Drought is a major abiotic stress that adversely affects the growth and productivity of plants. Malondialdehyde (MDA), a substance produced by membrane lipids in response to reactive oxygen species (ROS), can be used as a drought indicator to evaluate the degree of plasma membrane damage and the ability of plants to drought stress tolerance. Still measuring MDA is usually a labor- and time-consuming task. In this study, near-infrared (NIR) spectroscopy combined with partial least squares (PLS) was used to obtain rapid and high-throughput measurements of MDA, and the application of this technique to plant drought stress experiments was also investigated. Two exotic conifer tree species, namely, slash pine (Pinus elliottii) and loblolly pine (Pinus taeda), were used as plant material exposed to drought stress; different types of spectral preprocessing methods and important feature-selection algorithms were applied to the PLS model to calibrate it and obtain the best MDA-predicting model. The results show that the best PLS model is established via the combined treatment of detrended variable–significant multivariate correlation algorithm (DET-sMC), where latent variables (LVs) were 6. This model has a respectable predictive capability, with a correlation coefficient (R2) of 0.66, a root mean square error (RMSE) of 2.28%, and a residual prediction deviation (RPD) of 1.51, and it was successfully implemented in drought stress experiments as a reliable and non-destructive method to detect the MDA content in real time.
ABSTRACT. This is the first comprehensive study of the genetic analysis of the majority of oleoresin components of slash pine (Pinus elliottii). Pine oleoresin, the resin secreted from the pine tree, is a raw material widely used in industrial products. The objective of this study was to explore the genetic variation and correlation between the major oleoresin components of 50 open pollinated families of slash pine. The individual narrow-sense heritability of the 23 oleoresin components and genetic correlations between them were estimated using the residual maximum likelihood in the flexible mixed modeling program, ASReml-R. A high heritability of 0.424 was observed for β-pinene. Moderate levels of heritability were estimated for β-phellandrene, methyl abietate, estragole, 15-hydroxy-dehydroabietic acid, and isopimaric acid methyl ester at 0.303, 0.294, 0.27, 0.258, and 0.2, respectively. The heritabilities for pimaric acid methyl ester, abieta-8, 13-diene-18-oic acid methyl ester, sandaracopimaric acid, methyl ester, and camphene were relatively low and ranged from 0.11 to 0.17. Many negative genetic correlations were observed as unfavorable while the corresponding phenotypic correlations presented no significant relationships or positive phenotypic correlations. However, the heritabilities and genetic correlations showed that single or multiple component selections and improvement, directly or indirectly, were effective. We postulate that genetic parameters estimated in this study will work as a reference in breeding programs of oleoresin components, especially in slash pine.
Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program.
The planting of Pinus elliottii Engelm. has now reached close to three million ha in China. Molecular breeding as part of the improvement program for P. elliottii in southern China has been carried out in recent years. Third-generation sequencing (Pacbio sequencing technology, TGS) was used to obtain the exome of P. elliottii for molecular breeding. A total of 35.8 Gb clean reads were generated using TGS. After removing the redundant reads, we obtained 80,339 high-accuracy transcripts. Significantly, a total of 76,411 transcripts (95.1%) were blasted to public annotation databases. We predicted 65,062 intact coding sequences (CDSs), 8916 alternative splicing events, 1937 long non-coding RNAs, and 22,109 simple sequence repeats (SSRs) based on these obtained transcripts. Using the public databases and the data obtained above, 23 orthologous single-copy genes were identified to analyze the phylogenetic relationships for Pinus firstly including P. elliottii. Many positive selection genes involved in important biological processes and metabolism pathways were identified between P. elliottii and other pines. These positive selection genes could be candidate genes to be researched on the genetic basis of superior performance. Our study is the first to reveal the full-length and well-annotated transcripts of P. elliottii, which could provide reference for short transcriptome sequences in the research of genetics, phylogenetics, and genetic improvement for the non-reference genome species.Forests 2019, 10, 942 2 of 21 and are highly heterozygous. Like other conifers, the genome assembly of pines is also very difficult to determine because of our inability to obtain inbreeding lines [6]. The genome size of pines is about 17-35 gigabase pairs (Gb) [8]. The fist pine genome of Pinus taeda (22 Gb) was first published in 2014 [9,10]. Subsequently, the genome of Pinus lambertiana (31 Gb) was published [11]. The published pine genome contains highly abundant transposable elements. These published pine species genomes provide important genetic information for Pinus genetic study. However, interspecific divergences make it difficult for other pines to reference these published genomes. Whole genome sequencing is complex, time-consuming, and expensive. Thus, a better strategy is needed to obtain genome information for pines. Single-molecule, real-time (SMRT) sequencing developed by Pacific BioSciences (PacBio) is a third-generation sequencing (TGS) technology, more concisely referred to as "PacBio sequencing". PacBio sequencing has been widely used to sequence full-length transcripts and is well-suited for the non-reference species to obtain a complete transcriptional landscape [12]. TGS could generate full-length cDNA sequences, which would help provide a reference for second-generation sequencing (SGS) technologies in the assembling process and prediction of coding sequences (CDS), simple sequence repeat (SSR), long non-coding RNAs (long ncRNAs, lncRNAs), and alternative splicing (AS) events. Based on the full-length transcript ...
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