RESUMEN
Breeding rice varieties with a low phytic acid (LPA) content is an effective strategy to overcome micronutrient deficiency in a population which consume rice as a staple food. An LPA mutant, Pusa LPA Mutant 11 (PLM11), was identified from an ethyl methane sulfonate (EMS)-induced population of Nagina 22. The present study was carried out to map the loci governing the LPA trait in PLM11 using an F2:3 population derived from a cross between a high phytic acid rice variety, Pusa Basmati 6, with PLM11. The genotyping of the F2 population with 78 polymorphic SSR markers followed by the estimation of phytic acid content in the seeds harvested from 176 F2 plants helped in mapping a major QTL, qLPA8.1, explaining a 22.2% phenotypic variation on Chromosome 8. The QTL was delimited to a 1.96 cM region flanked by the markers RM25 and RM22832. Since there are no previous reports of a QTL/gene governing the LPA content in rice in this region, the QTL qLPA8.1 is a novel QTL. In silico analysis based on the annotated physical map of rice suggested the possible involvement of a locus, Os08g0274775, encoding for a protein similar to a phosphatidylinositol 3- and 4-kinase family member. This needs further validation and fine mapping. Since this QTL is currently specific to PLM11, the linked markers can be utilized for the development of rice varieties with reduced phytic acid (PA) content using PLM11 as the donor, thus enhancing the bioavailability of mineral micronutrients in humans.
RESUMEN
The semi-dwarfing allele, sd1-d, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), sd1-d, derived from a spontaneous mutation, has a 383-bp deletion in the SD1 gene. To date, as many as seven alleles of the SD1 gene have been identified and used in rice improvement, either with a functional single-nucleotide polymorphism (SNP), with insertion-deletions (InDels), or both. Here, we report discovery of a novel SNP in the SD1 gene from the rice genotype, Pusa 1652. Genetic analysis revealed that the inheritance of the semi-dwarfism in Pusa 1652 is monogenic and recessive, but it did not carry the sd1-d allele. However, response to exogenous gibberellic acid (GA3) application and the subsequent bulked segregant and linkage analyses confirmed that the SD1 gene is involved in the plant height reduction in Pusa 1652. Sequencing of the SD1 gene from Pusa 1652 revealed a novel transition in exon 3 (T/A) causing a nonsense mutation at the 300th codon. The stop codon leads to premature termination, resulting in a truncated protein of OsGA20ox2 obstructing the GA3 biosynthesis pathway. This novel recessive allele, named sd1-bm, is derived from Bindli Mutant 34 (BM34), a γ-ray induced mutant of a short-grain aromatic landrace, Bindli. BM34 is the parent of an aromatic semi-dwarf cultivar, Pusa 1176, from which Pusa 1652 is derived. The semi-dwarfing allele, sd1-bm, was further validated by developing a derived cleaved amplified polymorphic sequence (dCAPS) marker, AKS-sd1. This allele provides an alternative to the most widely used sd1-d in rice improvement programs and the functional dCAPS marker will facilitate marker-assisted introgression of the semi-dwarf trait into tall genotypes.