Fine mapping and candidate gene analysis of the up locus determining fruit orientation in pepper (Capsicum spp.).

Fang Hu,Jichi Dong,Jian Zhong,Jiaowen Cheng,Kailin Hu,Ziyan Zhou

doi:10.1007/s00122-021-03867-2

Abstract

The up locus determining fruit orientation was fine-mapped into a region with a physical length of ~169.51 kb on chromosome P12 in pepper. Capana12g000958, encoding a developmentally regulated G protein 2, was proposed as the strongest candidate via sequence comparison and expression analysis. Fruit orientation is an important horticultural and domesticated trait, which is controlled by a single semi-dominant gene (up) in pepper. However, the gene underlying up locus has not yet been identified. In this study, the previously detected major QTL UP12.1 was firstly verified using a backcross population (n = 225) stem from the cross of BB3 (C. annuum) and its wild relative Chiltepin (C. annuum var. glabriusculum) using BB3 as the recurrent parent. Then, a large BC1F2 population (n = 1827) was used for recombinant screening to delimit the up locus into an interval with ~ 169.51kb in length. Sequence comparison and expression analysis suggested that Capana12g000958, encoding a developmentally regulated G protein 2, was the most likely candidate gene for theup locus. There is no difference within the coding sequences of Capana12g000958 between BB3 and Chiltepin, while a SNP in the upstream of Capana12g000958 showed a complete correlation with the fruit orientation among a panel of 40 diverse pepper inbred lines. These findings will form a basis for gene isolation and reveal of genetic mechanism underlying the fruit orientation domestication in pepper.

Highlights

Plant organ orientation is governed by antagonistic interactions of the ubiquitous gravitropic mechanism and auxindependent antigravitropic offset mechanism (Roychoudhry et al 2013)
Fruit orientation phenotypes were evaluated with at least five flowers/fruits were recorded from stage S3 to S7 (Fig. 1) for each plant based on the ELV (E: erect, LP: lateral pendant, VP: vertical pendant) classification method as described previously (Cheng et al 2016a)
Chi-square tests revealed that the observed segregation in the BC1F1 population fitted the expected ratio 1:1 (χ2 = 0.04, P > 0.05). These findings indicated that variations in fruit orientation between BB3 and Chiltepin were controlled by a single semi-dominant gene

Summary

Introduction

Plant organ orientation is governed by antagonistic interactions of the ubiquitous gravitropic mechanism and auxindependent antigravitropic offset mechanism (Roychoudhry et al 2013). In Arabidopsis, several molecular regulators that govern alterations in pedicel orientation have been identified They include the BREVIPEDICELLUS (KNAT1/BP) (Douglas et al 2002; Venglat et al 2002), ASYMMETRIC LEAVES1/2 (AS1/2) (Xu et al 2003), CORYMBOSA1 (CRM1/BIG) (Yamaguchi et al 2007), KNOTTED-like2/6 (KNAT2/6) (Ragni et al 2008), ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1) (Li et al 2012) and LEAFY (LFY) (Yamaguchi et al 2012). In other non-model plants, NtSVP in tobacco, SlAGO7 in tomato, and CsUp in cucumber were found to participate in the developmental regulation of pedicel/fruit orientation (Wang et al 2015; Lin et al 2016; Sun et al 2019)

Methods

Results

Conclusion