Candidate Gene Selection for Cytoplasmic Male Sterility in Pepper (Capsicum annuum L.) through Whole Mitochondrial Genome Sequencing.

Peng Wang,Lang Wu,Yihao Wang,Tiantian Li,Jinqiu Liu,Yixin Ai,Qing Cheng,Huolin Shen,Liang Sun,Qiaohua Lu

doi:10.3390/ijms20030578

Abstract

Cytoplasmic male sterility (CMS), which is controlled by mitochondrial genes, is an important trait for commercial hybrid seed production. So far, genes controlling this trait are still not clear in pepper. In this study, complete mitochondrial genomes were sequenced and assembled for the CMS line 138A and its maintainer line 138B. The genome size of 138A is 504,210 bp, which is 8618 bp shorter than that of 138B. Meanwhile, more than 214 and 215 open reading frames longer than 100 amino acids (aas) were identified in 138A and 138B, respectively. Mitochondrial genome structure of 138A was quite different from that of 138B, indicating the existence of recombination and rearrangement events. Based on the mitochondrial genome sequence and structure variations, mitochondrion of 138A and FS4401, a Korean origin CMS line, may have inherited from a common female ancestor, but their CMS traits did originate separately. Candidate gene selection was performed according to the published characteristics of the CMS genes, including the presence SNPs and InDels, located in unique regions, their chimeric structure, co-transcription, and transmembrane domain. A total of 35 ORFs were considered as potential candidate genes and 14 of these were selected, with orf300a and 0rf314a as strong candidates. A new marker, orf300a, was developed which did co-segregate with the CMS trait.

Highlights

Heterosis plays an important role in crop production
Mitochondrial genomes of Cytoplasmic male sterility (CMS) line 138A and its maintainer line 138B were sequenced via Illumina PE and PacBio techniques
For the CMS lines, 138A was developed from a CMS plant which was discovered in the experimental field in China in 1986 [35] and the FS4401 was developed in Korea, their mitochondrial genome sequence and structure were highly similar to each other, suggesting they may originate from a common female ancestor

Summary

Introduction

Heterosis plays an important role in crop production. Hybrid crops produce 15–50% higher yields than the parent lines [1]. Heterosis has been widely used in the production of many cereal and horticultural crops, such as rice, maize, rapeseed, sorghum, sunflower, cucumber, watermelon, tomato as well as pepper [2]. The use of a male sterile line, which does not need emasculation during hybrid production, is a good solution for overcoming this problem. Since it was first successfully utilized in the production of hybrid corn (the maize CMS-T (Texas) system), the male-sterile-line-based hybrid technique has been applied in many other crops [3]

Methods

Results

Discussion

Conclusion