@article{walker_maynor_isik_heine_whetten_payn_quate_mckeand_2024, title={Stem Defect Rates and Ice Storm Damage for Families of Pinus taeda from Coastal and Piedmont Provenances Planted on a North Carolina Piedmont Site}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxae016}, DOI={10.1093/forsci/fxae016}, abstractNote={Abstract}, journal={FOREST SCIENCE}, author={Walker, Trevor D. and Maynor, Jessica A. and Isik, Fikret and Heine, Austin J. and Whetten, Ross W. and Payn, Kitt G. and Quate, T. Austin and McKeand, Steven E.}, year={2024}, month={Apr} }
 @article{shalizi_walker_heine_payn_isik_bullock_mckeand_2023, title={Performance Based on Measurements from Individual-Tree Progeny Tests Strongly Predicts Early Stand Yield in Loblolly Pine}, volume={2}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxad002}, DOI={10.1093/forsci/fxad002}, abstractNote={Abstract}, journal={FOREST SCIENCE}, author={Shalizi, Mohammad Nasir and Walker, Trevor D. and Heine, Austin J. and Payn, Kitt G. and Isik, Fikret and Bullock, Bronson P. and McKeand, Steven E.}, year={2023}, month={Feb} }
 @article{niknejad_bidese-puhl_bao_payn_zheng_2023, title={Phenotyping of architecture traits of loblolly pine trees using stereo machine vision and deep learning: Stem diameter, branch angle, and branch diameter}, volume={211}, ISSN={["1872-7107"]}, DOI={10.1016/j.compag.2023.107999}, abstractNote={Loblolly pine is one of the most planted forest tree species in the Southern United States for sawtimber production. The sawtimber yield potential of a pine tree is significantly impacted by its stem and branch architecture, which is of important focus in tree improvement programs. However, phenotyping these traits in the upper crown of pine trees is currently based on subjective visual assessments. This study investigated the feasibility of quantifying stem diameter, branch angle, and branch diameter of six-year-old loblolly pine trees in a progeny test using stereo 3D imaging, deep learning-based instance segmentation, and image and point cloud processing techniques. Instance segmentation of branches and stems was performed as well as principal component analysis (PCA) in 2D images, followed by 3D reconstruction of the segmented organs. The resulting 3D point clouds were further processed using random sample consensus (RANSAC) and statistical outlier removal to extract stem diameter, branch angle, and branch diameter. When compared to the manual ground-truth measurements, the three system-derived parameters achieved RMSEs of 0.055 m, 5.0˚, and 5.6 mm, respectively. In addition, Bland-Altman analyses showed that the stem diameter and branch angle estimations were found with limits of agreement of ± 0.098 m and ± 9.8˚, respectively, with nonsignificant biases. On the other hand, branch diameter estimation showed −12.1 mm and 9.3 mm for lower and upper limits of agreement with a bias. The proposed system demonstrates promising potential as a high-throughput low-cost precision phenotyping tool for the characterization of loblolly pine tree architecture under field conditions, facilitating the selection of superior genotypes with improved sawtimber properties.}, journal={COMPUTERS AND ELECTRONICS IN AGRICULTURE}, author={Niknejad, Nariman and Bidese-Puhl, Rafael and Bao, Yin and Payn, Kitt G. and Zheng, Jingyi}, year={2023}, month={Aug} }
 @article{shalizi_payn_isik_2022, title={Genetic linkage between the training and selection sets impacts the predictive ability of SNP markers in a cloned population of Pinus taeda L.}, volume={18}, ISSN={["1614-2950"]}, url={https://doi.org/10.1007/s11295-021-01532-9}, DOI={10.1007/s11295-021-01532-9}, number={1}, journal={TREE GENETICS & GENOMES}, publisher={Springer Science and Business Media LLC}, author={Shalizi, Mohammad Nasir and Payn, Kitt G. and Isik, Fikret}, year={2022}, month={Feb} }
 @article{shalizi_payn_walker_isik_heine_mckeand_2022, title={Long-term evaluation of intra- and inter-provenance hybrids of loblolly pine in the Piedmont region of the southeastern United States}, volume={522}, ISSN={["1872-7042"]}, url={http://dx.doi.org/10.1016/j.foreco.2022.120469}, DOI={10.1016/j.foreco.2022.120469}, abstractNote={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 (C×C, P×P) and their hybrids (C×P, P×C) were field tested for growth, sawtimber potential, and survival through age 19 years. The Coastal pure (C×C) families were the tallest, and the hybrid populations (C×P, P×C) were intermediate for height. The four populations did not differ for diameter at breast height. The hybrid C×P population, followed by the C×C population, showed significantly higher stand volumes per hectare. These two populations maintained higher survival and stand density compared to the Piedmont pure populations. Sawtimber potential was significantly higher in the Piedmont pure families at the coldest study sites, presumably due to defect in the C×C and C×P from cold damage. No significant genotype-by-environment interactions were detected for any traits. The genetic gain for height, stand volume, and survival was considerable in the C×C and C×P over the Piedmont source, suggesting potential for benefiting from the faster growth of the Coastal material in the Piedmont region. The performance of the Coastal intra- and inter-provenance populations was marginally affected by the minimum winter temperatures (MWT). These results indicate that the Coastal and the hybrid families can be planted in the Piedmont region with MWT’s of −13 °C or greater and where the difference in MWT between the origin of the Coastal parents and the test sites was not extreme (e.g., the difference did not exceed 2.8 °C). These MWT limits encompass the southern Piedmont of North Carolina (<35.615 °N) and the Piedmont of South Carolina, Georgia, and Alabama.}, journal={FOREST ECOLOGY AND MANAGEMENT}, publisher={Elsevier BV}, author={Shalizi, Mohammad Nasir and Payn, Kitt G. and Walker, Trevor D. and Isik, Fikret and Heine, Austin J. and McKeand, Steven E.}, year={2022}, month={Oct} }
 @misc{matallana-ramirez_whetten_sanchez_payn_2021, title={Breeding for Climate Change Resilience: A Case Study of Loblolly Pine (Pinus taeda L.) in North America}, volume={12}, ISSN={["1664-462X"]}, url={https://doi.org/10.3389/fpls.2021.606908}, DOI={10.3389/fpls.2021.606908}, abstractNote={Earth’s atmosphere is warming and the effects of climate change are becoming evident. A key observation is that both the average levels and the variability of temperature and precipitation are changing. Information and data from new technologies are developing in parallel to provide multidisciplinary opportunities to address and overcome the consequences of these changes in forest ecosystems. Changes in temperature and water availability impose multidimensional environmental constraints that trigger changes from the molecular to the forest stand level. These can represent a threat for the normal development of the tree from early seedling recruitment to adulthood both through direct mortality, and by increasing susceptibility to pathogens, insect attack, and fire damage. This review summarizes the strengths and shortcomings of previous work in the areas of genetic variation related to cold and drought stress in forest species with particular emphasis on loblolly pine (Pinus taedaL.), the most-planted tree species in North America. We describe and discuss the implementation of management and breeding strategies to increase resilience and adaptation, and discuss how new technologies in the areas of engineering and genomics are shaping the future of phenotype-genotype studies. Lessons learned from the study of species important in intensively-managed forest ecosystems may also prove to be of value in helping less-intensively managed forest ecosystems adapt to climate change, thereby increasing the sustainability and resilience of forestlands for the future.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Matallana-Ramirez, Lilian P. and Whetten, Ross W. and Sanchez, Georgina M. and Payn, Kitt G.}, year={2021}, month={Apr} }
 @article{lu_payn_pandey_acosta_heine_walker_young_2021, title={HYPERSPECTRAL IMAGING WITH COST-SENSITIVE LEARNING FOR HIGH-THROUGHPUT SCREENING OF LOBLOLLY PINE (PINUS TAEDA L.) SEEDLINGS FOR FREEZE TOLERANCE}, volume={64}, ISSN={["2151-0040"]}, url={http://dx.doi.org/10.13031/trans.14708}, DOI={10.13031/trans.14708}, abstractNote={Highlights}, number={6}, journal={TRANSACTIONS OF THE ASABE}, publisher={American Society of Agricultural and Biological Engineers (ASABE)}, author={Lu, Yuzhen and Payn, Kitt G. and Pandey, Piyush and Acosta, Juan J. and Heine, Austin J. and Walker, Trevor D. and Young, Sierra}, year={2021}, pages={2045–2059} }
 @article{pandey_payn_lu_heine_walker_acosta_young_2021, title={Hyperspectral Imaging Combined with Machine Learning for the Detection of Fusiform Rust Disease Incidence in Loblolly Pine Seedlings}, volume={13}, ISSN={["2072-4292"]}, url={https://doi.org/10.3390/rs13183595}, DOI={10.3390/rs13183595}, abstractNote={Loblolly pine is an economically important timber species in the United States, with almost 1 billion seedlings produced annually. The most significant disease affecting this species is fusiform rust, caused by Cronartium quercuum f. sp. fusiforme. Testing for disease resistance in the greenhouse involves artificial inoculation of seedlings followed by visual inspection for disease incidence. An automated, high-throughput phenotyping method could improve both the efficiency and accuracy of the disease screening process. This study investigates the use of hyperspectral imaging for the detection of diseased seedlings. A nursery trial comprising families with known in-field rust resistance data was conducted, and the seedlings were artificially inoculated with fungal spores. Hyperspectral images in the visible and near-infrared region (400–1000 nm) were collected six months after inoculation. The disease incidence was scored with traditional methods based on the presence or absence of visible stem galls. The seedlings were segmented from the background by thresholding normalized difference vegetation index (NDVI) images, and the delineation of individual seedlings was achieved through object detection using the Faster RCNN model. Plant parts were subsequently segmented using the DeepLabv3+ model. The trained DeepLabv3+ model for semantic segmentation achieved a pixel accuracy of 0.76 and a mean Intersection over Union (mIoU) of 0.62. Crown pixels were segmented using geometric features. Support vector machine discrimination models were built for classifying the plants into diseased and non-diseased classes based on spectral data, and balanced accuracy values were calculated for the comparison of model performance. Averaged spectra from the whole plant (balanced accuracy = 61%), the crown (61%), the top half of the stem (77%), and the bottom half of the stem (62%) were used. A classification model built using the spectral data from the top half of the stem was found to be the most accurate, and resulted in an area under the receiver operating characteristic curve (AUC) of 0.83.}, number={18}, journal={REMOTE SENSING}, publisher={MDPI AG}, author={Pandey, Piyush and Payn, Kitt G. and Lu, Yuzhen and Heine, Austin J. and Walker, Trevor D. and Acosta, Juan J. and Young, Sierra}, year={2021}, month={Sep} }
 @article{lu_walker_acosta_young_pandey_heine_payn_2021, title={Prediction of Freeze Damage and Minimum Winter Temperature of the Seed Source of Loblolly Pine Seedlings Using Hyperspectral Imaging}, volume={67}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxab003}, DOI={10.1093/forsci/fxab003}, abstractNote={Abstract}, number={3}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Lu, Yuzhen and Walker, Trevor D. and Acosta, Juan J. and Young, Sierra and Pandey, Piyush and Heine, Austin J. and Payn, Kitt G.}, year={2021}, month={Jun}, pages={321–334} }
 @article{maynor_isik_walker_whetten_heine_payn_mckeand_2021, title={Provenance and Family Variation in Biomass Potential of Loblolly Pine in the Piedmont of North Carolina}, volume={67}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxaa056}, DOI={10.1093/forsci/fxaa056}, abstractNote={Abstract}, number={3}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Maynor, Jessica A. and Isik, Fikret and Walker, Trevor D. and Whetten, Ross W. and Heine, Austin J. and Payn, Kitt G. and McKeand, Steven E.}, year={2021}, month={Jun}, pages={312–320} }
 @article{mhoswa_o'neill_mphahlele_oates_payn_slippers_myburg_naidoo_2020, title={A Genome-Wide Association Study for Resistance to the Insect Pest Leptocybe invasa in Eucalyptus grandis Reveals Genomic Regions and Positional Candidate Defense Genes}, volume={61}, ISSN={["1471-9053"]}, DOI={10.1093/pcp/pcaa057}, abstractNote={Abstract}, number={7}, journal={PLANT AND CELL PHYSIOLOGY}, author={Mhoswa, Lorraine and O'Neill, Marja M. and Mphahlele, Makobatjatji M. and Oates, Caryn N. and Payn, Kitt G. and Slippers, Bernard and Myburg, Alexander A. and Naidoo, Sanushka}, year={2020}, month={Jul}, pages={1285–1296} }
 @article{mckeand_payn_heine_abt_2020, title={Economic Significance of Continued Improvement of Loblolly Pine Genetics and Its Efficient Deployment to Landowners in the Southern United States}, volume={119}, ISSN={0022-1201 1938-3746}, url={http://dx.doi.org/10.1093/jofore/fvaa044}, DOI={10.1093/jofore/fvaa044}, abstractNote={Abstract}, number={1}, journal={Journal of Forestry}, publisher={Oxford University Press (OUP)}, author={McKeand, Steven E and Payn, Kitt G and Heine, Austin J and Abt, Robert C}, year={2020}, month={Dec}, pages={62–72} }
 @article{naidoo_christie_acosta_mphahlele_payn_myburg_külheim_2018, title={Terpenes associated with resistance against the gall wasp, Leptocybe invasa
, in Eucalyptus grandis}, volume={41}, ISSN={0140-7791}, url={http://dx.doi.org/10.1111/pce.13323}, DOI={10.1111/pce.13323}, abstractNote={Abstract}, number={8}, journal={Plant, Cell & Environment}, publisher={Wiley}, author={Naidoo, Sanushka and Christie, Nanette and Acosta, Juan J. and Mphahlele, Makobatjatji M. and Payn, Kitt G. and Myburg, Alexander A. and Külheim, Carsten}, year={2018}, month={Jun}, pages={1840–1851} }
 @article{fitza_payn_steenkamp_myburg_naidoo_2013, title={Chitosan application improves resistance to Fusarium circinatum in Pinus patula}, volume={85}, ISSN={0254-6299}, url={http://dx.doi.org/10.1016/j.sajb.2012.12.006}, DOI={10.1016/j.sajb.2012.12.006}, abstractNote={Fusarium circinatum is the causal agent for the disease, pitch canker, in Pinus patula. Commercial forestry incurs large economic losses from the pathogen, primarily as a result of post-planting mortality resulting in increased re-establishment costs. One means of enhancing defense is through pretreatment of seedlings with chemicals or biologically derived compounds that stimulate defense responses; a process collectively known as induced resistance. We compared the efficiency of ten inducers in improving defense against F. circinatum in P. patula seedlings. Chitosan (10 mg/ml) was effective in reducing and delaying disease symptoms of pitch canker in seedlings. Under both nursery and greenhouse conditions, chitosan application resulted in reduced lesion lengths in treated plants compared to non-treated plants over a period of six weeks (p < 0.05, Kruskal–Wallis). Reverse transcription-quantitative PCR expression analysis revealed that the reduction in lesion size in treated seedlings was accompanied by a four-fold increase in transcript abundance of the phenylalanine ammonia lyase transcript, which encodes an enzyme involved in the first committed step of the phenylpropanoid pathway. We suggest that the application of chitosan as part of an integrated management strategy, be further investigated for an effective approach to induce resistance in P. patula seedlings against F. circinatum.}, journal={South African Journal of Botany}, publisher={Elsevier BV}, author={Fitza, K.N.E. and Payn, K.G. and Steenkamp, E.T. and Myburg, A.A. and Naidoo, S.}, year={2013}, month={Mar}, pages={70–78} }
 @article{kanzler_payn_nel_2012, title={Performance of two Pinus patula hybrids in southern Africa}, volume={74}, ISSN={2070-2620 2070-2639}, url={http://dx.doi.org/10.2989/20702620.2012.683639}, DOI={10.2989/20702620.2012.683639}, abstractNote={Two Pinus patula hybrids, P. greggii × P. patula and P. patula × P. tecunumanii, were planted across a number of sites in southern Africa. The growth and survival for each species/taxon was assessed at either 5 or 8 years of age at each site and compared to the respective parental species. Pinus greggii, as a pure species, has greater drought tolerance and is better adapted to harsher sites than P. patula. At 8 years the P. greggii × P. patula hybrid had similar survival and was more productive than P. patula at the two sites where it was tested. Furthermore, the performance of the hybrid was better than pure species on the site with average poorer growth suggesting that this hybrid could be planted on poorer, more marginal sites not well suited to P. patula. Pinus tecunumanii is a productive species with good tolerance to the pitch canker fungus (PCF). Previous work has shown that the P. patula × P. tecunumanii hybrid is more tolerant to PCF after field inoculations. The latter hybrid was assessed at 5 years on three sites and compared to both parent species. The hybrid had similar survival and was more productive than both parent species. Large variation in performance between individual P. patula × P. tecunumanii families suggests that comprehensive testing and selection should be conducted in tandem with any operational deployment of this hybrid.}, number={1}, journal={Southern Forests: a Journal of Forest Science}, publisher={Informa UK Limited}, author={Kanzler, A and Payn, K and Nel, A}, year={2012}, month={Mar}, pages={19–25} }
 @article{fitza_myburg_steenkamp_payn_naidoo_2011, title={Induced resistance and associated defence gene responses in Pinus patula}, volume={5}, ISSN={1753-6561}, url={http://dx.doi.org/10.1186/1753-6561-5-s7-p82}, DOI={10.1186/1753-6561-5-s7-p82}, abstractNote={Background Plants are able to incite a type of broad spectrum resistance against pathogens upon pre-treatment with biological or chemical inducers. Systemic Acquired Resistance (SAR) and Induced Systemic Resistance (ISR) are two types of induced resistance which lead to the accumulation of specific pathogenesis-related (PR) proteins. Non-pathogenic rhizobacteria are inducing agents for ISR and increased levels of ethylene (ET) and jasmonate (JA) are associated with this pathway, whereas SAR is associated with an increase in salicylic acid (SA) levels [1]. Pinus patula and P. radiata are commercially planted conifer species in South Africa, but are both highly susceptible to the causal agent of pitch canker, Fusarium circinatum. Annually, the forestry sector suffers substantial economic losses due to this disease which affects 20-30% of the planting stock. Bonello et al. (2001) showed that repeated mechanical inoculation of P. radiata with F. circinatum activated induced resistance, enhancing the protection of the tree against subsequent pathogen challenge [2]. Detailed knowledge of the molecular mechanisms underlying induced resistance may be useful to develop strategies to control diseases of pine trees. This study aimed to compare the efficiency of ten biological and chemical inducers in inciting resistance against F. circinatum. Additionally the molecular basis of this induced resistance was investigated by analyzing the response of selected putative defence response genes.}, number={S7}, journal={BMC Proceedings}, publisher={Springer Nature}, author={Fitza, Katrin and Myburg, AA and Steenkamp, Emma and Payn, Kitt and Naidoo, Sanushka}, year={2011}, month={Sep} }
 @article{payn_dvorak_janse_myburg_2008, title={Microsatellite diversity and genetic structure of the commercially important tropical tree species Eucalyptus urophylla, endemic to seven islands in eastern Indonesia}, volume={4}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-007-0128-7}, number={3}, journal={TREE GENETICS & GENOMES}, author={Payn, Kitt G. and Dvorak, William S. and Janse, Bernard J. H. and Myburg, Alexander A.}, year={2008}, month={Jul}, pages={519–530} }
 @article{dvorak_hodge_payn_2008, title={The conservation and breeding of Eucalyptus urophylla: a case study to better protect important populations and improve productivity}, volume={70}, ISSN={["2070-2639"]}, DOI={10.2989/south.for.2008.70.2.3.531}, abstractNote={Eucalyptus urophylla is one of the most commercially important forest species in the world, primarily as a hybrid parent. However, the conservation status of the majority of the populations where it naturally occurs on seven islands in eastern Indonesia range from critically endangered to vulnerable. We examine the evolutionary forces that might have caused genetic variation within and between E. urophylla populations and link these findings to international provenance trial results and molecular marker studies. We demonstrate that one climatic type does not describe all E. urophylla populations. We suggest that volcanism played an important role in its distribution and levels of genetic diversity on the islands. We report significant provenance variation for survival and growth in trials established in Brazil, Colombia, Mexico, South Africa and Venezuela. Provenance differences for growth within a country are sometimes >50%. Based on these assessments, we develop an ex situ conservation strategy to protect populations that are most threatened but also show the greatest productivity across countries. We conclude that populations of E. urophylla will only be conserved ex situ if traditional and molecular tree breeders convince private industry of the economic importance to do so.}, number={2}, journal={SOUTHERN FORESTS-A JOURNAL OF FOREST SCIENCE}, author={Dvorak, W. S. and Hodge, G. R. and Payn, K. G.}, year={2008}, month={Aug}, pages={77–85} }
 @article{payn_dvorak_myburg_2007, title={Chloroplast DNA phylogeography reveals the island colonisation route of Eucalyptus urophylla (Myrtaceae)}, volume={55}, ISSN={0067-1924}, url={http://dx.doi.org/10.1071/bt07056}, DOI={10.1071/bt07056}, abstractNote={We present a study of the colonisation patterns of a tropical tree species among an island archipelago. Eucalyptus urophylla (S.T.Blake) is an economically important plantation species endemic to the volcanic slopes of seven islands in eastern Indonesia. In the present study, we investigated the geographical distribution of chloroplast DNA sequence variation in E. urophylla to gain insight into its historical seed-migration routes. DNA sequence data were obtained from 198 plants from which 20 haplotypes were identified. A moderate to high level of chloroplast genetic differentiation (GST = 0.581, NST = 0.724) and significant phylogeographic structure (NST > GST; P < 0.01) were observed, suggesting low levels of recurrent seed-mediated gene flow among the islands. The highest levels of haplotype diversity were observed on the eastern islands of Wetar and Timor. The two most westerly islands, Flores and Lomblen, were fixed for what appeared to be the ancestral haplotype. Chloroplast haplotype diversity therefore exhibited a decreasing trend from east to west in the species’ range, consistent with an east-to-west colonisation route across the seven islands. Environmental factors that may have contributed to the contemporary spatial distribution of chloroplast DNA haplotypes include island paleogeology, ocean currents, fluctuations in sea levels and possible hybridisation events.}, number={7}, journal={Australian Journal of Botany}, publisher={CSIRO Publishing}, author={Payn, Kitt G. and Dvorak, William S. and Myburg, Alexander A.}, year={2007}, pages={673} }