Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping

• Published in: Scientific reports Vol. 10; no. 1; p. 13695
• Main Authors: Kulkarni, Swapnil Ravindra, Balachandran, S. M., Ulaganathan, K., Balakrishnan, Divya, Praveen, M., Prasad, A. S. Hari, Fiyaz, R. A., Senguttuvel, P., Sinha, Pragya, Kale, Ravindra R., Rekha, G., Kousik, M. B. V. N., Harika, G., Anila, M., Punniakoti, E., Dilip, T., Hajira, S. K., Pranathi, K., Das, M. Ayyappa, Shaik, Mastanbee, Chaitra, K., Rao, P. Koteswara, Gangurde, Sunil S., Pandey, Manish K., Sundaram, R. M.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 13-08-2020; Nature Publishing Group
• Subjects: 631/208; 631/449; 631/61; Agricultural production; Agricultural research; Chromosome 3; Chromosome Mapping - methods; Chromosomes, Plant - genetics; Computer Simulation; Crop yield; Cultivars; Epistasis; Epistasis, Genetic; Gene mapping; Genes; Genetic Linkage; Genomes; Genotyping; Humanities and Social Sciences; Hybrids; Inbreeding; Microsatellite Repeats; multidisciplinary; Nucleotide sequence; Oryza - genetics; Oryza - growth & development; Phenotypic variations; Phenotyping; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Rice; Science; Science (multidisciplinary); Simple sequence repeats; Single-nucleotide polymorphism; Variance analysis
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-70637-3

The study was undertaken to identify the quantitative trait loci (QTLs) governing yield and its related traits using a recombinant inbred line (RIL) population derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R). A genetic map spanning 294.2 cM was constructed with 126 simple sequence repeats (SSR) loci uniformly distributed across the rice genome. QTL analysis using phenotyping and genotyping information identified a total of 22 QTLs. Of these, five major effect QTLs were identified for the following traits: total grain yield/plant (
qYLD3-1
), panicle weight (
qPW3-1),
plant height (
qPH12-1),
flag leaf width (
qFLW4-1)
and panicle length (
qPL3-1
), explaining 20.23–22.76% of the phenotypic variance with LOD scores range of 6.5–10.59. Few genomic regions controlling several traits (QTL hotspot) were identified on chromosome 3 for total grain yield/plant (
qYLD3-1)
and panicle length (
qPL3-1
). Significant epistatic interactions were also observed for total grain yield per plant (YLD) and panicle length (PL). While most of these QTLs were observed to be co-localized with the previously reported QTL regions, a novel, major QTL associated with panicle length (
qPL3-1
) was also identified. SNP genotyping of selected high and low yielding RILs and their QTL mapping with 1,082 SNPs validated most of the QTLs identified through SSR genotyping. This facilitated the identification of novel major effect QTLs with much better resolution and precision. In-silico analysis of novel QTLs revealed the biological functions of the putative candidate gene (s) associated with selected traits. Most of the high-yielding RILs possessing the major yield related QTLs were identified to be complete restorers, indicating their possible utilization in development of superior rice hybrids.