Abstract
BackgroundFirst flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.). The trait is controlled by quantitative trait loci (QTL); however, studies have been limited on QTL mapping and genes contributing to the trait.ResultsIn this study, we developed a high density genetic map using specific-locus amplified fragment sequencing (SLAF-seq), a high-throughput strategy for de novo single nucleotide polymorphism discovery, based on 146 recombinant inbred lines (RILs) derived from an intraspecific cross between PM702 and FS871. The map contained 9328 SLAF markers on 12 linkage groups (LGs), and spanned a total genetic distance of 2009.69 centimorgan (cM) with an average distance of 0.22 cM. The sequencing depth for the map was 72.39-fold in the male parent, 57.04-fold in the female parent, and 15.65-fold in offspring. Using the genetic map, two major QTLs, named Ffn2.1 and Ffn2.2, identified on LG02 were strongly associated with FFN, with a phenotypic variance explanation of 28.62 and 19.56%, respectively. On the basis of the current annotation of C. annuum cv. Criollo de Morelos (CM334), 59 candidate genes were found within the Ffn2.1 and Ffn2.2 region, but only 3 of 59 genes were differentially expressed according to the RNA-seq results. Eventually we identified one gene associated with the FFN based on the function through GO, KEGG, and Swiss-prot analysis.ConclusionsOur research showed that the construction of high-density genetic map using SLAF-seq is a valuable tool for fine QTL mapping. The map we constructed is by far the most saturated complete genetic map of pepper, and using it we conducted fine QTL mapping for the important trait, FFN. QTLs and candidate genes obtained in this study lay a good foundation for the further research on FFN-related genes and other genetic applications in pepper.
Highlights
First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.)
We identified two major quantitative trait loci (QTL) on chromosome 2, Ffn2.1 and Ffn2.2, with a phenotypic variance explanation of 28.62 and 19.56%, respectively, and another two minor QTLs, Ffn9 and Ffn12, on chromosome 9 and chromosome 12 separately. These results suggested that the FFN trait of pepper was regulated primarily by two major QTLs (Ffn2.1 and Ffn2.2) with four markers located at 169.09–169.49 Mb and 162.15–162.61 Mb separately on chromosome 2, which we considered to be the candidate genomic regions
Our present study for the construction of a high-density genetic map in pepper demonstrates that the Specific-length amplified fragments (SLAF)-seq strategy is a powerful method for marker discovery and high-density linkage map construction
Summary
First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.). Pepper (Capsicum annuum L.) is an economically important vegetable crop worldwide. The initiation of the first flower indicates the transition from vegetative to reproductive growth, which is a crucial. Zhang et al BMC Plant Biology (2019) 19:167 were identified on chromosome P02 and P09 [10]; QTLs for plant height were detected on chromosome 2, 4, 6, 7 and 8 [14]; QTLs for the lateral branch number were identified on the primary axis on chromosome 2 [14]; and QTLs for the number of leaves were detected on the main stem on all chromosomes except for P09 in pepper [10,11,12,13]. No QTL research on FFN has been conducted in pepper to date
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