The inheritance of genetic markers in microspore-derived plants of barley Hordeum vulgare L

Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods

Segregation distortion is the phenomenon in which genotypes deviate from expected Mendelian ratios in the progeny of a cross between two varieties or species. There is not currently a widely used consensus for the appropriate statistical test, or more specifically the multiple testing correction procedure, used to detect segregation distortion for high-density single-nucleotide polymorphism (SNP) data. Here we examine the efficacy of various multiple testing procedures, including chi-square test with no correction for multiple testing, false-discovery rate correction and Bonferroni correction using an in-silico simulation of a biparental mapping population. We find that the false discovery rate correction best approximates the traditional p-value threshold of 0.05 for high-density marker data. We also utilize this simulation to test the effect of segregation distortion on the genetic mapping process, specifically on the formation of linkage groups during marker clustering. Only extreme segregation distortion was found to effect genetic mapping. In addition, we utilize replicate empirical mapping populations of wheat varieties Avalon and Cadenza to assess how often segregation distortion conforms to the same pattern between closely related wheat varieties.

The identification of restriction fragment length polymorphisms linked to seed colour genes in Brassica napus

Restriction fragment length polymorphisms (RFLPs) linked to genes controlling seed colour were identified in rapeseed (Brassica napus). The efficiency of the RFLP analysis was enhanced by utilizing bulked segregant analysis, DNA clones that had previously been used to construct a RFLP map of B. napus, and a doubled-haploid (DH) population segregating for seed colour. Markers for two of the three seed colour genes segregating in the DH population were identified on the basis of χ2 analyses of marker distributions among visually classified black-, brown-, and yellow-seeded DH lines as well as ANOVA and quantitative trait locus analysis of light-reflectance measurements from seeds of the DH lines. The RFLP markers linked to seed colour that were identified in the present study will allow breeding strategies based on genotype selection to be developed for seed colour in rapeseed.

Molecular mapping of resistance to Leptosphaeria maculans in Australian cultivars of Brassica napus

Doubled haploid (DH) lines together with a cotyledon bioassay were employed for the molecular analysis of resistance to the blackleg fungus Leptosphaeria maculans in the Australian Brassica napus cultivars Shiralee and Maluka. We used bulked segregant analysis to identify 13 RAPD and two RFLP markers linked to the resistance phenotype and mapped these markers in the segregating DH population. Our data suggest the presence of a single major locus controlling resistance in the cultivar Shiralee, confirming our previous results obtained from Mendelian genetic analyses. In addition, preliminary mapping data for the cultivar Maluka also support a single locus model for resistance and indicate that the resistance genes from 'Shiralee' and 'Maluka' are either linked or possibly identical. The molecular markers identified in this study should be a useful tool for breeding blackleg resistant varieties using marker-assisted selection, and are the essential first step towards the map-based cloning of this resistance gene.

A comparison of RFLP maps based on anther culture derived, selfed, and hybrid progenies of Solanum chacoense

Comparative RFLP linkage maps were constructed using five segregating populations derived from two self-incompatible lines (termed PI 230582 and PI 458314) of diploid tuber-bearing Solanum chacoense Bitt. The analysis was based on 84 RFLP loci identified by 73 different cDNA clones. Distortion of expected Mendelian segregation ratios was observed; less than 10% of the markers showed a skewed segregation in the gametes forming the F1, hybrid population compared with 30% in the selfed population and 46 and 70% in the two populations produced by anther culture. For the anther culture derived populations, most of the skewed loci were scattered throughout the genome, whereas in the populations derived from selfing, they were found primarily in linkage group 1, around the S locus. In this study, we also found that the rate of meiotic recombination could differ between the male and female gametes produced by our parental lines. Thus, male gametes of line PI 458314 showed significantly less recombination as assessed by the total length of the map (206 cM for male gametes vs. 375 cM for female gametes) and the phenomenon was genome-wide. In contrast, the maps from the gametes of PI 230582 had about the same length, but some linkage groups were longer in the female gametes, while others were longer in the male gametes. Key words : Solanum chacoense, RFLP, anther culture, skewed segregation, self-incompatibility, sex differences in recombination.

Molecular mapping of segregation distortion loci in Aegilops tauschii

Distorted segregation ratios of genetic markers are often observed in progeny of inter- and intraspecific hybrids and may result from competition among gametes or from abortion of the gamete or zygote. In this study, 194 markers mapped in an Aegilops tauschii F2 population were surveyed for distorted segregation ratios. Region(s) with skewed segregation ratios were detected on chromosomes 1D, 3D, 4D, and 7D. These distorter loci are designated as QSd.ksu-1D, QSd. ksu-3D, QSd.ksu-4D, and QSd.ksu-7D. Three regions of segregation distortion identified on chromosome 5D were analyzed in two sets of reciprocal backcross populations to analyze the effect of sex and cytoplasm on segregation distortion. Extreme distortion of marker segregation ratios was observed in populations in which the F1 was used as the male parent, and ratios were skewed in favor of TA1691 alleles. There was some evidence of differential transmission caused by nucleo-cytoplasmic interactions. Our results agree with other studies stating that loci affecting gametophyte competition in male gametes are located on 5DL. The distorter loci on 5DL are designated as QSd.ksu-5D.1, QSd.ksu-5D.2, and QSd.ksu-5D.3.

In vitro androgenesis and segregation distortion inBrassica napus L.: spontaneous versus colchicine-doubled lines

A total of 750 plantlets were regenerated from 1,400 embryos produced through microspore cultures from one F₁ plant of the cross 'Darmor-bzh' x 'Yudal'. Fifty-three percent of the regenerants were evaluated by flow cytometric analysis, which revealed that 31% were spontaneous diploid (SD), 63% were still haploid and the remaining 6% plants had other ploidy levels. Available segregation data (266 markers) produced on this androgenic progeny were used to study the interference between segregation distortion and the mode of chromosome doubling of androgenc lines. On the basis of the present results it is not possible to conclude that distortions are peculiar to one type of regenerated plant; only a difference in the intensity of the bias might be assumed.

Comparative mapping of the barley genome with male and female recombination-derived, doubled haploid populations

Male (anther culture) and female (Hordeum bulbosum) derived, doubled haploid populations were used to map the barley genome and thus determine the different recombination rates occurring during meiosis in the F1 hybrid donor plants. The anther culture-derived (male recombination) population showed an 18% overall increase in recombination rate. This increased recombination rate was observed for every chromosome and most of the chromosome arms. Examination of linkage distances between individual markers revealed eight segments with significantly higher recombination in the anther culture-derived population, and one in the Hordeum bulbosum-derived population. Very strong distortions of single locus segregations were observed in the anther culture-derived population, but map distances were not affected significantly by these distortions. There were 1.047 and 0.912 recombinations per chromosome in the anther culture and Hordeum bulbosum-derived doubled haploid populations, respectively.

Study of microspore-culture responsiveness in oilseed rape (Brassica napus L.) by comparative mapping of a F2 population and two microspore-derived populations

RFLP segregation analyses were performed on a F2 population and two F1 microspore-derived populations from the same cross between a microspore culture-responsive parent ('Topas') and a non-responsive parent ('Westar'). A total of 145 loci were detected with 87 cDNA clones. Eighty-two markers were common across all three populations. A total of 66 markers was assembled into 18 linkage groups and 16 markers remained unlinked. Segregation distortions were significant for 29% of the markers in the F2 population and 23% and 31% in microspore-derived populations M3 and M5, respectively. An equivalent number of markers showed biased segregation towards each parental allele in the F2 population while more markers showed a significant deviation from the expected Mendelian ratio towards the responsive parent in both microspore-derived populations. Different subsets of markers showed segregation distortions in the three populations indicating that the selective pressures leading to microsporederived plants are different from those acting during selfing of the F1. Linkage groups 1 and 18 were identified as putative chromosomal regions associated with microspore-culture responsiveness.

RFLP markers linked to scald (Rhynchosporium secalis) resistance gene Rh2 in barley

Rhynchosporium secalis is the causal organism of barley scald disease. A number of resistance genes against the fungus are well known; one of them, the single dominant Rh2 resistance gene, has been mapped on the linkage map of barley using RFLP (restriction fragment length polymorphism) markers. The Rh2 gene was located on the distal part of chromosome arm 1S co-segregating with the RFLP marker CDO545 in 85 doubled-haploid progeny plants. The spring barley test population used was a cross between the 6-rowed American spring barley cv Atlas, C.I. 4118, carrying the Rh2 resistance gene, and a Bavarian 2-rowed malting barley cv Steffi, susceptible for R. secalis. The assessment of resistance versus susceptibility was based on artificial infections with a one-spore inoculum in greenhouse tests and with pathotype mixtures in field tests. By testing a pathotype mixture of German origin good resistance was found for the Rh2 gene in the field.

Mapping the genome of rapeseed (Brassica napus L.). I. Construction of an RFLP linkage map and localization of QTLs for seed glucosinolate content

A linkage map of the rapeseed genome comprising 204 RFLP markers, 2 RAPD markers, and 1 phenotypic marker was constructed using a F1 derived doubled haploid population obtained from a cross between the winter rapeseed varieties 'Mansholt's Hamburger Raps' and 'Samourai'. The mapped markers were distributed on 19 linkage groups covering 1441 cM. About 43% of these markers proved to be of dominant nature; 36% of the mapped marker loci were duplicated, and conserved linkage arrangements indicated duplicated regions in the rapeseed genome. Deviation from Mendelian segregation ratios was observed for 27.8% of the markers. Most of these markers were clustered in 7 large blocks on 7 linkage groups, indicating an equal number of effective factors responsible for the skewed segregations. Using cDNA probes for the genes of acyl-carrier-protein (ACP) and β-ketoacyl-ACP-synthase I (KASI) we were able to map three and two loci, respectively, for these genes. The linkage map was used to localize QTLs for seed glucosinolate content by interval mapping. Four QTLs could be mapped on four linkage groups, giving a minimum number of factors involved in the genetic control of this trait. The estimated effects of the mapped QTLs explain about 74% of the difference between both parental lines and about 61.7 % of the phenotypic variance observed in the doubled haploid mapping population.

Protein markers for anther culturability in barley

Two-dimensional electrophoresis of proteins from a recombinant population of anther culture-derived doubled haploid lines identified 4 loci or linkage groups showing a deviation from an expected 1∶1 segregation. It was hypothesized that these markers are linked to genes involved in the process of haploid plant production and that the deviation was due to a selection for alleles conferring higher anther culture response. To check this hypothesis, the anther culturability of 50 of the doubled haploid lines and their two inbred parents was assessed. It was found that 2 of the loci which had a distortion of segregation showed a significant effect on anther culture response, the most efficient allele being the most frequent in both loci. In addition, 2 more markers associated with anther culturability were found. One of the first mentioned 2 loci and one of the latter 2 were found to be linked to genes involved in both embryoid production and subsequent green plant regeneration. The remaining two were linked to genes involved only in green plant regeneration. Of the 4 favorable alleles 3 were inherited from one parent.

Molecular and morphological evaluation of doubled-haploid lines in maize. 2. Comparison with single-seed-descent lines

Doubled-haploid (DH) and single-seed-descent (SSD) lines in maize have been compared for quantitatively inherited traits and for RFLP markers. The comparisons of the distributions for agromorphological traits do not allow definite conclusions to be drawn on the similarity of the two reproductive systems. We have used more than 100 RFLP markers to provide a precise description of the parental allele frequency and the recombination fractions. A comparison of two DH populations shows that non-random meiotic reassortment is influenced by differences in the anther culture capacities of the two parental lines. For the DH lines derived from the cross DH5 x DH7, involving two responsive lines in anther culture, the distortion in segregation (P < 0.05) affected less than 20% of the genome with half of the deviations towards each parent. DH lines derived from the cross A188 x DH7, where A188 is a non-responsive line, showed more than twice this level of distortion and an excess of DH7 alleles was found for almost all of the skewed loci. The recombination fractions were homogeneous between the two DH populations for most of the genome. The genome sizes calculated with the DH and the SSD lines derived from the same cross, A188 x DH7, were also similar, which suggests that no selection against recombinant gametes occurs during anther culture. The observed recombination fraction after five meioses (SSD) is on average twice as large as after one meiosis (DH). No difference is observed for recombination fractions greater than 20%. Despite a precise description of the material at the molecular level, it has not been possible to make a definite conclusion as to whether or not the differences in some morphological characters are the consequences of differences in the segregation ratio and/or the recombination frequency. However, the agromorphological evaluation shows a narrow range in differences between the two types of lines and suggests that the use of DH lines is possible in breeding programmes.

Identification of RAPD markers linked to a Rhynchosporium secalis resistance locus in barley using near-isogenic lines and bulked segregant analysis

Three hundred random sequence 10-mer primers were used to screen a pair of near-isogenic lines of barley and their donor parent for markers linked to genes conferring resistance to Rhynchosporium secalis. One primer was identified which reproducibly generated a product, SC10-65-H400, from the donor parent and the Rhynchosporium-resistant near-isogenic line but not from the recurrent parent. Segregation analysis on a barley doubled haploid population and examination of a further three near-isogenic lines, their donor and recurrent parents confirmed that this marker was linked to the Rhynchosporium resistance locus (Rh) on chromosome 3L. The presence or absence of SC10-65-H400 was subsequently used along with the resistance phenotype to identify two groups of individuals in the doubled haploid population which possessed alternative alleles at both loci and defined a genetic interval between these two markers. Based on that information two bulked DNA samples were constructed by combining equal amounts of DNA from five individuals from each group. The two bulks and doubled haploid parental lines were screened with 700 10-mer primers. Seven products were identified which were present in the 'resistant' bulk and parent and were absent in the susceptible samples. Segregation analysis established their association with Rh. In addition co-segregation of the linked markers with a set of chromosome arm specific RFLPs confirmed the location of the Rh locus on the long arm of barley chromosome 3.

Detection and analysis of genetic variation in Hordeum spontaneum populations from Israel using RAPD markers

Randomly amplified polymorphic DNA (RAPD) markers were used to analyse genetic diversity within and between Hordeum spontaneum populations sampled from Israel. Nei's index of genetic differentiation was used to partition diversity into within and between population components. Fifty-seven per cent of the variation detected was partitioned within 10 H. spontaneum populations. Using principal component and multiple regression analysis, part of the variation detected between populations was seen to be associated with certain ecogeographical factors. Fifty-eight per cent of the distribution of the phenotypic frequencies of three RAPD phenotypes detected using a single primer in 20 H. spontaneum populations could be accounted for by four ecogeographical variables, suggesting adaptive variation at certain RAPD loci.

Random amplified polymorphic DNA and pedigree relationships in spring barley

We investigated random amplified polymorphic DNA (RAPD) in 27 inbred barley lines with varying amounts of common ancestry and in 20 doubled-haploid (DH) lines from a biparental cross. Of 33 arbitrary 10 base primers that were tested, 19 distinguished a total of 31 polymorphisms. All polymorphisms were scored as dominant genetic markers except for 1, where Southern analysis indicated the presence of two codominant amplification products. The inheritance of 19 RAPD polymorphisms and one morphological trait was studied in the DH lines. There was no evidence for segregation distortion, but a group of four tightly linked loci was detected. The frequencies of RAPD polymorphism in pairs of inbred lines were used to compute values of genetic distance (d), which were compared to kinship coefficients (r) between the same pairs of lines. A linear relationship between r and d was evident, but low values of r gave poor predictions of d. Cluster analysis showed that groups of inbred lines based on r were similar to those based on d with some notable exceptions. RAPD markers can be used to gain information about genetic similarities or differences that are not evident from pedigree information.

Construction of an RFLP map of barley

In order to construct an RFLP map of barley, two populations were analyzed using 251 genomic and cDNA markers: one population comprised 71 F1 antherderived double haploid (DH) individuals of an intraspecific cross (IGRI x FRANKA), and the other 135 individuals of an interspecific F2/F3 progeny (VADA x H. spontaneum). The distribution of nonrepetitive clones over the seven barley chromosomes revealed a maximum for chromosome 2H and a minimum for 6H. The polymorphism of the interspecific progeny (76%) clearly exceeded that of the intraspecific progeny (26%) although, based on their pedigrees, IGRI and FRANKA are only distantly related. The contribution of individual chromosomes of the DH parents to the overall polymorphism varied between 8% and 50%. A significant portion (44% versus 10% of the interspecific progeny) of the markers mapped on the DH offspring showed distorted segregation, caused mainly by the prevalence of variants originating from the parent that better responded to in vitro culture (IGRI). In contrast to the interspecific map, probes displaying skewed segregation were clustered on the DH map on discrete segments. The colinear arrangement of both maps covers a distance of 1,453 cM and identifies regions of varying map distances.

Water-soluble proteins of mature barley endosperm: genetic control, polymorphism, and linkage with β-amylase and spring/winter habit

Water-soluble proteins (WSP-2 and WSP-3) and β-amylase (β-AMY-1) were extracted from mature endosperms of 44 spring and 39 winter barley genotypes. The protein and enzyme isoforms were separated in isoelectric focusing gels with a pH gradient of 4-6.5. The Wsp-3 and β-Amy-1 loci were located to chromosomes 4H using the wheat/barley chromosome addition lines. Segregation analysis of F2 and doubled haploid populations showed Wsp-2 and β-Amy-1 to be tightly linked, with a map distance of 11 cMorgans. Isoforms of WSP-2 possessed similar pIs to that of WSP-3 and overlapping bands were observed in the gels. These bands segregated independently in F2 and doubled haploid populations, implying two unlinked genes. All three loci were found to be polymorphic: two alleles were detected at the Wsp-2 locus, three at Wsp-3 and two at β-Amy-1. The frequency of alleles at all three loci was found to be different in winter and spring genotypes. Spring genotypes possessed a wider range of phenotypes than winter genotypes. Spring and winter genotypes could be distinguished on the basis of WSP-3 and β- AMY-1 phenotypes. The linkage between Wsp-3 and β-Amy-1 loci and genes controlling spring/winter habit on chromosome 4H is discussed. It is concluded that Wsp-3 and β-Amy-1 can be used as genetic markers for spring/winter habit in barley genetic research and breeding.