Multi-trait association study identifies loci associated with tolerance of low phosphorus in Oryza sativa and its wild relatives.

We studied variation in adaptive traits and genetic association to understand the low P responses, including the symbiotic association of arbuscular mycorrhizal (AM) fungal colonization in Oryza species (O. sativa, O. nivara, and O. rufipogon). In the present experiment, we performed the phenotypic variability of the morphometric and geometric traits for P deficiency tolerance and conducted the association studies in GLM and MLM methods. A positive association between the geometric trait of the top-view area and root traits suggested the possibility of exploring a non-destructive approach in screening genotypes under low P. The AMOVA revealed a higher proportion of variation among the individuals as they belonged to different species of Oryza and the NM value was 2.0, indicating possible gene flow between populations. A sub-cluster with superior-performing accessions had a higher proportion of landraces (42.85%), and O. rufipogon (33.3%) was differentiated by four Pup1-specific markers. Association mapping identified seven notable markers (RM259, RM297, RM30, RM6966, RM242, RM184, and PAP1) and six potential genotypes (IC459373, Chakhao Aumbi, AC100219, AC100062, Sekri, and Kumbhi Phou), which will be helpful in the marker-assisted breeding to improve rice for P-deprived condition. In addition, total root surface area becomes a single major trait that helps in P uptake under deficit P up to 33% than mycorrhizal colonization. Further, the phenotypic analysis of the morphometric and geometric trait variations and their interactions provides excellent potential for selecting donors for improving P-use efficiency. The identified potential candidate genes and markers offered new insights into our understanding of the molecular and physiological mechanisms driving PUE and improving grain yield under low-P conditions.

Trait variations and expression profiling of OsPHT1 gene family at the early growth-stages under phosphorus-limited conditions.

To better understand the early response of genotypes to limited-phosphorus (P) conditions and the role of the phosphate transporter OsPHT1 gene family in the presence of PSTOL1, it is essential to characterize the level of tolerance in rice under limited-P conditions. In the present experiment, six rice genotypes were studied in three-way interactions [genotype (G) × phosphorus (P) × duration (D)] by comparing them at two instances (14 d and 28 d) under seven different concentrations of P (0.5‒10.0 ppm) in a hydroponic system. Trait differences and interactions of these traits were clearly distinguished among the various P rates. However, aboveground trait expression registered increased growth from 6.0 to 10.0 ppm of P. The major root-attributed traits in 0.5 ppm of P are significantly increased vis-à-vis 10 ppm of P. Analysis of variance displayed a significant difference between the genotypes for PSTOL1 and PHT1 expression. In low P, maximum root length with a shoot and root dry weight was observed in a new indigenous accession, IC459373, with higher expression of PSTOL1 than in Dular and IR64-Pup1 in 0.5 ppm of P at 14 d. Among the 13 PHT1 genes, OsPT1, OsPT2, OsPT6, and OsPT13 showed significant upregulation in IC459373, Dular, and IR64-Pup1. These results indicated that studying the expression levels of the PSTOL1 and PHT1 gene family at the early growth stages would be helpful in identifying superior donors to improve low-P tolerance and P-use efficiency in rice breeding programs.

Understanding interaction effect of arbuscular mycorrhizal fungi in rice under elevated carbon dioxide conditions.

Arbuscular mycorrhizal fungi (AMF), particularly the Glomerales group, play a paramount role in plant nutrient uptake, and abiotic and biotic stress management in rice, but recent evidence revealed that elevated CO2 concentration considerably reduces the Glomerales group in soil. In view of this, the present study was initiated to understand the interaction effect of native Glomerales species application in rice plants (cv. Naveen) under elevated CO2 concentrations (400 ± 10, 550 ± 20, and 700 ± 20 ppm) in open-top chambers. Three different modes of application of the AMF inoculum were evaluated, of which, combined application of AMF at the seedling production and transplanting stages showed increased AMF colonization, which significantly improved grain yield by 25.08% and also increased uptake of phosphorus by 18.2% and nitrogen by 49.5%, as observed at 700-ppm CO2 concentration. Organic acids secretion in rice root increased in AMF-inoculated plants exposed to 700-ppm CO2 concentration. To understand the overall effect of CO2 elevation on AMF interaction with the rice plant, principal component and partial least square regression analysis were performed, which found both positive and negative responses under elevated CO2 concentration.

Molecular Genetics and Breeding for Nutrient Use Efficiency in Rice.

In the coming decades, rice production needs to be carried out sustainably to keep the balance between profitability margins and essential resource input costs. Many fertilizers, such as N, depend primarily on fossil fuels, whereas P comes from rock phosphates. How long these reserves will last and sustain agriculture remains to be seen. Therefore, current agricultural food production under such conditions remains an enormous and colossal challenge. Researchers have been trying to identify nutrient use-efficient varieties over the past few decades with limited success. The concept of nutrient use efficiency is being revisited to understand the molecular genetic basis, while much of it is not entirely understood yet. However, significant achievements have recently been observed at the molecular level in nitrogen and phosphorus use efficiency. Breeding teams are trying to incorporate these valuable QTLs and genes into their rice breeding programs. In this review, we seek to identify the achievements and the progress made so far in the fields of genetics, molecular breeding and biotechnology, especially for nutrient use efficiency in rice.