Allele Mining and Molecular Breeding


The programme attempts to study molecular breeding for abiotic stress and molecular documentation of rice germplasms in NE India. As such, the programme attempts to study the germplasm systematically and tag the traits of interest and their variant alleles using markers for use in rice improvement programme through molecular breeding.

The objective of this programme is to:


  • Assess the nature and extent of genetic variation in the rice germplasm of Assam
  • Develop DNA fingerprint database of rice germplasms of AAU using SSR markers
  • Allele mining for genes related to important agronomic traits from existing rice germplasm
  • Identify the marker(s) linked to the gene(s) for the agronomic traits under study
  • Pyramid stress countering genes into elite varieties

Scientists Involved

Scientists involved with this programme are Dr. M K Modi, Dr. P Sen, Dr. A R Barooah, Dr. R N Sarmah, Dr. T Ahmed, Dr. S D Deka, Dr P K Pathak, Dr. S Baishya and Dr. K Das from AAU, Jorhat


Collaborative Scientists include Dr. N K Singh, NRCPB, New Delhi and Dr. A Patnaya, ICAR Complex, Barapani



Salient accomplishment:

  • Morphological data for 39 characters of 1400 (900 in Titabar and 500 in Karimganj) Sali lines recorded.
  • Morphological data for 39 characters of 1150 lines being recorded this season
  • 1013 lines were genotyped with 120 SSR markers
  • Phenotyping is in progress and allele mining will be done for drought tolerance
  • Two mapping populations from the following crosses were developed & genotyped
    • Ranjit x Banglami
    • Ranjit x Arc 10372
      • (Banglami a local drought tolerant line and ARC 10372 an Assam Rice Collection tolerant to drought and obtained from IRRI Progeny were Phenotyped for draught under rain-out shelter. QTls for drought will be identified)
  • Luit and Dishang was crossed with IRBB 60 for BLB resistance
  • Ranjit-Sub1 crossed with Improved Samba Masuri for BLB resistance


Future line of research:

  • Determine the population structure of the Rice germplasm maintained at AAU Jorhat using low density genome wide SNP markers
  • Develop a core set representing the entire diversity of the AAU rice germplasm
  • Extensive genotyping of the core using high density SNP chip.
  • Association mapping for identification of QTL for draught and flooding tolerance.
  • Develop Gel-based markers for the QTLs and introgress into advance breeding lines