Amanullah Sikandar, Li Shenglong, Osae Benjamin Agyei, Yang Tiantian, Abbas Farhat, Gao Meiling, Wang Xuezheng, Liu Hongyu, Gao Peng, Luan Feishi
College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China.
Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China.
Front Plant Sci. 2023 Jan 12;13:1034952. doi: 10.3389/fpls.2022.1034952. eCollection 2022.
Watermelon fruits exhibit a remarkable diversity of important horticultural phenotypes. In this study, we initiated a primary quantitative trait loci (QTL) mapping to identify the candidate regions controlling the ovary, fruit, and seed phenotypes. Whole genome sequencing (WGS) was carried out for two differentiated watermelon lines, and 350 Mb (96%) and 354 Mb (97%) of re-sequenced reads covered the reference genome assembly, individually. A total of 45.53% non-synonymous single nucleotide polymorphism (nsSNPs) and 54.47% synonymous SNPs (sSNPs) were spotted, which produced 210 sets of novel SNP-based cleaved amplified polymorphism sequence (CAPS) markers by depicting 46.25% co-dominant polymorphism among parent lines and offspring. A biparental F mapping population comprised of 100 families was used for trait phenotyping and CAPS genotyping, respectively. The constructed genetic map spanned a total of 2,398.40 centimorgans (cM) in length and averaged 11.42 cM, with 95.99% genome collinearity. A total of 33 QTLs were identified at different genetic positions across the eight chromosomes of watermelon (Chr-01, Chr-02, Chr-04, Chr-05, Chr-06, Chr-07, Chr-10, and Chr-11); among them, eight QTLs of the ovary, sixteen QTLs of the fruit, and nine QTLs of the seed related phenotypes were classified with 5.32-25.99% phenotypic variance explained (PVE). However, twenty-four QTLs were identified as major-effect and nine QTLs were mapped as minor-effect QTLs across the flanking regions of CAPS markers. Some QTLs were exhibited as tightly localized across the nearby genetic regions and explained the pleiotropic effects of multigenic nature. The flanking QTL markers also depicted significant allele specific contributions and accountable genes were predicted for respective traits. Gene Ontology (GO) functional enrichment was categorized in molecular function (MF), cellular components (CC), and biological process (BP); however, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were classified into three main classes of metabolism, genetic information processing, and brite hierarchies. The principal component analysis (PCA) of multivariate phenotypes widely demonstrated the major variability, consistent with the identified QTL regions. In short, we assumed that our identified QTL regions provide valuable genetic insights regarding the watermelon phenotypes and fine genetic mapping could be used to confirm them.
西瓜果实表现出多种重要的园艺表型。在本研究中，我们启动了初步的数量性状基因座（QTL）定位，以确定控制子房、果实和种子表型的候选区域。对两个分化的西瓜品系进行了全基因组测序（WGS），重新测序的 reads 分别覆盖了参考基因组组装的 350 Mb（96%）和 354 Mb（97%）。共发现 45.53%的非同义单核苷酸多态性（nsSNPs）和 54.47%的同义 SNPs（sSNPs），通过描绘亲本系和后代之间 46.25%的共显性多态性，产生了 210 组基于 SNP 的新型酶切扩增多态性序列（CAPS）标记。一个由 100 个家系组成的双亲 F 作图群体分别用于性状表型分析和 CAPS 基因分型。构建的遗传图谱全长共 2398.40 厘摩（cM），平均间距为 11.42 cM，基因组共线性为 95.99%。在西瓜的八条染色体（Chr-01、Chr-02、Chr-04、Chr-05、Chr-06、Chr-07、Chr-10 和 Chr-11）的不同遗传位置共鉴定出 33 个 QTL；其中，子房的 8 个 QTL、果实的 16 个 QTL 和种子相关表型的 9 个 QTL，解释的表型变异率（PVE）为 5.32 - 25.99%。然而，在 CAPS 标记的侧翼区域共鉴定出 24 个主效 QTL 和 9 个微效 QTL。一些 QTL 在附近的遗传区域紧密定位，解释了多基因性质的多效性效应。侧翼 QTL 标记还显示了显著的等位基因特异性贡献，并预测了各性状的相关基因。基因本体（GO）功能富集被分类为分子功能（MF）、细胞成分（CC）和生物过程（BP）；然而，京都基因与基因组百科全书（KEGG）途径被分为代谢、遗传信息处理和 BRITE 层次结构三个主要类别。多变量表型的主成分分析（PCA）广泛证明了主要变异性，与鉴定出的 QTL 区域一致。简而言之，我们认为我们鉴定出的 QTL 区域为西瓜表型提供了有价值的遗传见解，精细遗传图谱可用于确认它们。
