Molecular Breeding

, Volume 21, Issue 1, pp 49–65 | Cite as

Mapping of quantitative trait loci for basmati quality traits in rice (Oryza sativa L.)

  • Yellari Amarawathi
  • Rakesh Singh
  • Ashok K. Singh
  • Vijai P. Singh
  • Trilochan Mohapatra
  • Tilak R. Sharma
  • Nagendra K. Singh


Traditional basmati rice varieties are very low yielding due to their poor harvest index, tendency to lodging and increasing susceptibility to foliar diseases; hence there is a need to develop new varieties combining the grain quality attributes of basmati with high yield potential to fill the demand gap. Genetic control of basmati grain and cooking quality traits is quite complex, but breeding work can be greatly facilitated by use of molecular markers tightly linked to these traits. A set of 209 recombinant inbred lines (RILs) developed from a cross between basmati quality variety Pusa 1121 and a contrasting quality breeding line Pusa 1342, were used to map the quantitative trait loci (QTLs) for seven important quality traits namely grain length (GL), grain breadth (GB), grain length to breadth ratio (LBR), cooked kernel elongation ratio (ELR), amylose content (AC), alkali spreading value (ASV) and aroma. A framework molecular linkage map was constructed using 110 polymorphic simple sequence repeat (SSR) markers distributed over the 12 rice chromosomes. A number of QTLs, including three for GL, two for GB, two for LBR, three for aroma and one each for ELR, AC and ASV were mapped on seven different chromosomes. While location of majority of these QTLs was consistent with the previous reports, one QTL for GL on chromosomes 1, and one QTL each for ELR and aroma on chromosomes 11 and 3, respectively, are being reported here for the first time. Contrary to the earlier reports of monogenic recessive inheritance, the aroma in Pusa 1121 is controlled by at least three genes located on chromosomes 3, 4 and 8, and similar to the reported association of badh2 gene with aroma QTL on chromosome 8, we identified location of badh1 gene in the aroma QTL interval on chromosome 4. A discontinuous 5 + 3 bp deletion in the seventh exon of badh2 gene, though present in all the RILs with high aroma, was not sufficient to impart this trait to the rice grains as many of the RILs possessing this deletion showed only mild or no aroma expression.


Basmati Rice Grain and cooking quality QTL SSR markers 



Amylose content


Alkali spreading value


Cooked kernel elongation ratio


Grain length


Grain breadth


Grain length to breadth ratio


Simple sequence repeat


Quantitative trait locus



This work was done under National Bioscience Award to NKS by the DBT, Government of India. We are thankful to the financial support of ICAR through NPTC project, IARI and CSIR, New Delhi for fellowship supports to AY, and Dr. KV Prabhu for off-season multiplication of RILs in the National Phytotron Facility.

Supplementary material

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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Yellari Amarawathi
    • 1
  • Rakesh Singh
    • 1
    • 3
  • Ashok K. Singh
    • 2
  • Vijai P. Singh
    • 2
  • Trilochan Mohapatra
    • 1
  • Tilak R. Sharma
    • 1
  • Nagendra K. Singh
    • 1
  1. 1.Rice Genome Laboratory, National Research Centre on Plant BiotechnologyIndian Agricultural Research InstituteNew DelhiIndia
  2. 2.Division of GeneticsIndian Agricultural Research InstituteNew DelhiIndia
  3. 3.National Bureau of Plant Genetic ResourcesNew DelhiIndia

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