Early flowering is one of the major earliness traits in tomato and is also an important agronomical trait in crop plants; thus, this trait is important for plant breeding and crop improvement. With the innovation of rapid and cost-effective technologies, quantitative trait locus (QTL)-seq has become the preferred method of performing QTL identification. In the present study, we identified a candidate QTL of an early flowering trait in tomato (Solanum lycopersicum) using QTL-seq. Two DNA pools of the extreme phenotype of the F2 progeny from crosses between the ‘Bone MM’ cultivar (early flowering, P1) and ‘071-440’ cultivar (late flowering, P2) were bulked for sequencing and an alignment analysis. We observed 220 single nucleotide polymorphism markers, seven candidate QTLs, and genes that may be associated with early flowering located between 1.6 and 71.8 Mb on chromosome 1. Using traditional QTL analysis, the location of one QTL was confirmed in the physical region between 23.5 and 25.3 Mb, which corresponded to the region identified using QTL-seq, and was referred to as EF1 (Solyc01g017060). A real-time quantitative reverse transcription polymerase chain reaction analysis showed that EF1 was the most highly expressed among the candidate genes and significantly expressed in early flowering parents and furthermore, we found that EF1, which had a similar sequence to the Ycf2 gene, may relate to the early flowering phenotype.
QTL-seq has been successfully studied in identifying major QTLs, markers, and candidate genes associated with traits that are important for crop improvement. Tomato earliness is an economically important trait and is a major current research focus recently. This paper reports the identification of tomato early ripening fruit locus facilitated by QTL-seq using a novel next-generation sequencing technology. Two DNA pools of phenotypes of F2 offspring from crosses between the Bone ММ (early ripening fruit, P1) and 071-440 (late ripening fruit, P2) cultivars of (Solanum lycopersicum) were bulked for sequencing and alignment analysis. Sequencing results revealed 434 SNP markers on chromosome 11, a candidate QTL at position 52,048,208 bp (named er-fruit) and a candidate gene, Solyc11g071510.1.1. The “er-fruit” as confirmed by the traditional QTL method was related to the early fruit ripening trait in tomato. Additionally, BLAST analysis to known homologies for Solyc11g071510.1.1 gene encodes glycoside hydrolases (GHs). GHs are functionally associated with cell wall degradation, fruit softening and ripening. Thus, GHs may be important in fruit softening, stimulating early fruit ripening in tomato. Our results confirmed that QTL-seq is effective method to identify candidate QTL loci, candidate genes and candidate markers.
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