Hyperspectral and genome-wide association analyses of leaf phosphorus status in local Thai indica rice

Abstract

Phosphorus (P) is an essential mineral nutrient and one of the key factors determining crop productivity. P-deficient plants exhibit visual leaf symptoms, including chlorosis, and alter spectral reflectance properties. In this study, we evaluated leaf inorganic phosphate (Pi) contents, plant growth and reflectance spectra (420–790 nm) of 172 Thai rice landrace varieties grown hydroponically under three different P supplies (overly sufficient, mildly deficient and severely deficient conditions). We reported correlations between Pi contents and reflectance ratios computed from two wavebands in the range of near infrared (720–790 nm) and visible energy (green-yellow and red edge) (r > 0.69) in Pi-deficient leaves. Artificial neural network models were also developed which could classify P deficiency levels with 85.60% accuracy and predict Pi content with R2 of 0.53, as well as highlight important waveband sections. Using 217 reflectance ratio indices to perform genome-wide association study (GWAS) with 113,114 SNPs, we identified 11 loci associated with the spectral reflectance traits, some of which were also associated with the leaf Pi content trait. Hyperspectral measurement offers a promising non-destructive approach to predict plant P status and screen large germplasm for varieties with high P use efficiency.

Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice

“…These SNPs were found to be located on chromosomes 1-8 and 12 but not on chromosomes 9-11. It is worth noting that previous reports have mostly identified the BLB resistance gene on chromosome 11 [17,18,36,98]. However, our results indicate that SNPs on chromosome 11 were only detected at a low level of significance, with a q-value threshold of 5.71 and an FDR of 0.01 for the three Xoo isolates.…”

“…The four statistic methods were used as the mixed linear models (MLM) [75], Settlement of MLM Under Progressively Exclusive Relationship (SU-PER) [76], fixed and random model circulation probability unification (FarmCPU) [77], and the Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK) method [78] were used to control for false-negative results [71]. The threshold for identifying significant SNPs was determined using the False Discovery Rate (FDR) [18,25,36,79,80]. Gene annotations within a 100 kb region surrounding the highly associated SNPs were taken into consideration for SNP identification.…”

“…GWAS has become a powerful approach for unraveling the molecular genetics associated with natural phenotypic variation in rice. Various traits have been investigated using this technique, including agronomic traits, quality, and resistance to biotic and abiotic stresses [26,[33][34][35][36]. Data collected from a variety of populations, plant growth stages, and different Xoo variations have been utilized in GWAS for gene mining, QTL mapping, and searches for candidate SNPs for BLB resistant traits in rice.…”

Effect of phosphorus deficiency on allelopathic activity of lowland indica rice

“…1D-E). In a recent work, the inhibition of rice biomass by low P availability was not detected in three-week old rice seedlings, while leaf Pi contents were significantly reduced [31]. However, growth suppression due to P deficiency has been detected in rice seedlings of some rice cultivars, consistent with the higher transcription of Pi deficiencyresponsive genes such as OsIPS1, OsSPX1, OsSQD2, OsPAP10, and OsPT8 [32].…”

Rice straw-derived smoke water promotes rice root growth under phosphorus deficiency by modulating oxidative stress and photosynthetic gene expression

“…Modification of root system architecture in response to P deficiency is one of the strategies to improve P acquisition 10 . In rice ( Oryza sativa L.), the ability of roots to elongate under P deficiency varied greatly among rice populations 11 , 12 . Previous studies have shown that a gene encoding the protein kinase Pstol1 (Phosphorus-starvation tolerance 1), which is located in a major quantitative trait locus for P-deficiency tolerance, Pup1 , is responsible for enhanced root growth and large root system, contributing to increased nutrient uptake and P-deficiency tolerance 13 .…”