Genetical analysis of microspore derived plants of barley (Hordeum vulgare)

Extent and overlap of segregation distortion regions in 12 barley crosses determined via a Pool-GBS approach

Extent and overlap of segregation distortion regions in 12 barley crosses determined via a Pool-GBS approach. Segregation distortion is undesirable as it alters the frequency of alleles and can reduce the chances of obtaining a particular combination of alleles. In this work, we have used a pooled genotyping-by-sequencing (Pool-GBS) approach to estimate allelic frequencies and used it to examine segregation distortion in 12 segregating populations of barley derived from androgenesis. Thanks to the extensive genome-wide SNP coverage achieved (between 674 and 1744 markers), we determined that the proportion of distorted markers averaged 28.9 % while 25.3 % of the genetic map fell within segregation distortion regions (SDRs). These SDRs were characterized and identified based on the position of the marker showing the largest distortion and the span of each SDR. Summed across all 12 crosses, 36 different SDR peaks could be distinguished from a total of 50 SDRs and a majority of these SDRs (27 of 36) were observed in only one population. While most shared SDRs were common to only two crosses, two SDRs (SDR3.1 and SDR4.2) were exceptionally recurrent (seen in five and four crosses, respectively). Because of the broad span of most SDRs, an average of 30 % of crosses showed segregation distortion in any given chromosomal segment. In reciprocal crosses, although some SDRs were clearly shared, others were unique to a single direction. In summary, segregation distortion is highly variable in its extent and the number of loci underpinning these distortions seems to be quite large even in a narrow germplasm such as six-row spring barley.

Construction of an intraspecific integrated linkage map of pepper using molecular markers and doubled-haploid progenies

An integrated molecular linkage map of pepper (Capsicum annuum L.), including mainly RFLP and RAPD markers, has been constructed by alignment of three intraspecific linkage maps generated by segregating doubled-haploid progenies. A total of 85 markers covered approximately 820 cM in 14 linkage groups. Four linkage groups were assigned to 4 chromosomes. Two new genes of agronomic interest were located: L controlling hypersensitive resistance to TMV and up controlling the erect habit of the fruits. The C gene controlling the fruit pungency was more precisely located. This map is estimated to represent from 36 to 59% of the total pepper genome. An examination of segregation data has revealed several genomic regions with aberrant segregation ratios often favouring the agronomic big-fruited parents, particularly in crosses involving the exotic parent CM334, suggesting that these genome regions are subjected to selection during the process of doubled-haploid production. The suitability of doubled-haploid progenies for mapping projects and the differences observed between this intraspecific integrated map with earlier published interspecific pepper maps are discussed.

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.

A barley RFLP map: alignment of three barley maps and comparisons to Gramineae species

Several gene linkage maps have been produced for cultivated barley. We have produced a new linkage map for barley, based on a cross between Hordeum vulgare subsp. spontaneum and Hordeum vulgare subsp. vulgare (Hvs x Hvv), having a higher level of polymorphism than most of the previous barley crosses used for RFLP mapping. Of 133 markers mapped in the Hvs x Hvv F2 population, 69 were previously mapped on other barley maps, and 26 were mapped in rice, maize, or wheat. Two known gene clones were mapped as well as two morphological markers. The distributions of previously mapped markers were compared with their respective barley maps to align the different maps into one consensus map. The distributions of common markers among barley, wheat, rice and maize were also compared, indicating colinear linkage groups among these species.

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.

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.

Segregation distortion and linkage studies in microspore-derived double haploid lines of Hordeum vulgare L

A total of 62 doubled haploid (DH) lines was derived from a cross between tow lines of barley by anther culture. By two-dimensional electrophoresis of seedling proteins, the segregation of 28 loci in the population of DH lines was studied and a linkage map was constructed. The linkage map covered a large part of the length of the genome. A deviation to the 1∶1 segregation expected in the absence of selection was observed for at least one chromosome segment. This might be linked to a gene or group of genes selected because of their involvment in the process of haploid production.

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.

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

Biochemical, molecular and morphological markers have been used to monitor the segregation of alleles at major gene loci in microspore-derived lines of four spring barley crosses and their parents. Significant deviations from the expected Mendelian ratios were observed for four of the ten markers studied in the cross. Distorted ratios were associated with loci located on chromosomes 4H and 6H. The differential transmission of alleles was in favour of the responsive parent (Blenheim) used in the anther culture studies. For the α-Amy-1 locus on chromosome 6H, the preferential transmission of Blenheim alleles was most pronounced in the haploid regenerants that were colchicine treated. These results are discussed in relation to the genetic control of androgenetic response in barley and with respect to the exploitation of another culture in barley improvement.

Gametic selection in anther culture of rice (Oryza sauva L.)

The segregation and recombination of heterozygous isozyme markers have been monitored in anther culture derivatives (i.e., six nonmorphogenic microspore-derived callus [NMC] populations and two anther culture plant [ACP] populations) and F2 plants generated from six F1 hybrids of rice, including five japonica upland/improved indica tropical hybrids. The alleles in excess at some loci displaying skewed segregations in the F2s were consistently overrepresented in the NMC populations. These alleles were also generally found to be overabundant in the two ACP populations except for certain loci that contrastingly segregated in a 1∶1 ratio. Additional distortions were found to be specific to AC derivatives indicating the existence of in vitro gametic selection. Overall, however, the gametic selection in the ACP materials was neutral with regard to the indica and japonica differentiation. Estimates of linkages between markers borne by chromosome 6 using AC-derivative data were consistent with those noted in the F2s and with current knowledge of the isozyme locus linkage map. Given the average neutrality of gametic selection and the consistency of linkage relationships in the ACPs, their further use as rice molecular mapping and gene tagging populations can be investigated with confidence.