MOLECULAR MAPPING OF GENETIC LOCI ASSOCIATED WITH TOLERANCE TO LOW SOIL PHOSPHORUS IN RICE (Oryza sativa L.)
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Date
2019
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PROFESSOR JAYASHANKAR TELANGANA STATE AGRICULTURAL UNIVERSITY
Abstract
Rice is one of the most important cereal crops and occupies second prominent position in global agriculture. A significant proportion of rice growing soils across the world and in India is either phosphorus (P)-deficient or has a high P-fixing capacity resulting in reduced productivity levels. The basic mechanism plants follow for P utilization are P acquisition efficiency and internal P–use efficiency. Presence of genetic variability for P uptake has been reported in rice and a major QTL called Pup1 conferring tolerance to low soil P has been identified earlier. The present study was taken up in order to characterize available germplasm lines for low P tolerance and QTL mapping for low soil P tolerance in recombinant inbred line (RIL) mapping population developed by crossing, Wazuhophek (which has significant tolerance to low soil P condition and completely devoid of Pup1 genomic region) and Improved Samba Mahsuri (ISM; Which is highly sensitive to low soil P).
In the first objective, i.e. a set of 56 germplasm lines of rice were analyzed for their genotype with respect to markers spanning the Pup1 locus along with phenotypic characterization for low soil P tolerance. Significant genetic variability was observed with respect to plant height, number of productive tillers, root volume, dry root weight, dry shoot weight and grain yield under low P condition. Cluster analysis based on the stress indices and low soil P tolerance ability, grouped the genotypes into three groups, viz., highly tolerant, tolerant and sensitive. Genotyping of the rice lines with a set of Pup1 specific markers (viz., K46-1, K46-2, K52 and 46CG-1), revealed the presence of partial or complete Pup1 genomic region in most of the tolerant genotypes. A total of 15 genotypes showed tolerance to low soil P based on yield reduction in comparison to the tolerant and sensitive checks. Interestingly, the tolerant genotype line, IC216831 was observed to be completely devoid of Pup1, and hence it can be explored for identification and characterization of new loci underlying low soil P tolerance.
The second objective focused on SSR marker-based molecular mapping of genomic regions associated with low soil P tolerance in the non-Pup1 type, low P tolerant rice line from North-eastern part of India, Wazuhophek. Quantitative trait loci (QTLs) related to low soil P tolerance were identified in recombinant inbred lines (RILs), developed from cross Improved Samba Mahsuri/Wazuhophek. A total of 16 QTLs related to yield and other physio- morphological traits were identified under low soil P condition. Out of them, 10 QTLs were found on chromosome 8, spanning a 4.49 Mb region in the genomic interval of RM22554-RM8005. Two QTLs were identified on chromosome 7, spanning a 2.71 Mb (RM5847-RM22031) region and 11.31 Mb (RM21521-RM21103) region for root volume and P content of grains, respectively. Four QTLs were identified on chromosome 1, spanning a 9.2 Mb region in between the markersWR1.7-RM8105.
In silico analysis of identified genomic regions spanning the identified QTLs was carried out. A total of 538 genes were predicted in the QTL region on chromosome 8, of which eight genes related to phosphorus uptake or utilization, including genes related to auxin signalling, phosphatase activity and zinc figure transcription factor appear to be of interest.
A total of 1339 genes were predicted in the QTL region on chromosome 1, of which 14 genes related to phosphorus uptake or utilization, including auxin responsive genes and genes involved in maintenance of Pi homeostasis are of interest. A total of 712 genes were predicted in the QTL region controlling root volume, located on chromosome 7. Among them, 12 genes related to phosphorus uptake or utilization, including auxin responsive genes and transcription factors involved in regulation of stress related genes appear to be of interest. Similarly, in silico analysis of another QTL for P content in seed located on chromosome 7, predicated 570 genes. Among them, 16 were found to be possibly related to phosphorus uptake or utilization. All the QTLs detected in the present study, appear to be novel and did not overlap with the already reported genes/QTL. The novel low P tolerant rice line, IC216831, which is devoid of Pup1 can be subjected for genetic and molecular marker analysis to identify novel low P tolerance genes/QTLs. Further, the novel QTLs associated with low soil P tolerance identified from Wazuhophek, after their fine-mapping and validation, can be transferred into elite rice varieties and parental lines, which are sensitive to low soil P levels through marker-assisted breeding.
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D10,448