The use of sterility is common in plants and multiple loci for hybrid sterility have been identified in crops such as rice. In soybean, fine-mapping and research on the molecular mechanism of male sterility is limited. Here, we identified a male-sterile soybean line, which produces larger, abnormal pollen grains that stain poorly with I2-KI. In an inheritance test, all F1 plants were fertile and the F2 and F2:3 populations conformed with the expected segregation ratio of 3:1 (fertility:sterility) (p = 0.82) and showed a 1:2:0 ratio of homozygous fertile: heterozygous fertile: homozygous sterile genotypes (p = 0.73), suggesting that the sterility was controlled by a single recessive gene (designated “mst-M”). Bulked segregant analysis showed that almost all single-nucleotide polymorphisms (SNPs; 95.92%) were distributed on chromosome 13 and 868 SNPs (95.81%) were distributed in the physical region of Chromosome 13.21877872 to Chromosome 13.22862641. Genetic mapping revealed that mst-M was flanked by W1 and dCAPS-1 with genetic distances of 0.6 and 1.8 cM, respectively. The order of the consensus markers and known sterility genes was: Satt146 – (5.0 cM) – st5 – (2.5 cM) – Satt030 – (15.3 cM) – ms6 – (5.0 cM) – Satt149 – (39.5 cM) – W1 – (0.6 cM) – mst-M – (14.1 cM) – Satt516 (7.5 cM) – ms1 – (16.3 cM) – Satt595. These results suggest that mst-M is a newly identified male-sterility gene, which represents an alternative genetic resource for developing a hybrid seed production system for soybean.

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