Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations

Hyun-Seung Park,Sang-Choon Lee,Kihwan Song,Won Kyung Lee,Tae-Jin Yang,Jee Young Park,Hyun Oh Lee,Ho Jun Joh,Sunggil Kim

doi:10.1038/s41598-021-81988-w

Hyun-Seung Park, Sang-Choon Lee + Show 7 more

Open Access

https://doi.org/10.1038/s41598-021-81988-w

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Abstract

Both genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. To characterize the inheritance patterns of the organelle genomes in cucumber (Cucumis sativus var. sativus), two inbred lines and their reciprocal F1 hybrids were analyzed using an next generation whole genome sequencing data. Their complete chloroplast genome sequences were de novo assembled, and a single SNP was identified between the parental lines. Two reciprocal F1 hybrids have the same chloroplast genomes with their maternal parents. Meanwhile, 292 polymorphic sites were identified between mitochondrial genomes of the two parental lines, which showed the same genotypes with their paternal parents in the two reciprocal F1 hybrids, without any recombination. The inheritance patterns of the chloroplast and mitochondria genomes were also confirmed in four additional cucumber accessions and their six reciprocal F1 hybrids using molecular markers derived from the identified polymorphic sites. Taken together, our results indicate that the cucumber chloroplast genome is maternally inherited, as is typically observed in other plant species, whereas the large cucumber mitochondrial genome is paternally inherited. The combination of DNA markers derived from the chloroplast and mitochondrial genomes will provide a convenient system for purity test of F1 hybrid seeds in cucumber breeding.

Highlights

Both genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions
The average depths of the trimmed Next-generation sequencing (NGS) data mapped to the complete chloroplast genome sequences ranged from 540× to 690×
We generated approximately 1 Gb of NGS data, which is about three-fold the haploid genome coverage of Cucumis sativus[24]

Summary

Introduction

Both genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. Sativus), two inbred lines and their reciprocal F1 hybrids were analyzed using an generation whole genome sequencing data Their complete chloroplast genome sequences were de novo assembled, and a single SNP was identified between the parental lines. The inheritance patterns of the chloroplast and mitochondria genomes were confirmed in four additional cucumber accessions and their six reciprocal F1 hybrids using molecular markers derived from the identified polymorphic sites. While the nuclear genes show biparental Mendelian inheritance patterns, the chloroplast and mitochondrial genomes show non-Mendelian inheritance patterns, predominantly maternal inheritance[2]. Alternative chloroplast and mitochondria inheritance patterns have been reported in some plant species making it difficult to understand the inheritance patterns of their organelles[2]. The cucumber mitochondrial genome is almost 10 times longer than that of its chloroplast genome (~ 160 kb)

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