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Carol Loopstra

Carol Loopstra

Associate Professor

Department of Ecosystem Science & Management

2138 TAMU
College Station , TX 77843-2138
Office Phone: (979) 862-2200

Education:

  1. B.S., Forest Management (Science Option), Oregon State University, 1979
  2. M.S., Forest Science, Oregon State University, 1984
  3. Ph.D., Forestry and Genetics (co-majors), North Carolina State University, 1992

Biography:

Research Interests:

The Loopstra lab is interested in the molecular genetics of loblolly pine, particularly adaptation to drought and climate change. Loblolly pine is commercially the most important pine in the United States and is also a model system for gymnosperms. We are currently involved in two large USDA National Institute of Food and Agriculture (NIFA) projects. The PineRefSeq (Pine Reference Sequences) project (http://pinegenome.org/pinerefseq/) is sequencing the genomes and transcriptomes of loblolly pine and sugar pine, the two largest genomes sequenced to date. The Loopstra lab has been involved in the collection and treatment of tissues for the transcriptomes and is involved in the data analyses. PINEMAP (Pine Integrated Network: Education, Mitigation, and Adaptation project) (http://pinemap.org) integrates research, extension, and education to enable southern pine landowners to manage forests to increase carbon sequestration; increase efficiency of nitrogen and other fertilizer inputs; and adapt forest management approaches to increase forest resilience and sustainability under variable climates. The Loopstra lab is using exome capture to obtain DNA for SNP (single nucleotide polymorphism) discovery and genotyping in a population of 384 trees from though out the native range. We will look for associations with phenotypic characteristics important for adaptation and productivity as well as with climatic variables.

Select Publications:

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. David B Neale, 36 other authors including Carol Loopstra. Genome Biology 2014, 15:R59 

Wegrzyn JL, Liechty JD, Stevens KA, Wu L-S, Loopstra CA, and 17 others. (2014) Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics 196:891-909.

Eckert AJ, Wegrzyn JL, Liechty JD, Lee JM, Cumbie WP, Davis JM, Goldfarb B, Loopstra CA, Palle SR, Quesada T, Langley CH, Neale DB. (2013) The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae). Genetics 195: 1353-1372

Palle SR, Seeve CM, Eckert AJ, Wegrzyn JL, Neale DB, Loopstra CA. (2013) Association of loblolly pine xylem development gene expression with single nucleotide polymorphisms. Tree Physiology 33(7):763-74

Palle SR, Seeve CM, Eckert AJ, Cumbie WP, Goldfarb B, and Loopstra CA. (2011) Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.). Tree Genetics and Genomes 7: 193-206

Kovach AS, Wegrzyn JL, Parra G , Holt C, Bruening GE, Loopstra CA, Hartigan J,  Yandell M, Langley CH, Korf I, Neale DB (2010) The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 11:420 doi:10.1186/1471-2164-11-420

Sathyan P, Newton RJ, and Loopstra CA (2005) Genes induced by WDS are differentially expressed in two populations of aleppo pine (Pinus halepensis). Tree Genetics and Genomes 1(4):166-173

Yang S-H and Loopstra CA (2005) Seasonal variation in gene expression for loblolly pines (Pinus taeda L.) from different geographical regions. Tree Physiology 25:1063-1073

Yang S-H, Wang H, Sathyan P, Stasolla C, and Loopstra CA (2005) Real-time RT-PCR analysis of loblolly pine (Pinus taeda L.) arabinogalatactan protein and arabinogalactan-protein-like genes. Physiologia Plantarum 124: 94-126

Yang S-H, van Zyl L, No E-G, and Loopstra CA (2004) Microarray analysis of genes preferentially expressed in differentiating xylem of loblolly pine (Pinus taeda). Plant Science 166:1185-1195