Identification of self-incompatibility genotypes of almond by allele-specific PCR analysis

Tamura, M.; Ushijima, Koichiro; Sassa, Hidenori; Hirano, Hisashi; Tao, Ryutaro; Gradziel, Thomas M.; Dandekar, Abhaya M.

doi:10.1007/s001220051489

Cited by 138 publications

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“…Variation in the size of PCR amplification products of the first intron (Ortega et al 2005), the second intron (Tamura et al 2000;Channuntapipat et al 2001), or both introns can be used to identify S-alleles (Sutherland et al 2004). Degenerate primers designed using conserved sequences can be used to amplify alleles that have previously been identified or alleles that are thought to be new (De Cuyper et al 2005).…”

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“…These primers can distinguish among S-alleles due to size differences in the PCR products as well as their amplification pattern (Anderson 2005). However this method is unable to distinguish compatible alleles that are the same length but are different in sequence (Tamura et al 2000;Channuntapipat et al 2001;Lo´pez et al 2004;Ortega et al 2006). The cloning and sequencing of PCR amplified products is used to determine the S genotype by sequence comparisons (Janssens et al 1995;Richman and Kohn 1996;Verdoodt et al 1998;Ishimizu et al 1999;Tamura et al 2000;Ma and Oliveira 2001).…”

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“…However this method is unable to distinguish compatible alleles that are the same length but are different in sequence (Tamura et al 2000;Channuntapipat et al 2001;Lo´pez et al 2004;Ortega et al 2006). The cloning and sequencing of PCR amplified products is used to determine the S genotype by sequence comparisons (Janssens et al 1995;Richman and Kohn 1996;Verdoodt et al 1998;Ishimizu et al 1999;Tamura et al 2000;Ma and Oliveira 2001). To confirm a presumptive new S-allele that shows a new band pattern or to determine structural differences with previous alleles, S-alleles can be partially amplified by using consensus primers (Sonneveld et al 2003;De Cuyper et al 2005).…”

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Phylogenetic relationships among the first and second introns of selectedPrunus S-RNase genes

et al. 2015

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Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes. Can. J. Plant Sci. 95: 1145Á 1154. To identify and evaluate self-incompatible alleles in almonds and related germplasm, DNA from 15 Prunus species was amplified using two degenerate consensus primer pairs flanking first and second S-locus introns (PaConsI-FD'EMPc1ConsRD and EM-Pc2ConsFD'EM-Pc3ConsRD). Twenty-eight amplified PCR products were analyzed by automated sequencer capillary electrophoresis. Sequenced fragments were aligned against available Prunus S-locus sequences in the National Center for Biotechnology Information and S-alleles identities were determined. The phylogenetic relationships between S-alleles in the germplasm studied were determined by the homology between their sequences and dendrograms were obtained for each primer pair. The Maximum Likelihood (homology) ranged from 84 to 100%. Most sequences were similar to cultivated almond (Prunus dulcis) or to the European wild almond (P. webbii). Twenty-six alleles for the first and the second introns were registered in the database in the GenBank. Two sequences of the first and second introns, which were taken from Prunus nairica and had similarity in GenBank, were registered in the database under a common sequence of the first and second intron. Analysis of phylogenetic relationships (dendrograms) among S-alleles from wild almond species as well as S-alleles cluster relations showed most pairs of alleles well supported by bootstrap. Key words: Germplasm diversity, self-incompatibility, S-allele, PrunusRahemi, A., Gradziel T.M., Chaparro J.X., Folta, K.M., Taghavi, T., Fatahi, R., Ebadi, A. et Hassani, D. 2015. Liens phyloge´ne´tiques entre le premier et le deuxie`me intron des ge`nes de la S-RNase de certaines espe`ces du genre Prunus. Can. J. Plant Sci. 95: 1145Á1154. Les auteurs ont amplifie´l'ADN de 15 espe`ces du genre Prunus pour identifier puis e´valuer les alle`les auto-incompatibles dans l'amande et le mate´riel ge´ne´tique connexe. À cette fin, ils ont utilise´deux paires d'amorces consensuelles de´ge´ne´re´es, situe´es de part et d'autre du premier et du deuxie`me intron du locus-S (PaConsI-FD'EMPc1ConsRD et EM-Pc2ConsFD'EM-Pc3ConsRD). Vingt-huit produits amplifie´s de la PCR ont e´te´analyse´s par e´lectrophore`se capillaire a`se´quenc¸age automatique. Les fragments se´quence´s ont e´te´compare´s aux se´quences du locus-S du genre Prunus disponibles au National Center for Biotechnology Information et les alle`les ont e´te´identifie´s. Les liens phyloge´ne´tiques entre les alle`les-S du mate´riel ge´ne´tique a`l'e´tude ont e´te´e´tablis par homologie entre les se´quences, et les auteurs ont obtenu les dendrogrammes de chaque paire d'amorces. La fourchette de probabilite´maximale (homologie) varie de 84 a`100 pour cent. La plupart des se´quences ressemblent a`celles de l'amandier cultive´(Prunus dulcis) ou de l'amandier sauvage d'Europe (P. webbii). Vingt-six alle`les du premier et du deuxie`me intron ont e´te´enregistre´s dans la base de donne...

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Phylogenetic relationships among the first and second introns of selectedPrunus S-RNase genes

et al. 2015

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“…The development of new molecular techniques, such as the use of genomic DNA in PCR analysis (Tamura et al, 2000), has dramatically advanced the identification of S-alleles in almond. However, the primers developed by Tamura et al (2000) do not always distinguish alleles with a similar number of nucleotides, such as S 5 and S 25 (López et al, 2004), or S 3 and S f (Sánchez-Pérez et al, 2004).…”

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Short communication. Cloning and sequencing of partial genomic DNA fragments corresponding to the S11 and S12 alleles of the Spanish almond cultivar ‘Marcona’

Kodad¹,

Sánchez²,

Saibo³

et al. 2013

Span. j. agric. res.

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This paper reports the cloning and partial genomic DNA sequencing of two S-RNases (S11 and S12) of almond. DNA from the Spanish almond cultivar Marcona, the most highly appreciated in Spain, was amplified by PCR using the primer pair AS1II and AmyC5R designed for the conserved regions of almond S-alleles. The cloned and sequenced S11 allele of cv. Marcona appears to be identical to that of cvs. Rumbeta and Bertina (which have been previously cloned and sequenced). This is the first time, however, that S12 has been sequenced in almond. The amplified and cloned S12 allele fragment possessed 1080 bp corresponding to the second intron and 506 bp corresponding to the second and third exons. The product of PCR-specific amplification showed that cv. Marcona and the Portuguese cultivar Pestaneta carry the same S12 allele. Knowledge of the sequences of these alleles will be helpful in the design of specific primers for S11 and S12, and could be of use when employing antisense techniques in genetic engineering projects.

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“…However, this analysis still required flowering material (several years old). PCR-based strategies have also been developed for the identification of S-RNase alleles using genomic DNA (Tamura et al, 2000;Ushijima et al, 2003). Many almond S-RNase alleles have been cloned and sequenced (Ortega et al, 2006;Kodad et al, 2008;Halász et al, 2010a) using consensus primers (Sutherland et al, 2004).…”

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Review of genetic diversity studies in almond (Prunus dulcis)

Szikriszt

Hegedűs

Halász

2011

Acta Agronomica Hungarica

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Almond [Prunus dulcis (Mill.) D.A. Webb.] is cultivated for its nuts and is one of the oldest domesticated plants. Due to the genetically controlled self-incompatibility system that operates in this species, almond is characterized by great genetic diversity, the estimation of which has benefited from a range of marker techniques, including morphological characteristics, isoenzyme detection and molecular markers. Among the DNA-based molecular markers, simple sequence repeats (SSR) have been used most widely, although analyses have ranged from restriction fragment length polymorphism to the most recent single nucleotide polymorphism detection methods. Molecular markers have also been used to trace specific agronomic traits, e.g. self-(in)compatibility or kernel bitterness. Genetic diversity studies in almond have not revealed a direct relationship between the level of diversity and the origin of the germplasm. This might be explained by the relatively recent occurrence of self-compatibility in almond, which has not yet caused a serious loss of genetic diversity. The markers reviewed will be useful in monitoring and maintaining genetic diversity in almond breeding programmes, while others may permit marker-assisted selection for favourable agronomic traits. The cultivation, breeding and conservation of wild-growing almonds may equally benefit from the genetic diversity studies (especially those applying molecular markers).

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Identification of self-incompatibility genotypes of almond by allele-specific PCR analysis

Cited by 138 publications

References 21 publications

Phylogenetic relationships among the first and second introns of selectedPrunus S-RNase genes

Phylogenetic relationships among the first and second introns of selectedPrunus S-RNase genes

Short communication. Cloning and sequencing of partial genomic DNA fragments corresponding to the S11 and S12 alleles of the Spanish almond cultivar ‘Marcona’

Review of genetic diversity studies in almond (Prunus dulcis)

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