Abstract:【Objective】The watermelon root system is relatively weak and sensitive to salt stress during the seedling stage, which results in a significant decline in both yield and quality. Breeding new salt-tolerant watermelon varieties presents an effective solution to this issue. This study aims to identify key candidate genes associated with salt tolerance in watermelon, thereby providing a crucial foundation for understanding the mechanisms underlying watermelon responses to salt stress and for the cultivation of new salt-tolerant varieties.【Methods】The related indexes of salt tolerance of 121 watermelon core germplasm materials were measured.,which including 15 C.mucosospermus accessions, 3 C. amarus accessions, 1 C. ecirrhosus accession, 4 C. colocynthis accessions, 10 C. megalospermus accessions , and 88 C. lanatus accessions. The phenotypic indicators assessed included above ground fresh weight, above ground dry weight, root length, root surface area, chlorophyll content, root proline, root potassium ion (K+) content, root sodium ion (Na+) content, and root soluble sugar content. We employed the FaST-LMM (factored spectrally transformed linear mixed models) method to conduct a genome-wide association study (GWAS) on the phenotypic data, locating and displaying the single nucleotide polymorphisms (SNPs) associated with these phenotypic traits using a Manhattan plot. Additionally, we utilized the watermelon genome (http://cucurbitgenomics.org/organism/21) for gene expression analysis and gene function annotation, ultimately leveraging transcriptome data from both salt-tolerant and salt-sensitive materials to identify key candidate genes related to salt tolerance.【Results】The variation range of the nine phenotypic data ranged from 9.05% to 91.41%, among which the coefficient of variation of root soluble sugar was the largest, 91.41%, the variation range was 0.03 mg·g-1 to 7.06 mg·g-1 and the average value was 1.08 mg·g-1. The coefficient of variation of chlorophyll content was the smallest 9.05%, the variation range was 31.35 to 59.87, and the average value was 44.51. There were no significantly related SNP sites in the five indicators of above ground fresh weight, above ground dry weight, root length, chlorophyll content and root proline. However, there were SNP sites that were significantly associated with four traits: root surface area, root K+ content, root Na+content, and root soluble sugar content. One significant SNP site located on chromosome 2 was identified under the root surface area index, and twenty-three genes were obtained within the candidate interval, but only twenty genes were found to have expression levels in salt-tolerant and salt-sensitive materials, and Cla97C02G043360, Cla97C02G043200, Cla97C02G043190, Cla97C02G043250, Cla97C02G043350, Cla97C02G043290 and Cla97C02G043320 were induced by salt stress. Twenty-five significant SNP sites were identified under the root K+ content index, including four SNPs on chromosome 8 and twenty-one SNPs on chromosome 10. There were twenty-five genes were obtained in the candidate interval, and only twelve genes had expression levels, among them Cla97C08G145130, Cla97C10G191810, Cla97C08G145090, Cla97C08G145150, Cla97C08G145160 and Cla97C08G145120 were induced by salt stress. Two significant SNP sites located on chromosome 1 were identified under the root Na+ content index, and ten genes were obtained in the candidate interval and only seven genes had expression levels, among them Cla97C01G009540, Cla97C01G009490 and Cla97C01G009510 were induced by salt stress. One significant SNP site located on chromosome 4 was identified under the root soluble sugar content index, eighteen genes were obtained in the candidate interval, and seventeen genes had expression levels, among them Cla97C04G073310, Cla97C04G073220, Cla97C04G073240, Cla97C04G073230, Cla97C04G073290, Cla97C04G073280, Cla97C04G073190, Cla97C04G073210 and Cla97C04G073270 were induced by salt stress. In salt-tolerant and salt-sensitive materials before and after 150mM NaCl treatmentthe expression changes of fifty-six candidate genes were analyzed, and nine of them were differentially expressed genes (DEGs). Among them, Cla97C08G145130, Cla97C04G073300, Cla97C01G009540, Cla97C10G191810, Cla97C02G043360, Cla97C02G043190 and Cla97C04G073310 were significantly up regulated by salt stress, whereas Cla97C04G073170 and Cla97C02G043310 were significantly down regulated by salt stress. These nine genes can be divided into two classes. It is worth noting that in category I, Cla97C08G145130 (mannan endo-1, 4-beta-mannosidase 1-like, ManA1) had the most significant changes, and was increased by 255.82 and 7.80 times in salt-sensitive and salt-tolerant materials, respectively. It was followed by Cla97C04G073300 (dehydration-responsive element-binding protein 2A, DREB2A) and Cla97C01G009540 (phloem protein 2-like A9, PP2A9), which were increased by 31.63 and 9.18 times, 13.10 and 3.56 times in salt-sensitive and salt-tolerant materials, respectively.【Conclusion】It was speculated that these three genes may be key candidate genes related to watermelon salt tolerance, which provides a basis for analyzing the molecular mechanism of improving watermelon salt tolerance and developing molecular markers for assisted selection breeding.
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