Development of Whole Genome SNP-CAPS Markers and Preliminary QTL Mapping of Fruit Pedicel Traits in Watermelon

Abstract

Fruit pedicel (FP) is an important determinant of premium fruit quality that directly affects commercial market value. However, in-depth molecular and genetic basis of pedicel-related traits has not been identified in watermelon. Herein, a quantitative trait locus (QTL) mapping strategy was used to identify the potential genetic regions controlling FP traits based on newly derived whole-genome single nucleotide polymorphism based cleaved amplified polymorphism sequence (SNP-CAPS) markers. Next-generation sequencing based whole-genome re-sequencing of two watermelon parent lines revealed 98.30 and 98.40% of average coverage, 4,989,869 SNP variants, and 182,949 CAPS loci pairs across the reference genome, respectively. A total of 221 sets of codominant markers exhibited 46.42% polymorphism rate and were effectively genotyped within 100-F2:3 derived mapping population. The developed linkage map covered a total of 2,630.49 cM genetic length with averaged 11.90 cM, and depicted a valid marker-trait association. In total, 6 QTLs (qFPL4.1, qFPW4.1, qFPD2.1, qFPD2.2, qFPD8.1, qFPD10.1) were mapped with five major effects and one minor effect between the whole genome adjacent markers positioned over distinct chromosomes (02, 04, 08, 10), based on the ICIM-ADD mapping approach. These significant QTLs were similarly mapped in delimited flanking regions of 675.10, 751.38, 859.24, 948.39, and 947.51 kb, which collectively explained 8.64–13.60% PVE, respectively. A highly significant and positive correlation was found among the observed variables. To our knowledge, we first time reported the mapped QTLs/genes affecting FP traits of watermelon, and our illustrated outcomes will deliver the potential insights for fine genetic mapping as well as functional gene analysis through MAS-based breeding approaches.

Primary mapping of quantitative trait loci regulating multivariate horticultural phenotypes of watermelon (Citrullus lanatus L.)

“…In this experiment, two extremely divergent watermelon parent lines (W1-38 and PI542119) were used for genomic sequencing and a total of 3,784,650 SNPs and 172,151 CAPS loci pairs were detected; however, transition type SNPs were noticed higher than transversion type SNPs. A total of 210 sets of novel SNP-CAPS markers exhibited a moderate level of polymorphism (46.25%), and the obtained results are fairly comparable with the earlier reported genetic mapping studies in watermelon (Liu et al, 2015;Liu et al, 2016;Amanullah et al, 2021;Osae et al, 2021;Amanullah et al, 2022;Osae et al, 2022). Our constructed genetic map had a total length of 2,398.40 cM, an average interval length of 11.42 cM, and most physical intervals ranging from a minimum of 680.12 kb to a maximum of 950.70 kb, indicating lower recombination rate (Figures 3, 4).…”

“…Whole genome CAPS markers were derived based on major SNP sequences, as reported in our earlier study ( Amanullah et al., 2022 ). In brief, a total of 20–25 physical positions of SNP sequences “before and after 500 base pairs (bp)” of both parent lines were aligned across the whole gnome chromosomal length using SNP2CAPS software ( Thiel et al., 2004 ).…”

“…The suitable SNP sequences were chosen and converted into CAPS markers and DNA-based standard PCR primers were exported using the upgraded Primer Premier software (v6.25). The best quality primers were oligo-synthesized by Sangon Biotechology LTD., and then codominant polymorphic primers were screened based on distinct bands using the optimal CAPS PCR reactions in 10 μL mixture as previously stated ( Amanullah et al., 2022 ), e.g., 0.5 μL of each primer sequence (forward + reverse), 1 μL PCR buffer, 0.1 μL Taq DNA-polymerase, 0.15 μL dNTPs, 1 μL GDNA, and 6.75 μL deionized water. The enzyme digested PCR products were cleaved on gel electrophoresis, and the digested bands were captured on the Invitrogen iBright Imaging Systems.…”

“…The mapped QTLs with high LOD values (above 3) and phenotypic variance explained (PVE, >10%) were designated as major QTLs, and QTLs with low LODs and PVE (<10%) were designated as minor QTLs. Finally, the mapped QTLs were abbreviated as follows; the name of the trait, its position on the chromosome, and the number of QTLs, as reported earlier ( Amanullah et al., 2022 ).…”

“…Whole genome sequencing approach coupled with the published de novo reference genome assembly of watermelon has assisted in developing the base-by-base SNP markers and high-resolution genetic linkage mapping ( Guo et al., 2013 ). In recent years, SNP based codominant CAPS markers have been emerged as an efficient DNA markers for dissecting the major-effect QTLs of regulating the important qualitative and quantitative traits of melon and watermelon ( Bang et al., 2007 ; Liu et al., 2015 ; Cheng et al., 2016 ; Liu et al., 2016 ; Li et al., 2017 ; Zhang et al., 2018 ; Liu et al., 2019 ; Luan et al., 2019 ; Wang et al., 2019 ; Sun et al., 2020 ; Amanullah et al., 2020 ; Amanullah et al., 2021 ; Zhang et al., 2021 ; Pei et al., 2021 ; Osae et al., 2021 ; Yang et al., 2021 ; Amanullah et al., 2022 ; Osae et al., 2022 ; Lv et al., 2022 ).…”