Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time

Domestication drastically changed crop genomes,fixing alleles of interest and creating different genetic populations.Genome-wide association studies(GWASs)are a powerful tool to detect these alleles of interest(and so QTLs).In this study,we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions.Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups,all formed by accessions with a common origin.One of these groups was formed exclusively by Spanish accessions,while the rest were mainly formed by accessions from China,Italy,France,and the USA.These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases:Asiatic,Mediterranean,Californian,and southern hemisphere.In total,we found 13 independent QTLs for nut weight,crack-out percentage,double kernels percentage,and blooming time.Of the 13 QTLs found,only one had an additive effect.Through candidate gene analysis,we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage,Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage,and Prudul26A000954 as a candidate gene for the QTL found in blooming time.Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.

Prunus genetics and applications after de novo genome sequencing:achievements and prospects

Prior to the availability of whole-genome sequences,our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources.With public release of the peach genome and others that followed,significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued.In this review,we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences.Within the structural and evolutionary contexts,we summarize:(1)the current status of Prunus whole-genome sequences;(2)preliminary and ongoing work on the sequence structure and diversity of the genomes;(3)the analyses of Prunus genome evolution driven by natural and man-made selection;and(4)provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide.Functionally,we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits.These include phenology,fruit quality,allergens,disease resistance,tree architecture,and self-incompatibility.Translationally,we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement.Finally,we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae(GDR)and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.

Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes.However,in almond,little is known about the genetic variability in current breeding stocks,although several cases of inbreeding depression have been reported.To gain insights into the genetic structure in modern breeding programs worldwide,marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed.Inbreeding coefficients,pairwise relatedness,and genetic contribution were calculated for these genotypes.The results reveal two mainstream breeding lines based on three cultivars:“Tuono”,“Cristomorto”,and“Nonpareil”.Descendants from“Tuono”or“Cristomorto”number 76(sharing 34 descendants),while“Nonpareil”has 71 descendants.The mean inbreeding coefficient of the analyzed genotypes was 0.041,with 14 genotypes presenting a high inbreeding coefficient,over 0.250.Breeding programs from France,the USA,and Spain showed inbreeding coefficients of 0.075,0.070,and 0.037,respectively.According to their genetic contribution,modern cultivars from Israel,France,the USA,Spain,and Australia trace back to a maximum of six main founding genotypes.Among the group of 65 genotypes carrying the S f allele for self-compatibility,the mean relatedness coefficient was 0.125,with“Tuono”as the main founding genotype(24.7%of total genetic contribution).The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide.Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.

High-density mapping suggests cytoplasmic male sterility with two restorer genes in almond×peach progenies

Peach(Prunus persica)and almond(Prunus dulcis)are two sexually compatible species that produce fertile offspring.Almond,a highly polymorphic species,is a potential source of new genes for peach that has a strongly eroded gene pool.Here we describe the genetics of a male sterile phenotype that segregated in two almond(‘Texas’)×peach(‘Earlygold’)progenies:an F2(T×E)and a backcross one(T1E)to the‘Earlygold’parent.High-density maps were developed using a 9k peach SNP chip and 135 simple-sequence repeats.Three highly syntenic and collinear maps were obtained:one for the F2(T×E)and two for the backcross,T1E(for the hybrid)and E(for‘Earlygold’).A major reduction of recombination was observed in the interspecific maps(T×E and T1E)compared to the intraspecific parent(E).The E map also had extensive monomorphic genomic regions suggesting the presence of large DNA fragments identical by descent.Our data for the male sterility character were consistent with the existence of cytoplasmic male sterility,where individuals having the almond cytoplasm required the almond allele in at least one of two independent restorer genes,Rf1 and Rf2,to be fertile.The restorer genes were located in a 3.4 Mbp fragment of linkage group 2(Rf1)and 1.4 Mbp of linkage group 6(Rf2).Both fragments contained several genes coding for pentatricopeptide proteins,demonstrated to be responsible for restoring fertility in other species.The implications of these results for using almond as a source of novel variability in peach are discussed.

Fine mapping and identification of candidate genes for the peach powdery mildew resistance gene Vr3

Powdery mildew is one of the major diseases of peach(Prunus persica),caused by the ascomycete Podosphaera pannosa.Currently,it is controlled through calendar-based fungicide treatments starting at petal fall,but an alternative is to develop resistant peach varieties.Previous studies mapped a resistance gene(Vr3)in interspecific populations between almond(‘Texas’)and peach(‘Earlygold’).To obtain molecular markers highly linked to Vr3 and to reduce the number of candidate genes,we fine-mapped Vr3 to a genomic region of 270 kb with 27 annotated genes.To find evidence supporting one of these positional candidate genes as being responsible of Vr3,we analyzed the polymorphisms of the resequences of both parents and used near-isogenic lines(NILs)for expression analysis of the positional candidate genes in symptomatic or asymptomatic leaves.Genes differentially expressed between resistant and susceptible individuals were annotated as a Disease Resistance Protein RGA2(Prupe2G111700)or an Eceriferum 1 protein involved in epicuticular wax biosynthesis(Prupe2G112800).Only Prupe2G111700 contained a variant predicted to have a disruptive effect on the encoded protein,and was overexpressed in both heterozygous and homozygous individuals containing the Vr3 almond allele,compared with susceptible individuals.This information was also useful to identify and validate molecular markers tightly linked and flanking Vr3.In addition,the NILs used in this work will facilitate the introgression of this gene into peach elite materials,alone or pyramided with other known resistance genes such as peach powdery mildew resistance gene Vr2.