study of growth and...

Since 2009, deployment of full-sib families of loblolly pine (Pinus taeda L.) has gained prominence in the southeastern United States. To produce full-sib seed, a pollination bag is used to isolate female strobili from outside pollen contamination, and a known pollen is applied at the time of maximum female strobilus receptivity. The goal of this s...

The Cooperative Tree Improvement Program at North Carolina State University used the differential evolution algorithm developed for animal breeding (Kinghorn, Genet Sel Evol 43(1):4, Kinghorn 2011) to design the mating in the 4th cycle of loblolly pine (Pinus taeda L.) breeding. The mate selection algorithm optimizes genetic gain while putting cons...

Cloned progeny tests in forest tree breeding provide the ability to assess the same genotypes across multiple environments and partition observed phenotypic variance into additive and non-additive genetic effects. In this study, 2362 clones from 53 crosses of loblolly pine (Pinus taeda L.) were tested across eight locations in the Southern US. Alph...

A new epidemic disease caused by the rust fungus Uromycladium acaciae emerged in 2013/2014 causing defoliation, branch, and stem deformations in plantations of Acacia mearnsii (black wattle) in South Africa. This study investigated the level of genetic resistance to the rust fungus Uromycladium acaciae in six progeny tests from two different trial...

Higher genetic gains can be achieved through genomic selection (GS) by shortening time of progeny testing in tree breeding programs. Genotyping-by-sequencing (GBS), combined with two imputation methods, allowed us to perform the current genomic prediction study in Scots pine (Pinus sylvestris L.). 694 individuals representing 183 full-sib families...

Acoustic time of flight and drill resistance (surrogates for wood stiffness and density, respectively) were measured on 11,097 standing trees from 269 pollen-mix families of loblolly pine (Pinus taeda L.) in 6- to 9-year-old progeny tests at eight sites across the southeastern United States. Specific gravity was measured on two test sites. The phen...

Forest tree breeding has been successful at delivering genetically improved material for multiple traits based on recurrent cycles of selection, mating, and testing. However, long breeding cycles, late flowering, variable juvenile-mature correlations, emerging pests and diseases, climate, and market changes, all pose formidable challenges. Genetic...

A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 rea...

Fusiform rust is the most economically important disease of loblolly pine (Pinus taeda L.) in the southern United States. Estimates of family resistance to rust are critical for deployment decisions because 95% of loblolly pine plantations are established with individual families. If families show significant interactions with different pathogen in...

In this chapter we describe spatial analyses that deal with heterogeneity of errors in a post-hoc analysis, rather than in the experimental design. These spatial analyses can improve the estimation of genetic effects by modeling more accurately the spatial distribution of error effects in a field trial. Selecting an optimal model can be complicated...

Genetic data sets available to breeders are increasing in size, both in numbers of markers and in numbers of breeding individuals or lines genotyped. The scale of the data sets requires breeders to use software to perform quality control checks, visualize, and manipulate data. Breeders will often want to combine genetic marker data with physical or...

Multivariate models are commonly used to estimate phenotypic, genetic and environmental variances, covariances, and correlations for multiple traits in plant and animal breeding programs. When traits are correlated, breeding value predictions from a multivariate model can be more accurate than univariate models. In this chapter we introduce multiva...

The resemblance between individuals in a population has been traditionally estimated from pedigrees. High-throughput genotyping technology has enabled the use of large numbers of DNA markers to estimate the amount of genome shared by individuals. Genetic similarity estimates based on genetic markers are more precise than those based on pedigree inf...

The term ‘imputation’ refers to the estimation of values to replace missing observations in a data set. In this chapter, we are interested in imputing missing genotype values. The chapter is not intended as a rigorous treatment of the use and implications of imputation in breeding values prediction, but rather as a brief overview of some common str...

Understanding the matrix representations of variance-covariance models is important to be able to fit mixed models with complex variance structures. In particular, ASReml makes use of a notation for direct products of matrices to form some complex variance structures. The direct product notation can be applied both to the residual errors from the m...

ASReml has been become a default software for analysis of linear mixed models. The Average Information Sparse Matrix algorithm of ASReml makes the software very fast to solve large number of mixed model equations. The software is flexible to fit complex variance structures in mixed models. We introduce ASReml stand alone and a brief introduction to...

In this chapter we cover the basics of estimating breeding values from field progeny test data for half-sib family selection. The individual level or ‘animal’ model is introduced to demonstrate prediction of individual breeding values across generations. Modifications to the basic model are considered, such as maternal effects and genetic group eff...

Some mating designs, such as factorials and diallels produce full-sib families. These mating designs allow decomposing the observed genetic variance into additive and non-additive genetic effects. Selection among full-sib families is common in some plant and animal breeding programs. If full-sib families can be propagated, non-additive genetic effe...

Most field tests for plant breeding are replicated across different environments to measure the performance of breeding stocks across a range of environmental conditions to which a cultivar might be exposed. Multi-environment trials provide information about the adaptability of genotypes to specific environments or to sets of environments. The vari...

The whole genome regression approach to genomic selection is based on using large numbers of DNA markers to predict breeding values of individuals in animal and plant breeding programs. It is related to GBLUP introduced in Chapter 11, but it is distinguished from GBLUP by simultaneously modeling the effects of many DNA markers, and using the sum of...

In this chapter we will introduce the basic concepts and matrix algebra methods used to perform linear mixed models analysis. For readers who are more familiar with traditional analysis of variance (ANOVA) based on ordinary least squares methods, we first will review the ANOVA and compare ANOVA to mixed models analysis to help introduce this topic....

We wrote this book to fill the gap between textbooks of quantitative genetic theory and software manuals that provide details on analytical methods but little context or perspective on which methods may be most appropriate for particular applications. This book is intended for students in plant or animal breeding courses and for professional breede...

In Chile, an intensive Eucalyptus globulus clonal selection program is being carried out to increase forest productivity for pulp production. A breeding population was used to investigate the predicted ability of single nucleotide polymorphism (SNP) markers for genomic selection (GS). A total of 310 clones from 53 families were used. Stem volume an...

Provenance tests are a common tool in forestry designed to identify superior genotypes for planting at specific locations. The trials are replicated experiments established with seed from parent trees collected from different regions and grown at several locations. In this work, a Bayesian spatial approach is developed for modeling the expected rel...

[This corrects the article DOI: 10.1371/journal.pone.0165323.].

As part of a long-term project to develop a predictive model of lignin biosynthesis in the stem differentiating xylem of Populus trichocarpa, we explored the quantitative relationships of gene-specific monolignol pathway proteins and the amount of the lignin polymer. We determined the absolute abundance of monolignol pathway proteins in wild-type (...

The effects of imposed silvicultural treatments and genetics on growth and form traits were investigated in a 15-year-old loblolly pine (Pinus taeda L.) trial in southwestern Georgia, USA. The trial consisted of four treatment combinations and 25 open-pollinated first-and second-generation families. Average individual-tree stem volume ranged from 1...

Background The use of wood as an industrial raw material has led to development of plantation forestry, in which trees are planted, managed, and harvested as crops. The productivity of such plantations often exceeds that of less-intensively-managed forests, and land managers have the option of choosing specific planting stock to produce specific ty...

Background Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding populat...

Datasets for the F2 mapping population and the LD mapping population. (XLSX)

Design of the SNP arrays for the genotyping of the F2 mapping population. (PDF)

Statistics for the two VeraCode SNP arrays. (PDF)

Comparison between the composite map of P. pinaster and the F2 map (panel A), G2 male map (panel B) and G2 female map (panel C). The composite map is represented in blue and the parental maps of the F2 and G2 populations in green. The numbers at the top of each linkage group indicate the number of markers common to different maps for each linkage g...

Genetic location of the markers used for association mapping on the composite linkage map of Pinus pinaster established by de Miguel et al. (2015). The number of markers per linkage group is indicated beneath each linkage group. (PDF)

Distribution of the p-value of χ2 tests for the goodness-of-fit to the expected Mendelian segregation ratios of along the 12 linkage groups of F2 genetic map. Horizontal dotted lines represent the threshold above which SNPs are significantly distorted (p < 0.01). (PDF)

Scatterplot of additive relationship coefficients and genomic relationship coefficients within generations (G0 or G1) and between generations (G0-G1). (PDF)

List of the 248 mapped SNPs for the F2 mapping population. The following information is presented: the contig and SNP IDs, the associated dbSNP ss accession number, the genotyping platform used, the alleles considered, the designability score from Illumina (ADT software), the associated linkage group, and the position on the F2 map and on the Pinus...

Segregation for stem straightness (STR) in the F2 mapping population. (PDF)

Flowchart describing the different steps used to identify putative SNPs in the hybrid parent (H12) of the F2 progeny. (PDF)

Information obtained from MassArray assay design software (see separate supporting information file). (XLSX)

Average stem straightness (estimated as the deviation from verticality) as a function of genotype at three QTL loci on chromosomes 7 (sp_v3.0_unigene17779), 11 (sp_v3.0_unigene175515) and 12 (sp_v3.0_unigene20418). The genotype of the grandparents (Landes or Corsican) is indicated below the corresponding class. (PDF)

Single marker effects on total height and stem straightness, in ridge regression BLUP (RR-BLUP). The absolute values of markers are plotted on the 12 linkage groups of the Pinus pinaster composite map. (PDF)

Genotyping of the F2 mapping population. (PDF)

Descriptive statistics for the traits measured in the F2 and G2 mapping populations. For the F2 mapping population: stem straightness (STR) and height growth (HT) and for the G2 mapping population: annual height increment (HI) from 1985 to 1997. (PDF)

Spearman correlations for height increment in the G2 mapping population. Only significant correlations (p < 0.05) are listed. (PDF)

Current status of major international conifer genome sequencing projects. (PDF)

Background Genomic selection (GS) is a promising approach for decreasing breeding cycle length in forest trees. Assessment of progeny performance and of the prediction accuracy of GS models over generations is therefore a key issue. ResultsA reference population of maritime pine (Pinus pinaster) with an estimated effective inbreeding population siz...

Turkish fir (Abies bornmuelleriana Mattf.) and Trojan fir (Abies equi-trojani (Aschers. et Sint. ex Boiss) Mattf.) are economically and ecologically important endemic species to Turkey. These species are also becoming increasingly popular in Europe and North America due to their suitable characteristics for use as Christmas trees coupled with their...

p>Background Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding popul...