Identification of quantitative trait loci for cane splitting in red raspberry (Rubus idaeus)

Cane splitting, a normal feature of raspberry growth, can lead to plant infestation by cane midge followed by fungal infection, with losses in yield of up to 50 % if left untreated. The extent of splitting in the Latham × Glen Moy reference mapping population was assessed over six years and in three environments and quantitative trait loci (QTL) were identified across linkage groups (LG) 2, 3, 5 and 6. Cane splitting QTL on LG 3 and 5 co-locate with QTL for plant vigour. The cane splitting QTL on LG 6 is associated with the QTL for resistance to root rot caused by Phytophthora rubi. Broad-sense heritability for cane splitting ranged from 25.6 % in 2007 to 49.1 % in 2008 in this population. Season and environment were also found to influence cane splitting in this population. Several genes involved in general plant growth and in defence responses lie within these QTL. This is a first step towards identifying the genetic basis of cane splitting in raspberry and the development of genetic markers for use in raspberry breeding programmes.     

Mapping gene H controlling cane pubescence in raspberry and its association with resistance to cane botrytis and spur blight, rust and cane spot

Disease resistance is increasing in importance, as consumers require high-quality raspberry fruit at a time when chemical disease control is undesirable. Breeders have limited resources and rarely include a primary screen for each fungal disease. Marker-assisted breeding would facilitate the introduction of resistance into elite germplasm and breeding lines. An additional 20 simple sequence repeats have been added to the existing raspberry linkage map. Gene H, which determines cane pubescence (genotype HH or Hh), the recessive allele of which gives glabrous canes (genotype hh), has been mapped on to linkage group 2 and shown to be closely associated with resistance to cane botrytis and spur blight but not rust or cane spot. Other map regions on linkage groups 3, 5 and 6 associated with disease resistance are reported here. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers

Breeding in raspberry is time-consuming due to the highly heterozygous nature of this perennial fruit crop, coupled with relatively long periods of juvenility. The speed and precision of raspberry breeding can be improved by genetic linkage maps, thus facilitating the development of diagnostic markers for polygenic traits and the identification of genes controlling complex phenotypes. A genetic linkage map (789 cM) of the red raspberry Rubus idaeus has been constructed from a cross between two phenotypically different cultivars; the recent European cultivar Glen Moy and the older North American cultivar Latham. SSR markers were developed from both genomic and cDNA libraries from Glen Moy. These SSRs, together with AFLP markers, were utilised to create a linkage map. In order to test the utility of the genetic linkage map for QTL analysis, morphological data based on easily scoreable phenotypic traits were collected. The segregation of cane spininess, and the root sucker traits of density and spread from the mother plant, was quantified in two different environments. These traits were analysed for significant linkages to mapped markers using MapQTL and were found to be located on linkage group 2 for spines and group 8 for density and diameter. The availability of co-dominant markers allowed heterozygosities to be calculated for both cultivars.     

Insights to plant–microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes

Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant–microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant‐associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant–microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil‐borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere‐related traits, (c) the role of root exudation in microbe‐mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.     

A meta-analysis of genetic correlations between plant resistances to multiple enemies

Genetic correlations between plant resistances to multiple natural enemies are important because they have the potential to determine the mode of selection that natural enemies impose on a host plant, the structure of herbivore and pathogen communities, and the success of plant breeding for resistance to multiple diseases and pests. We conducted a meta-analysis of 29 published studies of 16 different plant species reporting a total of 467 genetic correlations between resistances to multiple herbivores or pathogens. In general, genetic associations between resistances to multiple natural enemies tended to be positive regardless of the breeding design, type of attacker, and type of host plant. Positive genetic correlations between resistances were stronger when both attackers were pathogens or generalist herbivores and when resistance to different enemies was tested independently, suggesting that generalists may be affected by the same plant resistance traits and that interactions among natural enemies are common. Although the mean associations between resistances were positive, indicating the prevalence of diffuse selection and generalized defenses against multiple enemies, the large variation in both the strength and the direction of the associations suggests a continuum between pairwise and diffuse selection.     

Breeding for immune responsiveness and disease resistance1

Animal production efficiency, and product volume and quality can be greatly increased by reducing disease losses. Genetic variation, a prerequisite for successful selection, has been found in animals and poultry exposed to a variety of viral, bacterial and parasitic infections. Breeding for disease resistance can play a significant role alone or in combination with other control measures including disease eradication, vaccination and medication. Feasibility of simultaneously improving resistance to specific diseases and production traits has been demonstrated. However, selection for specific resistance to all diseases of animals and poultry is impossible. Development of general disease resistance through indirect selection primarily on immune response traits may be the best long-term strategy but its applicability is presently limited by insufficient understanding of resistance mechanisms. Another hindrance may be negative genetic correlations among various immune response functions: phagocytosis, cell mediated and humoral immunity. To better assess the feasibility of increasing general disease resistance by indirect selection we must obtain estimates of heritability for immune response, disease resistance, and economic production traits, as well as genetic correlations among these traits. The present level of disease resistance in farm animals resulted from natural selection and from correlated responses to selection for production traits while the influence of artificial selection for resistance was minimal. Future research should be directed towards developing and applying breeding techniques that will increase resistance to diseases without compromising production efficiency and product quailty. This will require cooperation of immunogeneticists, veterinarians and animal and poultry breeders. Significant progress in the improvement of resistance to diseases may result from the application of new techniques of molecular genetics and cell manipulation.     

Breeding for Improved Disease Resistance in Organic Farming – Possibilities and Constraints

Lowered incidences of disease may be reached in several ways: management and rearing measures, vaccination programmes and preventive medications as well as breeding for improved disease resistance. Here the focus is on breeding for improved resistance to infectious diseases. In comparison to conventional farming, one has to acknowledge that the spectrum of diseases in animals reared under organic conditions is different and that the proportion of the breeding stock of animals in organic farming is considerably smaller. There are at least four different approaches that may be used in breeding towards resistance to infectious diseases. The most obvious is to record disease incidence in the progeny and select those parents that produce the progeny with the lowest incidences of disease. Another approach is to use breeders possessing certain major histo-compatibility complex antigens suggested being associated with resistance to certain infections. A third approach is to analyse the heritability of a set of immune functions or related traits crucial for resistance to infections and then use the traits with high heritability in breeding programmes. Finally, one may genetically select animals for high immune response using an index that combines estimated breeding values for several immunological traits. Examples of these various approaches are given and the feasibility for using these in organic farming are discussed.     

宠物抗病育种

宠物的抗病育种研究具有重要的意义,本文对开展抗病育种的必要性、宠物免疫抗病系统、疾病抗性遗传机制、免疫反应的遗传控制、宠物抗病常规育种、宠物抗病分子育种以及抗病育种方法的现状、存在的问题、展望进行了介绍。说明了对疾病抗性的选择有一个坚实基础。抗病育种是控制疾病的有效方法,应用前景美好。     

Inheritance of partial resistance to the leaf aphids Macrosiphum euphorbiae and Uroleucon sonchi in lettuce

The genetics of partial resistance (PR) of lettuce to the leaf aphid species Macrosiphum euphorbiae and Uroleucon sonchi was studied in F₁ and F₂ generations of six crosses between four cultivars. Partial resistance inherited mainly additively. With M. euphorbiae the estimates of broad-sense F₂ heritability were low and non-significant in crosses between parents of the same resistance level (S x S and PR x PR), and high (0.69-0.76) in crosses between parents of different resistance level (PR x S). The level of resistance in lettuce cultivars ‘Charan’ and ‘Marbello’ led to a marked reduction in percentage of plants with colonies of M. euphorbiae in a field experiment. With U. sonchi the highest estimates of F₂ heritability were found in ‘Charan x ‘Avoncrisp’ (0.51) and ‘Charan’ x ‘Chou de Naples' (0.48). In the cross ‘Charan’ x ‘Marbello’ (PR x PR) no significant segregation for resistance to M. euphorbiae was found, indicating that these cultivars may have the same genetic constitution for resistance to M. euphorbiae.‘Charan’ has additional genes for resistance to U. sonchi, that are not, or only weakly linked to the gene(s) for resistance to M. euphorbiae. The heritability estimates for the partial resistance to M. euphorbiae and U. sonchi indicate that it is possible to effectively select for these traits in plant breeding programmes.     

Mapping of A1 conferring resistance to the aphid Amphorophora idaei and dw (dwarfing habit) in red raspberry (Rubus idaeus L.) using AFLP and microsatellite markers

Background  

Raspberry breeding programmes worldwide aim to produce improved cultivars to satisfy market demands and within these programmes there are many targets, including increased fruit quality, yield and season, and improved pest and disease resistance and plant habit. The large raspberry aphid, Amphorophora idaei, transmits four viruses and vector resistance is an objective in raspberry breeding. The development of molecular tools that discriminate between aphid resistance genes from different sources will allow the pyramiding of such genes and the development of raspberry varieties with superior pest resistance. We have raised a red raspberry (Rubus idaeus) F₁ progeny from the cross 'Malling Jewel' × 'Malling Orion' (MJ × MO), which segregates for resistance to biotype 1 of the aphid Amphorophora idaei and for a second phenotypic trait, dwarf habit. These traits are controlled by single genes, denoted (A ₁) and (dw) respectively.     

Identification,characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs

Raspberry breeding is a long, slow process in this highly heterozygous out-breeder. Selections for complex traits like fruit quality are broad-based and few simple methodologies and resources are available for glasshouse and field screening for key pest and disease resistances. Additionally, the timescale for selection of favourable agronomic traits requires data from different seasons and environmental locations before any breeder selection can proceed to finished cultivar. Genetic linkage mapping offers the possibility of a more knowledge-based approach to breeding through linking favourable traits to markers and candidate genes on genetic linkage maps. To further increase the usefulness of existing maps, a set of 25 polymorphic SSRs derived from expressed sequences (EST-SSRs) have been developed in red raspberry (Rubus idaeus). Two different types of expressed sequences were targeted. One type was derived from a root cDNA library as a first step in assessing sequences which may be involved in root vigour and root rot disease resistance and the second type were ESTs from a gene discovery project examining bud dormancy release and seasonality. The SSRs detect between 2 and 4 alleles per locus and were assigned to linkage groups on the existing ‘Glen Moy’ × ‘Latham’ map following genotyping of 188 progeny and examined for association with previously mapped QTL. The loci were also tested on a diverse range of Rubus species to determine transferability and usefulness for germplasm diversity studies and the introgression of favourable alleles.     

Further studies on resistance to Leptosphaeria coniothyrium in the red raspberry and related species

Rubus pileatus and its F₁ hybrids with raspberry (R. idaeus) were resistant to cane blight (Leptosphaeriu conioth-yriurn), but little resistance was obtained in subsequent backcross generations apart from a hybrid identified in the second backcross. Two hybrids from backcrossing R. coreanus to raspberry also showed resistance. R. pileatus and its F, hybrids produced hard growth, unlike that of raspberries, which may have been associated with a form of resistance that could not easily be transferred to commercial raspberry cultivars. Some of the genotypes used as parents showed intermediate levels of resistance and it is possible that the highly resistant genotype identified in the second backcross arose from a recombination of genes for resistance. Plants with pubescent canes (gene H) were up to 20% more resistant to mycelial inoculation than those with non-pubescent canes (gene h), and the percentage of machine-harvester inflicted wounds with disease symptoms that resulted from natural infection was also less in genotypes with pubescent canes. Many genotypes with intermediate levels of resistance suffered only limited damage from mycelial inoculation and so there are good prospects for breeding cultivars with an effective resistance, despite the limited value of R. pileatus as a donor species.     

Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection

Sugarcane is an economically important crop for both food and biofuel industries. Marker-assisted breeding in sugarcane is becoming a reality with the recent development and deployment of markers linked with disease resistance genes. Large linkage disequilibrium in sugarcane makes genome-wide association studies (GWAS) a better alternative to biparental mapping to identify markers associated with agronomic traits. GWAS was conducted on a Louisiana core collection to identify marker-trait associations (MTA) for 11 cane yield and sucrose traits using single nucleotide polymorphism (SNP) and insertion-deletion (Indel) markers. Significant (P < .05) MTAs were identified for all traits where the top ranked markers explained up to 15% of the total phenotypic variation. High correlations (0.732 to 0.999) were observed between sucrose traits and 56 markers were found consistent across multiple traits. These markers following validation in more diverse populations could be used in marker-assisted selection of clones in sugarcane breeding program in Louisiana and elsewhere.     

Genetic and environmental variations in quantitative characters in fishes: a comparative analysis of monoclonal triploid and bisexual tetraploid spined loaches (<Emphasis Type="Italic">Cobitis</Emphasis>, Cobitidae)

The heritability estimates of 25 external morphometric characters and 23 craniometric indices are obtained by use of variances in monoclonal all-female triploids and bisexual tetraploids of spined loaches (genus Cobitis, Cobitidae) collected from the same breeding biotope. Most of studied traits demonstrate low heritability confirming previous conclusion on the similarity between external morphometric characters and craniological indices in relative effects of genetic and environmental components in their total phenotypic variation. Low heritability estimates in most of external morphological traits correspond to their low diagnostic value in Cobitis species. As a whole, in spite of certain deviations, studies on clonal forms do not refute the concept on higher heritability estimates in diagnostically significant traits in comparison with traits without diagnostic values in the same taxonomic group. Low heritability in most morphometric traits more probably is resulted from their low additive genetic variation caused by strong selection of evolutionary developed specific body shape in spined loaches, because strong selection should reduce the genetic variance in body proportions to minimal size. Sex differences observed in heritability estimates should be interpreted as a result of linkage of several additive genes controlling these traits to sex chromosomes. A few characters demonstrating high heritability estimates up to 0.492–0.580 are of great interest for taxonomic and phylogenetic studies in genus Cobitis and related taxa.     

Animal Board Invited Review: Meta-analysis of genetic parameters for resilience and efficiency traits in goats and sheep

Genetic selection focused purely on production traits has proven very successful in improving the productive performance of livestock. However, heightened environmental and infectious disease challenges have raised the need to also improve the resilience of animals to such external stressors, as well as their efficiency in utilising available resources. A better understanding of the relationship between efficiency and production and health traits is needed to properly account for it in breeding programmes and to produce animals that can maintain high production performance in a range of environmental conditions with minimal environmental footprint. The aim of this study was to perform a meta-analysis of genetic parameters for production, efficiency and health traits in sheep and goats. The dataset comprised 963 estimates of heritability and 572 genetic correlations collated from 162 published studies. A threelevel meta-analysis model was fitted. Pooled heritability estimates for milk production traits ranged between 0.27 ± 0.03 and 0.48 ± 0.13 in dairy goats and between 0.21 ± 0.06 and 0.33 ± 0.07 in dairy sheep. In meat sheep, the heritability of efficiency traits ranged from 0.09 ± 0.02 (prolificacy) up to 0.32 ± 0.14 (residual feed intake). For health traits, pooled heritability was 0.07 ± 0.01 (faecal egg count) and 0.21 ± 0.01 (somatic cell score) in dairy goats and 0.14 ± 0.04 (faecal egg count) and 0.13 ± 0.02 (somatic cell score) in dairy sheep. In meat sheep, the heritability of disease resistance and survival traits ranged between 0.07 ± 0.02 (mastitis) and 0.50 ± 0.10 (breech strike). Pooled estimates of genetic correlations between resilience and efficiency traits in dairy goats were not significantly different from zero with the exception of somatic cell score and fat content (?0.19 ± 0.01). In dairy sheep, only the unfavourable genetic correlation between somatic cell score and protein content (0.12 ± 0.03) was statistically significant. In meat sheep only, the correlations between growth and faecal egg count (?0.28 ± 0.11) as well as between growth and dagginess (?0.33 ± 0.13) were statistically significant and favourable. Results of this meta-analysis provide evidence of genetic antagonism between production and health in dairy sheep and goats. This was not observed in meat sheep where most of the pooled estimates had high standard errors and were non-significant. Based on the obtained results, it seems feasible to simultaneously improve efficiency and health in addition to production by including the different types of traits in the breeding goal. However, a better understanding of potential trade-offs between these traits would be beneficial. Particularly, more studies focused on reproduction and resilience traits linked to the animal’s multi-trait response to challenges are required.     

An Effective Method to Identify Heritable Components from Multivariate Phenotypes

Multivariate phenotypes may be characterized collectively by a variety of low level traits, such as in the diagnosis of a disease that relies on multiple disease indicators. Such multivariate phenotypes are often used in genetic association studies. If highly heritable components of a multivariate phenotype can be identified, it can maximize the likelihood of finding genetic associations. Existing methods for phenotype refinement perform unsupervised cluster analysis on low-level traits and hence do not assess heritability. Existing heritable component analytics either cannot utilize general pedigrees or have to estimate the entire covariance matrix of low-level traits from limited samples, which leads to inaccurate estimates and is often computationally prohibitive. It is also difficult for these methods to exclude fixed effects from other covariates such as age, sex and race, in order to identify truly heritable components. We propose to search for a combination of low-level traits and directly maximize the heritability of this combined trait. A quadratic optimization problem is thus derived where the objective function is formulated by decomposing the traditional maximum likelihood method for estimating the heritability of a quantitative trait. The proposed approach can generate linearly-combined traits of high heritability that has been corrected for the fixed effects of covariates. The effectiveness of the proposed approach is demonstrated in simulations and by a case study of cocaine dependence. Our approach was computationally efficient and derived traits of higher heritability than those by other methods. Additional association analysis with the derived cocaine-use trait identified genetic markers that were replicated in an independent sample, further confirming the utility and advantage of the proposed approach.     

红松优树半同胞子代家系生长、结实及抗病虫能力的变异特征

以吉林省露水河宏伟种子园的551个优株29年生红松半同胞子代家系为材料,对其生长性状(树高、胸径、冠幅)、结实性状(连续7个结实年份的球果总数)和抗病虫能力进行调查,利用多性状综合评价的方法,结合生长、结实和抗病虫能力等6个性状,优选出优良家系和单株.结果表明: 各性状在不同家系间和区组间的差异均达到极显著水平;各性状的表型变异系数变化范围为13.9%～61.0%,极显著的差异与高的变异系数有利于优良家系的评价和选择;材积、结实量和抗病虫能力的家系遗传力(分别为0.47、0.52和0.48)均大于单株遗传力(分别为0.37、0.07和0.10);红松家系生长性状、结实性状和抗病虫能力之间呈极显著正相关关系.以5%的入选率初步选出28个优良家系,其材积、结实量和抗病虫能力的遗传增益分别为16.8%、71.4%和0.5%;以2%的入选率在优良家系中初步选出7个优良单株,其材积、结实量和抗病虫能力的遗传增益分别为66.8%、80.9%和0.7%.这些初选的优良家系和单株表现出明显优势,可指导无性系种子园去劣疏伐,并为高世代种子园的营建提供繁殖材料.     

Combining ability for the traits of stem branching and plant height in linseed lines

Combining ability for the traits of stem branching and plant height has been studied in ten pure lines of flax under complete and incomplete diallel crosses. High heritability of the traits "plant height", "the number of lateral stems" and "the number of lateral shoots" and essential role of genes with dominant effects of interaction in genetic control of the traits of stem branching and plant height have been shown. On the basis of combining ability indexes the ways for usage of certain genotypes and crossing combinations in flax breeding were defined. As a result of individual selection from hybrid combinations some new complexes of habit traits and agriculturally valuable plant characteristics were obtained.