Abstract
Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production in many parts of the world. Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. KPY is positively correlated with growth measured as diameter at breast height (DBH) in both trials. In total, six RNA bulks from two treatments were sequenced on an Illumina HiSeq platform. At 5% false discovery rate level, 3953 transcripts showed differential expression in the same direction in both trials; 2551 (65%) were down-regulated and 1402 (35%) were up-regulated in low KPY samples. The genes up-regulated in low KPY trees were largely involved in biotic and abiotic stress response reflecting the low growth among low KPY trees. Genes down-regulated in low KPY trees mainly belonged to gene categories involved in wood formation and growth. Differential allelic expression was observed in 2103 SNPs (in 1068 genes) and of these 640 SNPs (30%) occurred in 313 unique genes that were also differentially expressed. These SNPs may represent the cis-acting regulatory variants that influence total gene expression. In addition we also identified 196 genes which had Ka/Ks ratios greater than 1.5, suggesting that these genes are under positive selection. Candidate genes and alleles identified in this study will provide a valuable resource for future association studies aimed at identifying molecular markers for KPY and growth.
Highlights
Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production (KPY) in many parts of the world [1]
Sequencing output RNA samples of E. nitens trees representing the Kraft pulp yield (KPY) extremes were collected in two trials, Meunna and Florentine
Sequencing reads from three bulks within a treatment were used as biological replicates in differential gene expression analyses
Summary
Eucalyptus nitens (shining gum) is a perennial forest tree species grown mainly for kraft pulp production (KPY) in many parts of the world [1]. A common feature of most agronomic traits in trees is that they are complex, and likely to be controlled by variation in many genes. There are two approaches being explored in trees for applying markers in breeding for improvement of complex traits. Markers potentially controlling the trait occurring within candidate genes are identified using association genetics in candidate genes. These associated markers are used to predict traits as in GS with random markers [6]. The discovery of high quality candidate genes is a crucial step in the discovery of polymorphisms associated with complex traits such as growth and pulp yield
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