Combined genome and transcriptome analysis of boll weight and lint percentage traits in Gossypium barbadense

Expression of sugar-related genes downregulated while hormone-related genes upregulated during the later stages of fiber development is related to the superior fiber quality but low fiber yield of G. barbadense. Compared to Gossypium hirsutum, G. barbadense exhibits superior fiber quality but relatively lower fiber yield. Exploring the genetic basis of yield-related traits could facilitate yield improvement in G. barbadense. Here, we conducted a genome-wide association study (GWAS) on two yield components, boll weight and lint percentage, using 246 G. barbadense accessions. We identified a total of 272 main-effect quantitative trait loci (qtls) and 34 QTL-by-environment interaction loci (qtlEs) for these traits, among which 57 qtls and 3 qtlEs overlapped with previously reported loci. To explore the potential mechanism between yield and fiber quality, we extracted the genes located within these loci and compared their expression patterns between G. barbadense accessions with extreme differences in fiber quality or yield traits. Gene ontology analysis of differentially expressed genes revealed that sugar- and hormone-related genes were antagonistically expressed during the later stages of fiber development, correlating with high yield and superior fiber quality, respectively. Local association analysis further identified 67 candidate genes associated with the two yield components, 20 of which were located within two introgression segments (ISs) from G. hirsutum into G. barbadense. Among them, A10-1-Y IS reduced the yield of G. barbadense, while D08-1-Y IS increased the yield of G. barbadense. Finally, we demonstrated that two haplotypes of the gene GB_A06G0815 (encoding beta-galactosidase 1), GB_A06G0815^C and GB_A06G0815^-, with a 1-bp insertion/deletion of C/- in the 10^th exon, were significantly associated with fiber yield. Overexpression of GB_A06G0815^C in Arabidopsis resulted in longer roots, larger leaves, higher yield, and more vigorous growth and development compared to the control. Our findings provide novel insight into the negative correlation between fiber quality and yield traits and offer potential genetic loci for high-yield breeding in G. barbadense.