Genomic selection in forest tree breeding

Genomic selection (GS) involves selection decisions based on genomic breeding values estimated as the sum of the effects of genome-wide markers capturing most quantitative trait loci (QTL) for the target trait(s). GS is revolutionizing breeding practice in domestic animals. The same approach and concepts can be readily applied to forest tree breeding where long generation times and late expressing complex traits are also a challenge. GS in forest trees would have additional advantages: large training populations can be easily assembled and accurately phenotyped for several traits, and the extent of linkage disequilibrium (LD) can be high in elite populations with small effective population size (N _e) frequently used in advanced forest tree breeding programs. Deterministic equations were used to assess the impact of LD (modeled by N _e and intermarker distance), the size of the training set, trait heritability, and the number of QTL on the predicted accuracy of GS. Results indicate that GS has the potential to radically improve the efficiency of tree breeding. The benchmark accuracy of conventional BLUP selection is reached by GS even at a marker density ~2 markers/cM when N _e ≤ 30, while up to 20 markers/cM are necessary for larger N _e. Shortening the breeding cycle by 50% with GS provides an increase ≥100% in selection efficiency. With the rapid technological advances and declining costs of genotyping, our cautiously optimistic outlook is that GS has great potential to accelerate tree breeding. However, further simulation studies and proof-of-concept experiments of GS are needed before recommending it for operational implementation.     

Effect of genomic prediction on response to selection in forest tree breeding

Through stochastic simulations, estimates of breeding values accuracies and response to selection were assessed under traditional pedigree-based and genomic-based evaluation methods. More specifically, several key parameters such as the trait’s heritability (0.2 and 0.6), the number of QTLs underlying the trait (100 to 200), and the marker density (1 to 10 SNPs/cM) were evaluated. Additionally, impact of two contrasting mating designs (partial diallel vs. single-pair mating) was investigated. Response to selection was then assessed in a seed production population (seed orchard consisting of unrelated selections) for different effective population sizes (N_e?=?5 to 25). The simulated candidate population comprised a fixed size of 2050 individuals with fast linkage disequilibrium decay, generally found in forest tree populations. Following the genetic/genomic evaluation, top-ranked individuals were selected to meeting the predetermined effective population size in target production population. The combination of low h², high N_e, and dense marker coverage resulted at maximum relative genomic prediction efficiency and the most efficient exploitation of the Mendelian sampling term (within-family additive genetic variance). Since genomic prediction of breeding values constitutes the methodological foundation of genomic selection, our results can be used to address important questions when similar scenarios are considered.     

Incorporation of competitive effects in forest tree or animal breeding programs

Competition among domesticated plants or animals can have a dramatic negative impact on yield of a stand or farm. The usual quantitative genetic model ignores these competitive interactions and could result in seriously incorrect breeding decisions and acerbate animal well-being. A general solution to this problem is given, for either forest tree breeding or penned animals, with mixed-model methodology (BLUP) utilized to separate effects on the phenotype due to the individuals' own genes (direct effects) and those from competing individuals (associative effects) and thereby to allow an optimum index selection on those effects. Biological verification was based on two lines of Japanese quail selected for 6-week weight; one line was selected only for direct effects (D-BLUP) while the other was selected on an optimal index for both direct and associative effects (C-BLUP). Results over 23 cycles of selection showed that C-BLUP produced a significant positive response to selection (b=0.52+/-0.25 g/hatch) whereas D-BLUP resulted in a nonsignificant negative response (b=-0.10+/-0.25 g/hatch). The regression of percentage of mortality on hatch number was significantly different between methods, decreasing with C-BLUP (b=-0.06+/-0.15 deaths/hatch) and increasing with D-BLUP (b=0.32+/-0.15 deaths/hatch). These results demonstrate that the traditional D-BLUP approach without associative effects not only is detrimental to response to selection but also compromises the well-being of animals. The differences in response show that competitive effects can be included in breeding programs, without measuring new traits, so that costs of the breeding program need not increase.     

Genomics of forest and ecosystem health in the Fagaceae: meeting report

A summary of 35 keynote, invited and volunteer papers delivered at a recent international conference is provided along with web links to PDFs of those presentations. Major conference themes targeted Genomic Tool Development for the Fagaceae and Application of Genomic Resources. The meeting provided a venue for reviewing the rapidly expanding knowledge base on Fagaceae genomics and for developing collaborations between scientists from Europe and North America.     

Best linear prediction of breeding values in a forest tree improvement program

Summary Best Linear Prediction (BLP) was used to predict breeding values for 1,396 parents from progeny test data in an operational slash pine breeding program. BLP rankings of parents were compared to rankings of averaged standard scores, a common approach in forestry. Using BLP rankings, selection of higher ranking parents tends to choose parents in a larger number of more precise progeny tests. The trend is the opposite with standard scores; higher ranking parents tend to be those in fewer, less precise tests. BLP and a related methodology, Best Linear Unbiased Prediction (BLUP), were developed by dairy cattle breeders and have not been used widely outside of animal breeding for predicting breeding values from messy progeny test data. Application of either of these techniques usually requires simplifying assumptions to keep the problem computationally tractable. The more appropriate technique for a given application depends upon which set of assumptions are better for the given problem. An assumption of homogeneous genetic and error variances and covariances, generally made by animal breeders when applying BLUP, was inappropriate for our data. We employed an approach that treated fixed effects as known and treated the same trait measured in different environments as different traits with heterogeneous variance structures. As tree improvement programs become more complex, the ease with which BLP and BLUP handle messy data and incorporate diverse sources of information should make these techniques appealing to forest tree breeders.     

生物多样性与林木育种

保护生物多样性在林木育种中必须予以重视。传统的林木育种主要考虑遗传增益。长期育种则以维持育种群体的变异性为主要目的。具有丰富生物多样性的天然森林群体是长期育种的基础。长期育种研究应以物种生物学、群体遗传学和居群生态学等为理论基础。主要研究森林群体的性质及群体的动态变化规律。传统林木育种的研究方向、研究内容及林木育种学的教学内容等都应予以适当的调整和补充。     

Needs and benefits of empirical power transformations for production and quality traits in forest tree breeding

Non-normality in the distribution of individual observations of production and quality traits in forest tree breeding may cause inaccurate selection and overestimation of predicted selection gain. The distribution of individual observations of traits such as height, diameter, branch diameter, branch angle and number of branches per whorl is not always normal. We investigated how the observations were distributed and to what degree it is possible to improve normality, homogeneity of error variance and additivity by using empirical power transformations. Computer simulations showed that a seriously skewed distribution impairs selection efficiency and exaggerates selection gain expectations. If the distribution is heavily skewed, transformation might be worthwhile. It does not seem possible to offer any general advice about which varities should be transformed, but in most cases there seems to be no need of any transformation.     

Asymptotic rates of response from forest tree breeding strategies using best linear unbiased prediction

 Genetic gain equations are developed for selection on multiple traits using either multi- or univariate best linear unbiased predictors (BLUP) and for selection under controlled and open pollination and polymix mating schemes. The equations assume an infinite population and account for the effects of selection. A comparison with simulated populations under the same mating schemes show that the gain equations predict selection response well, with the predictions having some upward bias. The gain equations are used to compare across mating schemes, to compare univariate to multivariate analyses, and to measure the reduction in the rate of genetic gain due to selection disequilibrium. Results show controlled pollination schemes can offer as much as a 56% advantage in genetic gain relative to open pollination. The reduction in the rate of genetic gain due to selection disequilibrium is approximately 27% under controlled pollination for the breeding goals studied. The results show a limited benefit in using multivariate analyses for predicting breeding values. Received: 20 April 1997 / Accepted: 8 October 1997     

Genomics progress will facilitate molecular breeding in soybean

<正>It has been suggested that the soybean(Glycine max[L.]Merr.)currently cultivated in commercial agriculture was domesticated from the wild soybean(G.soja Sieb.Zucc.)in China approximately 5,000 years ago.Because of its high protein and oil content,cultivated soybean has become a major economic crop by providing 69%and 30%of the world’s plant protein and oil.Soybean breeders have made     

Genotype by environment interactions in forest tree breeding: review of methodology and perspectives on research and application

Genotype by environment interaction (G×E) refers to the comparative performances of genotypes differing among environments, representing differences in genotype rankings or differences in the level of expression of genetic differences among environments. G×E can reduce heritability and overall genetic gain, unless breeding programmes are structured to address different categories of environments. Understanding the impact of G×E, the role of environments in generating G×E and the problems and opportunities is vital to efficient breeding programme design and deployment of genetic material. We review the current main analytical methods for identifying G×E: factor analytic models, biplot analysis and reaction norm. We also review biological and statistical evidence of G×E for growth, form and wood properties in forest species of global economic importance, including some pines, eucalypts, Douglas-fir, spruces and some poplars. Among these species, high levels of G×E tend to be reported for growth traits, with low levels of G×E for form traits and wood properties. Finally, we discuss possible ways of exploiting G×E to maximise genetic gain in forest tree breeding. Characterising the role of environments in generating interactions is seen as the basic platform, allowing efficient testing of candidate genotypes. We discuss the importance of level-of-expression interaction, relative to rank-change interaction, as being greater than in many past reports, especially for deployment decisions. We examine the impacts of G×E on tree breeding, some environmental factors that cause G×E and the strategies for dealing with G×E in tree breeding, and the future role of genomics.     

Avian responses to forest fragmentation during the breeding and non-breeding seasons

Forest fragmentation represents a threat to several bird species worldwide. Several factors can change across seasons (e.g. bird perception of the landscape, weather conditions, biotic interactions), which can modify the response of bird populations to forest fragmentation. However, most studies have been conducted only during the breeding season. Here we assessed the relationship between forest fragmentation (patch area and patch isolation) with population abundances of resident species during both the breeding and the non-breeding seasons. Bird population abundances (all species in the community, subsets of forest and habitat generalist species and for individual species) were estimated across a gradient of area-isolation in a semi-arid forest in Cordoba, Argentina. Population abundance of the overall avian community and of the subset of forest species declined with patch area reduction independently of the season. By contrast, the subset of habitat generalist species was not affected by patch area reduction or by the increase in patch isolation, either during the breeding or during the non-breeding season. When the analyses were carried out for individual species, we found four forest species and one habitat generalist species whose responses (the relationship between population abundance and patch area or with isolation) were different between breeding and non-breeding seasons. The negative effects of forest fragmentation were found mainly during the breeding season. Our results suggest that reduction of patch area may lead to a reduction of more than 65% of the population abundance of forest bird species, during both the breeding and the non-breeding season. Therefore, there is an urgent need to conserve large forest patches within the region as irreplaceable elements for the conservation of populations of several species.     

Biotechnological applications of tissue culture to forest tree improvement

Plant tissue culture techniques are of tremendous potential value to forest tree improvement. The technology is envisaged as playing a complementary role to traditional methods through exploiting spontaneous or induced genetic and epigenetic variability in culture, by use of haploidy and by the use of protoplasts. Haploids and protoplasts will aid in shortening breeding cycles and allow for unconventional crosses respectively. Clonal propagation is an integral part of any tree improvement program, and in addition can play an independent role in reforestation, clonal orchard establishment and in energy foresting. The goals, problems and limitations of these applications of tissue culture technology to forest tree improvement are indicated and assessed.     

从结构基因组学到功能基因组学

基因组学研究随着模式生物基因组全序列测定的完成由结构基因组学阶段发展到功能基因组学阶段,基因组学成为当今最为活跃、最有影响的前沿学科.以结构基因组学的研究成果为基础,功能基因组学中各学科因其原理不同及其关键技术的特点和优势,具有各自的应用范畴和发展趋势.功能基因组学不断渗透入现代科学的各领域,促成了适用于不同研究目的新兴学科的诞生.     

Variation in the breeding behavior of the dry forest tree Enterolobium cyclocarpum (guanacaste) in Costa Rica

We studied the breeding systems of four populations of Enterolobium cyclocarpum (guanacaste, earpod tree) in Costa Rica. Multilocus estimates of the outcrossing rate indicate that E. cyclocarpum is a predominant outcrossing species (t(m) ranged between 0.881 and 0.901) and biparental inbreeding is low (range between 0.058 and 0.079). Overall, our analyses showed significant differences in the gene frequencies between pollen and ovules and significant differences in pollen gene frequencies between the four populations. We also found significant differences in the pollen gene frequencies calculated for single trees in the same population. Outcrossing rates and pollen gene frequencies varied in two consecutive years in two populations of E. cyclocarpum. The correlated mating model revealed that there are differences in the correlation of paternity between populations and years. These findings indicate that there is variation in the average number of trees that father the seed crop of each tree and/or that some fathers are overrepresented in the seed crop of each tree. The implication of these findings for the development of strategies for conservation and management of this species are discussed.     

Improving wood quality in the western gulf forest tree improvement program: the problem of multiple breeding objectives

Currently, both industrial and private landowners in the Western Gulf Forest Tree Improvement Program (WGFTIP) area are compensated for their timber primarily based on the weight or volume of green wood reaching the mill gate. This places an immediate economic focus on adaptability and volume growth. However, selection for volume growth alone could result in decreased wood quality over time. Wood quality characteristics including stem straightness, wood specific gravity, and microfibril angle have either neutral or slightly unfavorable genetic correlations with volume growth in the WGFTIP loblolly pine (Pinus taeda L.) program. Since most WGFTIP members also consider wood quality an important selection criterion, the WGFTIP must define the best possible set of selection criteria given that (1) no single set of breeding objectives can be considered optimal for multiple products and (2) improvement in wood quality has no readily recognized economic importance in the existing market. To meet this challenge, the WGFTIP has implemented different strategies for its mainline breeding and deployment populations. In the mainline population, consistent breeding and selection criteria are used across members, while in the various deployment populations, selections are tailored to meet the specific needs of each member. The WGFTIP is also developing an elite wood quality population (WQEPop) based on backward selection. For the WQEPop to be successful, the economic importance of improved wood quality must be recognized, and landowners must be compensated for growing higher quality timber, especially if this results in reduced volume production. Improved methodology for within-family selection and for wood quality trait measurement is also important.     

Microclimate and tree community linked to differences in lepidopteran larval communities between forest fragments and continuous forest

Aim  We aim to assess the impact of forest fragmentation on lepidopteran larval community and study the associations of microclimate and tree community with lepidopteran assemblage.
Location  Kibale National Park, Uganda.
Methods  We investigated the effects of forest fragmentation on leaf herbivory, density of lepidopteran caterpillars, species richness and diversity as well as the composition of herbivorous lepidopteran larval community. Microclimate, size of the fragment, distance to the continuous forest, and tree diversity were studied as possible explanatory factors. We sampled 10 Neoboutonia macrocalyx Pax. (Euphorbiaceae) trees in each fragment during dry and rainy season, total of four times, in a year to cover the seasonal variation.
Results  The rates of herbivory, total larval density and species richness were significantly lower in the forest fragments than in the continuous forest but species diversity expressed as Fisher's alpha did not differ. The dominance structure and community composition of the larval communities in the fragments was different from that of the continuous forest. None of the differences we observed were related to the fragment area or distance to the continuous forest. Instead, we found an indication of association between the herbivore and the tree communities. The fragments had significantly lower humidity during most of the day and higher temperature during the afternoons (14–17 h), which might partially explain the differences in lepidopteran larval communities.
Main conclusions  Decreased larval density and species richness as well as differences in the community composition and structure all highlight the importance of large continuous forest areas for maintaining larval biodiversity.     

Organ formation in vitro as applicable to forest tree propagation

Literature concerning the influences of auxins, adenine, kinetin, light, heat, time, age, and physical characteristics of the medium onin vitro organ formation by sterile seed-plant fragments is reviewed and integrated.