Genetic Analysis of Diallel Tests of Loblolly Pine (Pinus Taeda L.).
Genetic Analysis of Diallel Tests of Loblolly Pine (Pinus Taeda L.).

Author:

Publisher:

Published: 2001

Total Pages:

ISBN-13:

DOWNLOAD EBOOK

A new approach was developed for analyzing diallel tests with SAS PROC MIXED and PROC IML. The new method can estimate variance components, obtain BLUE (best linear unbiased estimators) of fixed effects and BLUP (best linear unbiased predictors) of random genetic effects simultaneously. A new formula based on BLUP was further developed to predict individual tree breeding values. This new analytical method was validated using computer simulation and was compared with other existing programs. To analyze disconnected diallel mating designs with more than one diallel, simulated data generated with known parameters were analyzed using BLUP to compare three alternative models, which include diallel as fixed effect (Model 1), random effect (Model 2) or no diallel effect (Model 3). Both Model 1 and Model 3 produced unbiased GCA (general combining ability) variance estimates, while Model 2 resulted in downward biased GCA variance estimate. The accuracy of BLUP prediction for three models was very close, with Model 3 slightly better than the other two. Statistical approaches were also evaluated for combining multiple disconnected diallel test series in a given region. The best GCA sample variance prediction in the class of linear combination of local variance estimates was derived. Simulation study showed that a checklot adjustment was very critical to improve the prediction of genetic values obtained using BLUP analysis. Additional adjustment with improved GCA sample variance prediction could improve the correlation slightly beyond checklot adjustment. Analysis of annual measurement through age 8 from a total of 275 parents, 690 full-sib families from 23 diallel tests of loblolly pine in Northern, Coastal and Piedmont test regions showed: 1) dominance variance was small (20-40% of total genetic variance) relative to additive variance; 2) heritability increased over time, and the magnitude of heritabilities for diameter at breast height (DBH) and volume was comparable with the.

Gene Expression Analyses and Association Studies of Wood Development Genes in Loblolly Pine (pinus Taeda L.)
Gene Expression Analyses and Association Studies of Wood Development Genes in Loblolly Pine (pinus Taeda L.)

Author: Sreenath R. Palle

Publisher:

Published: 2011

Total Pages:

ISBN-13:

DOWNLOAD EBOOK

Gene expression analyses using native populations can provide information on the genetic and molecular mechanisms that determine intraspecific variation and contribute to the understanding of plant development and adaptation in multiple ways. Using quantitative real time - polymerase chain reaction (qRT-PCR), we analyzed the expression of 111 genes with probable roles in wood development in 400 loblolly pine individuals belonging to a population covering much of the natural range. Association mapping techniques are increasingly being used in plants to dissect complex genetic traits and identify genes responsible for the quantitative variation of these traits. We used candidate-gene based association studies to associate single nucleotide polymorphisms (SNPs) in candidate genes with the variation in gene expression. The specific objectives established for this study were to study natural variation in expression of xylem development genes in loblolly pine (Pinus taeda L.) using qRT-PCR, to associate SNPs in candidate genes with the variation in gene expression using candidate-gene based association analyses and to detect loblolly pine promoter polymorphisms and study their effect on gene expression. Out of the 111 genes analyzed using qRT-PCR, there were significant differences in expression among clones for 106 genes. Candidate-gene based association studies were performed between 3937 single nucleotide polymorphisms (SNPs) and gene expression to associate SNPs in candidate genes with the variation in gene expression. To the best of our knowledge, this is the first association genetic study where expression of a large number of genes, analyzed in a natural population, has been the phenotypic trait of interest. We cloned and sequenced promoters of 19 genes, 16 of which are transcription factors involved in wood development and drought response. SNP discovery was done in 13 of these promoters using a panel of 24 loblolly pine clones (unique genotypes). SNP genotyping is underway in the entire association population and association analyses will be done to study the effects of promoter SNPs on gene expression. The results from this project are promising and once these associations have been tested and proved, we believe that they will help in our understanding of the genetics of complex traits.

Gene Expression and Association Analyses of Stress Responses in Loblolly Pine (Pinus Taeda L.)
Gene Expression and Association Analyses of Stress Responses in Loblolly Pine (Pinus Taeda L.)

Author: Candace Marie Seeve

Publisher:

Published: 2012

Total Pages:

ISBN-13:

DOWNLOAD EBOOK

The molecular mechanisms underlying disease-resistance and drought-resistance in forest trees are not well understood. Linking variation in gene expression with genetic polymorphisms and with variations in disease- and drought-resistance phenotypes can provide information about these complex traits. We used real-time quantitative polymerase chain reaction (PCR) to detect variations in the expression of 88 disease- and drought-responsive genes within an association population of 354 loblolly pine trees (Pinus taeda L.). Using association genetics approaches, we then linked 3,938 single nucleotide polymorphisms (SNPs) in candidate genes with gene expression phenotypes to identify novel disease- and drought-responsive genes. To further examine differences in gene expression induced by drought, Fusarium circinatum (responsible for pitch canker disease), and drought +F. circinatum, the expression of 114 genes identified through comparative and association genetics approaches was analyzed on a subset of 24 loblolly pine trees possessing a range of pitch canker- and drought-resistance phenotypes. Significant differences in the uninduced expression of all 88 genes measured on the association population were observed among loblolly pine trees. Principal component analysis showed that some variation within the association population could be accounted for by population substructure of geographic origin. Hierarchical clustering of genes based on uninduced expression did not consistently group together functionally similar genes probably because expression was collected on unstressed stem tissue. This was supported in the smaller expression study as correlations between expression values of genes in the same functional networks were usually stronger when induced by a treatment compared with correlations between the uninduced expression of genes in the control group. Gene expression frequently changed by up to 4-fold in response to one or more treatments, but PtMYB12 was the only gene that exhibited a statistically significant change in response to treatments. ANOVA analyses of gene expression controlling for pitch canker resistance and for water use efficiency phenotypes identified differentially expressed genes suggesting that they may be contributing to these phenotypes. Finally, association genetics approaches detected 101 significant associations between SNPs in 94 candidate genes potentially involved in stress responses and 27 gene expression phenotypes.