Allele mining for the grain number gene An-1 in rice (Oryza sativa L.)

  • R. Shobica Priya,
  • T. Kalaimagal,
  • S. Rajeswari,
  • R. Ajay Prasanth and M. Raveendran


Rice yield has attained a plateau and hence the enhancement of grain yield is indispensable to feed the growing population, which could be achieved by the identification of superior alleles in the existing germplasm. Any variation in the pleiotropic gene, An-1 (yield gene) leads to enhanced grain number and grain size in rice. Hence, the gene was chosen for analyzing the allelic diversity/haplotype variation with 150 lines of 3K RG panel which revealed that, the gene An-1 has 20 Single Nucleotide Polymorphisms and 10 INDELs encompassing both intronic and exonic regions. The genotypes were divided into four haplotypes in the combination of seven SNPs with the maximum number of genotypes in the first haplotype and the least number of genotypes in fourth haplotype. From the study, H1 was identified as a superior haplotype. The haplo-pheno analysis identified the superior donors viz., SIGARDIS, GENIT and DAMNOEUB KAUN KHMOM harbouring superior haplotype combinations, which may be further utilized in haplotype-based breeding for the development of high yielding rice varieties.

Key words: rice, An-1, grain number, haplotype, SNPs, allelic diversity.

How to Cite
Priya, R. S., Kalaimagal, T., Rajeswari, S., & M. Raveendran, R. A. P. and. (2021). Allele mining for the grain number gene An-1 in rice (Oryza sativa L.). Electronic Journal of Plant Breeding, 12(3), 772-779. Retrieved from
Research Article