A Retrotransposon Insertion in GhMML3_D12 Is Likely Responsible for the Lintless Locus li3 of Tetraploid Cotton

Cotton (Gossypium) seed fibers can be divided into lint (long) or fuzz (very short). Using fiberless (fuzzless-lintless) mutants, the lint initiation gene Li-3 was identified by map-based cloning. The gene is an R2R3-MYB transcription factor located on chromosome D12 (GhMML3_D12). Sequence analysis revealed that li(3) is a loss-of-function allele containing a retrotransposon insertion in the second exon that completely blocks the gene's expression. The genetic loci n(2) and n(3) underlying the recessive fuzzless phenotype in Gossypium hirsutum were also mapped. The genomic location of n(3) overlapped with that of the dominant fuzzless locus N-1, and n(3) appeared to be a loss-of-function allele caused by a single nucleotide polymorphism (SNP) mutation in the coding region of GhMML3_A12. The n(2) allele was found to be co-located with li(3) and originated from G. babardense. n(2) and li(3) are possibly the multiple alleles of the GhMML3_D12 gene. Genetic analysis showed that Li-3 and N-3 are a pair of homologs with additive effects for the initiation of fibers (fuzz or lint). In addition, the presence of another locus was speculated, and it appeared to show an inhibitory effect on the expression of GhMML3. These findings provide new information about the genetic factors affecting the initiation of fibers in cotton.