Accuracy and responses of genomic selection on key traits in apple breeding

The application of genomic selection in fruit tree crops is expected to enhance breeding eficiency by increasing prediction accuracy,increasing selection intensity and decreasing generation interval.The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits.The training population comprised 977 individuals derived from 20 pedigreed fllsib families.Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an llumina 20K SNP array.From these data,a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application fllsib families.The application families had genotypes at 364 SNPs from a dedicated 512 SNP array,and these genotypic data were extended to the high-density level by imputation.These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values.Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19.The accuracies were strongly affected by the phenotypic distribution and heritability of traits.In the largest family,significant selection response was observed for traits with high heritability and symmetric phenotypic distribution.Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability.Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population.The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.

High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array

Dense genetic maps create a base for QTL analysis of important traits and future implementation of marker-assisted breeding.In tetraploid rose,the existing linkage maps include<300 markers to cover 28 linkage groups(4 homologous sets of 7 chromosomes).Here we used the 68k WagRhSNP Axiom single-nucleotide polymorphism(SNP)array for rose,in combination with SNP dosage calling at the tetraploid level,to genotype offspring from the garden rose cultivar‘Red New Dawn’.The offspring proved to be not from a single bi-parental cross.In rose breeding,crosses with unintended parents occur regularly.We developed a strategy to separate progeny into putative populations,even while one of the parents was unknown,using principle component analysis on pairwise genetic distances based on sets of selected SNP markers that were homozygous,and therefore uninformative for one parent.One of the inferred populations was consistent with self-fertilization of‘Red New Dawn’.Subsequently,linkage maps were generated for a bi-parental and a self-pollinated population with‘Red New Dawn’as the common maternal parent.The densest map,for the selfed parent,had 1929 SNP markers on 25 linkage groups,covering 1765.5 cM at an average marker distance of 0.9 cM.Synteny with the strawberry(Fragaria vesca)genome was extensive.Rose ICM1 corresponded to F.vesca pseudochromosome 7(Fv7),ICM4 to Fv4,ICM5 to Fv3,ICM6 to Fv2 and ICM7 to Fv5.Rose ICM2 corresponded to parts of F.vesca pseudochromosomes 1 and 6,whereas ICM3 is syntenic to the remainder of Fv6.

Knockdown of MLO genes reduces susceptibility to powdery mildew in grapevine

Erysiphe necator is the causal agent of powdery mildew(PM),one of the most destructive diseases of grapevine.PM is controlled by sulfur-based and synthetic fungicides,which every year are dispersed into the environment.This is why PM-resistant varieties should become a priority for sustainable grapevine and wine production.PM resistance can be achieved in other crops by knocking out susceptibility S-genes,such as those residing at genetic loci known as MLO(Mildew Locus O).All MLO S-genes of dicots belong to the phylogenetic clade V,including grapevine genes VvMLO7,11 and 13,which are upregulated during PM infection,and VvMLO6,which is not upregulated.Before adopting a gene-editing approach to knockout candidate S-genes,the evidence that loss of function of MLO genes can reduce PM susceptibility is necessary.This paper reports the knockdown through RNA interference of VvMLO6,7,11 and 13.The knockdown of VvMLO6,11 and 13 did not decrease PM severity,whereas the knockdown of VvMLO7 in combination with VvMLO6 and VvMLO11 reduced PM severity up to 77%.The knockdown of VvMLO7 and VvMLO6 seemed to be important for PM resistance,whereas a role for VvMLO11 does not seem likely.Cell wall appositions(papillae)were present in both resistant and susceptible lines in response to PM attack.Thirteen genes involved in defense were less upregulated in infected mlo plants,highlighting the early mlo-dependent disruption of PM invasion.

Transcriptional responses of Brassica nigra to feeding by specialist insects of different feeding guilds

Plants show phenotypic changes when challenged with herbivorous insects. The mechanisms underlying these changes include the activation of transcriptional responses, which are dependent on the attacking insect. Most transcriptomic studies on crucifer-insect interactions have focused on the model plant Arabidopsis thaliana, a species that faces low herbivore pressure in nature. Here, we study the transcriptional responses of plants from a wild black mustard （Brassica nigra） population to herbivores of different feeding guilds using an A. thaliana-based whole-genome microarray that has previously been shown to be suitable for transcriptomic analyses in Brassica. Transcriptional responses of B. nigra after infestation with either Pieris rapae caterpillars or Brevicoryne brassicae aphids are analyzed and compared. Additionally, the insect-induced expression changes of some individual genes are analyzed through quantitative real-time polymerase chain reaction. The results show that feeding by both insect species results in the accumulation of transcripts encoding proteins involved in the detoxification of reactive oxygen species, defensive proteins and glucosinolates and this is correlated with experimental evidence in the literature on such biochemical effects. Although genes encoding proteins involved in similar processes are regulated by both insects, there was little overlap in the induction or repression of individual genes. Furthermore, P. rapae and B. brassicae seem to affect different phytohormone signaling pathways. In conclusion, our results indicate that B. nigra activates several defense-related genes in response to P rapae or B. brassicae feeding, but that the response is dependent on the attacking insect species.

The Bemisia tabaci species complex： Additions from different parts of the world

Bemisia tabaci is one of the most threatening pests in many crops. We sequenced part of the mitochondrial cytochrome oxidase I gene from fifty whitefly populations collected in Indonesia, Thailand, India and China. Nineteen unique sequences （haplotypes） of the cytochrome oxidase I were identified in these populations. They were combined with sequences available in databases, resulting in a total of 407 haplotypes and analyzed together with nine outgroup accessions. A phylogenetic tree was calculated using the maximum likelihood method. The tree showed that all groups that were found in previous studies were also present in our study. Additionally, seven new groups were identified based on the new haplotypes. Most B. tabaci haplotypes grouped based on their geographical origin. Two groups were found to have a worldwide distribution. Our results indicate that our knowledge on the species complex around B. tabaci is still far from complete.

A potato late blight resistance gene protects against multiple Phytophthora species by recognizing a broadly conserved RXLR-WY effector

Species of the genus Phytophthora,the plant killer,cause disease and reduce yields in many crop plants.Although many Resistance to Phytophthora infestans(Rpi)genes effective against potato late blight have been cloned,few have been cloned against other Phytophthora species.Most Rpi genes encode nucleotide-binding domain,leucine-rich repeat-containing(NLR)immune receptor proteins that recognize RXLR(Arg-X-Leu-Arg)effectors.However,whether NLR proteins can recognize RXLR effectors from multiple Phytophthora species has rarely been investigated.Here,we identified a new RXLR-WY effector AVRamr3 from P.infestans that is recognized by Rpi-amr3 from a wild Solanaceae species Solanum americanum.Rpi-amr3 associates with AVRamr3 in planta.AVRamr3 is broadly conserved in many different Phytophthora species,and the recognition of AVRamr3 homologs by Rpi-amr3 activates resistance against multiple Phytophthora pathogens,including the tobacco black shank disease and cacao black pod disease pathogens P.parasitica and P.palmivora.Rpi-amr3 is thus the first characterized resistance gene that acts against P.parasitica or P.palmivora.These findings suggest a novel path to redeploy known R genes against different important plant pathogens.

Quantitative resistance against Bemisia tabaci in Solanum pennellii:Genetics and metabolomics

The whitefly Bemisia tabaci is a serious threat in tomato cultivation worldwide as all varieties grown today are highly susceptible to this devastating herbivorous insect.Many accessions of the tomato wild relative Solanum pennellii show a high resistance towards B. tabaci. A mapping approach was used to elucidate the genetic background of whiteflyresistance related traits and associated biochemical traits in this species. Minor quantitative trait loci（QTLs） for whitefly adult survival（AS） and oviposition rate（OR） were identified and some were confirmed in an F2BC1 population, where they showed increased percentages of explained variance（more than 30%）. Bulked segregant analyses on pools of whiteflyresistant and-susceptible F2 plants enabled the identification of metabolites that correlate either with resistance or susceptibility. Genetic mapping of these metabolites showed that a large number of them co-localize with whiteflyresistance QTLs. Some of these whitefly-resistance QTLs are hotspots for metabolite QTLs. Although a large number of metabolite QTLs correlated to whitefly resistance or susceptibility, most of them are yet unknown compounds and further studies are needed to identify the metabolic pathways and genes involved. The results indicate a direct genetic correlation between biochemical-based resistance characteristics and reduced whitefly incidence in S. pennellii.