Journal of Genetics

, 98:50 | Cite as

Detection of QTL for panicle architecture in \(\hbox {F}_{2}\) population of rice

  • Rohini BhatEmail author
  • Anil Kumar Singh
  • Romesh Kumar Salgotra
  • Manmohan Sharma
  • Muntazir Mushtaq
  • Sreshti Bagati
  • Sharmishta Hangloo
  • Amrinder Singh
Research Article


Panicle traits are the most important agronomic characters which directly relate to yield in rice. Panicle length (PL) being one of the major components of rice panicle structure is controlled by quantitative trait loci (QTLs). In our research, conducted at Research Farm of SKUAST-J, crosses of parental lines K 343 and DHMAS were made for generating \(\text {F}_{2}\) mapping population, which were then transplanted into the field using augmented design-I. The \(\text {F}_{2}\) population was used for phenotypic evaluation, development of linkage map and identification of QTLs on the chromosomes by using SSR markers. A total of 450 SSR markers were used for screening both the parents of which 53 highly polymorphic markers were selected and used for genotyping of 233 genotypes of \(\text {F}_{2}\) population. Linkage map was generated using MAPMAKER/EXP3.0 software, seven linkage groups were found distributed on 11 chromosomes of rice. QTLs were detected using QTL Cartographer (v2.5) software. Based on 1000 permutation tests, a logarithm of odds (LOD) threshold value 2.0 and 3.0 was set. Composite interval mapping was used to map QTLs in populations derived from bi-parental crosses. The phenotypic data, genotypic data and the genetic linkage map generated identified total three QTLs of which one was identified for PL qPL2, located at 85.01 cM position with 2.1 LOD value and in between the marker intervals RM324–RM208, this QTL explained the phenotype variation by 4.36%. The other two QTLs were identified for spikelet density (SD) qSD3.1 and qSD3.2, located at 28.91 and 39.51 cM, respectively, both with a flanking marker RM6832 on chromosome 3. The LOD value and phenotypic variation explained for qSD3.1 and qSD3.2 was 3.00 and 3.25; 9.70 and 12.34% respectively. The reported QTLs identified in the study suggested a less diversity in the parents used and also the rejection of not so useful markers from the used set of markers for PL and SD.


quantitativetrait loci logarithm of odds simple sequence repeats composite interval mapping 



The first author would like to thank the School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, J&K for allowing the successful conduction of the research problem.


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Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  • Rohini Bhat
    • 1
    Email author
  • Anil Kumar Singh
    • 1
  • Romesh Kumar Salgotra
    • 1
  • Manmohan Sharma
    • 1
  • Muntazir Mushtaq
    • 1
  • Sreshti Bagati
    • 1
  • Sharmishta Hangloo
    • 1
  • Amrinder Singh
    • 1
  1. 1.School of BiotechnologySher-e-Kashmir University of Agricultural Science and Technology of JammuChathaIndia

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