Asad Prodhan

Rice (Oryza sativa L.) is the staple crop for over half of the world's population and selection in different environmental and climatic conditions has led to the development of numerous local rice cultivars. In a changing environment, these local cultivars may need to be adapted to emerging stresses. Whole-genome sequences are available only for a small fraction of existing rice cultivars, limiting the opportunity for genomics-based marker-assisted selection (MAS) in most local cultivars. To efficiently develop locally-adapted rice cultivars resilient to adverse environmental conditions, our objective was to develop a pipeline for the analysis of re-sequencing data and the development of low-cost allele-specific markers that can be implemented in developing countries. This study focused on three rice cultivars (X265, F160, and Nerica4) commonly grown in Madagascar. We provide whole-genome sequencing data and identify sequence variations compared to publicly available sequences, followed by the development of simple PCR-based InDel and SNP markers. Their effectiveness in distinguishing different alleles at the Ghd7 locus controlling heading date was demonstrated, enabling us to employ these markers for MAS in a breeding population developed between X265 and a donor “Liu He Xi He”. In addition, we developed PCR-based SNP markers for the same population on qLFT-5, a quantitative trait locus for low-fertility tolerance in which the donor allele increases total panicle weight under low-input conditions. This study presents a practical pipeline for the utilization of next generation sequencing-derived large-scale data to accelerate low-cost marker development for MAS in rice and other crop species.
•Rice varieties popular in Madagascar were re-sequenced and variants were identified.•Practical markers useful for local breeders were designed and validated.•Multi-varietal comparison suggested a key amino acid critical for heading date.•This study suggests paths for decentralized breeding approach for local cultivars.

Polymerase chain reaction (PCR) amplicon sequencing allows for reliable identification of an organism by amplifying and analyzing a single conserved marker gene or DNA barcode. As this approach generally involves a single gene, it is an easier protocol to run compared with multilocus or whole-genome sequencing for diagnostic purposes, yet considerably reliable. Therefore, Sanger-based high-quality amplicon sequencing is widely deployed for species identification and high-throughput biosecurity surveillance. However, keeping up with the data analysis in large-scale surveillance or diagnostic settings could be a limiting factor because it involves manual quality control of the raw sequencing data, alignment of the forward and reverse reads, and, finally, a web-based Blastn search of all the amplicons. Here, we present a bioinformatics pipeline that automates the entire analysis. As a result, the pipeline is scalable with a high volume of samples and reproducible. Furthermore, the pipeline leverages the modern open-source Nextflow and Singularity concept; thus, it does not require software installation, except for Nextflow and Singularity, or any paid commercial software or programming expertise from the end users, making it widely adaptable.
[Formula: see text]

Pulse production is decreased when grown on waterlogged soil in rice-based cropping. This study evaluated four pulse crops-grass pea, field pea, cowpea and lentil-to find out their responses to waterlogging (WL) stress at emergence and vegetative stages. The treatment levels at emergence were drained control, 4-, 7- and 10-day WL, while in the vegetative stage they were drained control, 6-, 10- and 14-day WL. In the emergence stage, %emergence was significantly reduced as WL duration increased. After 10-day WL, emergence was reduced to 65% for grass pea, 30% for field pea, 5% for lentil and 7% for cowpea. At the vegetative stage, in both the WL and recovery phases, the WL treatment reduced plant height, tap root length, shoot and root dry mass compared to those in drained control with a significant difference in crops. In recovery as compared to the WL phase at 14-day WL, the chlorophyll content was increased 15% in cowpea and 14% in grass pea but decreased in field pea (26%) and lentil (35%). Similarly, in the recovery phase at 14-day WL, shoot relative growth rates (RGRs) of cowpea, grass pea, field pea and lentil were 20, 66, 10 and 5 mg plant-1 d-1; which were 66%, 70%, 8% and 14% of drained control, respectively. The RGR of root at 14-day WL was also higher in cowpea and grass pea with the rate of 13.8 and 16 mg-1 plant-1 d-1, respectively; in sharp contrast to a reduction of -4.3 mg-1 plant-1 d-1 in field pea and -3.9 mg-1 plant-1 d-1 for lentil than drained control. Furthermore, the higher number of adventitious roots was found in cowpea (14) and grass (9) pea than in field pea (6) and lentil (4). Comparison between growth stages, grass pea was tolerant to WL in both stages. Cowpea was WL sensitive at emergence, but tolerant to vegetative stage. Field pea was moderately tolerant to emergence but was sensitive at vegetative stage. Lentil was sensitive at WL at both stages. These novel insights will allow the fitting of winter pulses to various cropping systems according to the perceived risk of WL at various growth stages.

Heavy and costly use of phosphorus (P) fertiliser is often needed to achieve high crop yields, but only a small amount of applied P fertiliser is available to most crop plants. Hakea prostrata (Proteaceae) is endemic to the P-impoverished landscape of southwest Australia and has several P-saving traits. We identified 16 members of the Phosphate Transporter 1 (PHT1) gene family (HpPHT1;1-HpPHT1;12d) in a long-read genome assembly of H. prostrata. Based on phylogenetics, sequence structure and expression patterns, we classified HpPHT1;1 as potentially involved in Pi uptake from soil and HpPHT1;8 and HpPHT1;9 as potentially involved in Pi uptake and root-to-shoot translocation. Three genes, HpPHT1;4, HpPHT1;6 and HpPHT1;8, lacked regulatory PHR1-binding sites (P1BS) in the promoter regions. Available expression data for HpPHT1;6 and HpPHT1;8 indicated they are not responsive to changes in P supply, potentially contributing to the high P sensitivity of H. prostrata. We also discovered a Proteaceae-specific clade of closely-spaced PHT1 genes that lacked conserved genetic architecture among genera, indicating an evolutionary hot spot within the genome. Overall, the genome assembly of H. prostrata provides a much-needed foundation for understanding the genetic mechanisms of novel adaptations to low P soils in southwest Australian plants.

Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.

Phosphorus (P) is an essential plant nutrient. Most rice growing lands lack adequate P, requiring multiple P fertiliser applications to obtain expected yields. However, P fertiliser is environmentally damaging, and already unaffordable to the marginal farmers. This warrants developing P-efficient rice varieties that require less P to produce the expected yield. However, genetic factors underlying P-use efficiency (PUE) in rice remain elusive. Here, we conducted comparative transcriptome analysis using two rice varieties with contrasting PUE; a P-efficient landrace DJ123 and a P-inefficient modern cultivar IR64. We aimed to understand the transcriptomic responses in DJ123 that allow it to achieve a high PUE under low P conditions. Our results showed that both DJ123 and IR64 had replete tissue P concentrations after 48 h of P deprivation. Yet, DJ123 strongly responded to the external low P availability by inducing P starvation-inducible genes that included SPX2, PHO1, PAPs and SQDs, while these genes were not significantly induced in IR64. We envisage that the ability of DJ123 to rapidly respond to low P conditions might be the key to its high PUE. Our findings lay a valuable foundation in elucidating PUE mechanism in rice, thus will potentially contribute to developing P-efficient modern rice variety.

Phosphorus (P) fertilisers, made from rock phosphate, are used to attain high crop yields. However, rock phosphate is a finite resource and excessive P fertilisers pollute our environment, stressing the need for more P-efficient crops. Some Proteaceae have evolved in extremely P-impoverished environments. One of their adaptations is to curtail the abundance of ribosomal RNA, and thus protein, and tightly control the acquisition and assimilation of nitrogen (N) and sulfur. This differs fundamentally from plants that evolved in environments where N limits plant productivity, but is likely common in many species that evolved in P-impoverished landscapes. Here, we scrutinise the relevance of these responses towards developing P-efficient crops, focusing on plant species where 'P is in the driver's seat'.

The study was carried out to quantify and to evaluate the important chilli bioactive compounds from six different chilli varieties such as; Wild Capsicum, Cili Padi Thai, Cili Johor, Cili Padi Rangup, Cili Padi Putih and Cili Padi Centil collected from different locations of Malaysia. The antioxidant compounds; Total Phenolics, Total Flavonoids, Total Carotenoids, beta-carotenes and antioxidant activities were determined in these chilli varieties. Ferric Reducing Antioxidant Power assay (FRAP) and 1,1-Diphenyl-2-Picrylhydrazyl assay (DPPH) including capsaicin and dihydrocapsaicin were also conducted. Results revealed that, for both antioxidant compounds and activities, Cili Padi Rangup variety produced the highest value for total phenolic contents, total flavonoid contents, FRAP and DPPH activities expect for total carotenoid contents which was recorded high in Cili Padi Centil variety. Besides, the highest value for capsaicin and dihydrocapsaicin were determined in Cili Padi Putih. The phylogenetic tree produced based on morpho-physiological attributes showed that both of the high quality chilli varieties (Cili Padi Rangup and Cili Padi Putih) are originate from the same group. Therefore, these two chilli varieties can be recommended as having the highest content of antioxidant compounds, antioxidant activities, capsaicin and dihydrocapsaicin.

Hakea prostrata (Proteaceae) has evolved in extremely phosphorus (P)-impoverished habitats. Unlike species that evolved in P-richer environments, it tightly controls its nitrogen (N) acquisition, matching its low protein concentration, and thus limiting its P requirement for ribosomal RNA (rRNA). Protein is a major sink for sulfur (S), but the link between low protein concentrations and S metabolism in H. prostrata is unknown, although this is pivotal for understanding this species' supreme adaptation to P-impoverished soils.

Plants were grown at different sulfate supplies for 5 wk and used for nutrient and metabolite analyses.

Total S content in H. prostrata was unchanged with increasing S supply, in sharp contrast with species that typically evolved in environments where P is not a major limiting nutrient. Unlike H. prostrata, other plants typically store excess available sulfate in vacuoles. Like other species, S-starved H. prostrata accumulated arginine, lysine and O-acetylserine, indicating S deficiency.

Hakea prostrata tightly controls its S acquisition to match its low protein concentration and low demand for rRNA, and thus P, the largest organic P pool in leaves. We conclude that the tight control of S acquisition, like that of N, helps H. prostrata to survive in P-impoverished environments.

Hakea prostrata (Proteaceae) has evolved in an extremely phosphorus (P)-limited environment. This species exhibits an exceptionally low ribosomal RNA (rRNA) and low protein and nitrogen (N) concentration in its leaves. Little is known about the N requirement of this species and its link to P metabolism, despite this being the key to understanding how it functions with a minimal P budget. H.prostrata plants were grown with various N supplies. Metabolite and elemental analyses were performed to determine its N requirement. H.prostrata maintained its organ N content and concentration at a set point, independent of a 25-fold difference nitrate supplies. This is in sharp contrast to plants that are typically studied, which take up and store excess nitrate. Plants grown without nitrate had lower leaf chlorophyll and carotenoid concentrations, indicating N deficiency. However, H.prostrata plants at low or high nitrate availability had the same photosynthetic pigment levels and hence were not physiologically compromised by the treatments. The tight control of nitrate acquisition in H.prostrata retains protein at a very low level, which results in a low demand for rRNA and P. We surmise that the constrained nitrate acquisition is an adaptation to severely P-impoverished soils.