Articles
The frequent occurrence of null alleles hinders genotyping and selection in lemon breeding programs
Article number
1448_16
Pages
131 – 138
Language
English
Abstract
Given the polyembryony displayed by all lemon cultivars, the first step in breeding must be the differentiation of zygotic individuals from those with a nucellar origin (i.e., identical to the mother plant). Molecular characterization using genetic markers is a powerful tool to accomplish this, provided that reproducible and reliable markers capable of discriminating between the different genotypes are available.
But null alleles in one or a set of markers can cause incorrect genotyping of a progeny, as they can often go undetected in an initial characterization of parents, since heterozygotes with a null allele are indistinguishable from expected homozygotes in most genotyping technologies. Citrus limon has indeed proven to be highly heterozygous, and previous studies have detected the common appearance of null heterozygotes in lemon when using PCR-based markers.
In our lemon breeding program, we used SNP markers in order to identify true hybrids among the descendants of a cross ‘Verna 51’ × ‘Fino 49’. After a whole-genome sequencing of both parents, polymorphic SNPs were selected, and primers were designed for validation and to perform KASP analysis of the offspring.
Although these SNP markers were expected to segregate in a way in which the “aa” and “bb” genotypes of the parents would give rise to individuals either “aa” (nucellar) or “ab” (zygotic), we also found individuals with the unexpected genotype of the father, apparently “bb” in some of the markers.
The most likely explanation is that the real genotype of the parents is one or two null heterozygotes (“a0” × “b0”, or “a0” × “bb”) which would give rise to hybrids with the possible configurations “ab”, “a0”, “0b” or “00”. Segregation analysis confirmed that this was, in fact, the case.
As a consequence, more markers, up to 13 SNPs, were needed to confirm the hybrid nature of every descendant.
But null alleles in one or a set of markers can cause incorrect genotyping of a progeny, as they can often go undetected in an initial characterization of parents, since heterozygotes with a null allele are indistinguishable from expected homozygotes in most genotyping technologies. Citrus limon has indeed proven to be highly heterozygous, and previous studies have detected the common appearance of null heterozygotes in lemon when using PCR-based markers.
In our lemon breeding program, we used SNP markers in order to identify true hybrids among the descendants of a cross ‘Verna 51’ × ‘Fino 49’. After a whole-genome sequencing of both parents, polymorphic SNPs were selected, and primers were designed for validation and to perform KASP analysis of the offspring.
Although these SNP markers were expected to segregate in a way in which the “aa” and “bb” genotypes of the parents would give rise to individuals either “aa” (nucellar) or “ab” (zygotic), we also found individuals with the unexpected genotype of the father, apparently “bb” in some of the markers.
The most likely explanation is that the real genotype of the parents is one or two null heterozygotes (“a0” × “b0”, or “a0” × “bb”) which would give rise to hybrids with the possible configurations “ab”, “a0”, “0b” or “00”. Segregation analysis confirmed that this was, in fact, the case.
As a consequence, more markers, up to 13 SNPs, were needed to confirm the hybrid nature of every descendant.
Publication
Authors
N. Navarro-García, Y. Jiménez-Alfaro, P. Bretó-Monfort, O. Pérez-Tornero
Keywords
Citrus limon, marker assisted selection, apomixis, KASP
Groups involved
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