Articles
S-genotyping and de novo assembly of S-alleles in re-sequenced Japanese plum cultivars
Article number
1450_44
Pages
337 – 342
Language
English
Abstract
Japanese plum (hybrids of Prunus salicina Lindl.), like other Prunus species, has a gametophytic incompatibility system that prevents self-fertilization and promotes cross-pollination.
This system is regulated by the multiallelic S-locus, formed by two closely linked genes, one expressed in the pistil (S-RNase) and the other in the pollen tube (SFB). The identification of both S-alleles of a cultivar is essential to establish its pollination needs, as well as its suitability as a parent in breeding programs.
To date, 57 S-alleles have been described in P. salicina (42 S-RNase and 15 SFB), which has allowed the assignment of more than 200 cultivars to 26 incompatibility groups.
However, the identification of the S-genotype has not been possible in a number of cultivars, mainly because some S-alleles have not been previously sequenced.
In this work, we re-sequenced the genome of two Japanese plum cultivars ‘Laettitia’ and ‘Ebony 51’, filtered out non-S locus reads using a purpose-built Prunus S-loci database, and either genotyped the S-locus – via alignment to a P. salicina S-loci synthetic reference sequence – or de novo assembled all S-RNase and SFB genes.
The workflow proved to be robust in accurately determining the S-genotype and assembled all expected alleles previously identified by PCR analysis.
This complementary and more accurate procedure will facilitate the resolution of redundancies and inconsistencies commonly observed with traditional methods, and the unambiguous grouping of cultivars into their corresponding incompatibility group, necessary knowledge for an efficient selection of pollinator cultivars in plum orchards.
This system is regulated by the multiallelic S-locus, formed by two closely linked genes, one expressed in the pistil (S-RNase) and the other in the pollen tube (SFB). The identification of both S-alleles of a cultivar is essential to establish its pollination needs, as well as its suitability as a parent in breeding programs.
To date, 57 S-alleles have been described in P. salicina (42 S-RNase and 15 SFB), which has allowed the assignment of more than 200 cultivars to 26 incompatibility groups.
However, the identification of the S-genotype has not been possible in a number of cultivars, mainly because some S-alleles have not been previously sequenced.
In this work, we re-sequenced the genome of two Japanese plum cultivars ‘Laettitia’ and ‘Ebony 51’, filtered out non-S locus reads using a purpose-built Prunus S-loci database, and either genotyped the S-locus – via alignment to a P. salicina S-loci synthetic reference sequence – or de novo assembled all S-RNase and SFB genes.
The workflow proved to be robust in accurately determining the S-genotype and assembled all expected alleles previously identified by PCR analysis.
This complementary and more accurate procedure will facilitate the resolution of redundancies and inconsistencies commonly observed with traditional methods, and the unambiguous grouping of cultivars into their corresponding incompatibility group, necessary knowledge for an efficient selection of pollinator cultivars in plum orchards.
Publication
Authors
A. Torres, M.E. Guerra, J. Rodrigo, A. Hedhly
Keywords
Prunus salicina, self-incompatibility, SFB, S-locus, S-RNases
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