An epi-allele of SMS causes Sanming dominant genic male sterility in rice

Male sterility is an important trait in rice for hybrid rice (Oryza sativa) breeding. However, the factors involved in dominant male sterility are largely unknown. Here, we identified a gene from Sanming dominant genic male sterile rice, named Sanming dominant male sterility (SMS), and reported that an epi-allele of this locus contributes to male sterility. Segregation analysis attributed dominant male sterility to a single locus, SMS, which we characterized using a male-sterile near isogenic line (NIL) of rice cultivar 93-11. The SMS locus was heterozygous in the male-sterile 93-11 NIL, containing an epi-allele identical to that in 93-11, and an epi-allele identical to that in rice cultivar Nipponbare, which we refer to as SMS₉ and SMS_N, respectively. SMS₉ is silent and hyper-methylated, whereas SMS_N is expressed and hypo-methylated in the 93-11 NIL. Overexpressing SMS_N led to male sterility. Mutations in SMS rescued the male sterility of the 93-11 NIL. Interestingly, we observed the duplication of SMS_N in Nipponbare, but did not observe the duplication of SMS₉ in 93-11. Together, these findings suggest that the reduced methylation and enhanced expression of the SMS_N epi-allele in the 93-11 NIL is responsible for its role in conferring dominant male sterility.