In this study, microsatellite markers were developed for the genetic linkage mapping and breeding program of the black tiger shrimp Penaeus monodon. A total of 997 unique microsatellite-containing expressed sequence tags (ESTs) were identified from 10 100 EST sequences in the P. monodon EST database. AT-rich microsatellite types were predominant in the EST sequences. Homology searching by the blastn and blastx programs revealed that these 997 ESTs represented 8.6% known gene products, 27.8% hypothetical proteins and 63.6% unknown gene products. Characterization of 50 markers on a panel of 35-48 unrelated shrimp indicated an average number of alleles of 12.6 and an average polymorphic information content of 0.723. These EST microsatellite markers along with 208 other markers (185 amplified fragment length polymorphisms, one exon-primed intron-crossing, six single strand conformation polymorphisms, one single nucleotide polymorphism, 13 non-EST-associated microsatellites and two EST-associated microsatellites) were analysed across the international P. monodon mapping family. A total of 144 new markers were added to the P. monodon maps, including 36 of the microsatellite-containing ESTs. The current P. monodon male and female linkage maps have 47 and 36 linkage groups respectively with coverage across half the P. monodon genome.
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.
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