Genetic analysis and identification of QTLs associated with yield-enhancing traits in Oryza sativa IR64 × Oryza glaberrima interspecific backcross populations
Muralidhara Bharamappanavara A B # , Manoj Appaiah Chikkahosahalli B , Basavaraj Siddanagouda Patil
C , Ajitha Vijjeswarapu A , M. Siddaih Anantha A , Lokesha Ramappa B , Jayateertha Diwan B , Jayaprakash Mohan Nidagundi B , Umesh Rangappa Mathada B , Suma Chandrasekhara Talagunda B , Lokesh Yellaiah Guddalahalli B , Rajanna Byanna B , Santosha Rathod A , Raman Meenakshi Sundaram A , Lella Venkata Subbarao A , Mahender Kumar Rapolu A and Channappa Gireesh A # *
+ Author Affiliations
- Author Affiliations
A ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, India.
B University of Agricultural Sciences, Raichur 584104, Karnataka, India.
C ICAR-National Institute for Abiotic Stress Management, Baramati 413115, Maharashtra, India.
* Correspondence to: giri09@gmail.com
# These authors contributed equally to this paper
Handling Editor: Mohd. Kamran Khan
Crop & Pasture Science - https://doi.org/10.1071/CP22105
Submitted: 25 March 2022 Accepted: 3 November 2022 Published online: 6 January 2023
© 2023 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
Context: Broadening the gene pool of staple food crops by incorporating desirable genes from wild/relative species is way to achieve higher genetic gains. The African rice species Oryza glaberrima Steud. is a source of genes for genetic improvement of Oryza sativa L. to various biotic and abiotic stresses.
Aim: The study was undertaken to identify genomic regions associated with yield and yield-related traits in interspecific backcross mapping populations derived from variety IR64 (O. sativa indica) × O. glaberrima.
Methods: The BC1F2 and BC1F2:3 populations were phenotyped for days to 50% flowering, plant height, number of tillers, number of productive tillers, panicle length, spikelet fertility and grain yield under irrigated conditions. The BC1F2 population was genotyped with 99 genome-wide polymorphic SSR markers. Quantitative trait loci (QTLs) associated with yield-enhancing traits were identified through single marker analysis.
Key results: Significant genetic variability was observed with moderate to high heritability in mapping populations. Genotyping revealed the presence of segregation distortion and skewed genome composition. Single marker analysis identified 20 QTLs linked to the studied traits. A QTL linked to grain yield, qGY-4.1, derived from O. glaberrima was found in both populations with high phenotypic variance. The chromosome region around marker RM510 was identified as a QTL hotspot and putative candidate genes were identified.
Conclusions: Our study demonstrates that O. glaberrima can serve as a valuable genetic resource for genetic improvement of yield-enhancing traits in O. sativa cultivars.
Implications: The identified QTLs regions can be employed in molecular breeding. The promising introgression lines identified can be used as pre-breeding lines in future breeding programs.
Keywords: candidate genes, genome composition, grain yield, hotspots, mapping population, O. glaberrima, QTLs, simple sequence repeats.
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