Mapping of yield, yield stability, yield adaptability and other traits in barley using linkage disequilibrium mapping and linkage analysis

Plants is mostly done through linkage analysis. A segregating mapping population Identification and mappping of Quantitative Trait Loci (QTLs) in is created from a bi-parental cross and linkages between trait values and mapped markers reveal the positions ofQTLs. Inthisstudyweexploredlinkagedisequilibrium(LD)mappingof traits in a set of modernbarleycultivars. LDbetweenmolecularmarkerswasfoundup to a distance of 10 centimorgan,whichislargecomparedtootherspecies.Thelarge distancemightbeinducedby LDincreasingfactorssuchasinbreedingandthefactthatthepopulationismostlikelybasedon arathersmallset offoundinggenotypes. Associationsbetweenmarkersandtraitswerefoundforyield,yieldstability,leafrustresistance(LR),barleyyellowdwarfvirusresistance(BYD), plantheight,anddaystoheading.Trait-associatedmarkersfromLDanalysiswerelocatedinregionswherealreadyQTLsforthetraitconsideredhadbeenreportedfromstudiesbasedonbi-parentalcrosses. In addition, newQTLswerefoundforyield,yieldstability, LRandBYD.WeexpectthatLDmappingwillbecomeavaluableextension toconventionalQTLanalysisin plantbreeding.Specialattentionwasgivento traitsdescribinggenotype×environmentinteractions.Statisticalmodelswereusedtodefinemeasuresforyieldadaptabilityandyieldstabilitywithoutincludingenvironmentalfactorsdirectlyinthemodels.Adaptabilitywasdefinedastheresponsivenessofthegenotypetotheenvironment,andstabilitywasdefinedastheunexplaineddeviationfromthestatisticalmodel. LDmappinginbarleycultivarsresultedinmarker-traitassociations foryieldstability. In addition, linkage analyses in fourdoubled-haploidpopulationsresultedindetectionofmanyQTLsforadaptability, butonlya single QTL forstability.Weconcludedthatadaptabilitymeasuresweregeneticallybetterdefinedthanstabilitymeasuresandthatselectionforadaptabilityshouldbepossible

Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars

A set of 148 modern spring barley cultivars was explored for the extent of linkage disequilibrium (LD) between genes governing traits and nearby marker alleles. Associations of agronomically relevant traits (days to heading, plant height), resistance traits (leaf rust, barley yellow dwarf virus (BYD)), and morphological traits (rachilla hair length, lodicule size) with AFLP markers and SSR markers were found. Known major genes and QTLs were confirmed, but also new putative QTLs were found. The LD mapping clearly indicated the common occurrence of Rph3, a gene for hypersensitivity resistance against Puccinia hordei, and also confirmed the QTL Rphq2 for prolonging latency period of P. hordei in seedlings. We also found strong indication for a hitherto not reported gene for resistance or tolerance to BYD on chromosome 2, linked to SSR marker HVM054. Our conclusion is that LD mapping is a valuable additional tool in the search for applicable marker associations with major genes and QTLs

Integration of retrotransposons-based markers in a linkage map of barley

A deeper understanding of random markers is important if they are to be employed for a range of objectives. The sequence specific amplified polymorphism (S-SAP) technique is a powerful genetic analysis tool which exploits the high copy number of retrotransposon long terminal repeats (LTRs) in the plant genome. The distribution and inheritance of S-SAP bands in the barley genome was studied using the Steptoe · Morex (S · M) double haploid (DH) population. Six S-SAP primer combinations generated 98 polymorphic bands, and map positions were assigned to all but one band. Eight putative co-dominant loci were detected, representing 16 of the mapped markers. Thus at least 81 of the mapped S-SAP loci were dominant. The markers were distributed along all of the seven chromosomes and a tendency to cluster was observed. The distribution of S-SAP markers over the barley genome concurred with the knowledge of the high copy number of retrotransposons in plants. This experiment has demonstrated the potential for the S-SAP technique to be applied in a range of analyses such as genetic fingerprinting, marker assisted breeding, biodiversity assessment and phylogenetic analyses