Molecular markers provide an effective approach for studying complex disease resistances. In addition to various breeding applications, molecular markers tightly linked to a target gene can be used to construct linkage map and can also act as starting points for physical mapping and subsequent cloning of the gene (Tanksley et al. 1995). The most important use of linkage maps is to identify chromosomal locations containing genes and QTL associated with traits of interest, such maps are referred to as QTL maps and procedure of construction of QTL maps is known as QTL mapping. Genes or markers that are close together or tightly-linked will be transmitted together from parent to progeny more frequently than genes or markers that are located further apart. In a segregating population (mapping population), there is a mixture of parental and recombinant genotypes. In present study ‘Solan Lalima’ was used as susceptible parent and ‘EC-251649’ acted as resistant parent for buckeye rot disease of tomato which were used to produce F2 population of 100 individuals. Population sizes generally range from 50 to 250 individuals (Mohan et al. 1997), however for high-resolution mapping larger populations are required. F2 population is the mapping population of choice because it is the simplest type of mapping populations developed for self pollinating species. Their main advantages are that they are easy to construct and require a short time to produce.
With the development of saturated linkage maps, all regions of the genome can be assayed for the presence of a locus contributing for a particular trait (Tanksley 1993). In tomato, first RFLP linkage map was constructed by Tanksley et al. (1992). For linkage analysis of markers various software programs are used including MAPMAKER/ EXP and MapManager QTX, of which MAPMAKER/ EXP is most commonly used (Lee et al. 2016). MAPMAKER/ EXP was used to construct linkage groups in current study. The present study resulted in construction of tomato linkage map which consisted of 12 linkage groups. Only five linkage groups (LG2, 3, 6, 7, 10) were considered significant as they covered some portion of genome, while other linkage groups (LG1, 4, 5, 8, 9, 11, 12) were not considered significant as the distance between markers was 0 cM revealing further need to cover these linkage groups with more markers. Entire map covered a total of 4660.7 cM which represents a good coverage of genome and much higher than the marker densities of the genetic linkage maps of some other tomato cultivars in a few of the earlier studies (Grilli et al. 2007; Sharma et al. 2008; Foolad, 2015). The genome coverage was also calculated and found to be 96.55% for LG2, 60% for LG6 and 0.5% each for LG3, LG7, LG10 and 97.18% for the total map length. Sharma (2013) and Vaidya (2014) also reported high genome coverage of 96.5% in stevia and 98.03% in apple, respectively.
The phenotyping and genotyping studies were further used for QTL mapping using QTL Cartographer software. For mapping analysis many statistical programmes viz., simple interval mapping (SIM), interval mapping (IM) and CIM are used. More recently, CIM has become popular for mapping QTL (Collard et al. 2005; Show and Rajcan 2017). The main advantage of CIM is that it is more precise and effective at mapping QTL compared to single-point analysis and interval mapping, especially when linked QTL are involved. Many researchers have used QTL Cartographer for QTL mapping (Basten et al. 2001; Saxena 2010; Vaidya 2014; Dinesh et al. 2016). In tomato various QTL mapping studies have been conducted earlier for resistance to different diseases (Ji et al. 2009; Robbins et al. 2010; He et al. 2010; Sun et al. 2011; Yang et al. 2012; Zhang et al. 2013; Foolad, 2015), but present study is the very first study which found QTL for buckeye rot resistance. No other study has been reported for QTL identification for this disease. Thus, this study will significantly contribute toward buckeye rot resistance and facilitate the development of new resistant varieties through marker assisted selection (MAS) in near future.