Genome-wide association studies unveil candidate genes linked with fruit fiber traits in Calotropis procera

Calotropis procera is a vital emerging natural fiber crop exhibiting unique domestication traits, making it an ideal candidate for widespread cultivation. Fiber phenotypes across 32 populations from arid and barren environments were assessed to determine their quality. The soil physicochemical analysis of both ecological conditions revealed that fibers were more pronounced in the arid zone than in the barren zone, with nitrogen, phosphorus, and potassium having a negative impact. At the same time, total organic carbon reflected a positive correlation with its phenotypes. Genetic variations were investigated through GWAS to identify key alleles and genomic regions underlying potential fiber quality traits. The study uncovered 11,002 high-quality SNPs and 11 significant markers across the genome associated with fiber trait variations. The genomic region (Chr4:14050001_15050000) from cross populations of distinct ecologies was identified under selection, having candidate loci (Chr4:14,869,706) associated with fiber length. The Tajima's D values of these loci were estimated at 0.94 and 0.69 for the arid and barren zones, respectively, indicating differing selection pressures. The region harbors markers potentially shaped by environmental adaptation, offering insights into the genetic basis of fiber trait variation across dynamic ecology. This comprehensive study in C. procera set a new direction for domestication and molecular breeding efforts to enhance desirable fiber traits in arid ecology.