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Drought stress is a major cause of tree mortality in Mediterranean coniferous forests. This study aims to investigate the genetics of drought tolerance in ponderosa pine (Pinus ponderosa), a highly valuable species in the western United States. Genotype-to-environment (G2E) association investigates the statistical association between genetic variation at individual loci and the environment, while genotype-to-phenotype (G2P) association identifies loci linked to a particular phenotype by correlating genotypes at SNPs with the variation in certain traits. By combining G2E and G2P association genetics, this study can identify both the loci and traits that may explain variation in drought tolerance in this pine species. Single Nucleotide Polymorphism (SNP) markers have rapidly gained popularity due to their abundance in most genomes and their amenability to high-throughput genotyping techniques. Genotyping-by-sequencing (GBS) has been demonstrated to be a robust and cost-effective genotyping method. We first compared the performance of four GBS bioinformatics pipelines, two of which require a reference genome (TASSEL-GBS V2 and Stacks), two of which are de novo pipelines (UNEAK and Stacks), on this large-genome non-model organism. Stacks with a reference genome produced the highest number of SNPs with lowest proportion of paralogs. Over 4 million SNPs were identified with 223 ponderosa pine individuals using this method and the reference genome of loblolly pine (Pinus taeda). Then I ran a G2E analysis with these SNPs and five chosen climatic variables using LFMM2, which controls for the effects of demographic processes and population structure on the distribution of genetic variation. I found 213 SNPs strongly associated with mean maximum temperature of summer, 335 with mean minimum temperature of winter, 1798 with April 1st snow pack, and 120 SNPs with mean climatic water deficit. Protein functions linked to associated SNPs include ubiquitination, the abscisic acid (ABA) signaling pathway, cell division or growth of roots or shoots, cell wall organization, seed dormancy. The G2P analysis was carried out based on greenhouse experiment data. Seeds from 48 genotyped mother trees were planted in both dry and wet treatments. Eight phenotypic traits were measured during or after the greenhouse experiment. Six were drought-responsive, including root length, root-shoot dry mass ratio, stomata density on adaxial side, and number of stomatal rows on abaxial side (all higher in dry treatment), as well as shoot weight and height growth (lower). I found 153 SNPs strongly associated with root length, 80 with shoot weight, 145 with height growth, 42 with adaxial stomatal density, 85 with abaxial stomatal rows, and 1530 with root-to-shoot ratio. The identified SNPs reside in genes with a wide variety of functions, including ubiquitination, abscisic acid (ABA) signaling pathway, cell division or growth of roots or shoots, cell wall organization, which overlap with most of the identified protein functions in the G2E analysis. Potentially, future studies can develop molecular tools based on the associated genetic markers to assist breeders and gene resource managers in developing and managing adapted populations.
This handbook was designed as a reference tool for forest geneticists, tree breeders and other tree improvement personnel, as well as a textbook for university courses and short-courses at the graduate level in quantitative genetics. The chapters focus on the decision points faced by quantitative geneticists and breeders in designing programs and analyzing data. Beginning with a justification for the use of quantitative genetics in decision making in tree improvement programs, the book continues with a brief presentation of fundamental principles, followed by discussions and evaluations of mating designs and field test designs, the use of best linear predictors to estimate breeding values, the use of computer programs in the analysis of variance for genetic information, the deployment of genetically improved stock for capturing gains, the use of economic models for program justification, and the development of seed transfer guidelines.
Excerpt from Genetic Variation and Seed Transfer Guidelines for Ponderosa Pine in the Ochoco and Malheur National Forests of Central Oregon Guidelines for the Deschutes NF and adjoining area will be presented in a sub sequent report oh variation throughout the east side of the Cascades in Oregon. About the Publisher Forgotten Books publishes hundreds of thousands of rare and classic books. Find more at www.forgottenbooks.com This book is a reproduction of an important historical work. Forgotten Books uses state-of-the-art technology to digitally reconstruct the work, preserving the original format whilst repairing imperfections present in the aged copy. In rare cases, an imperfection in the original, such as a blemish or missing page, may be replicated in our edition. We do, however, repair the vast majority of imperfections successfully; any imperfections that remain are intentionally left to preserve the state of such historical works.