Tropical Plant Biology

Saeed-ur-Rahman, ; Khalid, Muhammad; Kayani, Sadaf-Ilyas; Jan, Farooq; Ullah, Ayaz; Tang, Kexuan

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09228-0

Artemisinins, as a class of bioactive molecules, are mainly derived from the extracts of Artemisia annua L. and are the mainstay for malaria treatment, including severe malaria, uncomplicated malaria and multi-drug resistant malaria. They are well-known for their good tolerability, safety and rapid onset of action. Their efficacy is not only limited to malaria but also extends to a variety of human diseases such as cancer, tuberculosis, viral diseases (e.g. Human cytomegalovirus), immune diseases and parasitic infections like schistosomiasis. Being a cheap and safe drug class, which saves millions of lives at risk from malaria around the globe, can also have significant potential in oncology as they have shown anti-cancer properties in both cell lines and animal models. Active derivatives (e.g. artesunate, artemether and arteether etc.) have also been synthesized which can be used for oral, rectal, intramuscular and intravenous administration. A comprehensive update on the non-malarial use of artemisinins and/or their derivatives and artemisinin-based drug development beyond anti-malarial is discussed in this review. With the collaborative efforts in the clinical pharmacology of artemisinins and novel synthesis of artemisinin analogues, it is likely that artemisinin-based drugs will become an important armamentarium impeding a number of diseases beyond malaria.

Xie, Yanning; Wang, Xinqi; Ren, Xiaoci; Yang, Xiangyu; Zhao, Rengui

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09227-1

The tassel architecture of maize (Zea mays L.), which plays an important role in F1 hybrid seed production and yield performance, is genetically controlled by quantitative trait loci (QTLs). Here, we constructed a high-density SNP-based genetic map using an F2 population containing 148 individuals. This genetic map included 7613 SNPs whose average genetic distance was 0.19 cM. On account of the F2 population, we detected 14 QTLs responsible for tassel branch number (TBN), tassel weight (TW), central spike length (CSL), and meristem length (ML); eight of these QTLs demonstrated a relatively high level of phenotypic variation explanation (PVE) (PVE ≥ 10%), at a high level of significance. qTW-2 was a major QTL (LOD = 10.11 and PVE = 28.82%), and this QTL and qTBN-2 shared the same region, indicating a possible pleiotropic effect. An F2:3 population was developed to further verify QTLs in the F2 population. Finally, qTBN-5, qTW-2 and qCSL_N-10 were detected reproducibly. To help screen potential candidate genes, we chose 12 genes within the regions of qTBN-5, qML-6, qCSL_N-7 and qTW-2 and that were possibly involved in tassel morphogenesis according to Gene Ontology (GO) annotation analysis and performed quantitative real-time polymerase chain reaction (qRT-PCR). The expression of eight of the 12 genes was significantly (P < 0.05) or extremely significantly different (P < 0.01) between parents of the F2 population during the young tassel development stage, suggesting that those eight were possible candidate genes. These results provide insights into the genetic mechanisms controlling tassel architecture and will benefit both tassel-related QTL fine mapping and causal gene cloning in maize.

He, Qing; Liu, Yanhui; Zhang, Man; Bai, Mengyan; Priyadarshani, S.; Chai, Mengnan; Chen, Fangqian; Huang, Youmei; Liu, Liping; Cai, Hanyang; Qin, Yuan

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09233-3

NAC [no apical meristem (NAM), Arabidopsis transcription activation factor (ATAF1/2) and cup-shaped cotyledon (CUC2)] proteins is one of the largest classes of plant specific transcription factors and plays a critical role in plant growth, development process, and abiotic/biotic stresses. In this study, 73 NAC genes (AcNACs) were identified from the pineapple genome. Phylogenetic analysis showed that AcNACs could be divided into 13 subgroups. Gene structure analysis showed that the number of introns varied from 0 to 12. Motif analysis revealed that all of the identified AcNACs had the conserved NAC domain and motif 6 is the conserved motif. Most of the AcNACs were located in chromosome except AcNAC68, AcNAC70, AcNAC71 and AcNAC72, which were presented on unanchored scaffolds. Furthermore, we analysed AcNAC expression patterns in vegetative organs and in sexual organs, namely ovules and stamens, at different developmental stages respectively. Five AcNAC genes (AcNAC6; AcNAC7; AcNAC48; AcNAC70; AcNAC71) were not detected in vegetative organs. AcNAC55 exhibited the highest expression level in vegetative organs. Six AcNAC genes (AcNAC11, AcNAC18, AcNAC27, AcNAC28, AcNAC40, and AcNAC55) showed high expression levels in all reproductive organs. Seven AcNAC genes (AcNAC26, AcNAC34, AcNAC40, AcNAC43, AcNAC63 and AcNAC65) were induced under abiotic stresses. These data provided a new insight of NAC gene family in pineapple and revealed the diverse function of NAC transcription factors in pineapple growth and development.

Alves-Pereira, Alessandro; Novello, Mariana; Dequigiovanni, Gabriel; Pinheiro, José; Brancalion, Pedro; Veasey, Elizabeth; Clement, Charles; Souza, Anete; Zucchi, Maria

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09229-z

The megabiodiversity of Brazil created opportunities for the domestication of a number of crop species, including some of major global importance. Considering the economic value of many Brazilian native crops, the genetic characterization of their populations is fundamental to support the utilization and conservation of their genetic resources, currently threatened by deforestation and the intensification of monuculture of exotic crops. Recent advances in DNA sequencing technologies have promoted the rapid genomic evaluation of non-model species, including those of only local importance. In this context, we evaluated the genomic diversity of three native Brazilian crops: manioc (Manihot esculenta), annatto (Bixa orellana) and the juçara palm (Euterpe edulis). Double-digest restriction site-associated DNA sequencing (ddRAD) was employed to identify thousands of SNP markers in each crop species (1952 in manioc, 3362 in annatto and 1040 in juçara). Population genomic analyses identified many loci putatively under selection, but the unavailability of genome sequences for annatto and juçara hampers further characterization for these crops. Nonetheless, the SNP markers identified were effective in the characterization of the genomic diversity and population structure. The levels of genomic diversity and inbreeding were compatible with the biology of each species. While wild and cultivated manioc were remarkably genetically divergent, the same was not observed between accessions of wild and cultivated annatto, and genetic differentiation was observed among juçara samples from different environments. The application of population genomic approaches may be valuable for the establishment of better practices of management of these crops, promoting the conservation and valorization of Brazilian native genetic resources.

Gandara, Flávio; Da-Silva, Paulo; Moura, Tânia; Pereira, Fernanda; Gobatto, Cláudia; Ferraz, Elza; Kageyama, Paulo; Tambarussi, Evandro

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09234-2

Cedrela fissilis Vell. has a wide distribution in South and Central America, and in neotropical forests the species occurs at a low density. Its wood is one of the most valued around the world, and the species is currently at risk of extinction due to both habitat fragmentation and illegal logging. Considering the need for conservation strategies, this study aims to investigate the genetic structure, diversity, and inbreeding in C. fissilis populations from the Atlantic Forest. To do this, nine microsatellite loci were used to genotype 289 individuals from eight undisturbed and disturbed fragments. Two of the eight populations harbor most of the genetic diversity: one includes most of the diversity present in all populations and the other is isolated but with high levels of diversity. Genetic diversity was higher within than among populations, with observed and expected heterozygosities ranging from 0.48 to 0.63 and from 0.55 to 0.70, respectively. We detected a significant fixation index, ranging from 0.08 to 0.24 and 32% of the observed alleles were exclusive of some population. The populations showed moderate genetic structure (F ST  = 0.10) and the Bayesian analysis grouped the studied individuals into three distinct genetic clusters that seem to be related to the presence of geographical barriers. The overall analyses of the results allow us to conclude that protecting only isolated fragments, either large or small, may be ineffective for conserving the C. fissilis gene pool in the studied region. This observation suggests that an appropriate strategy to conserve the gene pool of the species is to maintain both the Atlantic Forest green belt in the eastern portion of the Central and South region of this biome, where the forest is not highly fragmented, as well as the remaining forest areas to the west of the Paraná River.

Wei, Jinju; Xiu, Zhihui; Ou, Huiping; Chen, Junhui; Jiang, Huayan; Zhang, Xiaoqiu; Zhang, Ronghua; Zhou, Hui; Gui, Yiyun; Li, Haibi; Li, Yangrui; Yang, Rongzhong; Huang, Dongliang; Tan, Hongwei; Liu, Xihui

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09231-5

Sugarcane is an important industrial crop with a high sugar yield that has become a leading energy crop worldwide. It is widely cultivated in tropical and subtropical regions. Various diseases beset the cultivation of sugarcane. The molecular study of disease resistance in sugarcane is limited by its complicated genome. In our study, RNA-seq was employed to detect the mechanism of twisted leaf disease tolerance in modern cultivar sugarcane, which derived from Narenga porphyrocoma. We completed high-throughput transcriptomic sequencing of 12 samples, including three stages of a susceptible (NSBC1_T “H3–8”) and an unsusceptible cultivar (NSBC1_CK “H-19”) with two biological repeats, respectively. Using the Saccharum spontaneum genome as reference, the average mapping ratio of the clean data was over 70%. Among the differentially expressed genes between H3–8 and H3–19, we focused on the analysis of hormone pathways and resistance (R) genes. The results showed that twisted leaf disease triggers hormone networks and around 40% of R genes conditioned lower expression in the susceptible cultivar. One of the possible reasons for H3–8 being susceptible to twisted leaf disease might be the null/retarded response of R genes, especially in pre-onset stage (46% down-regulated) of pathogens infection.

Ali, Hina; Liu, Yanhui; Azam, Syed; Ali, Imran; Ali, Umair; Li, Weimin; Ashraf, Hafiza; Jie, Yang; Olsson, Stefan; Qin, Yuan

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09232-4

TALE (Three Amino-acid Loop Extension) transcription factors belong to a large gene family in plants and are also widespread in other Eukaryotes, including animals. We have in detail studied TALE genes in the economically important crop plant pineapple (Ananas comosus) but also compared these gene sequences with other plant TALE-genes. Using the webtool HMMER we found 18 TALE gene sequences in the pineapple genome, 33 genes in rice genome and 27 genes in Arabidopsis thaliana genome, 25 genes in Brachypodium distachyon genome, 22 genes in Vitis vinifera genome and 36 genes in Populus trichocarpa genome. The found TALE genes in pineapple genome were assigned to four groups (A, B, C, and D) based on similarity. The 18 TALE genes in pineapple were located on 11 of the 25 chromosomes. Structural heterogeneity was observed for the pineapple TALE genes and number of introns varied from 1 to 3 while the number of exons was 2–4. The pineapple TALE genes showed tissue specific expression. AcoTALE1 and AcoTALE15 were highly expressed in roots while AcoTALE16, AcoTALE2, and AcoTALE18 were highly expressed in fruit tissues. AcoTALE4 and AcoTALE7 were highly expressed at two different stages of stamen development. Abiotic shock treatment revealed that AcoTALE17 and AcoTALE8 were moderately upregulated by cold shock while heat shock firmly upregulated AcoTALE16 and AcoTALE5. AcoTALE2, AcoTALE4, AcoTALE12 and AcoTALE16 was highly expressed in response to salt shock while AcoTALE5 and AcoTALE12 was upregulated in response to osmotic (mannitol) shock. None of the TALE gene was differentially regulated in response to sudden darkness. Our study, identifying these TALE transcription factors and their involvement in different stress responses lays a foundation for the possible use of genetic modifications of TALE genes for pineapple crop improvements.

Dutta, Summi; Kumar, Manish; Mukhopadhyay, Kunal

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09235-1

MicroRNAs as regulators of gene expression have been known for over a decade and have been correlated with various types of abiotic and biotic stresses. IsomiRs are modified forms of typical miRNAs altered by one or few nucleotides as a result of post transcriptional modifications of miRNAs at terminals or SNPs containing miRNA sequences producing 5′/3′ isomiRs or SNP_isomiRs. These isoforms function exactly like miRNAs, but sometimes alter the target gene preference particularly when they differ in sequences within seed region. Existence of isomiRs was considered earlier as errors in sequencing techniques due to unavailability of proper detection tools. Bread wheat is the most cultivated cereal crop globally with a strong hold on world’s economy. Wheat production is frequently affected by rust diseases. Leaf rust, caused by Puccinia triticina, severely affects grain filling. Four small RNA libraries were prepared from leaves of two wheat Near Isogenic Lines, HD2329 (susceptible) and HD2329 + Lr24 (resistant) both under mock- and pathogen-inoculated conditions and sequenced using Illumina NGS. Several novel miRNAs were detected from these sequences. The present study focuses on identification of isomiRs derived from these miRNAs and their target genes. In total, 66 and 38 unique 5′ and 3′ isomiRs respectively were identified from 37 miRNAs. IsomiRs targeted genes with functions like amino acid metabolism, replication, transport, chelation of reactive oxygen species in wheat while genes with SunT and Structural Maintenance of Chromosome domain of Puccinia. This study will provide a basis for exploitation of isomiRs for genetic improvements in wheat.