Transcriptome analysis of oil palm (Elaeis guineensis Jacq.) roots under waterlogging stress

Abstract

Waterlogging seriously constrains growth and yields in oil palm. To date, the responsive molecular changes caused by waterlogging in oil palm remain elusive. To elucidate the molecular genetic mechanisms of waterlogging stress, two varieties of oil palm Deli x Lamé and Deli x Ghana were used. The transcriptome profiles of the roots under waterlogging stress and normal conditions were compared via Ion Torrent Sequencing. Four libraries (GNR, GSR, SNR, and SSR) of oil palm roots after 45 days of normal watering and waterlogging stress were constructed. Approximately 6.2 million sequenced reads per library were obtained, with 5.5 million mapped reads (88.64%) similar to the oil palm genome in the GenBank database. A comparison of GNR/GSR showed a high of 3,289 DEGs with most genes up-regulated (1,863 DEGs). The GO analysis revealed the distribution of the DEGs among various pathways, suggesting a wide spectrum of physiological processes impacted by waterlogging stress. Moreover, qRT-PCR showed strong expression of all selected RNA-seq genes in waterlogged Deli x Ghana (GSR), especially GST, SAPK10 and NAC29 that are reported for the time to respond to waterlogging stress. Thus, this study not only reveals the comprehensive mechanisms of waterlogging responsive transcription in oil palm, but also establishes Deli x Ghana as a highly-adaptable variety to waterlogging conditions.

Transcriptomic responses of oil palm (Elaeis guineensis) stem to waterlogging at plantation in relation to precipitation seasonality

“…Moreover, an expression heatmap revealed significant transcriptomic changes in the oil palm stem core ( Figure 3 ) whereas only minimal transcriptomic changes were detected in the leaves of the studied plants ( Figure 2 , S2 ). This was unexpected because the leaves of oil palm seedlings exhibited significant waterlogging-induced physiological and/or morphological changes in earlier studies ( Yulia and Sitorus, 2012 ; Rivera-Mendes et al., 2016 ; Cui et al., 2019 ; Nuanlaong et al., 2020 ). The reliability of these findings was evaluated using Fisher’s exact test, which indicated that genes associated with waterlogging were significantly overrepresented among the DEGs identified in the stem core, while the opposite was true for the leaves ( Figure 4A, B ).…”

“…Previous studies on waterlogging in oil palms have examined seedlings cultivated under controlled conditions ( Yulia and Sitorus, 2012 ; Rivera-Mendes et al., 2016 ; Cui et al., 2019 ; Nuanlaong et al., 2020 ; Nuanlaong et al., 2021 ). The goal of this study was to complement these works by studying waterlogging responses in adult palms growing under natural conditions, which is important because Poorter et al.…”

“…It is also crucial for stimulating the development of morphological-anatomical features that facilitate adaptation to or tolerance of waterlogging such as hypertrophied lenticels, adventitious roots, and aerenchyma ( Ali and Kim, 2018 ). Several genes associated with ethylene were highly expressed in waterlogged roots of Deli x Ghana (GSR) oil palms, including ACS3 , ACO , and ACO1 ( Nuanlaong et al., 2020 ). It is therefore notable that ACO1 (LOC105047965) was one of the PDEGs identified after heavy rainfall event in the plantation.…”

“…Oil palm yield loss is of particular concern because the oil palm has become a major cash crop in several countries, especially Indonesia and Malaysia. Nevertheless, waterlogging-response study of oil palm is still at its rudimentary stage and apparently investigated on oil palm seedlings grown under controlled conditions ( Rivera-Mendes et al., 2016 ; Cui et al., 2019 ; Nuanlaong et al., 2020 ; Nuanlaong et al., 2021 ); there have been no field studies on waterlogging responses in oil palms growing in real environments. Sessile plants have evolved complex response mechanisms that let them adapt to and survive environmental fluctuations that are not readily reproduced in controlled experiments.…”

“…Roots were proclaimed to be the very first part of plant system to discern water-deficiency or inundation, which then transmit various molecular signals to other parts of the plant via long-distance communication ( Takahashi et al., 2020 ; Yang et al., 2020 ). Consequently, most previous studies on waterlogging have focused primarily on the roots and rarely scrutinized into waterlogging responses of other plant parts ( Rivera-Mendes et al., 2016 ; Nuanlaong et al., 2020 ; Nuanlaong et al., 2021 ). Leaves may respond strongly to waterlogging because they are highly sensitive to osmotic stress and water deficiency in the atmosphere, and leaf morphological traits are well-established indicators of plant water status.…”