Research Report

Marker assisted selection for S5 neutral allele in inter-subspecific hybridization of rice  

Revathi P , Dinesh Chandra , Ram Deen , Arun Kumar Singh , Sohanvir singh , Moti Lal , Vijay pal bhadana , Ram Tilathoo
Directorate of Rice Research, Crop Improvement Section, Hyderabad, India
Author    Correspondence author
Molecular Plant Breeding, 2015, Vol. 6, No. 1   doi: 10.5376/mpb.2015.06.0001
Received: 11 Nov., 2014    Accepted: 19 Dec., 2014    Published: 27 Jan., 2015
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Preferred citation for this article:

Revathi et al., Marker assisted selection for S5 neutral allele in inter-subspecific hybridization of rice, Molecular Plant Breeding, 2015, Vol.6, No. 1 1-7 (doi: 10.5376/mpb.2015.06.0001)


The present level of heterosis in indica hybrids can be improved by exploiting inter-subspecific gene pool. Hybrid sterility in inter-subspecific hybridization is the major bottleneck, however use ofwide compatible varieties (WCVs) carrying neutral alleles helps in producing fertile hybrids. Conventionally WC varieties are identified by tedious test crossing. To identify WC varieties, 325 tropical japonica and 7 indica lines have been genotyped for the presence of S5n (neutral allele) with the help of S5-MMS (multiplex marker system) which clearly distinguish indica, japonica and S5 neutral allele. Of the 325 lines, 90 tropical japonica and Swarna (indica) showed the presence of S5n. One hundred and fifty F1 hybrids, indica × japonica (I × J), were evaluated for their hybrid sterility and spikelet fertility percentage ranged from 4 to 97%. The I × J hybrids with S5n showed higher spikelet fertility; however some hybrids without S5n showed higher spikelet fertility and among them few tropical japonica lines identified to carry indica allele by S5-MMS marker system, therefore this functional marker is a powerful tool for molecular screening of WC varieties. Hybrids with S5n showed higher sterility indicating existence of other than embryo sac sterility mechanism of I X J crosses, since S5n overcomes only embryo sac hybrid sterility. In wild rice O.rufipogon accessions the S5n allelic status was determined by using S5-MMS marker system. To conclude, S5-MMS is a powerful tool PCR based and with low cost, highly efficient as marker system in identifying WC varieties in different mapping populations including wild rice accessions. Whichsaves one year of breeder’s valuable time in inter-subspecific hybridization in rice.

Rice; Inter sub-specifiec hybridization; WC genotypes; S5 neutral allele; Molecular markers
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