A SNP variation in the Sucrose synthase (SoSUS) gene associated with sugar-related traits in sugarcane.

Background: Sugarcane (Saccharum spp.) is an economically significant crop for both the sugar and biofuel industries. Breeding sugarcane cultivars with high-performance agronomic traits is the most effective approach for meeting the rising demand for sugar and biofuels. Molecular markers associated with relevant agronomic traits could drastically reduce the time and resources required to develop new sugarcane varieties. Previous sugarcane candidate gene association analyses have found single nucleotide polymorphism (SNP) markers associated with sugar-related traits. This study aims to validate these associated SNP markers of six genes, including Lesion simulating disease 1 (LSD), Calreticulin (CALR), Sucrose synthase 1 (SUS1), DEAD-box ATP-dependent RNA helicase (RH), KANADI1 (KAN1), and Sodium/hydrogen exchanger 7 (NHX7), in a diverse population in 2-year and two-location evaluations. Methods: After genotyping of seven targeted SNP markers was performed by PCR Allelic Competitive Extension (PACE) SNP genotyping, the association with sugar-related traits and important cane yield component traits was determined on a set of 159 sugarcane genotypes. The marker-trait relationships were validated and identified by both t-test analysis and an association analysis based on the general linear model. Results: The mSoSUS1_SNPCh10.T/C and mSoKAN1_SNPCh7.T/C markers that were designed from the SUS1 and KAN1 genes, respectively, showed significant associations with different amounts of sugar-related traits and yield components. The mSoSUS1_SNPCh10.T/C marker was found to have more significant association with sugar-related traits, including pol, CCS, brix, fiber and sugar yield, with p values of 6.08 × 10-6 to 4.35 × 10-2, as well as some cane yield component traits with p values of 1.61 × 10-4 to 3.35 × 10-2. The significant association is consistent across four environments. Conclusion: Sucrose synthase (SUS) is considered a crucial enzyme involved in sucrose metabolism. This marker is a high potential functional marker that may be used in sugarcane breeding programs to select superior sugarcane with good fiber and high sugar contents.

The complete chloroplast genome sequence and phylogenetic analysis of Heritiera fomes Buch.-Ham. (Malvales: Sterculiaceae).

Heritiera fomes Buch.-Ham. (1800) is a species of mangrove in the family Malvaceae, widely distributed in the Indo-Pacific and listed as 'endangered' (EN) on the International Union for Conservation of Nature's (IUCN) red list. We reported the complete chloroplast genome sequence of H. fomes. The genome was 168,521 bp in length and included two inverted repeats (IRs) of 34,496 bp, separated by a large single-copy (LSC) region of 88,604 bp and a small single-copy (SSC) region of 10,925 bp, respectively. The genome contained 87 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes. The maximum-likelihood (ML) phylogenetic tree suggested that H. fomes is closely related to Heritiera angustata and Heritiera parvifolia with relatively high support bootstrap values of 86% and 100% with other species (Heritiera littoralis and Heritiera javanica), suggesting a relatively close genetic relationship between the five Heritiera plants. The chloroplast genome sequence provided a useful resource for conservation genetics studies of H. fomes and for phylogenetic studies of Heritiera.

The complete mitochondrial genome sequence of the karst-dwelling crab, Terrapotamon thungwa (Crustacea: Brachyura: Potamidae).

Terrapotamon thungwa is a new species of terrestrial long-legged crab discovered in a karst landscape of southern Thailand. Here, we report the first complete mitochondrial genome of this crab species. The mitochondrial genome size is 16,156 base-pairs (bp), including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA) genes. The AT and GC content of the mitochondrial genome sequence is 73.2% and 26.8%, respectively. Phylogenetic analysis with 26 crustacean species, based on 13 mitochondrial conserve genes, showed that T. thungwa was closely related to other freshwater crab species in the family Potamidae.

Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests.

Ceriops and Avicennia are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of Ceriops decandra, Ceriops zippeliana, and Ceriops tagal were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas Avicennia lanata was 148,264 bp in length. The gene content and gene order are highly conserved among these species. The chloroplast genome contains 125 genes in A. lanata and 129 genes in Ceriops species. Three duplicate genes (rpl2, rpl23, and trnM-CAU) were found in the IR regions of the three Ceriops species, resulting in expansion of the IR regions. The rpl32 gene was lost in C. zippeliana, whereas the infA gene was present in A. lanata. Short repeats (<40 bp) and a lower number of SSRs were found in A. lanata but not in Ceriops species. The phylogenetic analysis supports that all Ceriops species are clustered in Rhizophoraceae and A. lanata is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the rps7 gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three Ceriops species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in Ceriops and Avicennia species.

A SNP variation in an expansin (EgExp4) gene affects height in oil palm.

Oil palm (Elaeis guineensis Jacq.), an Aracaceae family plant, is utilized for both consumable and non-consumable products, including cooking oil, cosmetics and biodiesel production. Oil palm is a perennial tree with 25 years of optimal harvesting time and a height of up to 18 m. However, harvesting of oil palm fruit bunches with heights of more than 2-3 meters is challenging for oil palm farmers. Thus, understanding the genetic control of height would be beneficial for using gene-based markers to speed up oil palm breeding programs to select semi-dwarf oil palm varieties. This study aims to identify Insertion/Deletions (InDels) and single nucleotide polymorphisms (SNPs) of five height-related genes, including EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4, in short and tall oil palm groups by PacBio SMRT sequencing technology. Then, the SNP variation's association with height was validated in the Golden Tenera (GT) population. All targeted genes were successfully amplified by two rounds of PCR amplification with expected sizes that ranged from 2,516 to 3,015 base pair (bp), covering 5' UTR, gene sequences and 3' UTR from 20 short and 20 tall oil palm trees. As a result, 1,166, 909, 1,494, 387 and 5,384 full-length genomic DNA sequences were revealed by PacBio SMRT sequencing technology, from EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4 genes, respectively. Twelve variations, including eight InDels and four SNPs, were identified from EgDELLA1, EgGRF1, EgGA20ox1 and EgExp4. No variation was found for EgAPG1. After SNP through-put genotyping of 4 targeted SNP markers was done by PACE™ SNP genotyping, the association with height was determined in the GT population. Only the mEgExp4_SNP118 marker, designed from EgExp4 gene, was found to associate with height in 2 of 4 height-recordings, with p values of 0.0383 for height (HT)-1 and 0.0263 for HT-4. In conclusion, this marker is a potential gene-based marker that may be used in oil palm breeding programs for selecting semi-dwarf oil palm varieties in the near future.

A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome.

Mangroves are of great ecological and economical importance, providing shelters for a wide range of species and nursery habitats for commercially important marine species. Ceriops zippeliana (yellow mangrove) belongs to Rhizophoraceae family and is commonly distributed in the tropical and subtropical coastal communities. In this study, we present a high-quality assembly of the C. zippeliana genome. We constructed an initial draft assembly of 240,139,412 bases with an N50 contig length of 564,761 bases using the 10x Genomics linked-read technology. This assembly was further scaffolded with RagTag using a chromosome-scale assembly of a closely related Ceriops species as a reference. The final assembly contained 243,228,612 bases with an N50 scaffold length of 10,559,178 Mb. The size of the final assembly was close to those estimated using DNA flow cytometry (248 Mb) and the k-mer distribution analysis (246 Mb). We predicted a total of 23,474 gene models and 21,724 protein-coding genes in the C. zippeliana genome, of which 16,002 were assigned gene ontology terms. We recovered 97.1% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs analysis. The phylogenetic analysis based on single-copy orthologous genes illustrated that C. zippeliana and Ceriops tagal diverged approximately 10.2 million years ago (MYA), and their last common ancestor and Kandelia obovata diverged approximately 29.9 MYA. The high-quality assembly of C. zippeliana presented in this work provides a useful genomic resource for studying mangroves' unique adaptations to stressful intertidal habitats and for developing sustainable mangrove forest restoration and conservation programs.