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Enhancing rice yield in upland rice systems through genetic improvement remains a major challenge in the tropics. This review aims to provide the trends on upland rice cultivation over the last 30 years and recent distribution of upland rice in the tropics, and to report progress in studies on genetic improvement for enhancing productivity in Africa, Asia, and Latin America. While upland rice cultivation area has reduced in Asia and Latin America over the last 30 years, the area in Africa has increased. The current share of upland rice area in total rice area is related to rainfall and gross national income per capita, especially in Africa, and higher share is associated with lower rice self-sufficiency at national level. Breeding programs in Asia and Latin America have developed high-yielding varieties using indica materials as parents. In Africa, New Rice for Africa (NERICA) varieties were developed from crosses between improved tropical japonica and Oryza glaberrima. However, recent studies report that there is scope for improving existing NERICA using upland indica materials from Asia. In highlands of Africa, there are ongoing breeding programs using japonica varieties, such as the Nepalese Chhomrong Dhan. Key important plant traits used in the breeding programs are not largely different across regions, especially intermediate plant height and tillering capacity (which may be related to weed-suppressive ability), and high harvest index. In conclusion, we propose an international network for breeding upland rice with accelerating seed exchange across regions that could enhance upland rice productivity through genetic improvement.

Terracing is the oldest technique for water and soil conservation on natural hilly slopes. In Northern Thailand, terraced paddy fields were constructed long ago, but scientific questions remain on how terraced paddy fields and upland rice (non-terraced) differ for soil organic carbon (SOC) stocks, soil nutrients and soil erodibility. Therefore, this study aims to evaluate and compare SOC stocks, soil nutrients and soil erodibility between terraced paddy fields and upland rice at Ban Pa Bong Piang, Chiang Mai Province, Thailand. Topsoil (0–10 cm) was collected from terraced paddies and upland rice fields after harvest. Results showed that SOC stocks were 21.84 and 21.61 Mg·C·ha−1 in terraced paddy and upland rice fields, respectively. There was no significant difference in soil erodibility between terraced paddies (range 0.2261–0.2893 t·h·MJ−1·mm−1) and upland rice (range 0.2238–0.2681 t·h·MJ−1·mm−1). Most soil nutrients (NH4-N, NO3-N, available K, available Ca and available Mg) in the terraced paddy field were lower than those in the upland rice field. It was hypothesized that the continuous water flows from plot-to-plot until lowermost plot caused dissolved nutrients to be washed and removed from the flat surface, leading to a short period for accumulating nutrients into the soil. An increase in soil erodibility was associated with decreasing SOC stock at lower toposequence points. This study suggested that increasing SOC stock is the best strategy to minimize soil erodibility of both cropping systems, while proper water management is crucial for maintaining soil nutrients in the terraced paddy field.

Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources.

Aim: The experiment was conducted to maximize anther culture response in an upland indica rice cross amenable for drought tolerance breeding. Methodology: The cold pre-treated anthers of a cross Khandagiri (drought sensitive) x Dular (drought tolerant) were cultured on N6, SK3, MS and CIM media at varying concentration of hormones (2,4-D, Kn and NAA) to assess callusing response. Embryogenic calli were placed on regeneration medium (RM) with varying concentration of Kn, BAP and NAA for plant regeneration. The plantlets were acclimatized in half-strength MS basal liquid medium for one week before transferring to pot mixture (peat moss: perlite 2:1, v/v) for plant establishment in glasshouse under partial shade. Finally, the plantlets were checked for doubled haploid status by cytological study of root tips. Results: Anther culture response was found to be media and genotype-specific. F1-progenies responded better than either of the parents. A modified MS callus induction medium (CIM) with 1.5mg/l 2,4-D + 0.5mg/l Kn resulted impressively higher callusing response (30.2%) with nodular calli than SK3>MS>N6. High frequency (12.8%) of albino-free green plant regeneration with well developed rooting was achieved in RM medium (a modified MS) containing 2mg/l BAP and 0.5mg/l NAA. A total 129 doubled haploid (DH) plants (each with 12 pairs of chromosomes) were recovered which maintained normal growth, set seeds and resulted in true breeding DH lines. Interpretation: The high throughput regeneration system is amenable for doubled haploid production from indica crosses. Besides, the present doubled haploid stock can serve as an ideal mapping population and as such targeted for marker aided selection for early development of drought tolerant rice varieties.

Background Drought has become the major abiotic stress that causes losses in rice yields and consequently is one of the main environmental factors threatening food security. Long non-coding RNA (lncRNA) is known to play an important role in plant response to drought stress, while the mechanisms of competing endogenous RNA (ceRNA) in drought resistance in upland rice have been rarely reported. Results In our study, a total of 191 lncRNAs, 2115 mRNAs and 32 miRNAs (microRNAs) were found by strand-specific sequencing and small RNA sequencing to be differentially expressed in drought-stressed rice. Functional analysis of results indicate that they play important roles in hormone signal transduction, chlorophyll synthesis, protein synthesis and other pathways. Construction of a ceRNA network revealed that MSTRG.28732.3 may interact with miR171 in the chlorophyll biosynthesis pathway and affect the ability of plants to withstand drought stress by regulating Os02g0662700, Os02g0663100 and Os06g0105350. The accuracy of the regulatory network was verified by qRT-PCR. Conclusion Our results provide a theoretical basis for future studies on the potential function of lncRNA in plant drought resistance, and they provide new genetic resources for drought-resistant rice breeding.

Plant height (PH) is an important agronomical parameter to assess the growth status in upland rice fields. Recently, field-based phenotyping using unmanned aerial vehicles (UAVs) has received increasing attention as a cost-effective, well-suited sensing technology to measure PH. In this study, we evaluated feasibility of a low-cost small UAV for estimating PH in upland rice fields in Laos with a canopy height model (CHM). Images of the upland field, including 501 plots (= 167 accessions × 3 replicates), were captured by a commercial small UAV (DJI Phantom 4) before emergence and in the near-flowering stage to generate digital surface models (DSMs). The CHM was developed from the difference of the DSMs using UAV images obtained before emergence and before flowering. The CHM metrics of each plot were then calculated using 90-99th percentiles and the top 1-10% largest pixel values of CHM and were compared with the manually measured field PH (78.25-189.75 cm). The predictive accuracy was assessed in the 90-99th percentiles and top 1-10% values of CHM metrics with 5-fold cross-validation procedures. Simple linear regression analyses between the field PH and CHM metrics showed that the top 3% CHM metrics had the best correlation with the field PH (R 2  = 0.712, root-mean-square error (RMSE) = 9.142 cm, p < 0.001). Cross-validation procedures also confirmed that the top 3% CHM metrics were the best in terms of accuracy for estimating PH, with an error of 6.963% (8.823 cm) error.

Shanlan upland rice is an important landrace rice resource and is characterized with high drought stress (DS) tolerance relative to cultivated rice. However, the molecular mechanism of DS response in Shanlan upland rice remains unclear. In this study, we performed an integrated analysis of transcriptome and targeted metabolism to decipher the key biological pathways that responded to drought tolerance using two Shanlan upland rice lines. Results show that SL10 possesses 64% higher photosynthetic efficiency (Pn) and 2-fold higher water use efficiency (WUE) than that in SL1 exposed to DS. The decrease in Pn by DS is not due to stomatal limitation effects for SL1. Transcriptome analysis suggests photosynthesis relevant pathways (photosynthesis-antenna proteins and carbon fixation) and photorespiration relevant pathway (glycine, serine and threonine metabolism) in SL1 under DS were significantly enriched in the down-regulated and up-regulated DEGs list, respectively. There are 412 up-regulated and 233 down-regulated drought responsive genes (DRGs) in SL10 relative to SL1 induced by DS. Targeted metabolism results suggest that the contents across five metabolites related to carbon fixation pathway were declined by 36 and 8% in SL1 and SL10 caused by DS, respectively. We finally summarized the both gene expression and metabolites involved in photorespiration and carbon fixation pathways in response to DS in both rice lines. This study provides valuable information for better understanding the molecular mechanism underlying drought tolerance in Shanlan rice.

Summary Upland rice is a distinctive drought‐aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought‐aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high‐quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought‐resistant rice and the “blue revolution” in agriculture.

Purpose Upland rice production is often constrained by phosphorus deficiency (P) and drought events. Methods are needed to maximize P use efficiency, while promoting deep root development to mitigate drought. This study evaluates micro-dose P placement as a technique to enhance drought resilience of upland rice, thereby hypothesizing that P placement enhances deep root development, stimulated by the local P supply in the planting hole, compared to broadcast P. Methods Two pot experiments were conducted using P deficient upland soil in Tanzania (Expt.1) and Madagascar (Expt.2), with factorial combinations of P doses (control and two P levels), application method (placement versus broadcast), rice varieties (DJ123 & NERICA4) and water regimes (field capacity and drying periods). Results Micro-dose P placement strongly boosted the establishment of upland rice and enhanced P recovery rates (4- to 5-fold) and fertilizer use efficiency (9- to 14-fold) compared to broadcast P. Micro-dose P placements significantly enhanced the fraction of roots found at largest depth (> 30 cm, Expt. 1; >15 cm, Expt. 2) by 22- to 33 %. Surprisingly, shoot P concentrations were markedly lower under P placement than under broadcast at equivalent P doses or equivalent biomass, indicating a Piper-Steenbjerg effect. Conclusions This study is first in showing the enhanced deep rooting after basal P placement, and suggests replication at field scale where subsurface moisture may yield stronger benefits than in pots. The depleted shoot P concentrations induced by vigorous plant establishment under P placement may, however, counteract benefits at later growth stages and need further attention.