Population genetic analysis of two species of Distylium : D. racemosum growing in East Asian evergreen broad-leaved forests and D. lepidotum endemic to the Ogasawara (Bonin) Islands Abstract Although the genetic structures of populations in several model organisms have been studied even at the genomic level, quite a few ecologically important or evolutionary interesting species, such as endemic species on oceanic islands, exist whose genetic variations have not yet been studied. Genetic studies of those species may add new insights to our knowledge of evolution, especially when accompanied with ecological and geological knowledge of the species. In this study, we analyzed the genetic variation of two related species of Hamamelidaceae, Distylium racemosum and Distylium lepidotum, living in different habitats and possessing distinctive morphological characteristics. Distylium racemosum is one of the dominant trees of broad-leaved evergreen forests in Japan, and D. lepidotum is a dominant shrub in dry scrub endemic to the Ogasawara Islands. We analyzed the nucleotide variation at 112 protein-coding loci in 95 samples for the two Distylium species and inferred population structure and demographic history on the basis of these data. Our results showed that the samples from two Distylium species were genetically clustered into the following three groups: D. racemosum, D. lepidotum in the Chichijima Island, and D. lepidotum in the Hahajima Island. Furthermore, D. racemosum appears to have diverged first approximately 10 million years ago (MYA), and, then, the split of two populations of D. lepidotum occurred around 1 MYA. Additionally, we detected a few candidate loci that may contribute to adaptation of the species or local populations by exploring the pattern of the variation within and between species using the FST-outlier approach.

Recent, Late Pleistocene fragmentation shaped the phylogeographic structure of the European black pine ( Pinus nigra Arnold) Abstract Fragmentation acting over geological times confers wide, biogeographical scale and genetic diversity patterns to species, through demographic and natural selection processes. To test the effects of historical fragmentation on the genetic diversity and differentiation of a widespread forest tree, Pinus nigra Arnold, the European black pine, and to resolve its demographic history, we described and modelled its spatial genetic structure and gene genealogy. We then tested which Pleistocene event, whether recent or ancient, could explain its widespread but patchy geographic distribution. We used a set of different genetic markers, both neutral and potentially adaptive, and either bi-parentally or paternally only inherited, and we sampled natural populations across the entire species range. We analysed the data using both frequentist population genetic and Bayesian inference methods to calibrate realistic, demographic timed scenarios. We also considered how habitat suitability might have affected demography by correlating climate variables at different recent Pleistocene ages with genetic diversity estimates. Species with geographically fragmented distribution areas are expected to display significant among-population genetic differentiation and low within-population genetic diversity. Contrary to these expectations, we show that the current diversity of Pinus nigra and its weak genetic spatial structure result from the Late Pleistocene or Early Holocene fragmentation of one ancestral population into six distinct genetic lineages. Gene flow among the different lineages is strong across forests and many current populations are admixed between lineages. We propose to modify the currently accepted international nomenclature made of five sub-species and name these six lineages using regionally accepted sub-species-level names.

Extending the cacao ( Theobroma cacao L.) gene pool with underrepresented genotypes: growth and yield traits Abstract The narrow level of diversity of cacao varieties that are currently cultivated in West Africa has been suggested as one of the major problems to yield improvement of the crop in its major production countries. In this study, combining abilities and heritability for growth and yield traits in 12 underrepresented cacao parents of diverse genetic groups were estimated using these as females in crosses with three tester parents. Progenies obtained from a North Carolina II (NC II) incomplete factorial mating design together with three standard varieties were evaluated in a randomized complete block design with four replications at two contrasting locations for three growth traits (percentage survival, trunk cross-sectional area in the juvenile stage (TCSAj), and jorquette height) and four yield traits (bean weight, number of beans per pod, bean yield, and yield efficiency). Mean performance of the progenies was significant (p < 0.05) for all the traits involved and progenies of some specific crosses performed better than the best standard variety. The female GCA, male GCA, and SCA male × female interaction effects were significant, which suggest that both additive and dominant effects are important in the inheritance of traits. Heritability was moderate to high (H2 = 0.35–0.70) for broad sense and low (h2ns = 0.17–0.30) for narrow sense. This indicates that even though the expression of traits is controlled by genes, it may partly be influenced by the environment. Parental clones A1/197 and DOM 3 which had significant positive GCA effect consistently produced progenies with high SCA values for most of the traits. Results from the study indicate that the underrepresented cacao clones represent a suitable genetic resource for broadening parental clones of current cacao varieties cultivated in Ghana and beyond.

Extant population genetic variation and structure of eastern white pine ( Pinus strobus L.) in the Southern Appalachians Abstract Eastern white pine (Pinus strobus L.) is a widespread conifer in eastern North America. A novel dieback phenomenon, as well as increasing global temperatures contributing to the contraction of suitable habitat, is threatening this species’ long-term persistence in the Southern Appalachian Mountains. This southern extent of its current range is where P. strobus is hypothesized to have survived in refugial populations during the last glacial maximum. As a result, extant populations located here may have higher levels of ancestral genetic diversity, and by extension, adaptive potential. We genotyped 432 P. strobus individuals from 23 sites throughout the Southern Appalachians and another 34 individuals from two reference populations in the northern USA, using 10 established microsatellite markers. Levels of genetic diversity in the southern portion of the range were comparable but not higher than reference northern populations. There was an overall heterozygote deficiency and high inbreeding coefficient (FIS = 0.173); however, these values were comparable to published research of P. strobus throughout the northern range. There was low overall genetic differentiation (FST = 0.055) among populations in the Southern Appalachians and population structure was best explained by ecoregions. These results show that P. strobus in the Southern Appalachians is a fairly heterogenous and admixed species with relatively high genetic diversity mostly partitioned within populations. The Southern Appalachians remains an important area for P. strobus conservation, but not necessarily because it is genetically unique.

Chromosomal characterization of a potential model mini-Citrus ( Fortunella hindsii ) Abstract Mini-Citrus Fortunella hindsii (Hongkong kumquat), a member of the Rutaceae family, has the potential to be a model citrus due to its unique botanical features, including small plant size and short juvenility. However, data on its chromosomal characteristics, including karyotype and chromosomal homology, is lacking. Our research further investigates the chromosomal features of four Fortunella genotypes, F. crassifolia (JG), F. hindsii (PE1, PE2, and ME1), using chromosomal karyotyping, chromomycin A3(CMA) staining, 45S rDNA FISH, and hierarchical cluster analysis. The results showed high diversity of both CMA banding patterns and 45S rDNA physical mapping among these four genotypes. Based on chromosome ideograms, it was found that chromosomes of polyembryonic JG, PE1, and PE2 were heterozygous, while chromosomes of monoembryonic ME1 were homozygous. CMA band-based cluster analysis showed that all four Fortunella genotypes belonged to a single group, distinct from other Citrus genotypes. This work suggests that homozygous monoembryonic F. hindsii (ME1) is suitable for future development into a model plant for Citrus genetic and functional genomics research.

Independent QTL underlie resistance to the native pathogen Quambalaria pitereka and the exotic pathogen Austropuccinia psidii in Corymbia Abstract Fungal diseases such as the exotic myrtle rust (Austropuccinia psidii), and the native Quambalaria shoot blight (QSB; caused by Quambalaria species including Q. pitereka), constitute a significant threat to both native forests and Corymbia plantations in Australia and overseas. We here use quantitative trait loci (QTL) analysis to understand the genetic architecture of resistance to these pathogens in C. torelliana and C. citriodora subsp. variegata. QTL analysis was undertaken using 360 genotypes from two F1 crosses of C. torelliana × C. citriodora subsp. variegata, phenotyped by controlled inoculation with the strain of A. psidii present in Australia and independent inoculations with two strains of Q. pitereka (QSB1 & QSB2). A total of 22 QTL were identified, six for rust and 16 for QSB. The QTL for resistance to A. psidii and Q. pitereka in these pedigrees were independent from one another since they were generally in different parts of the genome, with only one case of co-location (QTL peak location within ± 2 MB). The QTL for the different QSB strains all mapped to discrete locations. The QTL for QSB were generally of a greater effect size than those for A. psidii. Several co-locations with QTL for resistance to rust and other fungal pathogens found in another eucalypt, Eucalyptus globulus, were detected and the implications of this observation are discussed.

Creation of an avocado unambiguous genotype SNP database for germplasm curation and as an aid to breeders Abstract Avocado (Persea americana) is an important tropical and subtropical fruit tree crop. Traditional tree breeding programs face the challenges of long generation times and significant expense in land and personnel resources. Avocado selection and breeding can be more efficient and less expensive through the development and application of molecular markers. A total of 1524 individuals were genotyped with 384 SNPs creating the largest SNP genotype database for avocado. These individuals correspond to four extensive germplasm collections including two housed in Florida and two in California. In addition, hybrids and selections from two rootstock breeding programs have been genotyped. Genotype data were analyzed using an affinity propagation method to define 155 groups. The 384 SNP markers provided accurate genotype data for individuals from different Persea species as well as half-siblings. Therefore, the majority of the genetic diversity of the avocado germplasm and related species that were genotyped has been captured. A simple visual method can also be used to identify self-pollinated individuals among the half-siblings of known maternal parents and, in some cases, to infer likely candidates for the paternal parent. Finally, this dataset is unambiguous so breeders can determine the genetic diversity of their breeding stock to optimize avocado breeding and selection programs by identifying outcrossed individuals at the seedling stage, thus increasing the efficiency of avocado genetic improvement.

Fourth cycle breeding and testing strategy for Pinus taeda in the NC State University Cooperative Tree Improvement Program Abstract 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 constraints on progeny inbreeding and coancestry level. The final mating list (4th cycle population) is expected to produce an index breeding value 63% higher than the candidate population mated at random. The average inbreeding coefficient in the candidate population was 0.000146. It increased to 0.000285 in the 4th cycle progeny. Only eight crosses out of 748 with progeny inbreeding value greater than zero were included in the mating list. One parent with a high index breeding value was used in 13 matings. A high majority of 421 individuals (75%) were mated two or more times; the remaining were mated once. The Cooperative also made significant changes in experimental design protocols to increase the efficiency of progeny testing by implementing an alpha-cyclic incomplete row-column design. Progeny test series across years were connected with a rolling front testing strategy by overlapping genetic entries across years. The Cooperative is expected to complete the 4th cycle in about 14 years, a significant reduction compared to previous cycles. With availability of high-throughput genotyping platforms, the Cooperative is moving toward implementation of genomic selection in the 5th cycle and beyond.

From mass selection to genomic selection: one century of breeding for quantitative yield components of oil palm ( Elaeis guineensis Jacq.) Abstract More efficient methods are required to breed oil palm (Elaeis guineensis Jacq.) for yield maximization in order to meet the increased demand for palm oil while limiting environmental impacts. This review article analyzes the evolution of breeding schemes for oil palm yield and its quantative components and the changes expected to take place with genomic selection (GS). Genetic improvement of oil palm yield started in the 1920s through mass selection. Later, several disruptive improvements dramatically increased the rate of genetic progress: (1) understanding the heredity of fruit form and the adoption of tenera, with thicker mesocarp, in plantations; (2) the discovery of hybrid vigor and the adoption of modified reciprocal recurrent selection; and (3) clonal selection, exploiting intra-hybrid variability. In addition, the use of linear mixed models to estimate genetic values has made selection more efficient. Today, GS appears to be a new disruptive improvement that can speed up breeding schemes by avoiding field trials in some cycles and increase selection intensity by evaluating more candidates. The genetic potential for oil palm yield has increased considerably over one century of breeding. GS is expected to bring the rate of genetic progress to a previously unprecedented level. The future studies on oil palm GS will aim at making it efficient for all yield components. For this purpose, they should focus in particular on the optimization of training populations and on the improvement of prediction models. Minimizing environmental impacts will also require improvement in other aspects (resistance to diseases, cultural practices, etc.).

TcMYB1 , TcMYB4 , and TcMYB8 participate in the regulation of lignan biosynthesis in Taiwania cryptomerioides Hayata Abstract Taiwania (Taiwania cryptomerioides Hayata) is a conifer species that is rich in bioactive secondary metabolites. Lignans, which are the major extracts, are especially important, but the biosynthetic gene regulation and downstream biosynthesis pathways remain unclear. In a previous study, we identified three pinoresinol-lariciresinol reductase (PLR) genes in Taiwanina, and in the present study, the regulation of these PLR genes was investigated. Through next-generation transcriptome sequencing, gene co-expression network analysis was performed to predict the relationship between putative transcription factor genes and upstream biosynthetic genes. Three MYB genes were identified as putative lignan biosynthetic regulators and named TcMYB1, TcMYB4, and TcMYB8. The gene expression of TcMYBs and TcPLRs was further confirmed with real-time PCR. Finally, an Agrobacteria-mediated transient overexpression experiment was conducted, and the activation of proTcPLR3::YFP by TcMYBs suggested that TcMYB1, TcMYB4, and TcMYB8 are biosynthetic regulators of lignan. These lignan regulators can be used in further research and applied to achieve a higher lignan content.