Regions Underlying Population Structure and the Genomics of Organ Size Determination in Capsicum annuum

Abstract

Fruits, as an important part of the human diet, have been under strong selection during domestication. In general, continued directed selection has led to varieties having larger fruit with greater shape variation and tremendous increases in fruit mass. Common cultivated peppers (Capsicum annuum L.) are found in a wide range of sizes and shapes. Analysis of genetic relatedness and population structure has shown that the large-fruited, nonpungent types have reduced diversity and comprise a highly structured group. To explore this population structure, a statistical method for detecting fixation within subpopulations was applied to a set of 21 pungent and 19 nonpungent lines that represent the pepper breeding germplasm. We have identified 17 blocks within the pepper genome that are conserved among nonpungent large-fruited varieties. To determine if these regions were fixed by selection on fruit size or pungency, quantitative trait loci (QTLs) from seven studies along with capsaicin biosynthesis genes and homologs of organ size regulatory genes were mapped onto the current pepper genome assembly. Of the 17 fixed regions, 14 overlapped with fruit size or shape QTLs. There were seven putative organ size regulators and seven capsaicin biosynthetic genes within these regions. This work defines genomic regions that underly structure within the nonpungent pepper germplasm and QTLs or genes that may have been selected for during the development of large-fruited nonpungent pepper varieties.

Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites

“…The other, a non-synonymous change on chromosome 3 in the gene Longifolia 1-like, is related fruit elongation and roundness. Both genomic regions overlap with QTLs linked to fruit shape and elongation previously identified in pepper [13,12,9,18]. In particular major QTL detected on chromosome 3 (fs3.1) and confirmed in several studies (Supplentary Table 1) is located 10 Mbp upstream from the non-synonymous change in Longifolia 1-like, while a QTL on chromosome 10 (fs10.1) is located 100 Mb downstream the cluster of variants on chromosome 10.…”

“…tomato, [5,6,7,8] the genetics underlying fruit shape in pepper is limited to findings from quantitative trait loci (QTL) analysis in a few biparental mapping populations ( Supplementary Table 1), mostly phenotyped with low-throughput techniques, [9,10,11,12,13,14,15,16] and/or limited to the identification of QTLs. [17,18,19,20] As a consequence, major genetic loci underlying Capsicum fruit variability have not yet been identified.…”

Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (Capsicum annuum)

“…The following are some of the more obvious candidate genes associated with our QTL regions. Big Brother is a gene that was found by screening the pepper genome sequence under Ft_1.1 , a QTL region from measurements of latitudinal sectional data, against the A. thaliana reference genomes (Hill et al, 2017). Big Brother encodes a RING‐finger domain protein that acts as an E3 ubiquitin‐ligase, which works with the putative ubiquitin‐binding protein ( DA1 ) to limit organ size by promoting the end of the cell proliferation stage and starting cell expansion (Disch et al, 2006; Li et al, 2008; Powell and Lenhard, 2012).…”

“…Unlike Big Brother , which functions in a cell‐autonomous manner, KLUH/CYP78A5 ( KLU ) requires coordination of signals between tissue layers or organs (Powell and Lenhard, 2012). The KLU gene that was detected on chromosome 3, associated with the Ft_3.1 region, was proposed to generate a transportable growth signaling molecule and control the timing to end the proliferation phase for avoiding the premature arrest in A. thaliana and tomato (Anastasiou et al, 2007; Chakrabarti et al, 2013; Hill et al, 2017). This gene encodes a cytochrome P450 monooxygenase protein (Anastasiou et al, 2007).…”

Genome‐wide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication

“…This pattern may be consistent with a QTL allele-such as one conferring a preferable freshuse phenotype-under selection in the Chile de Agua. Several loci on chromosome 6 are associated with fruit morphology (Han et al, 2016;Hill et al, 2017) including pericarp thickness (Rao, Chaim, Borovsky, & Paran, 2003), and flowering phenology traits (Yarnes et al, 2012), all of which might be under selective pressure in Chile de Agua. While such QTL could be potentially interesting candidates for follow-up research, a list of candidates from these data would be highly speculative and were thus not included.…”