QTL mapping of cucumber fruit flesh thickness by SLAF-seq

Abstract

Cucumber is an agriculturally and economically important vegetable crop worldwide. Fruit flesh thickness is an important trait for cucumber and also a central determinant of yield, yet little is known about the underlying mechanism of this trait. In this study, bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) was applied to finely map the gene that underlies fruit flesh thickness in cucumber. A 0.19-Mb-long quantitative trait locus on chromosome 2 controlling fruit flesh thickness (QTL fft2.1) was identified and further confirmed by simple sequence repeat (SSR) marker-based classical QTL mapping in 138 F2 individuals. Gene prediction of this 0.19-Mb region identified 20 genes. Quantitative RT-PCR revealed higher expression levels of Csa2 M058670.1 (SET domain protein-lysine methyltransferase) in D8 (thick fruit flesh parent) compared with that in XUE1 (thin fruit flesh parent) during fruit development. Sequence alignment analysis of Csa2M058670.1 from thick and thin fruit flesh cucumber lines revealed a 4-bp deletion mutation in the promoter region of this candidate gene, which may result in the loss of Csa2M058670.1 activation in thin fruit flesh lines. The data presented herein suggest that Csa2M058670.1 is a possible candidate gene for controlling flesh thickness in cucumber.

Identification of BnaYUCCA6 as a candidate gene for branch angle in Brassica napus by QTL-seq

“…Previous results showed that QTL-seq can be applied in RIL or F 2 populations to identify QTL for different agronomic traits undergone artificial or natural selective sweeps37. Since the first article published in yeast36, many QTL or candidate genes have been identified in different plant species by QTL-seq38394041424344. Previous results by genome wide association study (GWAS) showed that there are twenty-five QTL associated with branch angle in a diversity panel46.…”

“…Several QTL were rapidly identified by the combination of whole-genome re-sequencing with BSA, which was also referred as QTL-seq3738394041. Recently, more QTL and candidate genes for agronomic traits were identified by QTL-seq, verifying the effectiveness of this approach42434445.…”

Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA

“…The Δ(SNP_index) was calculated according to Hill et al (2013) and Xu et al (2015c), Δ(SNP_index) value was calculated as follows: SNP_index (ab) = Mab/(Pab+Mab), SNP_index(aa) = Maa/(Paa+Maa), and Δ(SNP_index) = SNP_index (aa)-SNP_index (ab); where Maa and Mab mean the depth of aa and ab populations derived from M, respectively, Paa and Pab mean the depth of aa and ab populations derived from P, respectively. The closer marker is associated with phenotype while the closer or equal Δ(SNP_index) is to 1.…”

Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley

“…Combining SLAF-seq with BSA identified chromosome regions related to 1000 grain weight in rice and the gene that control inflorescence meristem function in maize [50, 53]. Xu et al [54] reported that fruit flesh thickness in cucumber was fine-mapped by two SLAF markers in the 0.19 Mb genomic region. After anchoring the markers to the cucumber 9930 reference genome, 20 genes were predicted, and Csa2M058670.1 was identified as a good candidate gene due to its high expression level in thick fruit flesh varieties.…”

“…Specific-length amplified fragment sequencing (SLAF-seq) is considered an efficient and high-resolution genotyping method [49], which has identified major QTLs in maize [50], soybean [51], cucumber [52], rice [53] and candidate gene isolation in cucumber [54] and barley [44]. In this study, traditional marker assays and the combination of BSA with SLAF-seq were used to detect a genomic region in barley harboring the semi-dwarf gene ari-e .…”