Search

Anther culture (AC) is a valuable technique in rice breeding. However, the genetic mechanisms underlying anther culturability remain elusive, which has hindered its widespread adoption in rice breeding programs. During AC, microspores carrying favorable alleles for AC are selectively regenerated, leading to segregation distortion (SD) of chromosomal regions linked to these alleles in the doubled haploid (DH) population. Using the AC method, a DH population was generated from the japonica hybrid rice Shenyou 26. A genetic map consisting of 470 SNPs was constructed using this DH population, and SD analysis was performed at both the single- and two-locus levels to dissect the genetic basis underlying anther culturability. Five segregation distortion loci (SDLs) potentially linked to anther culturability were identified. Among these, SDL5 exhibited an overrepresentation of alleles from the female parent, while SDL1.1, SDL1.2, SDL2, and SDL7 displayed an overrepresentation of alleles from the male parent. Furthermore, six pairs of epistatic interactions (EPIs) that influenced two-locus SDs in the DH population were discovered. A cluster of genetic loci, associated with EPI-1, EPI-3, EPI-4, and EPI-5, overlapped with SDL1.1, indicating that the SDL1.1 locus may play a role in regulating anther culturability via both additive and epistatic mechanisms. These findings provide valuable insights into the genetic control of anther culturability in rice and lay the foundation for future research focused on identifying the causal genes associated with anther culturability. [ABSTRACT FROM AUTHOR]

Summary: Chinese perch, Siniperca chuatsi (Basilewsky), is one of the most commercially important cultured fishes in China. In the present study, a high‐density genetic linkage map of Chinese perch was constructed by genotyping‐by‐sequencing technique with an F1 mapping panel containing 190 progenies. A total of 2328 SNPs were assigned to 24 linkage groups (LGs), agreeing with the chromosome haploid number in this species (n = 24). The sex‐averaged map covered 97.9% of the Chinese perch genome, with the length of 1694.3 cM and a marker density of 0.7 cM/locus. The number of markers per LG ranged from 57 to 222, with a mean of 97. The length of LGs varied from 43.2 to 108.2 cM, with a mean size of 70.6 cM. The recombination rate of females was 1.5:1, which was higher than that of males. To better understand the distribution pattern of segregation distortion between the two sexes of Chinese perch, the skewed markers were retained and used to reconstruct the sex‐specific maps. The 16 segregation distortion regions were identified on 10 LGs of the female map, while 12 segregation distortion regions on eight LGs of the male map. Among these LGs, six LGs matched between the sex‐specific maps. This high‐density linkage map could provide a solid basis for identifying QTL associated with economically important traits, and for implementing marker‐assisted selection breeding of Chinese perch. [ABSTRACT FROM AUTHOR]

Segregation Distorter (SD) is a naturally occurring male meiotic drive system in Drosophila melanogaster, characterized by almost exclusive transmission of the SD chromosome owing to dysfunction of sperm receiving the SD+ homolog. Previous studies identified at least three closely linked loci on chromosome 2 required for distortion: Sd, the primary distorting gene; E(SD) (Enhancer of SD), which increases the strength of distortion; and Rsp (Responder), the apparent target of Sd. Strength of distortion is also influenced by linked upward modifiers including M(SD) (Modifier of SD) and St(SD) (Stabilizer of SD), and by various unlinked suppressors. Although Sd is known to encode a mutant RanGAP protein, none of the modifiers have been molecularly identified. This work focuses on the genetic and cytological characterization of a strong X-linked suppressor, Su(SD), capable of restoring Mendelian transmission in SD/SD+ males. Sd and its cohort of positive modifiers appear to act semiquantitatively in opposition to Su(SD) with distortion strength depending primarily on the total number of distorting elements rather than which particular elements are present. Su(SD) can also suppress male sterility observed in certain SD genotypes. To facilitate its eventual molecular identification, Su(SD) was localized by deletion mapping to polytene region 13C7-13E4. These studies highlight the polygenic nature of distortion and its dependence on a constellation of positive and negative modifiers, provide insight into the stability of Mendelian transmission in natural populations even when a drive system arises, and pave the way for molecular characterization of Su(SD) whose identity should reveal new information about the mechanism of distortion. [ABSTRACT FROM AUTHOR]

Hybridizations involving different species are often hindered because of incompatibility reactions. Although these reproductive barriers have been observed in many plant species, the underlying mechanisms remain to be comprehensively elucidated. In this study, we detected a hybridization barrier between apple (Malus × domestica) and pear (Pyrus spp.) belonging to different genera in the subtribe Malinae of the family Rosaceae. Pollination experiments revealed that Pyrus pyrifolia (Japanese pear) pollen is compatible with Malus pistils, whereas Pyrus communis (European pear) pollen is not. These results imply there is a distinct cross-(in)compatibility reaction occurring in Pyrus species. Based on the varying pollen tube behaviors among Pyrus species, genetic analysis was conducted to identify the genomic region responsible for the intergeneric barrier. Malus–Pyrus intergeneric hybrids were used to detect distorted segregation regions by combining genome sequencing and fine-scale genotyping data. We defined a single locus on chromosome 5, in which P. pyrifolia-derived alleles were exclusively inherited to the intergeneric hybrids from the Pyrus interspecific hybrid. Of the 235 genes in this genomic region, 80 exhibited a specific pollen-expression pattern, including genes involved in self-incompatibility reactions. These candidate genes are herein discussed regarding their possible functions related to reproductive isolation. [ABSTRACT FROM AUTHOR]

• Most sorghum domestication- and improvement-related traits were controlled by the QTLs with minor genetic effects. • One major QTL of plant height (ph1) was fine-mapped within a region of 24.5 kb on chromosome 1. • The variant of A1361T in the dw1 gene might originate from a same event not long time ago. • Parallel phenotypic changes across different species during domestication or improvement might share similar genetic basis. The genetic basis of domestication and improvement remains largely unknown in sorghum as a typical multiple-origins species. In this study, the F 2 and F 3 populations derived from a cross between Sorghum virgatum and domesticated sorghum were used to study the genetic architecture of domestication- and improvement-related traits. We found that human selection had greatly reshaped sorghum through the Quantitative Trait Loci (QTLs) with large genetic effects in the traits of harvest, plant architecture and grain taste including the reduction of shattering, few branches, short plant stature and the removal of polyphenols from seed. The expansion of seed width was selected to improve the yield through accumulating small-effect QTLs. Two major QTLs of plant height (QTI-ph1 and dw1) were narrowed down into 24.5-kilobase (kb) and 13.9-kb, respectively. DNA diversity analysis and association mapping of dw1 gene suggested the functional variant (A1361 T) might originate from the same event not long time ago. Our results supported that parallel phenotypic changes across different species during domestication and improvement might share the same genetic basis, QTL × QTL interactions might not play an important role in the reshaping of traits during sorghum domestication and improvement, and offered new views on transgressive segregation and segregation distortion. Our study greatly deepens our understandings of the genetic basis of sorghum domestication and improvement. [ABSTRACT FROM AUTHOR]

Background: The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. Results: We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species. Conclusions: GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS). [ABSTRACT FROM AUTHOR]

Catfish is the leading aquaculture species in the United States. The interspecific hybrid catfish produced by mating female channel catfish with male blue catfish outperform both of their parent species in a number of traits. However, mass production of the hybrids has been difficult because of reproductive isolation. Investigations of genome structure and organization of the hybrids provide insights into the genetic basis for maintenance of species divergence in the face of gene flow, thereby helping develop strategies for introgression and efficient production of the hybrids for aquaculture. In this study, we constructed a high-density genetic linkage map using the hybrid catfish system with the catfish 250K SNP array. A total of 26 238 SNPs were mapped to 29 linkage groups, with 12 776 unique marker positions. The linkage map spans approximately 3240 cM with an average intermarker distance of 0.25 cM. A fraction of markers (986 of 12 776) exhibited significant deviation from the expected Mendelian ratio of segregation, and they were clustered in major genomic blocks across 15 LGs, most notably LG9 and LG15. The distorted markers exhibited significant bias for maternal alleles among the backcross progenies, suggesting strong selection against the blue catfish alleles. The clustering of distorted markers within genomic blocks should lend insights into speciation as marked by incompatibilities between the two species. Such findings should also have profound implications for understanding the genomic evolution of closely related species as well as the introgression of hybrid production programs in aquaculture. [ABSTRACT FROM AUTHOR]

Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences., The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism ( SNP) array of 6000 markers evenly distributed along the E. grandis genome., The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy., This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome. [ABSTRACT FROM AUTHOR]

Abstract: In the study, we constructed a second generation genetic linkage map for silver carp (Hypophthalmichthys molitrix) using anonymous and EST-derived microsatellite markers in a mapping panel containing 156 “pseudo BC” progenies from two interspecific crosses between silver carp and bighead carp (Aristichthys nobilis). A total of 703 markers were ordered on 24 linkage groups (LGs) which are equal to chromosome numbers of the haploid genome of the species. The consensus map spanned 1561.1cM covering 93.1% of the silver carp genome with an average resolution of 2.2cM/locus. Length of LGs ranged from 42.1cM to 97.8cM (mean 65.0cM). Total number of markers on individual LG varied from 13 to 56 (mean 29.3). Estimated total length of the female map (1809.0cM) was 1.52 times longer than that of the male map (1188.5cM), and the recombination ratio between sexes (female vs. male) was 2.2, showing markedly higher recombination in the females. Percentage of distorted loci in the male map was obviously higher than that in the female map, and 5 segregation distortion regions were identified in the male linkage groups. This second generation genetic linkage map evidently extends previous genetic maps for silver carp, and provides a basis for such studies as quantitative trait locus mapping, comparative genomics and marker-assisted selection. [Copyright &y& Elsevier]

Background: Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. Results: Genotyping by Sequencing (GBS) was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs) linked these results to published maps for cross-validation and map comparison. Conclusions: GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation distortion in R. idaeus, which may help to identify deleterious alleles that are the basis of inbreeding depression in the species. [ABSTRACT FROM AUTHOR]

An endogenous meiotic driver in the dengue and yellow fever vector mosquito Aedes aegypti can cause highly male-biased sex ratio distortion in crosses from suitable genetic backgrounds. We previously selected a strain that carries a strong meiotic drive gene (D) linked with the male-determining allele (M) on chromosome 1 in A. aegypti. Here, we performed segregation analysis of the MD locus among backcross (BC1) progeny from a driver male and drive-sensitive females. Assessment of sex ratios among BC2 progeny showed ∼5.2% recombination between the MD locus and the sex determination locus. Multipoint linkage mapping across this region revealed consistent marker orders and recombination frequencies with the existing reference linkage map and placed the MD locus within a 6.5-cm interval defined by the LF159 locus and microsatellite marker 446GAA, which should facilitate future positional cloning efforts. [ABSTRACT FROM PUBLISHER]

Phytophthora root and stem rot caused by Phytophthora sojae, is one of the most damaging diseases of soybean, for which management is principally done by planting resistant cultivars with race specific resistance which are conferred by Rps (Resistance to Phytophthora sojae) genes. The Rps8 locus, identified in the South Korean landrace PI 399073, is located in a 2.23 Mbp region on soybean chromosome 13. In eight cv. Williams ( rps8/rps8) × PI 399073 ( Rps8/ Rps8) populations, this region exhibited strong segregation distortion. In a cross between the South Korean lines PI 399073 ( Rps8/ Rps8) and PI 408211B (multiple Rps genes) this region segregated in a Mendelian fashion. In this study, microsporogenesis was evaluated to identify meiotic abnormalities that may be associated with the segregation distortion of the Rps8 region. Pollen was collected from greenhouse-grown plants of the parental genotypes: Williams, PI 399073, and PI 408211B; as well as selected Rps8/ rps8 RILs from Williams × PI 399073 BCF and PI 399073 × PI 408211B F populations. There were no differences for pollen viability among the genotypes. However, for PI 399073, a mix of dyads, triads, tetrads and pentads was observed. A high frequency of meiotic abnormalities including fragments, laggards, multinucleated microspores; and microcytes containing DNA was also observed in Rps8/ rps8 Williams × PI 399073 BCF RILs. These meiotic abnormalities may contribute to the high degree of segregation distortion present in the Williams × PI 399073 populations. [ABSTRACT FROM AUTHOR]

chickpea F population of 593 plants derived from the intraspecific cross ILC3279 × WR315 was genotyped for markers closely linked to quantitative trait loci (QTLs) for ascochyta blight resistance (QTL and QTL located on linkage group 4 and QTL on linkage group 2). All the markers located on linkage group 4 exhibited strongly distorted segregation with respect to the expected Mendelian inheritance, towards the male parental line. This skewed segregation was also observed in a second F population of 50 plants derived from the same cross, confirming the presence of a region of distorted segregation on this linkage group and its heritability. The most skewed markers were SC-Y17 and TA72, which were tightly linked to each other, indicating that they may both be closely associated with the genetic factor responsible for segregation distortion in chickpea. To attempt to explain the non-Mendelian segregation, by identifying factors to which it could be attributed, three different chi-square tests were carried out to test different hypotheses using the data obtained from examining co-dominant markers associated with segregation distortion. According to our results, the distorted segregation could be caused by gametophytic factors that affect either male or female gametes. Pollen fertility and meiosis were also analysed to determine their relationship with segregation distortion; however, these not seem to be inducing factors in the non-Mendelian segregation reported in this study. [ABSTRACT FROM AUTHOR]

We further investigated genome macrosynteny for Brassica species and Arabidopsis thaliana. This work aimed at comparative map construction for B. oleracea and A. thaliana chromosomes based on 160 known A. thaliana probes: 147 expressed sequence tags (ESTs) and 13 full-length cDNA clones. Based on an in silico study of the A. thaliana genome, most of the selected ESTs (83%) represented unique or low-copy genes. We identified conserved segments by the visual inspection of comparative data with a priori assumptions, and established their significance with the LineUp algorithm. Evaluation of the number of B. oleracea gene copies per A. thaliana EST revealed a fixed upward trend. We established a segregation distortion pattern for all genetic loci, with particular consideration of the type of selection (gametic or zygotic), and discuss its possible impact on genetic map construction. Consistent with previous reports, we found evidence for numerous chromosome rearrangements and the genome fragment replication of B. oleracea that have taken place since the divergence of the two species. Also, we found that over 54% of the B. oleracea genome is covered by 24 segments conserved with the A. thaliana genome. The average conserved segment is composed of 5 loci covering 19.3 cM in the B. oleracea genetic map and 2.42 Mb in the A. thaliana physical map. We have also attempted to use a unified system of conserved blocks (previously described) to verify our results and perform a comprehensive comparison with other Brassica species. [ABSTRACT FROM AUTHOR]

To date, all linkage maps of hexaploid oat (Avena sativa L.) have been constructed using recombinant inbred lines (RILs). Doubled haploids (DHs), however, have the advantage over RILs of their comprehensive homozygosity. DHs have been used for mapping in several cereal species, but in oats the production of large DH populations has only recently become an option. A linkage map of hexaploid oat was constructed using an anther culture-derived DH population (137 individuals) from the F1 individuals of a cross between the Finnish cultivar ‘Aslak’ and the Swedish cultivar ‘Matilda’. The map is composed of 28 linkage groups containing 625 DNA markers: 375 AFLPs (amplified fragment length polymorphisms), 3 IRAPs (inter-retrotransposon amplified polymorphisms), 12 ISSRs (inter simple sequence repeats), 12 microsatellites, 57 RAPDs (random amplified polymorphic DNAs), 59 REMAPs (retrotransposon-microsatellite amplified polymorphisms), 105 SRAPs (sequence-related amplified polymorphisms), and 2 SNPs (single-nucleotide polymorphisms). The total map size is 1526 cM. Over half of the markers in the map showed distorted segregation, with alleles from ‘Aslak’ usually prevailing. This is explained by the better performance of ‘Aslak’ in anther culture. Quantitative trait loci affecting some important quality and agronomic traits are being localized on the map. À ce jour, toutes les cartes génétiques de l’avoine hexaploïde (Avena sativa L.) ont été produites avec des populations de lignées recombinantes fixées (« RIL »). Par rapport aux RIL, les haploïdes doublés (HD) ont cependant l’avantage d’une homozygotie exhaustive. Les HD ont été employés en cartographie chez plusieurs espèces de céréales, mais jusqu’à récemment il n’était pas possible de produire de grandes populations de lignées HD chez l’avoine. Une carte génétique de l’avoine hexaploïde a été produite grâce à une population de 137 lignées HD dérivées de la culture d’anthères à partir d’individus F1 issus du croisement entre le cultivar finlandais ‘Aslak’ et le cultivar suédois ‘Matilda’. La carte compte 28 groupes de liaison et totalise 625 marqueurs : 375 AFLP (polymorphismes de longueur de fragments amplifiés), 3 IRAP (polymorphismes d’amplification inter-rétrotransposons), 12 ISSR (polymorphismes d’amplification inter-microsatellites), 12 microsatellites, 57 RAPD (polymorphismes d’ADN amplifié au hasard), 59 REMAP (polymorphisme d’amplification rétrotransposon-microsatellite), 105 SRAP (polymorphismes d’amplification de séquences apparentées) et 2 SNP (polymorphismes mononucléotidiques). La taille totale de la carte est de 1526 cM. Plus de la moitié des marqueurs de la carte présentaient une ségrégation biaisée où les allèles du parent ‘Aslak’ étaient généralement favorisés. Ceci s’explique par la meilleure performance de ce cultivar en culture d’anthères. Des travaux de cartographie sont en cours en vue de localiser des QTL contrôlant certains caractères agronomiques et de qualité. [ABSTRACT FROM AUTHOR]

Molecular markers have been widely used to map quantitative trait loci (QTL). The QTL mapping partly relies on accurate linkage maps. The non-Mendelian segregation of markers, which affects not only the estimation of genetic distance between two markers but also the order of markers on a same linkage group, is usually observed in QTL analysis. However, these distorted markers are often ignored in the real data analysis of QTL mapping so that some important information may be lost. In this paper, we developed a multipoint approach via Hidden Markov chain model to reconstruct the linkage maps given a specified gene order while simultaneously making use of distorted, dominant and missing markers in an F2 population. The new method was compared with the methods in the MapManager and Mapmaker programs, respectively, and verified by a series of Monte Carlo simulation experiments along with a working example. Results showed that the adjusted linkage maps can be used for further QTL or segregation distortion locus (SDL) analysis unless there are strong evidences to prove that all markers show normal Mendelian segregation. [ABSTRACT FROM AUTHOR]

Genetic mapping techniques can be used to study the interaction between two different genomes after hybridization. This study investigated a Saccharum officinarum (Green German or GG, 2n≈11x≈110) × S. spontaneum (IND 81–146 or IND, 2n≈7x≈56) interspecific cross. Segregation of 193 microsatellite (SSR) loci was evaluated in the F1 progeny of 169 full-sibs of the cross. Following the two-way pseudo-testcross strategy and ‘cross pollination’ population type, linkage groups (LG) and phases were established for each parent map, using the criteria of LOD score ≥3.0 and a maximum recombination frequency of 0.35. Of the 193 markers analyzed, 61 were IND-specific, 106 were GG-specific, and 26 were heterozygous in both parents. About 78% of the markers segregated in a Mendelian fashion and 22% were distorted (as evaluated by χ2-tests, P≤0.01). The GG map included 91 marker loci arranged into 25 LG covering 1180 cM of the officinarum genome. The IND map consisted of 46 marker loci assembled into 10 LG, which spanned 614 cM of the spontaneum genome. A specific chromosome associated with segregation distortion was detected in the female (GG) genome only, probably as a result of double reduction. The segregation patterns of the marker loci indicated a centromere-driven distortion process with the shared allelic markers (as putative centromeres) regulating the placement and association of markers with opposite phase (coupling vs repulsion) and dosage on either side. Although incomplete, the framework maps were informative with respect to segregation distortion, chromosome fusion, rearrangements, and translocations, observed in both parental genomes as a result of their merger.Heredity (2006) 97, 366–375. doi:10.1038/sj.hdy.6800888; published online 16 August 2006 [ABSTRACT FROM AUTHOR]

Tef [ Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2 n = 4 x = 40) and a genome size of 730 Mbp. Ninety-four F9 recombinant inbred lines (RIL) derived from the interspecific cross, Eragrostis tef cv. Kaye Murri × Eragrostis pilosa (accession 30-5), were mapped using restriction fragment length polymorphisms (RFLP), simple sequence repeats derived from expressed sequence tags (EST–SSR), single nucleotide polymorphism/insertion and deletion (SNP/INDEL), intron fragment length polymorphism (IFLP) and inter-simple sequence repeat amplification (ISSR). A total of 156 loci from 121 markers was grouped into 21 linkage groups at LOD 4, and the map covered 2,081.5 cM with a mean density of 12.3 cM per locus. Three putative homoeologous groups were identified based on multi-locus markers. Sixteen percent of the loci deviated from normal segregation with a predominance of E. tef alleles, and a majority of the distorted loci were clustered on three linkage groups. This map will be useful for further genetic studies in tef including mapping of loci controlling quantitative traits (QTL), and comparative analysis with other cereal crops. [ABSTRACT FROM AUTHOR]

A genetic linkage map of an intraspecific cross between 2 Silene vulgaris s.l. ecotypes is presented. Three-hundred AFLP markers from 2 different restriction enzyme combinations were used to genotype an F2 mapping population. Maternal and paternal pure-coupling phase maps with 114 and 186 markers on 12 and 13 linkage groups, respectively, were constructed. Total map length of the paternal and maternal maps are 547 and 446 Kosambi cM, respectively. Nearly half of the markers (49%) exhibited significant transmission ratio distortion. Genome coverage and potential causes of the observed segregation ratio distortions are discussed. The maps represent a first step towards the identification of quantitative trait loci associated with habitat adaptation in the non-model species Silene vulgaris. [ABSTRACT FROM AUTHOR]

Viability selection will change gene frequencies of loci controlling fitness. Consequently, the frequencies of marker loci linked to the viability loci will also change. In genetic mapping, the change of marker allelic frequencies is reflected by the departure from Mendelian segregation ratio. The non-Mendelian segregation of markers has been used to map viability loci along the genome. However, current methods have not been able to detect the amount of selection (s) and the degree of dominance (h) simultaneously. We developed a method to detect both s and h using an F2 mating design under the classical fitness model. We also developed a quantitative genetics model for viability selection by proposing a continuous liability controlling the viability of individuals. With the liability model, mapping viability loci has been formulated as mapping quantitative trait loci. As a result, nongenetic systematic environmental effects can be easily incorporated into the model and subsequently separated from the genetic effects of the viability loci. The quantitative genetic model has been verified with a series of Monte Carlo simulation experiments.Heredity (2005) 94, 347-355. doi:10.1038/sj.hdy.6800615 Published online 10 November 2004 [ABSTRACT FROM AUTHOR]

Five genetic linkage maps were constructed for the parents of three progenies: Citrus aurantium (A) × Poncirus trifoliata var. Flying Dragon (Pa), C. volkameriana (V) × P. trifoliata var. Rubidoux (Pv) and a self-pollination of P. trifoliata var. Flying Dragon (Pp). The number of polymorphic markers assayed ranged from 48 for Pa to 120 for A according to the heterozygosity of each parental. As our focus was on genome comparison, most of the markers were newly generated simple sequence repeats. Inter-retrotransposon amplified polymorphisms based on four retrotransposon sequences isolated from Citrus spp were also used to saturate the maps. These polymorphisms were much more frequent in A (53) than in Pa (15) and randomly distributed throughout both genomes. Since comparative genomics and quantitative trait locus analysis applicability depends on the reliability of marker ordering, the causes of variation in marker order were investigated. Around 25% of the markers showed gametal segregation distortions. Segregation distortions were also observed at the zygotic level towards a reduction in the observed frequency of homozygotes from that expected in linkage groups 5 and 7. The presence of balanced lethal factors or gametal incompatibility genes in those genomic regions would explain a zygotic advantage of heterozygotes at these specific regions. Four differences in genomic organization were observed; three are putative translocations and affect homeologous linkage groups 3, 7 and 11, where highly distorted markers are found. Other causes of variation in marker order are also discussed: the introduction of new markers in the map, lowering the LOD score and the mapping software. These results represent the first comparative mapping analysis among Citrus and Poncirus species. [ABSTRACT FROM AUTHOR]

Segregation distortion skews the genotypic frequencies from their Mendelian expectations. Our objectives in this study were to assess the frequency of occurrence of segregation distortion in maize, identify chromosomal regions consistently associated with segregation distortion, and examine the effects of gametophytic factors on linkage mapping. We constructed a simple sequence repeat (SSR) linkage map for a LH200/LH216 F2Syn3 (i.e., random-mated three times) population, and compared the segregation distortion in this map with the segregation distortion in three published linkage maps. Among 1,820 codominant markers across the four mapping populations, 301 (17%) showed segregation distortion (P < 0.05). The frequency of markers showing segregation distortion ranged from 19% in the Tx303/CO159 mapping population to 36% in the B73/Mo17 mapping population. A positive relationship was found between the number of meioses and the frequency of segregation distortion detected in a population. On a given chromosome, nearly all of the markers showing segregation distortion favored the allele from the same parent. A total of 18 chromosomal regions on the ten maize chromosomes were associated with segregation distortion. The consistent location of these chromosomal regions in four populations suggested the presence of segregation distortion regions (SDRs). Three known gametophytic factors are possible genetic causes of these SDRs. As shown in previous research, segregation distortion does not affect the estimate of map distance when only one gametophytic factor is present in an SDR. [ABSTRACT FROM AUTHOR]

Two complementary segregating plant populations of Coffea canephora were produced from the same clone. One population (DH) comprised 92 doubled haploids derived from female gametes, while the other population (TC) was a test cross consisting of 44 individuals derived from male gametes. Based on the DH population, a genetic linkage map comprising 160 loci was constructed. Eleven linkage groups that putatively correspond to the 11 gametic chromosomes of C. canephora were identified. The mapped loci included more than 40 specific sequence-tagged site markers, either single-copy RFLP probes or microsatellites, that could serve as standard landmarks in coffee-genome analyses. Furthermore, comparisons for segregation distortion and recombination frequency between the two populations were performed. Although segregation distortions were observed in both populations, the frequency of loci exhibiting a very pronounced degree of distortion was especially high in the DH population. This observation is consistent with the hypothesis of strong zygotic selection among the DH population. The recombination frequencies in both populations were found to be almost indistinguishable. These results offer evidence in favour of the lack of significant sex differences in recombination in C. canephora.Key words: coffee, mapping, sex differences, segregation distortion, recombination frequency.Deux populations complémentaires de plantes en ségrégation ont été produites à partir d'un même clone de Coffea canephora. Une population (DH) comprend 92 haploïde-doublés dérivés des gamètes femelles, tandis que l'autre (TC) consiste en 44 individus issus des gamètes mâles. Sur la base de la population DH, une carte génétique de liaison, comprenant 160 loci, a été construite. Onze groupes de liaison correspondant très vraisemblablement aux 11 chromosomes de C. canephora ont été identifiés. Parmi les loci cartographiés sont inclus 40 marqueurs « séquence-spécifiques », constitués par des sondes associées à du polymorphisme de fragments de restriction ou par des microsatellites, qui pourraient servir de balises de référence dans les études portant sur le génome des caféiers. Par ailleurs, une comparaison, entre les deux populations, des distorsions de ségrégation et des fréquences de recombinaison a été réalisée. Bien que des distorsions de ségrégation aient été observées au sein des deux populations, la fréquence des loci montrant un fort degré de distorsion est particulièrement élevée chez la population DH. Cette observation est cohérente avec l'hypothèse d'une forte sélection zygotique au sein de la population DH. Les fréquences de recombinaison apparaissent globalement similaires au sein des deux populations. Ces résultats suggèrent l'absence de différences sexuelles significatives pour la recombinaison chez C. canephora.Mots clés : caféier, cartographie, différences sexuelles, distorsion de ségrégation, fréquence de recombinaison. [ABSTRACT FROM AUTHOR]

A phenotypically polymorphic barley (Hordeum vulgare L.) mapping population was developed using morphological marker stocks as parents. Ninety-four doubled-haploid lines were derived for genetic mapping from an F1 using the Hordeum bulbosum system. A linkage map was constructed using 12 morphological markers, 87 restriction fragment length polymorphism (RFLP), five random amplified polymorphic DNA (RAPD), one sequence-tagged site (STS), one intron fragment length polymorphism (IFLP), 33 simple sequence repeat (SSR), and 586 amplified fragment length polymorphism (AFLP) markers. The genetic map spanned 1,387 cM with an average density of one marker every 1.9 cM. AFLP markers tended to cluster on centromeric regions and were more abundant on chromosome 1 (7H). RAPD markers showed a high level of segregation distortion, 54% compared with the 26% observed for AFLP markers, 27% for SSR markers, and 18% for RFLP markers. Three major regions of segregation distortion, based on RFLP and morphological markers, were located on chromosomes 2 (2H), 3 (3H), and 7 (5H). Segregation distortion may indicate that preferential gametic selection occurred during the development of the doubled-haploid lines. This may be due to the extreme phenotypes determined by alleles at morphological trait loci of the dominant and recessive parental stocks. Several molecular markers were found to be closely linked to morphological loci. The linkage map reported herein will be useful in integrating data on quantitative traits with morphological variants and should aid in map-based cloning of genes controlling morphological traits. [ABSTRACT FROM AUTHOR]

Genetic research in fishes is poised to contribute a vast amount of information on the structural organization and function of vertebrate genomes. Recent advances in molecular biology have made possible the widescale characterization of genomes in all living organisms. This includes defining chromosomes at the cytological level down to their linear composition at individual nucleotide base pairs. Pioneering gene mapping studies into the genomes of fishes will only serve as the starting point for more detailed studies into the function of these genomes. Future research directed at understanding the mechanisms of gene actions and interactions will benefit all areas of biology, including ecology, ethology, evolution, and physiology. Gene mapping data from brown trout and rainbow trout are used to exemplify how basic information on gene transmission in a species may help to localize centromeres onto a genetic map and identify chromosomal regions possessing a high degree of segregation distortion. Genetic maps may also be used to identify differences in recombination levels among individuals and between the sexes when multiple mapping families are utilized in studies. Observations of this type are the antecedents to more complex biological investigations on the genetic architecture underlying these phenomena. [ABSTRACT FROM AUTHOR]

Due in large part to the data accumulated from years of classic genetic analysis, petunia (Petunia hybrida Vilm) has remained a useful model system, particularly for studies of gene regulation and genome structure. We have used three segregating populations of petunia, including those serving as the source of an earlier actin gene RFLP map, for RFLP mapping of several additional genes. Twenty-seven loci have been merged with 11 previously mapped morphological and biochemical markers. Our results contribute additional evidence to reports of a high degree of genome plasticity and segregation distortion in this species and suggest that petunia may be a useful plant system for detailed analysis of plant genome organization, activity and evolution. [ABSTRACT FROM AUTHOR]

A linkage map of Lablab purpureus consisting of 127 RFLP and 91 RAPD loci was constructed in an F2 population of 119 individuals. This population was derived from a cross between ’Rongai’ (an annual cultivar) and CPI 24973 (a perennial wild accession). The map comprises 17 linkage groups and covers 1610 centiMorgans (cM) with an average distance of 7 cM between markers. Severe segregation distortions were observed, with the very extreme situation where no paternal type was recovered from the mapping population. These results strongly suggest the presence of a gene conferring preferential transmission from the maternal parent ’Rongai’. It was also clear that, while the majority of RAPD markers are valuable when used together with RFLP or other stringent marker systems, they could be problematic when used solely in mapping exercises. [ABSTRACT FROM AUTHOR]

Oryza glaberrima is an endemic African cultivated rice species. To provide a tool for evaluation and utilisation of the potential of O. glaberrima in rice breeding, we developed an interspecific O. glaberrima×Oryza sativa genetic linkage map. It was based on PCR markers, essentially microsatellites and STSs. Segregation of markers was examined in a backcross (O. sativa/O. glaberrima//O. sativa) population. Several traits were measured on the BC1 plants, and major genes and QTLs were mapped for these traits. Several of these genes correspond well to previously identified loci. The overall map length was comparable to those observed in indica×japonica crosses, indicating that recombination between the two species occurs without limitation. However, three chromosomes show discrepancies with the indica×japonica maps. The colinearity with intraspecific maps was very good, confirming previous cytological observations. A strong segregation-distortion hot spot was observed on chromosome 6 near the waxy gene, indicating the presence of s10, a sporo-gametophytic sterility gene previously identified by Sano (1990). The main interests of such a PCR-based map for African rice breeding are discussed, including gene and QTL localisation, marker-assisted selection, and the development of interspecific introgression lines. [ABSTRACT FROM AUTHOR]

• Through the genotyping-by-sequencing (GBS) technology, a high-density genetic linkage map was constructed. • Twenty-seven stable quantitative trait loci (QTL) were obtained for fiber yield and quality. • A severe segregation distortion ratio was found on chromosome D08, reaching 99.39 %. • Segregation distortion markers on chromosome D08 were significantly associated with fiber strength. • An alien fragment introgressed from G. thurberi potentially improved fiber strength. Cotton (Gossypium) is a worldwide natural fiber crop. Fiber quality improvement lags far behind that of fiber yield. Although interspecific hybridization contributes significantly to improve fiber quality, the mechanism of alien genomic introgression to improve fiber quality has rarely been reported. In this study, a superior fiber-strength line (J02−508) derived from interspecific hybridization was used to dissect the genetic and genomic bases for fiber quality by forward-genetics technologies. Both F 2 and F 2:5 populations were developed from a cross between superior line J02−508 and a weak fiber-quality line (ZRI015). Based on the linkage map constructed from the F 2:5 population, 27 stable quantitative trait loci (QTL) were detected for fiber yield and quality. Unexpectedly, an abnormally high segregation distortion ratio was found for all chromosomes (reaching an average of 83.13 % for each chromosome), and the highest ratio of segregation distortion markers (SDMs) was on chromosome D08, reaching 99.39 %. Taking the SDMs into account, a distinct genome region on chromosome D08 was identified, which had a sizeable physical interval (∼53 Mb length) with low recombination frequency and was significantly associated with fiber strength (named qFS_D08 , LOD value = 11.49). Additionally, by integrating different approaches, we initially confirmed that this region was an alien fragment introgressed from wild diploid cotton, G. thurberi (D 1), accounting for nearly 77 % of the length of chromosome D08 in the J02−508 genome. We provided molecular evidence for fiber strength improvement caused by introgression. This study is also beneficial to understand the importance of interspecific hybridization for improving fiber strength during cotton breeding. [ABSTRACT FROM AUTHOR]

Transmission ratio distortion (TRD) is defined as the allele transmission deviation from the heterozygous parent to the offspring from the expected Mendelian genotypic frequencies. Although TRD can be a confounding factor in genetic mapping studies, this phenomenon remains mostly unknown in pigs, particularly in traditional breeds (i.e., the Iberian pig). We aimed to describe the maternal TRD prevalence and its genomic distribution in two Iberian varieties. Genotypes from a total of 247 families (dam and offspring) of Entrepelado (n = 129) and Retinto (n = 118) Iberian varieties were analyzed. The offspring were sired by both ungenotyped purebred Retinto and Entrepelado Iberian boars, regardless of the dam variety used. After quality control, 16,246 single-nucleotide polymorphisms (SNPs) in the Entrepelado variety and 9744 SNPs in the Retinto variety were analyzed. Maternal TRD was evaluated by a likelihood ratio test under SNP-by-SNP, adapting a previous model solved by Bayesian inference. Results provided 68 maternal TRD loci (TRDLs) in the Entrepelado variety and 24 in the Retinto variety (q < 0.05), with mostly negative TRD values, increasing the transmission of the minor allele. In addition, both varieties shared ten common TRDLs. No strong evidence of biological effects was found in genes with TRDLs. However, some biological processes could be affected by TRDLs, such as embryogenesis at different levels and lipid metabolism. These findings could provide useful insight into the genetic mechanisms to improve the swine industry, particularly in traditional breeds. [ABSTRACT FROM AUTHOR]