Fine Mapping and Candidate Gene Analysis of Two Major Quantitative Trait Loci, qFW2.1 and qFW3.1, Controlling Fruit Weight in Pepper (Capsicum annuum)

Fruit weight is an important agronomic trait in pepper production and is closely related to yield. At present, many quantitative trait loci (QTL) related to fruit weight have been found in pepper; however, the genes affecting fruit weight remain unknown. We analyzed the fruit weight-related quantitative traits in an intraspecific <i>Capsicum annuum</i> cross between the cultivated species blocky-type pepper, cv. Qiemen, and the bird pepper accession, "129-1" (<i>Capsicum annuum</i> var. <i>glatriusculum</i>), which was the wild progenitor of <i>C. annuum</i>. Using the QTL-seq combined with the linkage-based QTL mapping approach, QTL detection was performed; and two major effects of QTL related to fruit weight, <i>qFW2.1</i> and <i>qFW3.1</i>, were identified on chromosomes 2 and 3. The <i>qFW2.1</i> maximum explained 12.28% of the phenotypic variance observed in two F₂ generations, with the maximum LOD value of 11.02, respectively; meanwhile, the <i>qFW3.1</i> maximum explained 15.50% of the observed phenotypic variance in the two F₂ generations, with the maximum LOD value of 11.36, respectively. <i>qFW2.1</i> was narrowed down to the 1.22 Mb region using homozygous recombinant screening from BC₂S₂ and BC₂S₃ populations, while <i>qFW3.1</i> was narrowed down to the 4.61Mb region. According to the transcriptome results, a total of 47 and 86 differentially expressed genes (DEGs) in the candidate regions of <i>qFW2.1</i> and <i>qFW3.1</i> were identified. Further, 19 genes were selected for a qRT-PCR analysis based on sequence difference combined with the gene annotation. Finally, <i>Capana02g002938</i> and <i>Capana02g003021</i> are the most likely candidate genes for <i>qFW2.1</i>, and <i>Capana03g000903</i> may be a candidate gene for <i>qFW3.1</i>. Taken together, our results identified and fine-mapped two major QTL for fruit weight in pepper that will facilitate marker-assistant breeding for the manipulation of yield in pepper.