Fine mapping of a major QTL controlling early flowering in tomato using QTL-seq

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...

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Bibliographic Details
Published in:Canadian journal of plant science 2018-06, Vol.98 (3), p.672-682
Main Authors: Ruangrak, Eaknarin, Su, Xiaomei, Huang, Zejun, Wang, Xiaoxuan, Guo, Yanmei, Du, Yongchen, Gao, Jianchang
Format: Article
Language:English
Subjects:
Chromosome 1
Crop improvement
Cultivars
early flowering loci
Expressed sequence tags
Flowering
Gene mapping
Gene polymorphism
Genetic crosses
locus de la floraison hâtive
Phenotypes
Plant breeding
Plant sciences
Polymerase chain reaction
QTL-seq
Quantitative trait loci
Reverse transcription
Single-nucleotide polymorphism
Solanum lycopersicum
tomate
tomato
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Summary: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.
ISSN:0008-4220
1918-1833
DOI:10.1139/cjps-2016-0398