Self-incompatibility (SI) in plants has evolved independently multiple times and S-RNase-based gametophytic self-incompatibility (GSI) is most common. The Rosaceae family possesses both self-recognition (Prunus) and nonself-recognition (Malus) GSI systems, and the latter is widespread in flowering plants. Gillenia trifoliata is a Rosaceae species related to Prunus and Malus, providing utility for understanding SI evolution. Gillenia is sister taxon to Malus, but unlike Malus, has not undergone polyploidisation. In addition, the common ancestor of Gillenia and Prunus is close to the origin of the subfamily. Using a highly contiguous Gillenia genome, orthologous regions to both Malus and Prunus S-loci were identified. Only the Prunus-like S-locus was highly polymorphic and had signatures of a functional S-locus including positive selection of the S-RNase. This suggests a self-recognition system controls SI in Gillenia, and the common ancestors of Gillenia and Prunus, and Gillenia and the apple tribe, likely had a self-recognition SI system. Comparative genomics between Gillenia and Malus suggest apple lost the self-recognition mechanism, and a nonself-recognition mechanism evolved independently from a rudimentary locus with at least one male S-determinant. Repetitive sequences in the Malus-like S-locus in Gillenia may facilitate illegitimate recombination, suggesting putative mechanisms of evolution of nonself-recognition S-loci.

Knowledge of the genotypes for the self-incompatibility locus (S-locus) in apple varieties and in genotypes being used as parents is critical for breeding and commercial production. We present a high-throughput set of molecular markers for the identification of 13 common S-RNase alleles (S1, S2, S3, S5, S7, S8, S9, S10, S20, S23, S24, S25 and S28). This set is composed of seven allele-specific quantitative PCR-based High-Resolution Melting assays and four multi-allelic SSR markers. Validation of these markers was performed using 86 apple accessions, including cultivars with known S-genotypes and recent commercial varieties arising from the Plant & Food Research (PFR) cultivar breeding programme. We also characterized the S-genotypes of 183 genotypes representing some of the most valuable parents within PFR's cultivar breeding programme. The results of this work demonstrate the practical usefulness of this marker set to provide accurate cross-compatibility information to optimise choice of pollenisers in commercial apple orchard design, and to identify compatible parents and guide parental selection when executing apple breeding programmes, to optimise fruit crop yield and quality.

Background The genetic control of sex determination in teleost species is poorly understood. This is partly because of the diversity of mechanisms that determine sex in this large group of vertebrates, including constitutive genes linked to sex chromosomes, polygenic constitutive mechanisms, environmental factors, hermaphroditism, and unisexuality. Here we use a de novo genome assembly of New Zealand silver trevally ( Pseudocaranx georgianus ) together with sex-specific whole genome sequencing data to detect sexually divergent genomic regions, identify candidate genes and develop molecular makers. Results The de novo assembly of an unsexed trevally (Trevally_v1) resulted in a final assembly of 579.4 Mb in length, with a N50 of 25.2 Mb. Of the assembled scaffolds, 24 were of chromosome scale, ranging from 11 to 31 Mb in length. A total of 28,416 genes were annotated after 12.8 % of the assembly was masked with repetitive elements. Whole genome re-sequencing of 13 wild sexed trevally (seven males and six females) identified two sexually divergent regions located on two scaffolds, including a 6 kb region at the proximal end of chromosome 21. Blast analyses revealed similarity between one region and the aromatase genes cyp19 (a1a/b) (E-value < 1.00E-25, identity > 78.8 %). Males contained higher numbers of heterozygous variants in both regions, while females showed regions of very low read-depth, indicative of male-specificity of this genomic region. Molecular markers were developed and subsequently tested on 96 histologically-sexed fish (42 males and 54 females). Three markers amplified in absolute correspondence with sex (positive in males, negative in females). Conclusions The higher number of heterozygous variants in males combined with the absence of these regions in females support a XY sex-determination model, indicating that the trevally_v1 genome assembly was developed from a male specimen. This sex system contrasts with the ZW sex-determination model documented in closely related carangid species. Our results indicate a sex-determining function of a cyp19a1a -like gene, suggesting the molecular pathway of sex determination is somewhat conserved in this family. The genomic resources developed here will facilitate future comparative work, and enable improved insights into the varied sex determination pathways in teleosts. The sex marker developed in this study will be a valuable resource for aquaculture selective breeding programmes, and for determining sex ratios in wild populations.

[目的]利用已开发的矮化性状分子标记(Dw1/Dw2)筛选中国实生和自育无性系苹果砧木,探明各个砧木品种的矮化基因型,为苹果砧木育种工作中亲本选择及矮化分子辅助育种提供帮助.[方法]以不同地区采集的24份中国实生和自育的无性系苹果砧木、147份新疆野苹果(李2-3)×'M9'和345份山荆子(野1-2)×'M9'杂交后代单株的叶片DNA为模板,以矮化砧木'M9''M116'和'MM106'为对照,利用己经开发的Dw1和Dw2矮化标记的SSR引物进行PCR扩增,然后用毛细管电泳检测PCR产物,分析确定各个样品的矮化基因型.[结果]在24份中国苹果砧木中鉴定出8份携带Dw1矮化基因,5份携带Dw2矮化基因,3个自育杂交品种同时携带Dw1和Dw2矮化基因;新疆野苹果(李2-3)×'M9'组合的147个杂种实生苗中有48株携带Dw1矮化基因,14株同时携带Dw1和Dw2基因,山荆子(野1-2)×'M9'的345个杂交后代中仅有11个单株携带Dw1基因型,其余单株均不携带任一矮化基因.[结论]试验中检测的八棱海棠(房2-3)、山荆子(野1-2)和平邑甜茶(野2-22)等中国常用实生砧木均不携带Dw1或Dw2基因,仅新疆野苹果(李2-3)中含有Dw2矮化基因;中国自育的杂交砧木品种中,以'M9'等矮化品种为亲本的后代大多携带Dw1或Dw2;双亲都含有矮化基因的杂交组合后代能获得更多的携带矮化基因的单株.

Current control strategies for the major apple disease European canker (EC) are laborious and expensive, and often do not prevent progression of the disease, which can lead to loss of trees and therefore production. Hence, the development of resistant cultivars is a significant goal for breeders supporting growers in maritime climates conducive to the disease. With genetic markers increasingly being used as a tool in marker-assisted selection for parental and seedling selection, genetic mapping of major effect loci controlling resistance to the pathogen is integral to most breeding programmes. We report the genetic mapping of EC resistance in a bi-parental progeny derived from a cross between moderately EC-resistant ‘Malling 9’ (‘M9’) and highly resistant Malus ‘Robusta 5’ (R5) using two resistance phenotyping techniques. Field inoculation of rasp wounds on the stem and lateral shoots of replicated plants grown on their own roots with a suspension of Neonectria ditissima conidia proved both easier to perform and more effective than inoculation onto leaf scars. Rasp wound phenotype data combined with a previously reported genetic map enabled us to identify a large-effect QTL for control of resistance to EC on linkage group 14 of R5, which we named Rnd1. The position of this QTL was confirmed using leaf scar phenotyping data from the field and glasshouse inoculations. We have developed new SNP markers for this locus, using a novel bioinformatic SNP filtering tool that searches aligned genomic sequences of multiple apple accessions. We have converted one of these markers into a high-throughput version for application in marker-assisted selection of apple.

A multi-allelic genetic marker resource for future genetics studies in m (a) over bar nuka (Leptospermum scoparium) and its close relatives has been developed by mining simple sequence repeats (SSR) from a preliminary draft genome assembly of L. scoparium 'Crimson Glory'. In total, 469 and 169 trinucleotide and dinucleotide repeats, respectively, were detected in a set of 89,619 predicted gene models. Polymerase chain reaction primer pairs were designed for 32 loci exhibiting high sequence similarity to Eucalyptus grandis. These 32 primer pairs were screened over a population of m (a) over bar nuka and 3 accessions of sympatric, related k (a) over bar nuka (genus Kunzea). The 15 polymorphic SSR markers that were successfully developed are now available for genetic analysis in Myrtaceae.

Background: Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for fire blight resistance has been reported on linkage group 3 of Malus 'Robusta 5'. In this study we identified markers derived from putative fire blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases.Results: When several defined E. amylovora strains were used to inoculate three progenies from international breeding programs, all with 'Robusta 5' as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand 'Malling 9' X 'Robusta 5' population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein (MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German 'Idared' X 'Robusta 5' population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene (HSP90). In the US 'Otawa3' X 'Robusta5' population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in fire blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with fire blight resistance. However, this QTL was not observed in the New Zealand or German populations.Conclusions: The results suggest that the upper region of 'Robusta5' linkage group 3 contains multiple genes contributing to fire blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and other factors. Mapping markers derived from putative fire blight resistance genes has proved a useful aid in defining these QTLs and developing markers for marker-assisted breeding of fire blight resistance.

Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programmes, as options are limited for management of this destructive disease of caused by the bacterial pathogen Erwinia amylovora. Genetic mapping of quantitative trait loci (QTLs) for resistance has been a first step towards enabling marker assisted selection for fire blight resistance. A large effect QTL for fire blight resistance has been previously reported on Linkage Group (LG) 3 of Malus 'Robusta 5' (Peil et al. 2007, 2008). In this study, we first re-considered the quantification of the complex disease phenotype in two 'Robusta 5' mapping populations used in previous studies and then employed both composite interval mapping (CIM) for analysis of single QTLs and the additional QTL mapping (addqtl) function of R/qtl software. CIM enabled the resolution of individual QTLs at distinct locations in the two populations with peaks located 6 cM apart. The upper of these two QTL co-located with a leucine-rich repeat receptor-like protein (MxdRLP1) candidate resistance gene. Subsequent analysis with addqtl enabled the detection of an additional QTL in one of the mapping populations where a single QTL had previously been mapped. The additional QTL was in a similar location to the upper of the two QTL detected by CIM. Allelotypic differences within LG3 that were detected between the 'Robusta 5' clones used in the study are believed to underlie the differential effects in the two mapping populations. (Texte integral)

Apple is host to a wide range of pests and diseases, with several of these, such as apple scab, powdery mildew and woolly apple aphid, being major causes of damage in most areas around the world. Resistance breeding is an effective way of controlling pests and diseases, provided that the resistance is durable. As the gene pyramiding strategy for increasing durability requires a sufficient supply of resistance genes with different modes of action, the identification and mapping of new resistance genes is an ongoing process in breeding. In this paper, we describe the mapping of an apple scab, a powdery mildew and a woolly apple aphid gene from progeny of open-pollinated mildew immune selection. The scab resistance gene Rvi16 was identified in progeny 93.051 G07-098 and mapped to linkage group 3 of apple. The mildew and woolly aphid genes were identified in accession 93.051 G02-054. The woolly aphid resistance gene Er4 mapped to linkage group 7 to a region close to where previously the genes Sd1 and Sd2, for resistance to the rosy apple leaf-curling aphid, had been mapped. The mildew resistance gene Pl-m mapped to the same region on linkage group 11 where Pl2 had been mapped previously. Flanking markers useful for marker-assisted selection have been identified for each gene.

Molecular markers associated with gene coding regions are useful tools for bridging functional and structural genomics. Due to their high abundance in plant genomes, single nucleotide polymorphisms (SNPs) are present within virtually all genomic regions, including most coding sequences. The objective of this study was to develop a set of SNPs for the apple by taking advantage of the wealth of genomics resources available for the apple, including a large collection of expressed sequenced tags (ESTs). Using bioinformatics tools, a search for SNPs within an EST database of approximately 350,000 sequences developed from a variety of apple accessions was conducted. This resulted in the identification of a total of 71,482 putative SNPs. As the apple genome is reported to be an ancient polyploid, attempts were made to verify whether those SNPs detected in silico were attributable either to allelic polymorphisms or to gene duplication or paralogous or homeologous sequence variations. To this end, a set of 464 PCR primer pairs was designed, PCR was amplified using two subsets of plants, and the PCR products were sequenced. The SNPs retrieved from these sequences were then mapped onto apple genetic maps, including a newly constructed map of a Royal Gala×A689-24 cross and a Malling 9×Robusta 5, map using a bin mapping strategy. The SNP genotyping was performed using the high-resolution melting (HRM) technique. A total of 93 new markers containing 210 coding SNPs were successfully mapped. This new set of SNP markers for the apple offers new opportunities for understanding the genetic control of important horticultural traits using quantitative trait loci (QTL) or linkage disequilibrium analysis. These also serve as useful markers for aligning physical and genetic maps, and as potential transferable markers across the Rosaceae family.