Genome-Wide Association Study Reveals Functional Association of GhRBB1_A07 Gene with Superior Fiber Quality in Cotton

A multi-parent advanced generation inter-cross (MAGIC) population was developed through random-mating of 11 diverse cultivars for five generations has the ability to break the negative correlation between yield and fiber quality. In this study, fiber quality data obtained from four environments and 6,071 Single Nucleotide Polymorphic (SNP) markers generated via Genotyping-by-Sequencing (GBS) and 224 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS). By conducting a mixed linear model, GWAS enabled us to identify markers significantly associated with fiber quantitative trait loci (QTL). We identified and validated one QTL cluster associated with four fiber quality traits (short fiber content, strength, length and uniformity) on chromosome A07. Gene expression and amino acid substitution analysis suggested that a regeneration of bulb biogenesis 1 (GhRBB1_A07) gene is a candidate for superior fiber quality in Upland cotton. The DNA marker CFBid0004 designed from an 18 bp deletion in the coding sequence of GhRBB1_A07 in Acala Ultima is associated with the improved fiber quality in the MAGIC RILs and 105 additional commercial Upland cotton cultivars. Using GBS and a MAGIC population enabled more precise fiber QTL mapping in Upland cotton. The fiber QTL and associated markers identified in this study can be used to improve fiber quality through marker assisted selection in a cotton breeding program. Target manipulation of the GhRBB1_A07 gene through biotechnology or gene editing may potentially improve cotton fiber quality.