Table_1_A Major QTL Located in Chromosome 8 of Cucurbita moschata Is Responsible for Resistance to Tomato Leaf Curl New Delhi Virus.XLSX

Tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite whitefly transmitted begomovirus, responsible since 2013 of severe damages in cucurbit crops in Southeastern Spain. Zucchini (Cucurbita pepo) is the most affected species, but melon (Cucumis melo) and cucumber (Cucumis sativus) are also highly damaged by the infection. The virus has spread across Mediterranean basin and European countries, and integrated control measures are not being enough to reduce economic losses. The identification of resistance genes is required to develop resistant cultivars. In this assay, we studied the inheritance of the resistance to ToLCNDV previously identified in two Cucurbita moschata accessions. We generated segregating populations crossing both resistant pumpkins, an American improved cultivar Large Cheese (PI 604506) and an Indian landrace (PI 381814), with a susceptible C. moschata genotype (PI 419083). The analysis of symptoms and viral titers of all populations established the same monogenic recessive genetic control in both resistant accessions, and the allelism tests suggest the occurrence of alleles of the same locus. By genotyping with a single nucleotide polymorphism (SNP) collection evenly distributed along the C. moschata genome, a major quantitative trait locus (QTL) was identified in chromosome 8 controlling resistance to ToLCNDV. This major QTL was also confirmed in the interspecific C. moschata × C. pepo segregating populations, although C. pepo genetic background affected the resistance level. Molecular markers here identified, linked to the ToLCNDV resistance locus, are highly valuable for zucchini breeding programs, allowing the selection of improved commercial materials. The duplication of the candidate region within the C. moschata genome was studied, and genes with paralogs or single-copy genes were identified. Its synteny with the region of chromosome 17 of the susceptible C. pepo revealed an INDEL including interesting candidate genes. The chromosome 8 candidate region of C. moschata was also syntenic to the region in chromosome 11 of melon, previously described as responsible of ToLCNDV resistance. Common genes in the candidate regions of both cucurbits, with high- or moderate-impact polymorphic SNPs between resistant and susceptible C. moschata accessions, are interesting to study the mechanisms involved in this recessive resistance.

番茄曲叶新德里病毒（Tomato leaf curl New Delhi virus, ToLCNDV）是一种双分体基因组、由烟粉虱传播的菜豆金色花叶病毒属病毒，自2013年起已对西班牙东南部的葫芦科作物造成严重危害。西葫芦（Cucurbita pepo）是受影响最严重的物种，但甜瓜（Cucumis melo）与黄瓜（Cucumis sativus）也会因该病毒侵染遭受严重损失。该病毒已扩散至地中海盆地及欧洲多国，现有综合防治措施仍不足以降低其引发的经济损失，亟需鉴定抗病基因以培育抗病品种。本研究针对此前在两个中国南瓜（Cucurbita moschata）种质中鉴定出的抗ToLCNDV性状的遗传规律展开分析：通过将两份抗病南瓜材料——美国改良品种‘Large Cheese（PI 604506）’与印度地方品种PI 381814——分别与感病中国南瓜种质PI 419083进行杂交，构建了分离群体。通过对所有分离群体的症状表现与病毒滴度进行分析，证实两份抗病种质均受单基因隐性遗传调控；等位性测验结果表明，二者的抗病基因位于同一基因座的等位变异。通过使用均匀分布于中国南瓜基因组的单核苷酸多态性（single nucleotide polymorphism, SNP）标记集进行基因分型，研究人员在第8号染色体上鉴定到一个控制抗ToLCNDV的主效数量性状位点（quantitative trait locus, QTL）。该主效QTL在中国南瓜×西葫芦（C. moschata × C. pepo）的种间分离群体中也得到了验证，不过西葫芦的遗传背景会对抗病性水平产生影响。本研究鉴定到的与ToLCNDV抗病基因座连锁的分子标记，可有效应用于西葫芦育种项目，助力优良商业化材料的选育。研究人员对中国南瓜基因组内的候选区域进行了重复序列分析，鉴定出了存在旁系同源基因的区域以及单拷贝基因；该候选区域与感病西葫芦第17号染色体区域的共线性分析结果显示，存在一段包含多个潜在候选基因的插入缺失（insertion-deletion, INDEL）区域。中国南瓜第8号染色体的候选区域与此前报道的、与抗ToLCNDV相关的甜瓜第11号染色体区域也存在共线性关系。在两份中国南瓜种质的抗病与感病材料间存在高影响或中影响多态性SNP的两种葫芦科作物候选区域的共有基因，可用于进一步解析该隐性抗病性的分子机制。