CONFIRMATION AND FINE MAPPING OF MAJOR QTL FOR GRAIN SIZE IN BASMATI RICE

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dc.contributor.advisorANURADHA, G
dc.contributor.authorANNE KITTY DEBORAH, D
dc.date.accessioned2016-06-07T11:55:33Z
dc.date.available2016-06-07T11:55:33Z
dc.date.issued2011
dc.description.abstractBasmati rice is a unique varietal group that has gained wider acceptance as a speciality rice all over the world by virtue of its unique quality traits. Grain size plays a crucial role in determining the grain quality in Basmati rice. Genetic control of basmati grain quality traits is quite complex, but breeding of new varieties having Basmati grain quality characters can be greatly facilitated by the use of molecular markers tightly linked to these traits. Hence, in the present investigation 155 recombinant inbred lines (RILs) developed from a cross between Basmati370 and Jaya were used for confirmation and fine mapping of a major QTL for grain size in Basmati rice using SSR markers derived from inside and near the genomic region associated with grain size in the marker interval of RM289 and RM18600 on chromosome 5, that was already identified by Vemireddy (2008) using F2 population developed from the same cross. The parents used for mapping, Basmati370 and Jaya differed significantly with respect to all the three traits viz., grain length (GL), grain breadth (GB) and Length- Breadth ratio (LBR). Transgressive segregation of 45.8 % in grain length, 21.93 % in grain breadth and 12.25 % in LB ratio was observed in the RILs. All the three traits exhibited normal distribution in the RIL population indicating quantitative inheritance of these traits. Correlation analysis among the grain characters studied in RILs revealed a highly significant negative association of LB ratio with grain breadth and significant positive correlation with grain length. Out of 52 SSR and 1 INDEL markers used, 23 (43.40 %) were polymorphic, 27 (39.62 %) were monomorphic and 9 (16.98 %) were not amplified between Basmati370 and Jaya. The RILs were genotyped for these 23 polymorphic markers and the linkage map employing phenotypic and genotypic data of the RILs was constructed using MAPMAKER v 3.0. The QTLs were identified using interval mapping (IM) and composite interval mapping (CIM) methods of QTL Cartographer v 2.5 software with 2.5 as LOD threshold for detecting a QTL. A minor QTL for grain length qGL5.1 was identified by IM in the marker interval of RM6024 and RM1237 with Phenotypic Variance (PVE) of 3.7 %. A single QTL designated as qGB5.1 was detected for grain MAPMAKER v 3.0. The QTLs were identified using interval mapping (IM) and composite interval mapping (CIM) methods of QTL Cartographer v 2.5 software with 2.5 as LOD threshold for detecting a QTL. A minor QTL for grain length qGL5.1 was identified by IM in the marker interval of RM6024 and RM1237 with Phenotypic Variance (PVE) of 3.7 %. A single QTL designated as qGB5.1 was detected for grain breadth in the marker interval of RM1237 and RM18582 with PVE of 3.58 % in CIM and 4.51 % in IM and a QTL qGLB5.1 for Length- Breadth Ratio was identified with PVE of 11.8 %. The genetic distance of the flanking markers harbouring QTL cluster in the previous study conducted by Vemireddy (2008) was 26.5 cM whereas in the present study it was narrowed down to 15.7 cM. The physical distance also has come down from 11,128 kb to 685 kb. Comparision of rice genome database revealed that LOC_OS05g31920 (zinc ion binding protein), LOC_OS05g31930 (retrotransposon protein, putative, unclassified), LOC_OS05g31940 (retrotransposon protein, putative, unclassified), LOC_OS05g31950 (retrotransposon protein, putative, Ty3-gypsy subclass), LOC_OS05g31959 (hypothetical protein) and LOC_OS05g31970 (expressed protein) genes are present at this region. Interestingly, two predicted genes closure to this region viz., AP2 transcription factor and RING E3 ligase were reported to be involved in controlling the seed size and weight by earlier studies. In the present study, one microsatellite marker i.e., RM18582 showed close association with the grain size QTLs. This marker has potential to be used in markerassisted improvement of the grain size in Basmati rice. Though the present study was carried out in single environment, together with the results of F2 population of the same cross, it could be concluded that these three QTLs associated with grain size traits of Basmati could be considered as stable QTLs. These QTLs, apart from their suitability in improvement of the traits concerned, can also serve as potential candidates for fine mapping. These stable QTLs also facilitate development of Nearā€isogenic lines and advanced breeding lines.en_US
dc.identifier.urihttp://krishikosh.egranth.ac.in/handle/1/66916
dc.language.isoenen_US
dc.publisherACHARYA N.G. RANGA AGRICULTURAL UNIVERSITYen_US
dc.relation.ispartofseriesD8841;
dc.subAgricultural Biotechnology
dc.subjectgrain, rice, genetics, chromosomes, genes, proteins, genomes, crossing over, genetic structures, phenotypesen_US
dc.subjectBasmathi,en_US
dc.these.typeM.Sc
dc.titleCONFIRMATION AND FINE MAPPING OF MAJOR QTL FOR GRAIN SIZE IN BASMATI RICEen_US
dc.typeThesisen_US
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