Abstract
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.
Highlights
A very strong and positive phenotypic correlation was observed between total grain yield/plant (YLD) and panicle weight (PW) (r = 0.89) and plant height (PH) (r = 0.35) at 1% level of significance
The traits total grains/ panicle (GP), fertile grains/panicle (FGP), test grain weight (TGW), flag leaf length (FLL), flag leaf width (FLW), number of productive tillers (PT), panicle length (PL) showed the positive and significant phenotypic correlation at 5% level of significance with total grain yield/plant (YLD) whereas negative correlation was observed between YLD and Days to fifty percent flowering (DFF)
This study identified several major and minor effect quantitative trait loci (QTL) from both male and female parents of Karnataka Rice Hybrid-2 (KRH-2), which co-localized with QTLs, discovered in earlier studies, indicate that the genomic regions underlying the QTLs could be possible hotspots for yield heterosis associated traits
Summary
Abbreviations QTL Quantitative trait loci RIL Recombinant inbred line SSR Simple sequence repeats ICIM Inclusive composite interval mapping SNP Single nucleotide polymorphism GWAS Genome wide association mapping GBS Genotyping-by-sequencing KRH-2 Karnataka rice hybrid-2 RARS Regional Agricultural Research Station KMR-3R Karnataka Mandya rice-3R SSD Single seed descent DFF Days to fifty percent flowering (DFF) YLD Total grain yield per plant GP Total number of grains per panicle FGP Fertile grains per panicle TGW Test (thousand) grain weight PW Panicle weight PH Plant height PL Panicle length FLL Flag leaf length FLW Flag leaf width PT Productive tillers BM Biomass CV% Coefficient of variation in percentage STAR Statistical Tool for Agricultural Research (STAR) software version 2.0.1 ANOVA Analysis of variance DNA Deoxy ribose nucleic acid CTAB Cetyl trimethyl ammonium bromide PCR Polymerase chain reaction TrisHCl Tris aminomethane hydrochloric acid KCl Potassium chloride mM Milli molar MgCl2 Magnesium chloride dNTP Deoxyribonucleotide triphosphate pmol Pico mole pH Potential of hydrogen ng Nano gram U Unit v/v Volume/volume °C Degree centigrade EST Expressed sequence tags LOD Log-likelihood ratio PVE Phenotypic variation explained cM Centi Morgan SAM file Sequence alignment map file MAF Minor allele frequency GLM method General linear model method WA-CMS line Wild abortive-cytoplasmic male sterile line. QTL mapping, a method that identifies the number, position and effect of loci on the expression of specific traits[15] has been extensively used for the identification of novel QTLs in rice by various research g roups[16] This problem was addressed using a combination of conventional and molecular breeding approaches such as the marker assisted selection (MAS) which led to the identification of yield enhancing. The MAS strategy has been used to address biotic s tresses[27] and introgression of five genes that confer resistance to biotic stress into the japonica cultivar were well characterized The characterization of such novel QTLs is crucial in understanding the genetic basis of traits’ expressions but are important from breeding perspectives[28]. The present study was carried out with an objective to map novel genomic regions for the yield and its allied parameters with recombinant inbred line (RIL) population derived from an elite hybrid KRH-2 with the help of SSR and SNP markers
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