A high-throughput method for genotyping S-RNase alleles in apple

Abstract

We present a new efficient screening tool for detection of S-alleles in apple. The protocol using general and multiplexed primers for PCR reaction and fragment detection on an automatized capillary DNA sequencer exposed a higher number of alleles than any previous studies. Analysis of alleles is made on basis of three individual fragment sizes making the allele interpretation highly accurate. The method was employed to genotype 432 Malus accessions and exposed 25 different S-alleles in a selection of Malus domestica cultivars of mainly Danish origin (402 accessions) as well as a selection of other Malus species (30 accessions). The allele S3 (28 %) was the most common among the Danish cultivars followed by S1 and S7 (both 27 %). The alleles S36 and S40 not previously reported from M. domestica were found in 6 and 17 cultivars, respectively. Complete allelic composition was found in 91 % of the 369 diploid accessions and in 86 % of the 63 triploids concerned. We further identified a relatively high frequency of S33 and S34, which has not been considered by most previous studies. The protocol presented here is easy to adopt and saves both time and work effort compared to previous methods. The robustness is illustrated by the great accuracy and a high number of S-alleles presented.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-016-0448-0) contains supplementary material, which is available to authorized users.

Finding a Compatible Partner: Self-Incompatibility in European Pear (Pyrus communis); Molecular Control, Genetic Determination, and Impact on Fertilization and Fruit Set

“…The DNA sequence encoding this hexapeptide has frequently been used for the development of consensus primers for PCR-based S-genotyping (DeFranceschi et al., 2012). S-RNase genotyping by PCR is commonly used in Rosaceae species to determine incompatibility relations between cultivars, often in combination with field-controlled pollination assays (Zuccherelli et al., 2002; Larsen et al., 2016; Herrera et al., 2018). Figure 3 displays a schematic representation of the protein sequence of the S-RNase of Pyrus, Prunus , and Solanaceae.…”

Identification and characterization ofS-RNasegenes in apple rootstock and the diversity ofS-RNasesinMalusspecies

“…Whether those S-RNases sequences have unique functions or not yet known, since some of them are rather similar to previously described S-RNases. Here, Larsen et al (2016) followed the same nomenclature of Matsumoto (2013) where the above mentioned alleles were not included. However, they had used the names as S44 dom and S44 syl with different functions.…”

Detection of Self Incompatibility Genotypes in Prunus africana: Characterization, Evolution and Spatial Analysis

“…A total of 22 alleles were identified in Prunus lannesiana var . speciosa [ 26 ].Twenty alleles were retrieved from 20 Sorbus aucuparia individuals, whereas 16, 17 and 22 alleles were found in Prunus avium [ 27 ], Crataegus monogyna [ 28 ] and Malus domestica [ 29 ] respectively. All these above Rosaceae species being diploid, a similar number of specificities was also found in the polyploidy Prunus spinosa [ 16 ].…”