S -Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S -Loci Reference Sequence.
Afif HedhlyMaría Engracia GuerraJérôme GrimpletJavier RodrigoPublished in: International journal of molecular sciences (2023)
Self-incompatibility in Prunus species is governed by a single locus consisting of two highly multi-allelic and tightly linked genes, one coding for an F-box protein-i.e., SFB in Prunus - controlling the pollen specificity and one coding for an S-RNase gene controlling the pistil specificity. Genotyping the allelic combination in a fruit tree species is an essential procedure both for cross-based breeding and for establishing pollination requirements. Gel-based PCR techniques using primer pairs designed from conserved regions and spanning polymorphic intronic regions are traditionally used for this task. However, with the great advance of massive sequencing techniques and the lowering of sequencing costs, new genotyping-by-sequencing procedures are emerging. The alignment of resequenced individuals to reference genomes, commonly used for polymorphism detection, yields little or no coverage in the S -locus region due to high polymorphism between different alleles within the same species, and cannot be used for this purpose. Using the available sequences of Japanese plum S -loci concatenated in a rosary-like structure as synthetic reference sequence, we describe a procedure to accurately genotype resequenced individuals that allowed the analysis of the S -genotype in 88 Japanese plum cultivars, 74 of them are reported for the first time. In addition to unraveling two new S -alleles from published reference genomes, we identified at least two S -alleles in 74 cultivars. According to their S -allele composition, they were assigned to 22 incompatibility groups, including nine new incompatibility groups reported here for the first time (XXVII-XXXV).
Keyphrases
- genome wide
- genetic diversity
- genome wide association study
- dna methylation
- single cell
- high throughput
- copy number
- high throughput sequencing
- transcription factor
- minimally invasive
- binding protein
- genome wide identification
- randomized controlled trial
- amino acid
- systematic review
- protein protein
- health insurance
- structural basis
- genome wide analysis
- genome wide association
- affordable care act
- quantum dots