Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq

Abstract

Bulk segregant analysis coupled with whole genome sequencing is a powerful approach and cost-effective method to identify loci controlling fruit traits in tomato. Domestication of fruit and vegetable crops was accompanied by selection for weight of the edible parts. Increases in fruit weight are controlled by multiple quantitative trait loci (QTL). To date, only two fruit weight genes have been cloned and a third has been fine-mapped. Genes that control locule number also impact fruit weight and two of them are known. To efficiently identify additional tomato fruit weight (FW) and locule number (LC) loci, six F2 populations were generated from crosses between closely related tomato accessions for which the alleles of the cloned FW and LC genes were known. We employed the bulk segregant approach coupled to whole genome sequencing (QTL-seq) which led to the identification of three highly significant and newly mapped FW QTL. fw11.2 was located in the distal part of chromosome 11 above the known loci fas and fw11.3; fw1.1 in the pericentromeric region of chromosome 1; and fw3.3 located ~1.6 Mb below the known fruit weight gene, SlKLUH/FW3.2. In addition, we mapped three LC QTL (lcn2.4, lcn5.1, and lcn6.1) although their significance was generally low. To confirm the location of the gene underlying fw11.2, we developed additional markers and conducted progeny tests. These results allowed us to narrow down the fw11.2 QTL to a region of ~750 kb corresponding to 66 candidate genes. Our research approach provided a cost-effective and time-efficient method for the identification of additional genes involved in FW and LC that could be used for both fruit development studies and crop improvement programs.

Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits

“…This would reduce the number of associations detected to 69 (nine ‘interactive’, 44 ‘specific’, and 16 ‘constitutive’). With this stringent threshold, we would not have recovered some well-described tomato QTLs, such as, for example, FW11.2 and FW11.3 on chromosome 11 (fruit FW QTLs: Huang and van der Knaap, 2011; Illa-Berenguer et al , 2015). The need for more permissive thresholds in GWASs is often claimed.…”

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

“…The SNP/SSR-index and Δ (SNP/SSR-index)-based QTL-seq strategy was employed at a target major QTL genomic region to identify major rice GW QTL in accordance with previously defined recommended parameters (Takagi et al, 2013; Lu et al, 2014; Das et al, 2015; Illa-Berenguer et al, 2015). The Δ (SNP/SSR-index) was measured based on subtraction of SNP/SSR-index between LGWB and HGWB.…”

Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis

“…QTL-seq is proposed as an efficient strategy for rapid identification of QTLs, which takes advantage of bulked-segregant analysis and high-throughput genotyping using next-generation sequencing (NGS). This approach has been applied to detecting QTLs in rice, cucumber, tomato, and chickpea1516171819. Previously we constructed a high-density cucumber genetic map compromising 1800 SNPs using F 2 populations derived from CC3 × NC76.…”