Identification of Early Tomato Fruit Ripening Loci by QTL-seq

Eaknarin Ruangrak ,Jianchang Gao,Pimpan Pimorat,Nang Myint Phyu Sin Htwe,Yan Du

doi:10.5539/jas.v11n2p51

Abstract

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 &ldquo;er-fruit&rdquo; 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.

Highlights

Earliness in tomato is one of the factors that needs much concern in recent years due to climatic changes and increased world’s population
The early fruit ripening time was scored from the days after anthesis to the ripening of fruit of 1200 individuals of F2 obtained from crossing Bone ММ (P1) to 071-440 (P2) cultivars (Figure A1)
The results of the alignment suggested that the reference genome size is 781666411 bp, and the mapping rate of the aligned samples varied from 93.14% to 96.3%, for the reference genome (Table B2)

Summary

Introduction

Earliness in tomato is one of the factors that needs much concern in recent years due to climatic changes and increased world’s population. Earliness in tomatoes consists of three stages; (1) flowering time, (2) fruit setting time, and (3) fruit ripening time (Powers, 1941) The environmental factors such as temperature and light intensity play a significant role in the expression of any components for early maturity (Kerr, 1955; Adams et al, 2001). It has been reported “Early Cherry’ alleles caused reductions in both ripening time and fruit weight by using RAPD marker analysis in F2 population derived from a cross between Lycopersicon esculentum’E6203’ (normal ripening) and Lycopersicon esculentum’Early Cherry’ (early ripening) (Doganlar et al, 2000). The important fruit ripening phenotypes have been distinguished by rin, nor, Nr and Cnr mutants that have been jas.ccsenet.org

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