Characterization of quantitative trait loci from DJ123 () independently affecting panicle structure traits in rice cultivar IR64.

Unlabelled: The rice panicle is the principal organ to influence productivity and traits affecting panicle architecture determine sink size and yield potential. Improving panicle architecture may be effective in increasing yield under low-input conditions, but which traits are of importance under such conditions and how they are genetically controlled is not well understood. Using recombinant inbred lines (RILs) derived from a cross between a modern variety IR64 and a low fertility tolerant accession DJ123, quantitative trait locus (QTL) mapping was conducted under high soil fertility in Japan and low fertility in Madagascar.

Novel QTL for Lateral Root Density and Length Improve Phosphorus Uptake in Rice (Oryza sativa L.).

The rice root system consists of two types of lateral roots, indeterminate larger L-types capable of further branching, and determinate, short, unbranched S-types. L-type laterals correspond to the typical lateral roots of cereals whereas S-type laterals are unique to rice. Both types contribute to nutrient and water uptake and genotypic variation for density and length of these laterals could be exploited in rice improvement to enhance adaptations to nutrient and water-limited environments.

Corrigendum: QTL mapping for early root and shoot vigor of upland rice ( L.) under P deficient field conditions in Japan and Madagascar.

[This corrects the article DOI: 10.3389/fpls.2022.

QTL mapping for early root and shoot vigor of upland rice ( L.) under P deficient field conditions in Japan and Madagascar.

Upland rice production is limited by the low phosphorus (P) availability of many highly weathered tropical soils and P deficiency is likely to become increasingly limiting in future drier climates because P mobility decreases sharply with soil moisture. Good seedling root development will be crucial to cope with the combined effects of low P and water availability. Upland rice genebank accession DJ123 was used as a donor for P efficiency and root vigor traits in a cross with inefficient local variety Nerica4 and a set of backcross lines were used to characterize the seedling stage response of upland rice to low P availability and to identify associated QTL in field trials in Japan and Madagascar.

Comparative transcriptome analysis reveals a rapid response to phosphorus deficiency in a phosphorus-efficient rice genotype.

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.

Genomic prediction of zinc-biofortification potential in rice gene bank accessions.

A genomic prediction model successfully predicted grain Zn concentrations in 3000 gene bank accessions and this was verified experimentally with selected potential donors having high on-farm grain-Zn in Madagascar. Increasing zinc (Zn) concentrations in edible parts of food crops, an approach termed Zn-biofortification, is a global breeding objective to alleviate micro-nutrient malnutrition. In particular, infants in countries like Madagascar are at risk of Zn deficiency because their dominant food source, rice, contains insufficient Zn.

Phenotyping of a rice (Oryza sativa L.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in Madagascar.

Rice (Oryza sativa L.) is a staple food of Madagascar, where per capita rice consumption is among the highest worldwide. Rice in Madagascar is mainly grown on smallholder farms on soils with low fertility and in the absence of external inputs such as mineral fertilizers.

Leaf phosphorus fractionation in rice to understand internal phosphorus-use efficiency.

Background And Aims: Phosphorus (P) availability is often limiting for rice (Oryza sativa) production. Improving internal P-use efficiency (PUE) is crucial to sustainable food production, particularly in low-input systems. A critical aspect of PUE in plants, and one that remains poorly understood, is the investment of leaf P in different chemical P fractions (nucleic acid-P, lipid-P, inorganic-P, metabolite-P and residual-P).

From gene banks to farmer's fields: using genomic selection to identify donors for a breeding program in rice to close the yield gap on smallholder farms.

Despite phenotyping the training set under unfavorable conditions on smallholder farms in Madagascar, we were able to successfully apply genomic prediction to select donors among gene bank accessions. Poor soil fertility and low fertilizer application rates are main reasons for the large yield gap observed for rice produced in sub-Saharan Africa. Traditional varieties that are preserved in gene banks were shown to possess traits and alleles that would improve the performance of modern variety under such low-input conditions.

Identification of Loci Through Genome-Wide Association Studies to Improve Tolerance to Sulfur Deficiency in Rice.

Sulfur (S) is an essential nutrient for plant growth and development; however, S supply for crop production is decreasing due to reduced inputs from atmospheric deposition and reduced application of S-containing fertilizers. Sulfur deficiency in soil is therefore becoming a widespread cause of reduced grain yield and quality in rice ( L). We therefore assessed the genotypic variation for tolerance to S deficiency in rice and identified loci associated with improved tolerance.

Phosphorus uptake commences at the earliest stages of seedling development in rice.

Seed phosphorus (P) reserves are essential for seedling development; however, we hypothesise that the quantity of P in seeds will lose importance in cultivars that rapidly acquire it via their roots. Our objective in this study was therefore to investigate the onset of seedling P uptake in rice (Oryza sativa). This was addressed through 33P-labelled supply and through measuring P depletion in combination with the detection of P transporter activity in the root tissue of three rice cultivars during early development.

Genome-wide association and gene validation studies for early root vigour to improve direct seeding of rice.

Elucidation of the genetic control of rice seedling vigour is now paramount with global shifts towards direct seeding of rice and the consequent demand for early vigour traits in breeding programmes. In a genome-wide association study using an indica-predominant diversity panel, we identified quantitative trait loci (QTLs) for root length and root number in rice seedlings. Among the identified QTLs, one QTL for lateral root number on chromosome 11, qTIPS-11, was associated with a 32.

The role of root size versus root efficiency in phosphorus acquisition in rice.

In rice, genotypic differences in phosphorus (P) uptake from P-deficient soils are generally proportional to differences in root biomass or surface area (RSA). It is not known to what extent genotypic variation for root efficiency (RE) exists or contributes to P uptake. We evaluated 196 rice accessions under P deficiency and detected wide variation for root biomass which was significantly associated with plant performance.

Unmasking Novel Loci for Internal Phosphorus Utilization Efficiency in Rice Germplasm through Genome-Wide Association Analysis.

Depletion of non-renewable rock phosphate reserves and phosphorus (P) fertilizer price increases has renewed interest in breeding P-efficient varieties. Internal P utilization efficiency (PUE) is of prime interest because there has been no progress to date in breeding for high PUE. We characterized the genotypic variation for PUE present within the rice gene pool by using a hydroponic system that assured equal plant P uptake, followed by mapping of loci controlling PUE via Genome-Wide Association Studies (GWAS).

A novel allele of the P-starvation tolerance gene OsPSTOL1 from African rice (Oryza glaberrima Steud) and its distribution in the genus Oryza.

We have developed allele-specific markers for molecular breeding to transfer the PSTOL1 gene from Kasalath to African mega-varieties, including NERICAs, to improve their tolerance to P-deficient soil. The deficiency of phosphorus (P) in soil is a major problem in Sub-Saharan Africa due to general nutrient depletion and the presence of P-fixing soils. Developing rice cultivars with enhanced P efficiency would, therefore, represent a sustainable strategy to improve the livelihood of resource-poor farmers.

The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency.

As an essential macroelement for all living cells, phosphorus is indispensable in agricultural production systems. Natural phosphorus reserves are limited, and it is therefore important to develop phosphorus-efficient crops. A major quantitative trait locus for phosphorus-deficiency tolerance, Pup1, was identified in the traditional aus-type rice variety Kasalath about a decade ago.

Root metabolic response of rice (Oryza sativa L.) genotypes with contrasting tolerance to zinc deficiency and bicarbonate excess.

Plants are routinely subjected to multiple environmental stresses that constrain growth. Zinc (Zn) deficiency and high bicarbonate are two examples that co-occur in many soils used for rice production. Here, the utility of metabolomics in diagnosing the effect of each stress alone and in combination on rice root function is demonstrated, with potential stress tolerance indicators identified through the use of contrasting genotypes.

Leaf ascorbic acid level--is it really important for ozone tolerance in rice?

Leaf ascorbic acid (ASA) level is thought to be an important trait conferring stress tolerance in plants, but definite evidence regarding its effectiveness in the breeding of stress tolerant crops is lacking. Therefore, the stress response of a rice TOS17 insertion mutant (ND6172) for a GDP-D-mannose-3',5'-epimerase gene, which is involved in ASA biosynthesis, was tested. Two fumigation experiments were conducted, in which rice plants (Oryza sativa L.

Revisiting the role of organic acids in the bicarbonate tolerance of zinc-efficient rice genotypes.

It has been hypothesised that enhanced organic acid release from the roots of zinc-efficient rice (Oryza sativa L.) genotypes plays a strong role in plant tolerance to both bicarbonate excess and Zn deficiency. To address several uncertainties in the literature surrounding the tolerance of rice to bicarbonate, we initially assessed the tolerance of six rice genotypes to bicarbonate stress under field conditions and in solution culture.

The Frustration with Utilization: Why Have Improvements in Internal Phosphorus Utilization Efficiency in Crops Remained so Elusive?

Despite the attention internal phosphorus utilization efficiency (PUE) of crops has received in the literature, little progress in breeding crop cultivars with high PUE has been made. Surprisingly few studies have specifically investigated PUE; instead, genotypic variation for PUE has been investigated in studies that concurrently assess phosphorus acquisition efficiency (PAE). We hypothesized that genotypic differences in PAE confound PUE rankings because genotypes with higher PAE suffer a lower degree of P stress, resulting in lower PUE.

Mechanisms of ozone tolerance in rice: characterization of two QTLs affecting leaf bronzing by gene expression profiling and biochemical analyses.

High surface ozone concentration is increasingly being recognized as a factor that negatively affects crop yields in Asia. However, little progress has been made in developing ozone-tolerant genotypes of rice-Asia's major staple crop. This study aimed to identify possible tolerance mechanisms by characterizing two quantitative trait loci (QTLs) that were previously shown to influence visible leaf symptoms under ozone exposure (120 nl l(-1), 7 h d(-1), 13 d).

Response to zinc deficiency of two rice lines with contrasting tolerance is determined by root growth maintenance and organic acid exudation rates, and not by zinc-transporter activity.

*Zinc (Zn)-deficient soils constrain rice (Oryza sativa) production and cause Zn malnutrition. The identification of Zn-deficiency-tolerant rice lines indicates that breeding might overcome these constraints. Here, we seek to identify processes underlying Zn-deficiency tolerance in rice at the physiological and transcriptional levels.

Nitrification inhibition activity, a novel trait in root exudates of rice.

Background And Aims: Nitrification is an important process in soil--plant systems for providing plant-available nitrate (NO(3) (-)). However, NO(3) (-) is less stable in soils compared with ammonium (NH(4) (+)) and is more easily lost through leaching, runoff or denitrification. This study tested whether biological nitrification inhibition (BNI) activity is present in the root exudates of rice (Oryza sativa) and also the extent of variation between different genotypes.

Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure.

The phosphorus uptake 1 (Pup1) locus was identified as a major quantitative trait locus (QTL) for tolerance of phosphorus deficiency in rice. Near-isogenic lines with the Pup1 region from tolerant donor parent Kasalath typically show threefold higher phosphorus uptake and grain yield in phosphorus-deficient field trials than the intolerant parent Nipponbare. In this study, we report the fine mapping of the Pup1 locus to the long arm of chromosome 12 (15.