Potential for marker-assisted selection for forest tree breeding: lessons from 20 years of MAS in crops

For the most part, molecular markers and detection of quantitative trait loci have been developed for forest tree species in view to performing marker-assisted selection (MAS). However, MAS has not been applied to forest trees until now. In parallel, some success stories of MAS in crop breeding have been reported. Recently, genotyping techniques have undergone a tremendous increase in throughput, moving the trend from MAS to genomic selection. We analyzed 250 papers reporting the use of MAS in plant breeding and found that the most popular schemes used were gene pyramiding and marker-assisted backcross manipulating a single or very few genomic regions which have a major impact on crop value. We reviewed theoretical and simulation studies to identify the parametric space in which MAS is expected to bring about significant advantages over phenotypic selection. Then, we tried to explain why MAS has not been applied to forest trees and discuss the opportunities offered by recent advances in these species.     

Evaluating genetic resources of forest trees by means of life history traits – a Norwegian example

Additive variation in adaptive traits is a prerequisite for selectionand adaptation to future environmental changes, but distribution of adaptivegenetic variability between and within populations is poorly known in mostforest trees. Owing to this deficiency, life history traits such as geographicrange, pollination vector and seed dispersal capability, which significantlyaffect gene flow and thus the distribution of genetic variability, were used toevaluate the genetic resources in 23 Norwegian native forest tree species. Basedon the combination of life history traits the species' genetic resourceswere classified either as viable, potentially vulnerable or vulnerable, assuminga decrease in within-population variability in this sequence. Twelve widelydistributed species with generally effective dispersal of pollen and seeds wereconsidered viable (Pinus sylvestris, Picea abies,Juniperus communis, Betula pubescens, B. pendula,Alnus incana, A. glutinosa, Salix caprea, Populustremula, Corylus avellana, Sorbus aucuparia, Prunus padus)and have as such no particular conservation needs. Effective seed dispersal of these species, asinferred from post-glacial migration rates, may be partly responsible for theirgenerally early post-glacial appearance, and may, in combination with the wideranges and relatively large evolutionary potential, indicate that viable speciesare best able to cope with climatic change. Among species with restricted rangesand more limited gene flow eight were considered potentially vulnerable (Quercuspetraea, Q. robur, Fraxinus excelsior, Acer platanoides,Taxus baccata, Ilexaquifolium, Fagus sylvatica, Ulmus glabra) and threewere considered vulnerable (Tiliacordata, Malus sylvestris, P. avium). Application of differentintensities of a multiple population breeding system (MPBS) is considered the most appropriate mode of conservinggenetic resources in these species.     

Tissue culture of forest trees—Clonal propagation of mature trees of Eucalyptus citriodora Hook,by tissue culture

Multiple shoots were obtained from terminal buds of 20-year-old trees of Eucalyptus citriodora Hook on Murashige and Skoog's medium supplemented with calcium pantothenate, biotin, benzylaminopurine and kinetin. Rooting could be induced by naphthalene-acetic acid in shoot cultures only after they had undergone three subcultures. Incubation at 15°C with continuous illumination followed by growth in agitated liquid cultures was essential for inducing shoot development in the primary terminal buds. These treatments were not necessary in later subcultures or with explants from seedlings obtained from seeds. Fifteen subcultures have so far been carried out and healthy viable plantlets obtained in each subculture. It is estimated that over 100 000 plants can be obtained by this method in a year from a single bud of mature Eucalyptus citriodora trees.     

Carved trees in grazed forests in boreal Sweden—analysis of remaining trees, interpretation of past land-use and implications for conservation

Culturally modified trees (CMTs) provide unique insights into traditional knowledge and uses of the forest ecosystems. In close relation to pre-industrial livestock herding in central Sweden, it was a custom to carve text and symbols on trees and use them as notice boards in the forest. The main aim of this study was to document and analyse remaining carved trees in a managed forest landscape of 160 km². The same area was surveyed twice, once in 1986 and once in 2003. 488 carved trees were documented and classified into legible themes that were interpreted in the light of past herding practices. Name was the most common theme, found in 85% of the carvings. Most of the carvings were made in the period from the 1750s until the early 1900s. The custom of carving on trees was closely related to important grazing areas and the need to establish rights to them. The main losses of carved trees nowadays are due to their natural death and decay as most of the carved trees are located in areas that are not targeted for management. A primary recommendation for preservation is therefore to continue documentation of the trees because of the noticeable deterioration in readability of the carvings.     

Don’t miss the forest for the trees! Evidence for vertical differences in the response of plant diversity to disturbance in a tropical rain forest

Ecological studies in tropical rain forests traditionally focus on trees above a threshold diameter at breast height (dbh), since ignoring plant species of the other structural compartments is believed to be an acceptable tradeoff between exhaustiveness and effectiveness. However, the consequences of missing species below a threshold dbh value have been largely neglected so far. We evaluated whether the response of species diversity of ≥10-cm dbh trees was similar to the response of other structural ensembles (namely treelets, saplings, and terricolous herbs) in a lowland tropical rain forest, to three disturbance regimes: natural gap dynamics (control), and selective logging with and without additional thinning. We studied forest vegetation composition and diversity in a 20-yr replicated field experiment comprising nine 1 ha permanent plots established in a semi-deciduous rain forest of the Congo Basin and equally distributed among the three treatments. Once corrected by stem density, species richness was similar between logged (20 years since logging) and untouched old-growth forest stands with respect of trees, but higher with respect of treelets. As disturbance intensity increased, species richness increased within sapling layers but decreased within herb layers, while species spatial turnover (beta diversity) increased in both cases. Regarding the parameters of the partitioned rarefaction curves and relative abundance distribution curves, no correlation was found between trees and any of the other structural compartments. Whilst tree and treelet species composition was similar among treatments, the understories still reflected past disturbance intensity, with a strong response of the sapling and herb layers. These results show that ecological studies based solely on tree layers (dbh ≥ 10 cm) are misleading because their response to disturbance cannot be used as a surrogate for the response of other structural ensembles. Long-lasting effects of anthropogenic disturbance on the sapling bank and the herb layer may durably influence the long-term forest dynamics. Since overstory but not understory plant communities have recovered from human disturbances 20 years after silvicultural operations, African tropical rain forest ecosystems may not be as resilient to selective logging as previously thought.     

Recurrent selection alternating with haploid steps — a rapid breeding procedure for combining agronomic traits in inbreeders

Summary Doubled haploid lines are increasingly used in practical breeding programs. Depending on the nature of the starting material as well as on the breeding aims, one or more haploid steps are recommended, and F₁ hybrids or selfed progenies in later generations serve as starting material for the haploidization. It is demonstrated that one haploid step followed by selection in the greenhouse and in the field during the first androgenetic (A₁) and two subsequent selfed generations (A₂; A₃) is the most efficient procedure, if characters from related varieties are to be combined. For breeding programs that include wild types or unrelated genotypes, recurrent selection alternating with several haploid steps is the most efficient. A prerequisite for successful application of this combination of repeated haploidization and selection steps alternating with backcrosses is an effective selection system. The different approaches are demonstrated on a winter barley breeding program, with the central aim of combining the qualitatively inherited character resistance to barley yellow mosaic virus with quantitatively inherited complexes, particularly yield.     

Elite athletes’ genetic predisposition for altered risk of complex metabolic traits

Background

Genetic variants may predispose humans to elevated risk of common metabolic morbidities such as obesity and Type 2 Diabetes (T2D). Some of these variants have also been shown to influence elite athletic performance and the response to exercise training. We compared the genotype distribution of five genetic Single Nucleotide Polymorphisms (SNPs) known to be associated with obesity and obesity co-morbidities (IGF2BP2 rs4402960, LPL rs320, LPL rs328, KCJN rs5219, and MTHFR rs1801133) between athletes (all male, n = 461; endurance athletes n = 254, sprint/power athletes n = 207), and controls (all male, n = 544) in Polish and Russian samples. We also examined the association between these SNPs and the athletes’ competition level (‘elite’ and ‘national’ level). Genotypes were analysed by Single-Base Extension and Real-Time PCR. Multinomial logistic regression analyses were conducted to assess the association between genotypes and athletic status/competition level.

Results

IGF2BP2 rs4402960 and LPL rs320 were significantly associated with athletic status; sprint/power athletes were twice more likely to have the IGF2BP2 rs4402960 risk (T) allele compared to endurance athletes (OR = 2.11, 95% CI = 1.03-4.30, P <0.041), and non-athletic controls were significantly less likely to have the T allele compared to sprint/power athletes (OR = 0.62, 95% CI =0.43-0.89, P <0.0009). The control group was significantly more likely to have the LPL rs320 risk (G) allele compared to endurance athletes (OR = 1.26, 95% CI = 1.05-1.52, P <0.013). Hence, endurance athletes were the “protected” group being significantly (p < 0.05) less likely to have the risk allele compared to sprint/power athletes (IGF2BP2 rs4402960) and significantly (p < 0.05) less likely to have the risk allele compared to controls (LPL rs320). The other 3 SNPs did not show significant differences between the study groups.

Conclusions

Male endurance athletes are less likely to have the metabolic risk alleles of IGF2BP2 rs4402960 and LPL rs320, compared to sprint/power athletes and controls, respectively. These results suggest that some SNPs across the human genome have a dual effect and may predispose endurance athletes to reduced risk of developing metabolic morbidities, whereas sprint/power athletes might be predisposed to elevated risk.     

Interfamily variation in amphibian early life-history traits: raw material for natural selection?

The embryonic development and time to hatching of eggs can be highly adaptive in some species, and thus under selective pressure. In this study, we examined the underlying interfamily variation in hatching timing and embryonic development in a population of an oviparous amphibian, the rough-skinned newt (Taricha granulosa). We found significant, high variability in degree of embryonic development and hatching timing among eggs from different females. Patterns of variation were present regardless of temperature. We also could not explain the differences among families by morphological traits of the females or their eggs. This study suggests that the variation necessary for natural selection to act upon is present in the early life history of this amphibian.     

Genomic selection for fruit quality traits in apple (Malus×domestica Borkh.)

The genome sequence of apple (Malus×domestica Borkh.) was published more than a year ago, which helped develop an 8K SNP chip to assist in implementing genomic selection (GS). In apple breeding programmes, GS can be used to obtain genomic breeding values (GEBV) for choosing next-generation parents or selections for further testing as potential commercial cultivars at a very early stage. Thus GS has the potential to accelerate breeding efficiency significantly because of decreased generation interval or increased selection intensity. We evaluated the accuracy of GS in a population of 1120 seedlings generated from a factorial mating design of four females and two male parents. All seedlings were genotyped using an Illumina Infinium chip comprising 8,000 single nucleotide polymorphisms (SNPs), and were phenotyped for various fruit quality traits. Random-regression best liner unbiased prediction (RR-BLUP) and the Bayesian LASSO method were used to obtain GEBV, and compared using a cross-validation approach for their accuracy to predict unobserved BLUP-BV. Accuracies were very similar for both methods, varying from 0.70 to 0.90 for various fruit quality traits. The selection response per unit time using GS compared with the traditional BLUP-based selection were very high (>100%) especially for low-heritability traits. Genome-wide average estimated linkage disequilibrium (LD) between adjacent SNPs was 0.32, with a relatively slow decay of LD in the long range (r(2)?=?0.33 and 0.19 at 100 kb and 1,000 kb respectively), contributing to the higher accuracy of GS. Distribution of estimated SNP effects revealed involvement of large effect genes with likely pleiotropic effects. These results demonstrated that genomic selection is a credible alternative to conventional selection for fruit quality traits.     

Root–shoot allometry of tropical forest trees determined in a large-scale aeroponic system

Background and Aims

This study is a first step in a multi-stage project aimed at determining allometric relationships among the tropical tree organs, and carbon fluxes between the various tree parts and their environment. Information on canopy–root interrelationships is needed to improve understanding of above- and below-ground processes and for modelling of the regional and global carbon cycle. Allometric relationships between the sizes of different plant parts will be determined.

Methods

Two tropical forest species were used in this study: Ceiba pentandra (kapok), a fast-growing tree native to South and Central America and to Western Africa, and Khaya anthotheca (African mahogany), a slower-growing tree native to Central and Eastern Africa. Growth and allometric parameters of 12-month-old saplings grown in a large-scale aeroponic system and in 50-L soil containers were compared. The main advantage of growing plants in aeroponics is that their root systems are fully accessible throughout the plant life, and can be fully recovered for harvesting.

Key Results

The expected differences in shoot and root size between the fast-growing C. pentandra and the slower-growing K. anthotheca were evident in both growth systems. Roots were recovered from the aeroponically grown saplings only, and their distribution among various diameter classes followed the patterns expected from the literature. Stem, branch and leaf allometric parameters were similar for saplings of each species grown in the two systems.

Conclusions

The aeroponic tree growth system can be utilized for determining the basic allometric relationships between root and shoot components of these trees, and hence can be used to study carbon allocation and fluxes of whole above- and below-ground tree parts.     

From genome to phenome—Simple inborn errors of metabolism as complex traits

Sporadically, patients with a proven defect in either mFAO or OXPHOS are described presenting with a metabolic profile and clinical phenotype expressing concurrent defects in both pathways. Biochemical linkages between both processes are tight. Therefore, it is striking that concurrent dysfunction of both systems occurs so infrequent. In this review, the linkages between OXPHOS and mFAO and the hypothesized processes responsible for concurrent problems in both systems are reviewed, both from the point of view of primary biochemical connections and secondary cellular responses, i.e. signaling pathways constituting nutrient-sensing networks. We propose that affected signaling pathways may play an important role in the phenomenon of concurrent defects. Recent data indicate that interference in the affected signaling pathways may resolve the pathological phenotype even though the primary enzyme deficiency persists. This offers new (unexpected) prospects for treatment of these inborn errors of metabolism. This article is part of a Special Issue entitled: From Genome to Function.     

Sexual selection in an anadromous population of threespine sticklebacks — no role for parasites

Summary We examined the hypothesis that trematode parasites played a role in the evolution of the red colour of male threespine sticklebacks (Gasterosteus aculeatus L.) and whether the parasites affected female fitness. Parasites (blackspot disease) played no role either in determining the outcome of male—male competition for breeding territories or in female mate choice. Among males with territories, mating success was highly variable. Some males obtained over 3000 eggs (approximately 10 matings) whereas others received none. In 1 year of the 2 year study, males with the greatest amount of red nuptial coloration had the greatest mating success. Although male colour may sometimes affect female choice in this system, this preference has probably not evolved because of the Hamilton—Zuk mechanism of sexual selection. The parasites had small, but statistically significant effects on female fitness. Females with high parasite loads were in poorer condition and produced fewer eggs than less parasitized fish.     

Expression of embryonic hemoglobin genes in mice heterozygous for α-thalassemia or β-duplication traits and in mice heterozygous for both traits

Hemoglobins of mouse embryos at 11.5 through 16.5 days of gestation were separated by electrophoresis on cellulose acetate and quantitated by a scanning densitometer to study the effects of two radiation-induced mutations on the expression of embryonic hemoglobin genes in mice. Normal mice produce three kinds of embryonic hemoglobins. In heterozygous α-thalassemic embryos, expression of EI (x₂y₂) and EII (α₂y₂) is deficient because the x- and α-globin genes of one of the allelic pairs of Hba on chromosome 11 was deleted or otherwise inactivated by X irradiation. Simultaneous inactivation of the x- and α-globin genes indicates that these genes must be closely linked. Reduced x- and α-chain synthesis results in an excess of y chains that associate as homotetramers. This unique y₄ hemoglobin also appears in β-duplication embryos where excess y chains are produced by the presence of three rather than two functional alleles of y- and β-globin genes. In double heterozygotes, which have a single functional allele of x- and α-globin genes and three functional alleles of y- and β-globin genes, synthesis of α and non-α chains is severely imbalanced and half of the total hemoglobin is y₄. Mouse y₄ has a high affinity for oxygen, P₅₀ of less than 10 mm Hg, but it lacks cooperativity so is inefficient for oxygen transport. The death of double heterozygotes in late fetal or neonatal life may be due in large part to oxygen deprivation to the tissues.     

Can we find the genes involved in complex traits?

A report on the third Complex Trait Consortium meeting, Bar Harbor, USA, 6-9 July 2004.     

Microclimate of tree cavities during winter nights—implications for roost site selection in birds

We examined the relationships between cavity temperature, ambient temperature outside the cavity and structural characteristics of 70 cavities measured for 1 night to determine if cavity roosting birds may potentially select warmer tree cavities for wintertime roosting. The mean temperature increment of the cavity (=cavity-ambient temperature) varied from −2.4 to 4.9°C and increased with higher day-to-night fluctuations in the ambient temperature, smaller cavity entrance and better health status of the cavity tree. Cavities in healthy trees were warmer than those in dead trees, but this difference disappeared with rising mean ambient temperatures. This interaction between the effects of tree health status and mean ambient temperature, as well as the effect of day-to-night fluctuations in the ambient temperature, were supported by the analysis of repeated measurements of temperature taken on 12 consecutive nights in five cavities. The variability in cavity microclimates makes the selection of warmer roost sites possible, and the predictors of microclimate may provide indirect cues to prospecting birds.     

Does canopy position affect wood specific gravity in temperate forest trees?

The radial increases in wood specific gravity known in many tree species have been interpreted as providing mechanical support in response to the stresses associated with wind loading. This interpretation leads to the hypothesis that individuals reaching the canopy should (1) be more likely to have radial increases in specific gravity and (2) exhibit greater increases than individuals in the subcanopy. Wood specific gravity was determined for three species of forest trees (Acer rubrum, Fagus grandifolia and Tsuga canadensis) growing in central Massachusetts, USA. Acer rubrum shows radial increases in specific gravity, but these increases are not more pronounced in canopy trees; the other two species show a pattern of radial decreases. The degree of radial increase or decrease is influenced by tree height and diameter. Of the dominant tree species for which we have data, A. rubrum, Betula papyrifera and Pinus strobus show radial increases in specific gravity, whereas F. grandifolia, T. canadensis and Quercus rubra show decreases. The occurrence of radial increases in B. papyrifera and P. strobus, which are often canopy emergents, suggests that it is overall adaptive strategy that is important rather than position (canopy vs. subcanopy) of any individual tree. It is suggested that radial increases in specific gravity are associated with early-successional status or characteristics and decreases with late-successional status or persistence in mature forest.