Toward Cloning LIGON LINTLESS-2 (Li2), a Gene Involved in Cotton Fiber Elongation

Long fiber is what makes cotton useful for the textile industry. Ligon lintless-2 (Li₂) is a dominant mutant with short lint fiber (< 5 mm). Cloning such genes is important for understanding the pathways and mechanisms that differentiate spinnable cotton from its progenitors. A population of 1532 F2 plants derived from a cross between Pima S-7 (G. barbadense) and an Li₂ mutant line (G. hirsutum) was used to fine map the Li₂ region on chromosome 18. A total of 58 SSR and CISP markers known to locate in the Li₂ region were screened in a small subset of the population for polymorphism and to determine their approximate map position, then 8 markers were used to screen the whole population. CISP15 was 0.3 cM from Li₂  and SSR18 showed complete linkage with Li₂. Eleven genes in this small region were selected for further investigation of possible roles in fiber growth and development, annotated as cell wall proteins, cell wall enzymes, secondary metabolism genes, hormonal regulatory genes and post-transcriptional modification genes. For these eleven genes we examined non-synonymous SNPs between non-fiber (D and F) and fiber producing (A, At and Dt) genomes, performed qPCR and VIGS (Virus Induce Gene Silencing) and prioritized a subset of genes for further investigation. This research provides new insight into the identity of Li₂ and the functions of other genes related to fiber development which may be important for cotton breeding and genetics.