Development of molecular markers for genetic male sterility in Gossypium hirsutum

Genetic male sterility (GMS) in cotton mediated by two homozygous recessive genes, ms5ms5 and ms6ms6, is expressed as non-dehiscent anthers and unviable pollen grains. Sequence analysis on ms5 and ms6 loci in Gossypium hirsutum was conducted to reveal genomic variation at these two loci between GMS and wild-type G. hirsutum inbred lines, and sequence polymorphism linked to ms5 on A12 and ms6 on D12 was revealed. A haplotype marker set that consisted of four SNPs targeting both ms5 and ms6 gene regions was developed and validated for association with GMS in cotton. Predictability of GMS phenotype by this haplotype SNP set was over 99 %. GMS haplotype marker set can serve as a high-throughput molecular breeding tool to select GMS individuals and improve hybrid production efficiency.