Emanating candidate genes responsible for fruit quality traits in citrus through GBS-based genome wide association studies

High throughput genotyping-by-sequencing (GBS) and genome-wide association studies (GWAS) serve as two powerful approaches to delineate the complexity of the biology among citrus genera. The most attributable character in citrus is the fruit quality which is determined by the combination of physical and chemical traits contributing towards the ripening phase, hence crop improvement. Both GBS and GWAS were employed on highly diverse eighty-two different citrus genotypes to study twenty-three fruit quality traits aiming towards the genetic improvement of citrus fruit traits. GBS generated 215 million-reads covering 38.78Gb of sequence data, with an average of 2.8 million-reads per sample. Eventually, 44,229 high-confidence SNPs were found that spanned on the all the chromosomes from 1 to 9 which were further used for GWAS analysis. Association mapping resulted in the detection of 354 significant loci linked to twenty-three fruit quality traits. Thirty-six pleiotropic SNPs were found and more genetic loci were found to be associated with mesocarp width (MS), seed weight per fruit (SW), juice content in endocarp (JCE), average number of seeds per fruit (ANSF), leaf lamina length (LLL), leaf lamina width (LLW) and ratio of leaf length to leaf width (RLW) on chromosome 5. Twelve candidate genes associated within the 5 Mb linkage disequilibrium (LD) region of these 36 pleiotropic quantitative trait nucleotides (QTNs) were reported. These candidate genes were associated with the fruit quality traits viz. MS, JCE, fruit weight (FW), SW, ANSF, average number of segments per fruit (NSPF), PC, JCE, LLL, LLW and RLW in citrus. We found that the majorly identified candidate gene with loci Cs2g_pb011080 and Cs7g_pb024190 were responsible for controlling pleotropic traits i.e. MS, PC and JCE exhibiting oxidoreductase activity, vital for reducing the bitterness in citrus and promoting fruit quality among citrus genera. This study suggested that the identified significant loci could be exploited for the selection of desirable character at early stages in future citrus breeding programmes promoting fruit quality attributes leading to accelerated acceptability of citrus.