A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.)

Phosphorus use efficiency (PUE) is a complex trait, governed by many minor quantitative trait loci (QTLs) with small effects. Advances in molecular marker technology have led to the identification of QTLs underlying PUE. However, their practical use in breeding programs remains challenging due to the unstable effects in different genetic backgrounds and environments, interaction with soil status, and linkage drag. Here, we compiled PUE QTL information from 16 independent studies. A total of 192 QTLs were subjected to meta-QTL (MQTL) analysis and were projected into a high-density SNP consensus map. A total of 60 MQTLs, with significantly reduced number of initial QTLs and confidence intervals (CI), were identified across the rice genome. Candidate gene (CG) mining was carried out for the 38 MQTLs supported by multiple QTLs from at least two independent studies. Genes related to amino and organic acid transport and auxin response were found to be abundant in the MQTLs linked to PUE. CGs were cross validated using a root transcriptome database (RiceXPro) and haplotype analysis. This led to the identification of the eight CGs (OsARF8, OsSPX-MFS3, OsRING141, OsMIOX, HsfC2b, OsFER2, OsWRKY64, and OsYUCCA11) modulating PUE. Potential donors for superior PUE CG haplotypes were identified through haplotype analysis. The distribution of superior haplotypes varied among subspecies being mostly found in indica but were largely scarce in japonica. Our study offers an insight on the complex genetic networks that modulate PUE in rice. The MQTLs, CGs, and superior CG haplotypes identified in our study are useful in the combination of beneficial alleles for PUE in rice

Assessing the Effect of a Major Quantitative Locus for Phosphorus Uptake (<i>Pup1</i>) in Rice (<i>O. sativa</i> L.) Grown under a Temperate Region

Water and phosphorus (P) fertilizer are two of the most critical inputs in rice cultivation. Irrigation and chemical fertilizers are becoming limiting factors under climate change and urbanization, which is leading to significant losses in yield. The Pup1 quantitative trait locus (QTL) confers tolerance to P starvation through enhanced early-stage root vigor and P uptake in indica rice grown in the tropics. Whether the QTL works in temperate rice genetic backgrounds grown in temperate regions remains to be elucidated. To address this question, we introgressed the Pup1 QTL into three temperate rice varieties—MS11, TR22183, and Dasanbyeo—using marker-assisted backcrossing and high-density genotyping. The selected lines all harbored the full Pup1 QTL with recurrent parent genome recovery rates ranging from 66.5% to 99.8%. Under the rainfed and P non-supplied conditions, Pup1 introgression lines did not show clear advantages over the recurrent parents in terms of vegetative growth and grain yield per plant, but exhibited enhanced yield responses to P application, except in Dasanbyeo, which a temperate rice that is genetically similar to indica. Our results suggest that Pup1 confers enhanced P uptake in temperate rice and that the efficacy of Pup1 might depend on the subspecific genomic background of the rice, whether it is japonica or indica

Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p &lt; 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding