RNA-Seq Using Two Populations Reveals Genes and Alleles Controlling Wood Traits and Growth in Eucalyptus nitens

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.

Genetic effect in leaf and xylem transcriptome variations among Eucalyptus urophylla x grandis hybrids in field conditions

“…In total, 20,984±43 genes, that is about 58 % of E. grandis identified genes, were evenly expressed in the three E. urophylla x E. grandis hybrid genomes. The much higher number of non-DE genes compared to DE genes is consistent with findings of Thavamanikumar et al (2014) in xylem of E. nitens, and may be at least partly attributable to housekeeping genes that are constitutive genes required for the maintenance of basic cellular function and are expressed at relatively constant levels. Nevertheless such a low proportion of DE genes in our experiment was not expected given the natural differential expression existing between the urophylla and grandis parental species (Salazar et al, 2013), the disturbance in the regulation of gene expression often observed in interspecific hybrids (Hegarty et al, 2008) notably concerning the trans-regulatory mechanisms, the possible allele-specific expression mechanism (Song, 2016), and the open field cultivation conditions.…”

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

“…Complementing genetic information with molecular phenotypes (e.g., transcript levels) can contribute to a better mechanistic understanding of trait variation (24,26,27). Expression QTL (eQTL) analysis (28) allows the identification of genomic loci associated with variation in molecular phenotypes.…”

Biological significance of RNA-seq and single-cell genomic research in woody plants

“…RNA-seq technology has been used to investigate the development and 38 E. grandis genes are identified to locate in bona fide lignification clades and 17 genes may be involved in lignin biosynthesis in E. grandis (Carocha et al 2015). In E. nitens, 3953 transcripts have identified to be involved in biotic and abiotic stress response (Thavamanikumar et al 2014). In Eucalyptus grandis and E. urophylla, integrated analysis of transcript and trait variation in eucalypt hybrids could be useful in investigation of wood property traits (Kullan et al 2012).…”