Predicting Pollen Sterility Using SNP Markers in Single and Two Gene Recessive Inheritance of Photoperiod and Thermosensitive Genetic Male Sterile Rice.

Genetic male sterility has been used successfully in Asia to achieve high grain yields in hybrids vs. pure line varieties. Information is lacking concerning performance and inheritance of environmentally sensitive genetic male sterility under U.S. field conditions. The objectives of our research were to investigate inheritance of photoperiod, thermo-sensitive male sterility (PTGMS) under field plot conditions and to evaluate SNP-based markers for utility in hybrid rice breeding programs. The PTGMS lines 2008s and 2009s evaluated in this study were 100% pollen sterile under Louisiana conditions in 2012 and 2013. A total of 609 and 540 F₂ plants derived from 2009s and 2008s were crossed to fertile tropical japonica lines and randomly sampled in three separate studies in 2012-2013 to determine fertile: sterile plant segregation ratios. Based on pollen sterility, 2008s F₂ population segregation ratios fit a 15 fertile: 1 sterile, two-gene recessive model across both years in LA while 2009s F₂ population ratios fit a 3 fertile: 1 sterile, single gene recessive model in 2013. The 2008s genotyping of SNP markers at pms1(t) and pms3 loci showed two-gene recessive segregation with significant interactions affecting pollen fertility across 2012-2013. Combined marker main effects and their interactions explained 54% of observed variation. Predictive ability of pms1(t) and pms3 markers in the 2008s F₂ populations ranged from 43% to 85%. Sterile plants genotyped with SNP markers at the ptgms2-1 locus correctly predicted 97% of sterile phenotypes in the 2009s F₂ populations.  Results indicated that the ptgms2-1 SNP-based marker can be used for hybrid development under Louisiana conditions, while utility of the two-gene based markers can be variable across different environments.