Whole-Genome Sequencing and Variant Discovery of Citrus reticulata ‘Kinnow’ from Pakistan

Citrus is a source of many nutritional and medicinal advantages, which is cultivated worldwide with major citrus groups of sweet oranges, mandarins, grapefruits, kumquats, lemons and limes. Pakistan produces all of its major citrus groups with mandarin (Citrus reticulata) being the prominent group that includes local commercial cultivars such as Feutral’s Early, Dancy, Honey and Kinnow. The present study was designed to understand the genetic architecture of this unique variety of Citrus reticulata -’Kinnow’. The whole-genome resequencing and variant calling was performed to map the genomic variability that might be responsible for its particular characteristics like taste, seededness, juice content, thickness of peel and its shelf-life. A total of 139,436,350 raw sequence reads using Illumina platform were generated with 20.9 Gb data in Fastq format having 98% effectiveness and 0.2% base call error rate. Overall, a total of 3,503,033 SNPs, 176,949 MNPs, 323,287 INS and 333,083 DEL were identified using GATK4 variant calling pipeline against Citrus clementina as a reference genome. Further, g:Profiler bioinformatics tool was applied for annotating the newly found variants, harbor genes/transcripts and their involved pathways. A total of 73,864 transcripts harbors 4,336,352 variants, most of the observed variants were predicted in non-coding regions and 1,009 transcripts were found well annotated by different databases. Out of total aforementioned transcripts, 588 involved in biological processes, 234 in molecular functions and 167 transcripts involved in cellular components in Citrus reticulata. In a nutshell, 18,153 high-impact variants and 216 genic-variants found in the current study which may be used for marker assisted breeding programs of ‘Kinnow’ to identify this particular variety among others and to propagate its valued traits to improve the contemporary citrus varieties as well. Graphical Abstract