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Onion (Allium cepa) is not highly tractable for development of molecular markers due to its large (16 gigabases per 1C) nuclear genome. Single nucleotide polymorphisms (SNPs) are useful for genetic characterization and marker-aided selection of onion because of codominance and common occurrence in elite germplasm. We completed genotyping by sequencing (GBS) to identify SNPs in onion using 46 [F.sub.2] plants, parents of the [F.sub.2] plants (Ailsa Craig 43 and Brigham Yellow Globe 15-23), two doubled haploid (DH) lines (DH2107 and DH2110), and plants from 94 accessions in the USDA National Plant Germplasm System (NPGS). SNPs were called using the TASSEL 3.0 Universal Network Enabled Analysis (UNEAK) bioinformatics pipeline. Sequences from the [F.sub.2] and DH plants were used to construct a pseudo-reference genome against which genotypes from all accessions were scored. Quality filters were used to identify a set of 284 high quality SNPs, which were placed onto an existing genetic map for the F2 family. Accessions showed a moderate level of diversity (mean [H.sub.e] = 0.341) and evidence of inbreeding (mean F = 0.592). GBS is promising for SNP discovery in onion, although lack of a reference genome required extensive custom scripts for bioinformatics analyses to identify high quality markers. Key words: genetic map, doubled haploid lines, genotyping by sequencing, germplasm, single nucleotide polymorphism, population genetics. L'oignon (Allium cepa) ne se prete pas facilement au developpement de marqueurs moleculaires en raison de la grande taille de son genome nucleaire (16 gigabases pour 1C). Les polymorphismes mononucleotidiques (SNP) sont utiles pour la caracterisation genetique et la selection assistee chez l'oignon en raison de leur codominance et de leur abondance au sein du materiel ameliore. Les auteurs ont realise un genotypage par sequencage (GBS) pour identifier des SNP chez l'oignon au moyen de 46 plantes [F.sub.2], des parents des [F.sub.2] (Ailsa Craig 43 et Brigham Yellow Globe 15-23), de deux lignees haplo'ides doublees (DH; DH2107 et DH2110), ainsi que de 94 accessions du USDA National Plant Germplasm System (NPGS). Les SNP ont ete appeles en utilisant le pipeline bioinformatique TASSEL 3.0 UNEAK ('Universal Network Enabled Analysis'). Les sequences des plantes [F.sub.2] et DH ont ete employees pour construire un pseudo-genome de reference a l'aide duquel les genotypes ont ete appeles pour toutes les accessions. Des filtres de qualite ont ete identifies un ensemble de 284 SNP de haute qualite, lesquels ont ete positionnes sur une carte genetique existante pour la famille F2. Les accessions presentaient un niveau modere de diversite genetique (indice [H.sub.e] moyen = 0,341) et des evidences de consanguinite (indice F moyen = 0,592). Le GBS se montre prometteur pour l'identification de SNP chez l'oignon, bien que l'absence d'un genome de reference necessite de nombreux scripts maison pour l'analyse bioinformatique afin d'identifier des SNP de haute qualite. [Traduit par la Redaction] Mots-cles: carte genetique, lignees haplo'ides doublees, genotypage par sequencage, germoplasme, polymorphisme mononucleotidique, genetique des populations., Introduction Bulb onion (Allium cepa L.) is a widely produced and highly valuable vegetable crop (FAO 2018). Onion cultivars have been selected for bulbing and flowering across diverse day-length and [...]

Seed weight in lucerne (Medicago sativa) may affect subsequent seedling vigour and stand establishment. A landrace of lucerne (Oman 2) from Oman has a 100-seed weight over 60% larger than the largest seeded parent used in previous studies. Crosses were made between Oman 2 and the smaller-seeded cultivar Titan 9, and segregating families were produced for genetic analysis and measurement of response to selection for seed size. There were significant differences in 100-seed weights between the parents (Oman 2 and Titan 9) and subsequent families. Regression of 100-seed weights of F2 families versus F1 parents was highly significant (p < 0.001), as well as 100-seed weights of the F3 families versus F1 parents. Analysis of diallel crossing among large and small-seeded F1 plants revealed highly significant general (GCAs) and specific (SCAs) combining abilities, as well as highly significant reciprocals. The GCA effect was much greater than the SCA effect with a GCA/SCA ratio of 15.9. This large ratio agrees with the significant regression coefficients and indicates that 100-seed weight in lucerne has high heritability. The significance of reciprocals was due to a large maternal effect in which large-seeded maternal parents produced progenies with significantly larger seeds relative to small-seeded parents. These results indicate that large-seeded plants should be used as the maternal parents in crosses and for recurrent selection to increase the seed size of progenies. [ABSTRACT FROM AUTHOR]

Chromosome 5 of onion carries major quantitative trait loci (QTL) that control dry-matter content, pungency and storability of bulbs, amounts and types of epicuticular waxes, and resistances to abiotic factors, all of which are of interest to breeders. SNPs, SSRs, and RFLPs in expressed regions of the onion genome have been genetically mapped, and we used these clones and sequences from the NCBI database to develop DNA probes for in situ hybridization to integrate the genetic and physical maps of onion chromosome 5. We produced genomic amplicons from expressed regions of the onion genome that carried both exons and introns in order to increase the hybridization specificity of the probes and to enlarge the target DNA sizes. Tyramide-FISH technique was used to increase the detection sensitivity of relatively short target DNA regions, which range from 950 to 2100 bp. Through the integration of genetic and chromosomal maps, we were able to estimate the distribution of recombination events along onion chromosome 5. We demonstrated the efficiency of chromosomal in situ mapping of exon-intron genomic clones for the extremely large genome of onion. Keywords: Allium cepa, Tyramide-FISH, chromosome, EST, recombination. Resume : Le chromosome 5 de l'oignon porte plusieurs locus de caractere quantitatif (QTL) majeurs qui sont d'interet pour les selectionneurs dont la teneur en matiere seche, le gout releve et la duree d'entreposage des bulbes, la teneur et les types de cires epicuticulaires, ainsi que des resistances a plusieurs stress abiotiques. Des marqueurs SNP, SSR et RFLP situes dans les regions exprimees du genome de l'oignon ont ete positionnes sur la carte genetique. Les auteurs ont employe ces clones ou ces sequences tirees de la base de donnees NCBI comme sondes pour realiser des hybridations in situ afin d'integrer les cartes genetiques et physiques du chromosome 5 chez l'oignon. Les auteurs ont produit des amplicons genomiques contenant a la fois des exons et des introns afin d'augmenter la specificite de l'hybridation des sondes et pour accroitre la taille des cibles. La technique Tyramide-FISH a ete employee afin d'augmenter la sensibilite de detection des regions ciblees puisque celles-ci etaient relativement courtes, allant de 950 a 2100 pb. L'integration des cartes genetique et chromosomique a permis d'estimer la distribution des evenements de recombinaison tout au long du chromosome 5. Les auteurs on demontre l'efficience de la cartographie chromosomique in situ a l'aide de sondes genomiques exoniquesintroniques chez le tres grand genome de l'oignon. [Traduit par la Redaction] Mots-cles : Allium cepa, Tyramide-FISH, chromosome, EST, recombinaison., Introduction Integrated genetic maps use data from classical and molecular genetics and genomics. Integrated recombination and physical maps have been created for several important crops. Different approaches used for developing [...]

Male-sterile (S) cytoplasm of onion is an alien cytoplasm introgressed into onion in antiquity and is widely used for hybrid seed production. Owing to the biennial generation time of onion, classical crossing takes at least 4 years to classify cytoplasms as S or normal (N) male-fertile. Molecular markers in the organellar DNAs that distinguish N and S cytoplasms are useful to reduce the time required to classify onion cytoplasms. In this research, we completed next-generation sequencing of the chloroplast DNAs of N- and S-cytoplasmic onions; we assembled and annotated the genomes in addition to identifying polymorphisms that distinguish these cytoplasms. The sizes (153 538 and 153 355 base pairs) and GC contents (36.8%) were very similar for the chloroplast DNAs of N and S cytoplasms, respectively, as expected given their close phylogenetic relationship. The size difference was primarily due to small indels in intergenic regions and a deletion in the accD gene of N-cytoplasmic onion. The structures of the onion chloroplast DNAs were similar to those of most land plants with large and small single copy regions separated by inverted repeats. Twenty-eight single nucleotide polymorphisms, two polymorphic restriction-enzyme sites, and one indel distributed across 20 chloroplast genes in the large and small single copy regions were selected and validated using diverse onion populations previously classified as N or S cytoplasmic using restriction fragment length polymorphisms. Although cytoplasmic male sterility is likely associated with the mitochondrial DNA, maternal transmission of the mitochondrial and chloroplast DNAs allows for polymorphisms in either genome to be useful for classifying onion cytoplasms to aid the development of hybrid onion cultivars. Key words: Allium cepa, cytoplasmic male sterility, molecular markers. Le cytoplasme male sterile (S) de l'oignon provient de l'introgression d'un cytoplasme etranger dans l'antiquite et il est largement employe pour la production de semence hybride. En raison de la nature bisannuelle de l'oignon, un schema classique de croisement necessitera au moins 4 ans pour classifier un cytoplasme comme etant du type S ou N (pour normal et male fertile). Des marqueurs moleculaires provenant des organites et permettant de distinguer les cytoplasmes N et S permettent de reduire le temps requis pour classifier les cytoplasmes. Dans ce travail, les auteurs ont realise un sequen^age complet des ADN chloroplastiques chez les oignons a cytoplasme N et S; ils ont assemble et annote les genomes en plus d'identifier des polymorphismes qui distinguent ces cytoplasmes. La taille du genome chloroplastique (153 536 vs. 153 355 pb) et son contenu en GC (36,8 %) etaient tres semblables chez les deux types de cytoplasmes, tel qu'attendu en raison de leur proximite phylogenetique. La difference de taille provenait principalement de petits indels dans les regions intergeniques et d'une deletion au sein du gene accD chez l'oignon a cytoplasme N. La structure du genome chloroplastique etait semblable a celle retrouvee chez la plupart des plantes terrestres avec une grande et une petite region a simple copie, lesquelles sont separees d'une region repetee inversee. Les auteurs ont choisi vingt-huit polymorphismes mononucleotidiques, deux polymorphismes de site de restriction, et un indel repartis parmi les 20 genes chloroplastiques dans une grande et une petite region a simple copie. Ces marqueurs ont ete valides au sein de diverses populations d'oignons deja classifiees comme etant NouSia l'aide de polymorphismes de fragments de restriction. Bien que la sterilite male cytoplasmique soit vraisemblablement associee a l'ADN mitochondrial, la transmission maternelle des ADN mitochondriaux et chloroplastiques rendent utiles des polymorphismes observes dans l'un ou l'autre genome pour la classiication des cytoplasmes chez l'oignon et pour aider au developpement de cultivars hybrides. [Traduit par la Redaction] Mots-cles: Allium cepa, sterilite male cytoplasmique, marqueurs moleculaires., Introduction Onion (Allium cepa L.) is a member of the family Alliaceae in the order Asparagales, a large monophyletic group within the monocots. Within the Asparagales, the Alliaceae has been [...]

Cucumber (Cucumis sativus) has one of the largest mitochondrial genomes known among all eukaryotes, due in part to the accumulation of short 20 to 60 by repetitive DNA motifs. Recombination among these repetitive DNAs produces rearrangements affecting organization and expression of mitochondrial genes. To more efficiently identify rearrangements in the cucumber mitochondrial DNA, we built two nonoverlapping 800 and 220 kb BAC contigs and assigned major mitochondrial genes to these BACs. Polymorphism carried on the largest BAC contig was used to confirm paternal transmission. Mitochondrial genes were distributed across BACs and physically distant, although occasional clustering was observed. Introns in the nad1, nad4, and nad7 genes were larger than those reported in other plants, due in part to accumulation of short repetitive DNAs and indicating that increased intron sizes contributed to mitochondrial genome expansion in cucumber. Mitochondrial genes atp6 and atp9 are physically close to each other and cotranscribed. These physical contigs will be useful for eventual sequencing of the cucumber mitochondrial DNA, which can be exploited to more efficiently screen for unique rearrangements affecting mitochondrial gene expression. Key words: Cucumis sativus, bacterial artificial chromosome, FPC, organellar genome. Le concombre (Cucumis sativus) possede fun des plus grands genomms mitochondriaux chez les eucaryotes en raison, en partie, dune accumulation de courts motifs repetitifs d'ADN de 20 a 60 pb. La recombinaison entre ces sequences repetees produit des rearrangements qui affectent l'organisation et (expression des genes mitochondriaux. Afin d'identifier plus efficacement les rearrangements au sein de l'ADN mitochondrial du concombre, les auteurs ont assemble deux contigs totalisant 800 et 220 kb de clones BAC sans chevauchements et ont assigne les principaux genes mitochondriaux a ces BAC. Le polymorphisme present sur le plus grand contig BAC a ete employe pour en confirmer la transmission paternelle. Les genes mitochondriaux etaient distrbbues sur les BAC et separes dune grande distance physique, bien que quelques groupements aient ete observes. Les Introns dens les genes nad1, nad4 et nad7 etaient plus grands que leurs homologues chez d'autres plantes en raison, en partie, de l'accumulation de courts motifs repetes d'ADN, ce qui indique que des Introns de taille accrue ont contribue a l'expansion du genome mitochondrial chez le concombre. Les genes mitochondriaux atp6 et atp9 sont physiquement proches l'un de l'autre et co-transcrits. Ces contigs physiques seront utiles en vue du sequencage de l'ADN mitochondrial du concombre qu'il serait possible d'exploiter pour identifier efficacement des rearrangements uniques affectent (expression de genes mitochondriaux. Mots-cles : Cucumis sativus, chromosome bacterien artifcial, FBC, genome d'organite. [Traduit par la Redaction], Introduction Plant mitochondrial genomes are larger than those of most other eukaryotes, even though the numbers of mitochondrially encoded genes are similar (Unseld et al. 1997; Kubo et al. 2000; [...]