RESUMO
KEY MESSAGE: Proof of concept of Bayesian integrated QTL analyses across pedigree-related families from breeding programs of an outbreeding species. Results include QTL confidence intervals, individuals' genotype probabilities and genomic breeding values. Bayesian QTL linkage mapping approaches offer the flexibility to study multiple full sib families with known pedigrees simultaneously. Such a joint analysis increases the probability of detecting these quantitative trait loci (QTL) and provide insight of the magnitude of QTL across different genetic backgrounds. Here, we present an improved Bayesian multi-QTL pedigree-based approach on an outcrossing species using progenies with different (complex) genetic relationships. Different modeling assumptions were studied in the QTL analyses, i.e., the a priori expected number of QTL varied and polygenic effects were considered. The inferences include number of QTL, additive QTL effect sizes and supporting credible intervals, posterior probabilities of QTL genotypes for all individuals in the dataset, and QTL-based as well as genome-wide breeding values. All these features have been implemented in the FlexQTL(™) software. We analyzed fruit firmness in a large apple dataset that comprised 1,347 individuals forming 27 full sib families and their known ancestral pedigrees, with genotypes for 87 SSR markers on 17 chromosomes. We report strong or positive evidence for 14 QTL for fruit firmness on eight chromosomes, validating our approach as several of these QTL were reported previously, though dispersed over a series of studies based on single mapping populations. Interpretation of linked QTL was possible via individuals' QTL genotypes. The correlation between the genomic breeding values and phenotypes was on average 90 %, but varied with the number of detected QTL in a family. The detailed posterior knowledge on QTL of potential parents is critical for the efficiency of marker-assisted breeding.
Assuntos
Cruzamentos Genéticos , Malus/genética , Locos de Características Quantitativas , Teorema de Bayes , Cruzamento , Mapeamento Cromossômico , Cromossomos de Plantas , Frutas/anatomia & histologia , Frutas/genética , Estudos de Associação Genética , Ligação Genética , Genótipo , Malus/anatomia & histologia , LinhagemRESUMO
Apple ( Malus x domestica Borkh.) sequences sharing homology with known resistance genes were cloned using a PCR-based approach with degenerate oligonucleotide primers designed on conserved regions of the nucleotide-binding site (NBS). Sequence analysis of the amplified fragments indicated the presence of at least 27 families of NBS-containing genes in apple, each composed of several very similar or nearly identical sequences. The NBS-leucine-rich repeat homologues appeared to include members of the two major groups that have been described in dicot plants: one possessing a toll-interleukin receptor element and one lacking such a domain. Genetic mapping of the cloned sequences was achieved through the development of CAPS and SSCP markers using a segregating population of a cross between the two apple cultivars Fiesta and Discovery. Several of the apple resistance gene homologues mapped in the vicinity, or at least on the same linkage group, of known loci controlling resistance to various pathogens. The utility of resistance gene-homologue sequences as molecular markers for breeding purposes and for gene cloning is discussed.
Assuntos
Mapeamento Cromossômico , Genes de Plantas/genética , Imunidade Inata/genética , Malus/genética , Filogenia , Polimorfismo Genético , Sequência de Aminoácidos , Clonagem Molecular , Análise por Conglomerados , Primers do DNA , Marcadores Genéticos/genética , Dados de Sequência Molecular , Reação em Cadeia da Polimerase/métodos , Polimorfismo Conformacional de Fita Simples , Alinhamento de Sequência , Análise de Sequência de DNARESUMO
A cDNA clone encoding a leucine-rich repeat (LRR) receptor-like protein kinase (LRPKm1) of Malus x domestica cv. Florina has been isolated using as a heterologous probe a cloned gene encoding a polygalacturonase-inhibiting protein (PGIP) of Phaseolus vulgaris L. A genomic clone containing the 5'-regulatory region and a 5' portion of the open reading frame of the LRPKm1 gene has also been isolated. An open reading frame of 2997 nt (999 amino acids) was present in the cDNA clone, encoding a receptor-like protein comprising a 21 amino acid signal peptide for secretion, a leucine zipper, 23 LRRs, a putative membrane-spanning region and a serine/threonine protein kinase domain. LRPKm1 shows homology to the A. thaliana receptor-like protein kinase RLK5 and, to a minor extent, to PGIP. The LRPKm1 region from +5 to +600 exhibits an alternative reading frame that encodes a product corresponding to a proline-rich protein fragment homologous to several hydroxyproline-rich proteins. Southern blot analysis showed that LRPKm1 belongs to a multigene family and that there is length polymorphism of the hybridizing restriction fragments among different M. x domestica cultivars. Northern blot analysis was carried out on mRNA extracted from infected leaves of either cv. Florina (resistant to Venturia inaequalis) or cv. Golden Delicious (susceptible to V. inaequalis), and from tissues treated with salicylic acid. A 3500 bp transcript hybridizing at high stringency with the LRPKm1 cDNA accumulated in response to infection or salicylic acid treatment. Transcript accumulation was more intense in the incompatible interaction than in the compatible one. The possible involvement of this receptor-like protein kinase in resistance of apple to phytopathogenic fungi is discussed.