Tropical Plant Biology

Pushpalatha, Raji; Gangadharan, Byju

2020 Tropical Plant Biology

doi: 10.1007/s12042-020-09255-2

Climate change and its impact on agriculture are one of the ongoing research areas, and the major task among agricultural managers is to meet the food demand in the future in the context of the production gap of major food grain crops. Literature analysis is carried out to understand the climate resilience of cassava, one of the major tuber crops and is considered to bridge the food demand gap in the near future. Systematic analysis of literature includes influence of changing environmental parameters such as temperature, solar radiation, photoperiod, air humidity, soil water deficit, salinity, elevated ozone and CO2, combined effects of elevated CO2 with temperature, water deficit and salinity to the growth and yield of cassava along with its resilience to biotic stresses and its climate suitability. Studies indicate cassava can tolerate a temperature level of up to 40 °C, and thereafter the rate of photosynthesis decreases. Cassava can be cultivated in regions with variations in solar radiation without much compromise in its yield in the context of global dimming of sunshine duration. The resilience to water stress and air humidity variations are adapted by reducing stomatal conductance without influencing the rate of photosynthesis. Cassava has also an inbuilt mechanism to cope with water scarcity by leaf drooping. Already established cassava can tolerate a salinity level of up to 150 mM and the younger ones can tolerate up to a level of 40 mM. Studies also indicate a strong positive influence of elevated CO2 of up to 700 ppm on the rate of photosynthesis and yield of cassava. Elevated CO2 enhances the resilience of cassava to water stress and salinity. Similarly, the combined effect of elevated CO2 and higher temperatures also increases the yield attributes of cassava. These all indicate the resilience of cassava to the changing climate and it ensures as an insurance crop as well as food security crop in the near future. Studies show its resilience to biotic stresses as well. Climate suitability studies also show its suitability in the present locations in the near future as well as its adaptation to other areas. However, the research gap is identified in areas of influence of elevated ozone on growth characteristics of cassava. This study also recommends identifying the extent of tolerance level of cassava to the influence of the combined effect of salinity and elevated CO2. Further, researchers need to concentrate on developing biotic as well as abiotic stress-tolerant genes in cassava varieties to increase its production irrespective of the changing climatic conditions.

Ibrahim, Aminu Kurawa; Zhang, Liwu; Niyitanga, Sylvain; Afzal, Muhammad Zohaib; Xu, Yi; Zhang, Lilan; Zhang, Liemei; Qi, Jianmin

2020 Tropical Plant Biology

doi: 10.1007/s12042-020-09261-4

Association mapping (AM) is an approach that accounts for thousands of polymorphisms to evaluate the effects of quantitative trait loci (QTL). It is an important instrument for identification of alleles and new genes as well as dissection of complex characters. AM is more advantageous than linkage analysis due to the comparatively high-resolution provided, which is based on the structure of linkage disequilibrium (LD). Marker density, population, sample sizes and population structure are among the critical factors that should be considered when AM is used. It is necessary to note that, the choice of germplasm, genotypic and phenotypic data quality, the use of appropriate statistical analysis for marker-phenotype association detections and verifications are key to association analysis. Great potentials to enhance crop genetic improvement are offered by AM. However, to understand its application, extensive research is needed, such as improvements in computational and statistical methods and its integration with gene annotation data or functional analysis. Statistical apparatuses that are user-friendly and genetic resources are also needed and must be enhanced. Rare allele/variant analysis is an important area to be considered to enhance AM studies. Joint linkage association mapping has now been proposed to improve linkage-based QTL mapping and AM limitations. In the future, new candidate genes and QTL can be easily identified if genome-wide association studies (GWAS) are combined with functional genomics. As such, this review describes association mapping, its utilization in plant breeding, limitations as well as advantages over linkage mapping.

da Costa, Cláudia Militz; dos Santos, Railson Schreinert; Marini, Naciele; da Maia, Luciano Carlos; Vanier, Nathan Levien; Elias, Moacir Cardoso; de Oliveira, Maurício; Costa de Oliveira, Antonio

2020 Tropical Plant Biology

doi: 10.1007/s12042-019-09252-0

The quality concept for cooked rice (Oryza sativa L.) varies according to customers culture and habits, varying from stickier, in Asia, to looser grains, more appreciated in South America. This parameter, no matter the taste, is an important factor in the evaluation of what constitutes a good rice grain. Higher grain stickiness is associated not only with lower amylose content, but also with amylopectin chain length and the net of proteins reinforced by intra and intermolecular disulfide bonds around the rice starch granule. Therefore, the present study compared four rice genotypes and the effectiveness of seed zinc coating treatments: T0 (without zinc sulfate) and TZnSO4 (with 8.81 g of ZnSO4.7H2O. kg−1 of seeds). Here we show that both treatments affect transcript accumulation of important sulfur-metabolism-enzymes. However, the higher levels of transcripts from these genes did not result in higher cysteine or serine levels. The adhesiveness of cooked mature rice grains is greatly impacted by genotype, but no evidence that transcript up-regulation could be associated to stickiness.

Thioune, El-Hadji; Strickler, Susan; Gallagher, Thomas; Charpagne, Aline; Decombes, Patrick; Osborne, Bruce; McCarthy, James

2020 Tropical Plant Biology

doi: 10.1007/s12042-020-09254-3

Climate change is expected to result in more frequent periods of both low rainfall and above normal temperatures for many coffee growing regions. To understand how coffee reacts to such change, we studied the physiological and gene expression responses of the clonal variety C. canephora FRT07 exposed to water deficits under two different temperature regimes. Variations in the time-dependent impact of water deficits on leaf stomatal conductance and carbon assimilation were significantly different under the 27 °C and 27 °C/42 °C conditions examined. The physiological responses 24 h after re-watering were also different for both conditions. Expression analysis of genes known to respond to water deficits indicated that drought-related signaling occurred at both temperatures. Deeper insights into the response of coffee to water deficits was obtained by RNASeq based whole transcriptome profiling of leaves from early, late, and recovery stages of the 27 °C experiment. This yielded expression data for 13,642 genes and related differential expression analysis uncovered 362 and 474 genes with increased and decreased expression, respectively, under mild water deficits, and 1627 genes and 2197 genes, respectively, under more severe water deficits. The data presented, from a single clonal coffee variety, serves as an important reference point for future comparative physiological/transcriptomic studies with clonal coffee varieties with different sensitivities to water deficits and high temperatures. Such comparative analyses will help predict how different coffee varieties respond to changing climatic conditions, and may facilitate the identification of alleles associated with high and low tolerance to water deficits, enabling faster breeding of more climate-smart coffee trees.

Liu, Wenping; Zhao, Biligen-Gaowa; Chao, Qing; Wang, Baichen; Zhang, Qian; Zhang, Chunxiao; Li, Shufang; Jin, Fengxue; Yang, Deguang; Li, Xiaohui

2020 Tropical Plant Biology

doi: 10.1007/s12042-020-09259-y

Drought is a main factor affecting plant growth and crop production. APETALA2/Ethylene Responsive Element Binding Protein (AP2/EREBP) transcription factors (TFs) are involved in the response to abiotic stress and their functions in ABA signaling and the regulation of drought response have been intensively studied. However, AP2/EREBP TFs have been limited in the maize. The objective of our study was to identify the function of the novel maize AP2/EREBP gene ZmEREB160. Expression levels analysis in maize revealed that ZmEREB160 is significantly induced by PEG6000, NaCl and ABA treatment. ZmEREB160 localized to the nucleus when transiently expressed in Arabidopsis leaf protoplasts. ZmEREB160 activated the reporter gene and exhibited transcriptional activation activity in yeast cells. When overexpression of ZmEREB160 in Arabidopsis significantly enhanced tolerance to osmotic and ABA stress, overexpressed seedlings were longer roots under ABA and mannitol treatments compared with wild type. In addition, overexpression of ZmEREB160 Arabidopsis seedlings was found to elevate survival rate compared with wild type plants under drought stress. During the drought treatment, qRT-PCR assays showed that the expression levels of ABA/drought stress-related genes, ABI2, ABI5, COR15, DREB2A and RD29B were up-regulated in ZmEREB160 transgenic plants, transgenic plants accumulated more proline content than wild type plants. These results indicate that ZmEREB160 functions in response to drought and ABA stresses, and participates in ABA signaling pathway and may enhance drought tolerance.

Lu, Shi; Li, Mu; Zhang, Mo; Lu, Ming; Wang, Xinqi; Wang, Piwu; Liu, Wenguo

2020 Tropical Plant Biology

doi: 10.1007/s12042-020-09258-z

Both plant height (PH) and ear height (EH) are key agronomic traits in maize that are associated with plant lodging resistance and population density. To explore the genetic basis for PH and EH in maize, we conducted a genome-wide association study (GWAS) based upon 1.49 × 106 single nucleotide polymorphisms (SNPs) identified following the sequencing of 80 backbone inbred maize lines in Jilin Province. By comparing genotypic data and these two traits of interest, we identified 27 total SNPs significantly associated with PH and EH (P < 0.000001). Of these SNPs, 12 were significantly associated with PH and were found on chromosomes 1, 3, 4, 6, 7, and 9, accounting for 25.8% of the phenotypic variability for this trait. The remaining 15 SNPs were significantly linked with EH and were located on chromosomes 1, 2, 4, 6, 7, 8, 9, and 10, accounting for 30% of the phenotypic variability for this trait. Within a mean linkage disequilibrium (LD) distance of 9.7 kb from these SNP loci, we identified 5 candidate genes associated with PH, with one of these candidate genes harboring a significant SNP. Similarly, we identified 12 candidate genes associated with EH, of which 3 harbored significant SNPs. We then isolated RNA from 8 different inbred maize lines from this GWAS study cohort and assessed the expression of these candidate genes of interest via quantitative real-time PCR (qRT-PCR). Through this analysis, we were able to verify that there were significant differences in the expression of these four SNP-harboring candidate genes in plants with a range of EH and PH phenotypes.

de Queiroz, Claudia Afras; da Silva Matos, Kedma; Lobo, Igor Kelvyn Cavalcante; de Sousa, Sandra Barbosa; Muniz, Celli Rodrigues; Beleza Yamagishi, Michel E.; Zocolo, Guilherme Julião; Hanada, Rogério Eiji; Gasparotto, Luadir; Sousa, Nelcimar Reis; de Andrade, Edmar Vaz; Cordeiro, Isabelle Bezerra; Melo, Anderson Adriano Martins; da Silva, Gilvan Ferreira

2020 Tropical Plant Biology

doi: 10.1007/s12042-020-09256-1

Oversprouting is a poorly studied disease of guarana plant (Paullinia cupana var. sorbilis), a native species from Amazon Rainforest caused by Fusarium decemcellulare (FDC) that affects the plant growth and reproduction, severely compromising productivity. The sorbilis variety of guarana is anciently cultivated and is used today for the industry of soft drinks, cosmetic and pharmaceutical. Transcriptome, proteome, light and electron microscopy were used to compare symptomatic and asymptomatic tissues and reveal anatomical, histological and cytological alterations resultant from the disease. Disease symptoms described here include a marked reduction in the longitudinal axis and the formation of “capsules”, named as this for the first time here, which display hard thickened external walls and contain extremely malformed floral organs and/or poorly differentiated vegetative primordia when occurring isolate in individual branching points. The aggregate of multiple “capsules” in a same branch point produces galls. The production of indol-acetic acid (IAA) in vitro by F. decemcellulare was for the first time reported and the comparative transcriptome and preliminary proteome data from symptomatic and asymptomatic tissues, support the occurrence of hormonal imbalance identified through several plant hormone-related genes and proteins differentially expressed only in symptomatic tissues. Auxin signaling mechanism, as well as auxin-responsive genes associated to cell cycling, division and proliferation also occurred differentially in infected tissues. Oversprouting and the reduction of the longitudinal axis in malformed cells and organs are related to hormonal unbalance are discussed in this paper.

Wang, Haiyan; Shen, Xu; Lu, Cheng; Li, Kaimian; Wang, Wenquan

2020 Tropical Plant Biology

doi: 10.1007/s12042-020-09257-0

Chloroplastic pyruvate phosphate dikinase (PPDK) (chlPPDK) is a key enzyme in the photosynthesis of C4 plants. PPDK is expressed in high abundance in C4 plants but only in trace amounts in C3 plants. The existing research reveals a higher expression of MechlPPDK in cultivated cassava varieties than that in wild cassava W14. However, knowledge about the transcriptional regulation of the MechlPPDK gene in cassava (Manihot esculenta Crantz) is insufficient. Therefore, we aim to identify the transcription profile of MechlPPDK and the core promoter region of MechlPPDK. We cloned the MechlPPDK coding sequence and its 5′-flanking sequence from the cassava variety Ku50. A series of deletion constructions fused to a uidA reporter gene were performed in the 5′-flanking sequence and stably transformed into tobacco. We found that P1 (from −590 bp to +114 bp) had the highest promoter activity among P1 to P3. The 5′-flanking sequence of MechlPPDK responded differently to varied abiotic stresses. Our results will further the understanding of the regulation of MechlPPDK expression.