@article{eckert_wegrzyn_cumbie_goldfarb_huber_tolstikov_fiehn_neale_2012, title={Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome}, volume={193}, ISSN={["1469-8137"]}, DOI={10.1111/j.1469-8137.2011.03976.x}, abstractNote={The metabolome of a plant comprises all small molecule metabolites, which are produced during cellular processes. The genetic basis for metabolites in nonmodel plants is unknown, despite frequently observed correlations between metabolite concentrations and stress responses. A quantitative genetic analysis of metabolites in a nonmodel plant species is thus warranted. Here, we use standard association genetic methods to correlate 3563 single nucleotide polymorphisms (SNPs) to concentrations of 292 metabolites measured in a single loblolly pine (Pinus taeda) association population. A total of 28 single locus associations were detected, representing 24 and 20 unique SNPs and metabolites, respectively. Multilocus Bayesian mixed linear models identified 2998 additional associations for a total of 1617 unique SNPs associated to 255 metabolites. These SNPs explained sizeable fractions of metabolite heritabilities when considered jointly (56.6% on average) and had lower minor allele frequencies and magnitudes of population structure as compared with random SNPs. Modest sets of SNPs (n = 1-23) explained sizeable portions of genetic effects for many metabolites, thus highlighting the importance of multi-SNP models to association mapping, and exhibited patterns of polymorphism consistent with being linked to targets of natural selection. The implications for association mapping in forest trees are discussed.}, number={4}, journal={NEW PHYTOLOGIST}, author={Eckert, Andrew J. and Wegrzyn, Jill L. and Cumbie, W. Patrick and Goldfarb, Barry and Huber, Dudley A. and Tolstikov, Vladimir and Fiehn, Oliver and Neale, David B.}, year={2012}, month={Mar}, pages={890–902} }
 @article{cumbie_eckert_wegrzyn_whetten_neale_goldfarb_2011, title={Association genetics of carbon isotope discrimination, height and foliar nitrogen in a natural population of Pinus taeda L}, volume={107}, ISSN={0018-067X 1365-2540}, url={http://dx.doi.org/10.1038/hdy.2010.168}, DOI={10.1038/hdy.2010.168}, abstractNote={Loblolly pine, Pinus taeda L., is one of the most widely planted, commercially and ecologically important tree species in North America. We took an association genetics approach, using an unimproved population of 380 clonally replicated unrelated trees, to test 3,938 single nucleotide polymorphisms (SNPs) in as many genes for association with phenotypic variation in carbon isotope discrimination, foliar nitrogen concentration and total tree height after two growing seasons. Best linear unbiased prediction (BLUP) was used with a spatial adjustment to remove environmental variation from phenotypic data derived from a common garden experiment. After correction for multiple testing, a total of 14 SNPs were associated with the traits of carbon isotope discrimination (n = 7), height (n = 1) and foliar nitrogen concentration (n = 6) using 380 clones. Tails of the population phenotypic distribution were compared for allele frequency differences, revealing 10 SNPs with allele frequency in at least one tail significantly different from the overall population. Eight associated SNPs were in sequences similar to known genes, such as an AP2 transcription factor related to carbon isotope discrimination and glutamate decarboxylase associated with foliar nitrogen concentration, and others were from unknown genes without homologs in Arabidopsis.}, number={2}, journal={Heredity}, publisher={Springer Science and Business Media LLC}, author={Cumbie, W P and Eckert, A and Wegrzyn, J and Whetten, R and Neale, D and Goldfarb, B}, year={2011}, month={Jan}, pages={105–114} }
 @article{cumbie_isik_li_goldfarb_2011, title={Effects of propagule type on genetic parameters of wood density and growth in a loblolly pine progeny test at ages 10 and 11 years}, volume={7}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/s11295-011-0402-6}, DOI={10.1007/s11295-011-0402-6}, number={6}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Cumbie, W. Patrick and Isik, Fikret and Li, Bailian and Goldfarb, Barry}, year={2011}, month={Jul}, pages={1147–1158} }
 @article{palle_seeve_eckert_cumbie_goldfarb_loopstra_2011, title={Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.)}, volume={7}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-010-0325-7}, abstractNote={Gene expression analyses using native populations can contribute to the understanding of plant development and adaptation in multiple ways. These include the identification of candidate genes and genetic polymorphisms affecting expression and phenotypic traits and characterization of transcriptional networks. We analyzed the expression of 111 genes with probable roles in xylem/wood development in a population of loblolly pine (Pinus taeda L.) covering much of the natural range. Loblolly pine is one of the most commercially important forest tree species in the United States, and the discovery of genes and alleles contributing to desirable wood properties would be valuable. Of the 111 genes analyzed using quantitative reverse transcription–polymerase chain reaction, there were significant differences in gene expression between clones for 106 genes. Genes encoding lignin biosynthetic enzymes and arabinogalactan proteins were more variable than those encoding cellulose synthases or those involved in signal transduction. Several groups of genes with related functions form clusters. A network analysis identified transcription factors that may be key regulators of xylem development in pine. Secondary wall-associated NAC domain protein 1 (SND1) in particular appears to be involved in the regulation of many other genes. The cluster analysis using clones did not result in discrete populations but did identify some expression differences between regions. In the future, the gene expression data will be used for association analyses and promoter studies to understand how these gene expression differences are associated with specific genetic polymorphisms in other genes and promoters.}, number={1}, journal={TREE GENETICS & GENOMES}, author={Palle, Sreenath Reddy and Seeve, Candace M. and Eckert, Andrew J. and Cumbie, W. Patrick and Goldfarb, Barry and Loopstra, Carol A.}, year={2011}, month={Feb}, pages={193–206} }
 @article{quesada_gopal_cumbie_eckert_wegrzyn_neale_goldfarb_huber_casella_davis_2010, title={Association Mapping of Quantitative Disease Resistance in a Natural Population of Loblolly Pine (Pinus taeda L.)}, volume={186}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.110.117549}, abstractNote={Abstract}, number={2}, journal={GENETICS}, author={Quesada, Tania and Gopal, Vikneswaran and Cumbie, W. Patrick and Eckert, Andrew J. and Wegrzyn, Jill L. and Neale, David B. and Goldfarb, Barry and Huber, Dudley A. and Casella, George and Davis, John M.}, year={2010}, month={Oct}, pages={677–U336} }