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

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.

Figure 1

Schematic representation of mitochondrial and chloroplast genome of Cucumis sativus. (a) Each colored bar indicates the mitochondrial chromosome 2 retrieved from NCBI (NC_016005.1) and chloroplast genome of the inbred line MGL in this study. One of the pair of the inverted repeat regions in chloroplast genome was removed. Genes transcribed clockwise and counterclockwise are located on the outside and inside of the bar, respectively. The 292 mitochondrial and 1 chloroplast polymorphisms between two parental lines, MGL and CFL, are represented as black lines for SNP and red lines for InDels. The mitochondrial plastid DNAs and their plastid origins are linked with gray line. The positions of six InDel markers (M1 to M6) are labeled with red triangles. (b) Genotype comparison of the 292 polymorphic sites in mitochondrial genome of parental lines and F₁ hybrids of reciprocal cross. The same color indicates the same genotype for polymorphic sites among parental lines and F₁ hybrids. Gray-mitochondrial indicates the genotype of the reference mitochondrial genome (NC_016005.1).

Figure 2

Validation of molecular markers to confirm inheritance pattern of organelles in cucumber. Eight molecular markers (Cp-SNP-01 to Mt-InDel-06) were designed based on chloroplast and mitochondrial sequence polymorphisms and validated using genomic DNA PCR analyses with seven cucumber samples. Two nuclear InDel markers, Nu-InDel-01 and Nu-InDel-02, were used to confirm heterozygous genotypes of F₁ hybrid nuclear genomes. M, 100-bp size marker; MGL, a Korean solid green-type inbred line; CFL, a Chinese long green-type inbred line; F1(MGLxCFL), an F₁ hybrid between MGL (maternal) and CFL (paternal); F1(CFLxMGL), an F₁ hybrid between CFL (maternal) and MGL (paternal); BP15, a Beith alpha-type inbred line; F1(MGLxBP15), an F₁ hybrid between MGL (maternal) and BP15 (paternal); F1(BP15xMGL), an F₁ hybrid between BP15 (maternal) and MGL (paternal).

Figure 3

Summarized inheritance patterns of chloroplast and mitochondria in cucumber. Organelle inheritance from parental inbred lines to their two reciprocal F₁ progeny was elucidated through whole-organelle genome- and polymorphic marker-based genotyping, confirming that cucumber chloroplasts were inherited maternally while mitochondria were inherited paternally. Colors indicate genotypes.