An intact mitochondrial cox1 gene and a pseudogene with different genomic configurations are present in apple cultivars ‘Golden Delicious’ and ‘Delicious’: Evolutionary aspects
Highlights
► The mitochondrial cox1 genes in two apples Golden Delicious and Delicious were characterized. ► There are two intact cox1 (G-cox1 and D-cox1) and two truncated copies (G-φcox1 and D-φcox1). ► A common 1115-bp segment was shared among the four cox1 sequences. ► Delicious bears substoichiometric amounts of G-cox1 and G-φcox1 besides D-cox1 and D-φcox1. ► Substoichiometric molecules carrying D-φcox1 were present in the Golden Delicious.
Introduction
The cultivated apple (Malus x domestica) is a complex interspecific hybrid (Korban and Skirvin, 1984, Way et al., 1990). Its primary wild ancestor has been considered to be Malus sieversii whose range is centered at the border between western China and the former Soviet Union (Hokanson et al., 1997). Other Malus species which have contributed to the genetic makeup of apple including the wild Caucasian apple (Malus orientalis), as well as crab apples from Europe (Malus sylvestris), Siberia (Malus baccata), Manchuria (Malus mandshurica), and China (Malus prunifolia) (Janick et al., 1996, Hokanson et al., 1997). This theory of the primary ancestor has recently been challenged, however, by Coart et al. (2006), who found the extensive sharing of plastome types between M. x domestica and M. sylvestris. They also reported that the main plastome types shared by both species were nearly absent from M. sieversii.
As with other important fruit crops, it is difficult to determine exactly when the apple was first domesticated, but the Greeks and Romans were growing apples at least 2500 years ago (Hancock, 2004). Ten thousand or more named apple cultivars are documented, yet only a few dozen are grown on a commercial scale world-wide (Janick et al., 1996). We should also note that the world production of apples is mostly based on two cultivars: ‘Delicious’ and its red sports, and ‘Golden Delicious’, with their seedlings making up a high proportion of the new cultivars (Janick et al., 1996, Hokanson et al., 1997). The two cultivars originated in the USA as chance seedlings in the late 19th century (Way et al., 1990). ‘Delicious’ may have reportedly an old US cultivar ‘Yellow Bellflower’ in its parentage, while ‘Golden Delicious’ seems to be derived from a cross between ‘Grimes Golden’ and ‘Golden Reinette’ (Way et al., 1990). Moreover, Savolainen et al. (1995) described that the ‘Red Delicious’ family including ‘Delicious’ might have a cytoplasmic origin in a landrace ‘Yellow Transparent’ grown in Russia and the Baltic states. We previously used mitochondrial DNA (mtDNA) polymorphisms to characterize the cytoplasmic diversity within a range of apple cultivars and landraces (Ishikawa et al., 1992, Kato et al., 1993). The distribution of mtDNA polymorphism patterns allowed the classification of the apple genotypes into four distinct cytoplasmic groups. The four groups were described by representative cultivar or landrace within each group: ‘Golden Delicious’-type, ‘Delicious’-type, ‘McIntosh’-type, and ‘Dolgo Crab’-type.
As part of our effort to understand the molecular basis of mitochondrial genome variation giving rise to these diverse cytoplasm types, we investigated the genomic regions that distinguished the ‘Golden Delicious’-type and ‘Delicious’-type cytoplasms from each other. We present herein an analysis of the mtDNA rearrangement involving the cox1 (cytochrome c oxidase subunit 1) locus. The implications of our data are discussed with respect to the evolutionary mechanisms for the generation of mitochondrial genome diversity in apples.
Section snippets
Plant material and nucleic acid preparation
Eight apple cultivars representing each of the ‘Golden Delicious’-and ‘Delicious’-type cytoplasms were chosen for our analysis: the former cytotype cultivars were ‘Golden Delicious’, ‘Tsugaru’ (‘Golden Delicious’ × ‘Jonathan’), ‘Jonagold’ (‘Golden Delicious’ × ‘Jonathan’) and ‘Fuji’ (‘Ralls Janet’ × ‘Delicious’); and the latter cytotype cultivars were ‘Delicious’, ‘Hopa Crab’, ‘Red Astrachan’ and ‘Cellini’ (Kato et al., 1993, Harada et al., 1993). Total genomic DNA was prepared from young fresh
Sequence and expression of the cox1 gene in ‘Golden Delicious’
Kato et al. (1993) previously described that a heterologous cox1 probe from sugarbeet hybridized to 10.0-kb and 4.2-kb HindIII fragments in ‘Golden Delicious’, which were not present in ‘Delicious’, which instead showed hybridization to 9.1-kb and 5.0-kb HindIII fragments. Hybridization of PstI-digested DNAs to the same probe detected 13.0-kb and 6.5-kb fragments in ‘Golden Delicious’, but not in ‘Delicious’, where 17.0-kb and 2.5-kb fragments were identified (data not shown). First, the 6.5-kb
Acknowledgements
Leaf samples were kindly supplied by Drs. Takeo Harada (Faculty of Agriculture and Life Science, Hirosaki University, Japan) and Megumi Igarashi (Aomori Prefectural Industrial Technology Research Center, Japan). We are grateful to Dr Mineo Senda (Faculty of Agriculture and Life Science, Hirosaki University, Japan) for providing sugarbeet cox1 gene. This work was supported in part by Grants-in-Aids for Scientific Researches from Ministry of Education, Science, and Culture, Japan.
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2013, Scientia HorticulturaeCitation Excerpt :The results are not unexpected, considering that the ‘Dolgo Crab’ group was composed primarily of Chinese crab apples, as opposed to the other three groups, which contained a large number of European, the US and Canadian ancient cultivars and their pedigrees. We previously designed four oligonucleotide primers (named P1 through P4, see Table S1), combination of which allowed the discrimination between predominant (intensively amplified) and substoichiometric forms of G-cox1, G-Ψcox1, D-cox1 and D-Ψcox1 sequences (Wakatsuki et al., 2011): these four sequences can be amplified specifically with primer pairs P3/P2, P1/P4, P1/P2, and P3/P4, respectively. In this study, genomic DNA was prepared from eight ‘McIntosh’ and six ‘Dolgo Crab’ type accessions, and subjected to PCR analysis using the above primer pairs.
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Cytoplasmic genome diversity in the cultivated apple - Short communication
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Authors contributed equally to this work.