Jaiswal Namrata, Zia Bazgha, Chanda Bidisha, Gilliard Andrea, Shi Ainong, Ling Kai-Shu
United States Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC, 29414, USA.
United States Department of Agriculture-Agricultural Research Service, Crop Production and Pest Control Research, West Lafayette, IN, 47907, USA.
Theor Appl Genet. 2025 Jul 22;138(8):190. doi: 10.1007/s00122-025-04974-0.
Tomato (Solanum lycopersicum L.), one of the most widely grown vegetables in the world, has been seriously impacted in the past decade by the emerging tomato brown rugose fruit virus (ToBRFV). ToBRFV is a seed-borne tobamovirus, with ability to overcome the commonly used Tm-2 resistance gene in tomato. The objective of this study was to conduct quantitative trait locus (QTL) mapping and identify single-nucleotide polymorphism (SNP) markers associated with ToBRFV resistance in tomato. Two F populations were used for QTL mapping: One derived from a cross between S. pimpinellifolium USVL333 (PI 390718) × USVL332 (PI 390717) and another from 'Moneymaker' × USVL332 (PI 390717), with population sizes of 195 and 79 plants, respectively. The resistance trait was derived from the S. pimpinellifolium accession USVL332 (PI 390717). A major QTL for ToBRFV resistance was identified on chromosome 11 (SL4.0ch11), with the peak located at approximately 46.84 Mbp. This QTL spans a 22-kb interval between 46,825,788 bp and 46,847,421 bp, as determined through both genome-wide association study (GWAS) and QTL linkage mapping. Three SNP markers, SL4.0ch11_46825788, SL4.0ch11_46847421, and SL4.0ch11_46850215, demonstrated the most significant association with high LOD values (LOD = 13 in the Blink model) in GWAS analysis. In this genomic region, two disease resistance gene analogs, Solyc11g062150 (TIR-NBS-LRR resistance protein, Toll-Interleukin receptor) and Solyc11g062180 (disease resistance protein, leucine-rich repeat), were identified, which may serve as candidates for ToBRFV resistance. The QTL identified in this study could be valuable for plant breeders in facilitating tomato breeding with ToBRFV resistance.
番茄（Solanum lycopersicum L.）是世界上种植最广泛的蔬菜之一，在过去十年中受到新出现的番茄褐色皱纹果病毒（ToBRFV）的严重影响。ToBRFV是一种种传烟草花叶病毒，能够克服番茄中常用的Tm-2抗性基因。本研究的目的是进行数量性状位点（QTL）定位，并鉴定与番茄对ToBRFV抗性相关的单核苷酸多态性（SNP）标记。两个F群体用于QTL定位：一个来自醋栗番茄USVL333（PI 390718）×USVL332（PI 390717）的杂交后代，另一个来自“Money maker”×USVL332（PI 390717）的杂交后代，群体大小分别为195株和79株。抗性性状来自醋栗番茄种质USVL332（PI 390717）。在11号染色体（SL4.0ch11）上鉴定到一个主要的ToBRFV抗性QTL，峰值位于约46.84 Mbp处。通过全基因组关联研究（GWAS）和QTL连锁图谱分析确定，该QTL跨越46,825,788 bp至46,847,421 bp之间的22 kb区间。三个SNP标记，SL4.0ch11_46825788、SL4.0ch11_46847421和SL4.0ch11_46850215，在GWAS分析中显示出与高LOD值（Blink模型中LOD = 13）最显著的关联。在该基因组区域，鉴定到两个抗病基因类似物，Solyc11g062150（TIR-NBS-LRR抗性蛋白，Toll-白细胞介素受体）和Solyc11g062180（抗病蛋白，富含亮氨酸重复序列），它们可能是ToBRFV抗性的候选基因。本研究中鉴定的QTL对于植物育种者促进抗ToBRFV番茄育种可能具有重要价值。
