Physical distribution of recombination in B-genome chromosomes of tetraploid wheat

Summary Several studies have indicated a noncorrespondence between genetic and physical distances in wheat chromosomes. To study the physical distribution of recombination, polymorphism for C-banding patterns was used to monitor recombination in 67 segments in 11 B-genome chromosome arms of Triticum turgidum. Recombination was absent in proximal regions of all chromosome arms; its frequency increased exponentially with distance from the centromere. A significant difference was observed between the distribution of recombination in physically short and physically long arms. In physically short arms, recombination was almost exclusively concentrated in distal segments and only those regions were represented in their genetic maps. In physically long arms, while a majority of the genetic distance was again based upon recombination in distal chromosome segments, some interstitial recombination was observed. Consequently, these regions also contributed to the genetic maps. Such a pattern of recombination, skewed toward terminal segments of chromosomes, is probably a result of telomeric pairing initiation and strong positive chiasma interference. Interference averaged 0.81 in 35 pairs of adjacent segments and 0.57 across the entire recombining portions of chromosome arms. The total genetic map lengths of the arms corresponded closely to those expected on the basis of their metaphase-I chiasma frequencies. As a consequence of this uneven distribution of recombination there can be a 153-fold difference (or more) in the number of DNA base pairs per unit (centiMorgan) of genetic length.     

T-DNA mediated disruption of essential gametophytic genes in Arabidopsis is unexpectedly rare and cannot be inferred from segregation distortion alone

Many genes are thought to be expressed during the haploid phase in plants, however, very few haploid-specific genes have been isolated so far. T-DNA insertion mutagenesis is a powerful tool for generating mutations that affect gametophyte viability and function, as disruption of a gene essential for these processes should lead to a defect in the transmission of the gametes. Mutants can therefore be screened on the basis of segregation distortion for a reporter resistance gene contained in the T-DNA. We have screened the Versailles collection of Arabidopsis transformants for 1:1 Kan^R:Kan^S segregation after selfing, focussing on gametophyte mutations which show normal transmission through one gametophyte and cause lethality or dysfunction of the other. Only 1.3% (207) of the 16,000 lines screened were scored as good candidates. Thorough genetic analysis of 38 putative T-DNA transmission defect lines (Ttd) identified 8 defective gametophyte mutants, which all showed 0 to 1% T-DNA transmission through the pollen. During the screen, we observed a high background of low-penetrance mutations, often affecting the function of both gametophytes, and many lines which were likely to carry chromosomal rearrangements. The reasons for the small number of retained lines (all male gametophytic) are discussed, as well as the finding that, for most of them, residual T-DNA transmission is obtained through the affected gametophyte. Received: 27 July 1998 / Accepted: 16 September 1998     

Sex-ratio distortion in Drosophila simulans: co-occurence of a meiotic drive and a suppressor of drive

A sex-ratio distortion factor was found at high frequency in D. simulans strains from Seychelles and New Caledonia. This factor is poorly or not expressed within those strains which are resistant to it. Its presence was detected by crossing females from New Caledonia or the Seychelles with males from a different geographic origin. Most of the F1 males obtained produced an excess of females (up to 99%) in their progeny. The two strains are infected with Wolbachia, but these micro-organisms are not involved in the sex-ratio distortion. The sex-ratio factor is shown to be an X-linked meiotic driver; nuclear resistance factor(s) act by suppressing the drive. It is likely that the same X-located driver invaded the two populations, which subsequently developed resistance factor(s) against it.     

Common features of segregation distortion in plants and animals

Segregation distortion is increasingly recognized as a potentially powerful evolutionary force. This runs counter to the perception that non-Mendelian genes are rare genetic curiosities, a view that seems to be supported by the near ubiquity of the Mendelian system of inheritance. There are several reasons why segregation distortion may be more important than is evidenced by known empirical examples. One possibility is that the types of segregation distorters we have found are only a subset of a broader range of non-Mendelian systems, many of which go undetected. In this paper, we review what is known about the sex-linked meiotic drive system in the plant, Silene latifolia, and present some data on the mechanism of segregation distortion. We outline the general features that segregation distorters in plants and animals have in common. In some cases, such as the paucity of systems that directly alter meiotic segregation, there are likely to be inherent constraints on the range of systems that can possibly occur. Other generalities, however, support the notion that many forms of meiotic drive are possible, and that the known examples of segregation distortion are likely to be only subset of those that can possibly occur. Non-Mendelian genes may therefore have greater evolutionary importance than their current abundance in nature would suggest.     

Geographic distribution of alleles at the Ga2 locus for segregation distortion in barley

Summary A distorted segregation of esterase alleles at the complex loci, Est1, Est2 and Est4, was found in an F₂ population. This distortion is typical for cross combinations between the Ga2Ga2 and ga2ga2 genotypes responsible for segregation distortion, since the Ga2 locus is linked with the complex loci encoding the esterase isozymes. The segregation of esterase isozyme patterns in F₂ populations between 473 varieties of barley and a tester of ga2ga2 genotype was examined, and the genotypes inducing segregation distortion were detected. Varieties with a ga2ga2 genotype are widely distributed throughout the world, whereas Ga2Ga2 varieties are found only in eastern and southern regions of Asia, from Japan to North India, with a low frequency. In varieties collected from these regions, some associations were detected between alleles at the Ga2 locus and esterase isozyme patterns. Additionally, most of the Ga2 barley varieties are naked and possess a BtBtbt2bt2 genotype for a non-brittle rachis.     

Modeling segregation distortion for viability selection I. Reconstruction of linkage maps with distorted markers

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.     

Segregation distortion of isozyme loci in cherimoya (Annona cherimola Mill)

The allelic segregation of 13 isozyme loci in hand-fertilized heterozygous cherimoya trees (Annona cherimola Mill.) has been studied. We analyzed 63 locus x progeny combinations and found non-Mendelian segregation in 12 cases. The sequential Bonferroni method revealed only eight cases of non-Mendelian segregation; these have been investigated with several chi-square tests to discover what processes were involved. Gametic selection appears to be the main contributor, although zygotic selection seems also to play a part.     

Segregation,linkage, and diversity of allozymes in knobcone pine

Summary Female gametophytes of knobcone pine were used to study genetic variation at 58 loci in 26 enzyme systems. Mendelian segregation and linkage were tested at 21 loci. Got1, Pgi2, Mnr3, Adh2, and Lap2 were linearly arrayed in a single linkage group. Est and Acp3, and Flest and Lap1, formed two independent linkage groups. Although Mendelian segregation was the rule, several cases of segregation distortion were observed. Pooled over trees, Lap1 and Aap1 showed significant distortion. Of 11 cases of distortion observed for individual trees, 10 showed an excess of common alleles. Pooled over both loci and trees, giving a total sample of 17,183 gametes, the common alleles were significantly overrepresented by 1.1%, and heterogeneity was highly significant. Our results, and others in the literature, suggest that segregation distortion may affect the genetic structure of conifer populations.     

The location of major genes and associated quantitative trait loci on chromosome arm 5BL of wheat

Summary Chromosome 5B of bread wheat is known to carry two major genes giving rise to genetic disorders, Ne1 for hybrid necrosis and Vg for winter variegation. Additionally, in many european winter wheat varieties this chromosome is represented in a translocated form, with 5BL-7BL, 5BL-7BS chromosomes rather than the normal 5B and 7B forms of the standard variety Chinese Spring. Genetic analysis has been carried out to map these genes and the translocation break point, and to investigate their pleiotropic effects or those of linked quantitative trait loci (qtl) for economically important characters. This was facilitated by the development of single chromosome recombinant lines between a normal and translocated karyotype, and growing these in field experiments over two seasons. There was differential segregation in favour of the translocated karyotype in the population of recombinant lines. Linkage analysis revealed that the two morphological markers and the isozyme locus Ibf-B1 were located on the long arm of 5B with a gene order of: breakpoint — Ne1 — Vg — Ibf-B1. Analysis of quantitative characters using these genes as landmarks showed pleiotropic effects of Ne1 or effects of tightly linked qtl on most of the quantitative characters related to grain yield. An additional qtl determining spikelet and grain number/ear appeared to be linked to the centromere. Effects on ear emergence time were associated with both Ne1 and Vg, and these interacted with environments. Similarly, effects on plant height were associated with Ne1 and Vg. In addition, there was a further unlocated locus (loci) for height acting independently of the markers.     

Segregation distortion at marker loci: variation during microspore embryogenesis in maize

In the present study, we analyzed the segregation distortions of markers during in vitro androgenesis in maize. This was based on four segregating populations derived from the A188×DH7 one-way-cross. These populations consisted of very young androgenetic embryos, well-developed calluses, haploid regenerated plantlets and spontaneous diploid plantlets. These structures all represented different developmental stages, from that of microspores to the regenerated plantlets. This study complemented a previous one by Murigneux et al. 1994, where distorted segregations of RFLP markers were detected in a single-seed-descent population and in a doubled-haploid population derived from the same cross. The weakly biased SSD maize genetic map was used as a reference to locate 145 AFLP loci whose allelic segregations were also analyzed in the androgenetic segregating populations. Segregation distortions were determined based on chi-square analysis (P<0.01 and P<0.001). Regions on chromosomes 2 and 8 showed distortions from the beginning of embryo formation, with large effects throughout the process. Regions on chromosomes 3, 4, 6 and 10 could control callus formation from microspores. Other deviations of marker genotypes on chromosomes 1, 4, 6 and 10 could be associated with the regeneration phase. Moreover, the statistical method of Cheng et al. for mapping a lethal factor locus inside segments of linked distorted markers was used to estimate the position of seven partial lethal androgenetic factors on chromosomes 1, 2, 8 and 10. These factors could represent selective genes actively involved in maize androgenesis. Received: 31 July 2000 / Accepted: 2 January 2001     

Interspecific genetic linkage map, segregation distortion and genetic conversion in coffee (Coffea sp.)

An interspecific partial genetic linkage map of Coffea sp. based on 62 backcross hybrids is presented. F₁ hybrids were generated by a cross between the wild C. pseudozanguebariae and the anciently cultivated C. liberica var. dewevrei (DEW); progeny were then derived from a backcross between F₁ hybrid and DEW. The map construction consisted of a two-step strategy using 5.5 and 3.1 LOD scores revealed by simulation file. The map consisted of 181 loci: 167 amplified fragment length polymorphism (AFLP) and 13 random fragment length polymorphism (RFLP) loci. The markers were assembled into 14 linkage groups, each with 4–31 markers covering 1,144 cM. Segregation distortion was observed for 30% of all loci, in particular 3:1 and 1:3 ratios equally favouring each of the two parents. The existence of such ratios suggests genetic conversion events. This map also represents an initial step towards the detection of quantitative trait loci. Received: 4 Janaury 2000 / Accepted: 17 January 2000     

Determination of the frequency of wheat-rye chromosome pairing in wheat x rye hybrids with and without chromosome 5B

Genomic in-situ hybridization (GISH) was used to determine the amount of wheat-rye chromosome pairing in wheat (Triticum aestivum) x rye (Secale cereale) hybrids having chromosome 5B present, absent, or replaced by an extra dose of chromosome 5D. The levels of overall chromosome pairing were similar to those reported earlier but the levels of wheat-rye pairing were higher than earlier determinations using C-banding. Significant differences in chromosome pairing were found between the three genotypes studied. Both of the chromosome-5B-deficient hybrid genotypes showed much higher pairing than the euploid wheat hybrid. However, the 5B-deficient hybrid carrying an extra chromosome 5D had significantly less wheat-rye pairing than the simple 5B-deficient genotype, indicating the presence of a suppressing factor on chromosome 5D. Non-homologous/non-homoeologous chromosome pairing was observed in all three hybrid genotypes. The value of GISH for assessing the level of wheat-alien chromosome pairing in wheat/alien hybrids and the effectiveness of wheat genotypes that affect homoeologous chromosome pairing is demonstrated.     

Cytological and molecular characterization of a chromosome interchange and addition lines in Cadet involving chromosome 5B of wheat and 6Ag of Lophopyrum ponticum

Efforts to transfer wheat curl mite (Eriophyes tulipae Keifer) resistance from Lophopyrum ponticum 10X (Podb.) Love to bread wheat (Triticum aestivum L.) have resulted in the production of a number of cytogenetic stocks, including an addition line of 6Ag, a ditelo addition line, and a wheat-Lophopyrum translocation line. Characterization of these lines with C-banding, in situ hybridization with a Lophopyrum species-specific repetitive DNA probe (pLeUCD2), and Southern blotting with pLeUCD2 and a 5S ribosomal DNA probe (pScT7) confirmed that the distal portion of the short arm of 6Ag was translocated onto the distal portion of 5BS (5BL. 5BS-6AgS). It was also determined that the ditelo addition was an acrocentric chromosome of 6AgS.     

Genetic and physical characterization of grain texture-related loci in diploid wheat

Endosperm texture, i.e. the hardness or softness of the grain, is an important quality criterion in cereals because it determines many grain end-use properties. Grain softness is the dominant trait and is mainly controlled by the Ha locus on the short arm of chromosome 5D in hexaploid bread wheat. Genes for puroindoline a (Pina-D1), puroindoline b (Pinb-D1), and grain softness related protein (Gsp-D1) have been shown to be linked to the Ha locus in different mapping populations and have been associated with the expression of grain softness. The study of the linkage relationships among these genes has been limited by the low level of polymorphism in the D genome of hexaploid Triticum aestivum. In the present study, a highly polymorphic Triticum monococcum mapping population was used to analyze linkage relationships among these three genes. Gsp-A ^m 1 and Pina-A ^m 1 were found to be completely linked and lie 0.14 cM distal to Pinb-A ^m 1 in the distal region of the short arm of chromosome 5A^m. The tight genetic linkage among these three genes was paralleled by their physical proximity within a single 105-kb clone isolated from a T. monococcum bacterial artificial chromosome (BAC) library. A restriction map of this BAC clone showed that Pina-A ^m 1 is located between Pinb-A ^m 1 and Gsp-A ^m 1. Partial sequences of the T. monococcum genes showed a high degree of similarity with their T. aestivum counterparts (≥ 94%). Marker-assisted selection strategies based on the tight linkage among Ha-related genes are discussed. Received: 27 June 1999 / Accepted: 18 August 1999     

Selection and segregation distortion in a sex-differentiated population

We extend the classical model for selection at an autosomal locus in a sex-differentiated population to include segregation distortion. The equations remain the same, but the fitness parameters are interpreted differently and refer to alleles instead of genotypes. We derive conditions for internal and external stability of the equilibria, i.e., stability with respect to perturbations of alleles that are already present at equilibrium and stability with respect to invasion attempts by newly arising alleles. We show that, in a sex-differentiated population, external stability of an equilibrium can be judged on the basis of Shaw--Mohler criteria. Throughout, we compare the situation in populations with and without sex differentiation. Interestingly, internal stability is more difficult to achieve in a population without sex differentiation than in a population in which selection and segregation distortion are restricted to one sex. In a companion paper we show how the general results of the present paper can lead to new insights into specific systems such as the t complex of the house mouse.     

Two loci on wheat chromosome 5A regulate the differential cold-dependent expression of the cor14b gene in frost-tolerant and frost-sensitive genotypes

Although cold acclimation in cereals involves the expression of many cold-regulated genes, genetic studies have shown that only very few chromosomal regions carry loci that play an important role in frost tolerance. To investigate the genetic relationship between frost tolerance and the expression of cold-regulated genes, the expression and regulation of the wheat homolog of the barley cold-regulated gene cor14b was studied at various temperatures in frost-sensitive and frost-tolerant wheat genotypes. At 18/15 °C (day/night temperatures) frost-tolerant plants accumulated cor14b mRNAs and expressed COR14b proteins, whereas the sensitive plants did not. This result indicates that the threshold temperature for induction of the wheat cor14b homolog is higher in frost-resistant plants, and allowed us to use this polymorphism in a mapping approach. Studies made with chromosome substitution lines showed that the polymorphism for the threshold induction temperature of the wheat cor14b homolog is controlled by a locus(i) located on chromosome 5A of wheat, while the cor14b gene was mapped in Triticum monococcum on the long arm of chromosome 2A^m. The analysis of single chromosome recombinant lines derived from a cross between Chinese Spring/Triticum spelta 5A and Chinese Spring/Cheyenne 5A identified two loci with additive effects that are involved in the genetic control of cor14b mRNA accumulation. The first locus was tightly linked to the marker psr911, while the second one was located between the marker Xpsr2021 and Frost resistance 1 (Fr1). Received: 20 July 1999 / Accepted: 15 November 1999     

Linkage of the hordein loci Hor1 and Hor2 with the powdery mildew resistance loci Ml-k and Ml-a on Barley chromosome 5

Summary The linkage relationship among the loci Hor1, Hor2, Ml-k and Ml-a on the short arm of chromosome 5 was studied by progeny testing the F₂ generation of two crosses. The loci Hor1 and Hor2 code for polypeptides of the storage protein hordein (prolamin) and the loci Ml-k and Ml-a determine the resistance reaction with some powdery mildew fungi cultures. The order of the loci is Ml-k, Hor1, Ml-a, and Hor2, the first named being nearest the centromere. The recombination percentage between Hor1 and Hor2 was determined in the F₁ and F₂ generations in both crosses, the combined estimate being 7.4±0.9 per cent. The recombination percentage estimated between Ml-k and Hor1 was 4.0±1.3, between Hor1 and Ml-a, 5.3±1.1, and between Ml-a and Hor2, 6.1±1.2. The estimates involving the Ml- loci were all probably a little too high.     

A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits

Background

Genotyping-by-sequencing (GBS) is a high-throughput genotyping approach that is starting to be used in several crop species, including bread wheat. Anchoring GBS tags on chromosomes is an important step towards utilizing them for wheat genetic improvement. Here we use genetic linkage mapping to construct a consensus map containing 28644 GBS markers.

Results

Three RIL populations, PBW343 × Kingbird, PBW343 × Kenya Swara and PBW343 × Muu, which share a common parent, were used to minimize the impact of potential structural genomic variation on consensus-map quality. The consensus map comprised 3757 unique positions, and the average marker distance was 0.88 cM, obtained by calculating the average distance between two adjacent unique positions. Significant variation of segregation distortion was observed across the three populations. The consensus map was validated by comparing positions of known rust resistance genes, and comparing them to wheat reference genome sequences recently published by the International Wheat Genome Sequencing Consortium, Rye and Ae. tauschii genomes. Three well-characterized rust resistance genes (Sr58/Lr46/Yr29, Sr2/Yr30/Lr27, and Sr57/Lr34/Yr18) and 15 published QTLs for wheat rusts were validated with high resolution. Fifty-two per cent of GBS tags on the consensus map were successfully aligned through BLAST to the right chromosomes on the wheat reference genome sequence.

Conclusion

The consensus map should provide a useful basis for analyzing genome-wide variation of complex traits. The identified genes can then be explored as genetic markers to be used in genomic applications in wheat breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1424-5) contains supplementary material, which is available to authorized users.     

Genetic linkage between C-bands and storage protein genes in chromosome 1B of tetraploid wheat

Summary Genetic mapping of polymorphic C-bands allows direct comparisons between genetic and physical maps. Eleven C-bands and two seed storage protein genes on chromosome 1B, polymorphic between Langdon durum and four accessions of T. dicoccoides, were used to study the distribution of recombination along the entire length of the chromosome. Recombination in the short arm was almost completely restricted to the satellite, two-thirds of the arm's length from the centromere; the Gli-B1 gene was found to be tightly linked to the telomeric C-band. In the long arm, the distal 51.4% of the arm accounted for 88% of recombination; the proximal half of the arm accounted for the remaining 12%. While the amount of crossing-over differed significantly between the four T. dicoccoides 1B chromosomes, there were no significant differences in the relative distributions of crossing-over along the chromosome. Consequently, the genetic maps obtained from the four individual T. dicoccoides chromosomes were combined to yield a consensus map of 14 markers (including the centromere) for the chromosome.     

Recombination mapping of some chromosome 1A-, 1B-, 1D- and 6B-controlled gliadins and low-molecular-weight glutenin subunits in common wheat

 Inheritance of low-molecular-weight glutenin subunits (LMW GS) and gliadins was studied in the segregating progeny from several crosses between common wheat genotypes. The occurrence of a few recombinants in the F₂ grains of the cross Skorospelka Uluchshennaya×Kharkovskaya 6 could be accounted for by assuming that the short arm of chromosome 1D contains two tightly linked loci each coding for at least one gliadin plus one C-type LMW GS. These loci were found to recombine at a frequency of about 2%, and to be linked to the Glu-D3 locus coding for B-type LMW GS. Some proteins showing biochemical characteristics of D-type or C-type LMW GS were found to be encoded by the Gli-B1 and Gli-B2 loci, respectively. Strongly stained B-type LMW GS in cvs Skorospelka Uluchshennaya and Richelle were assigned to the Glu-B3 locus, but recombination between this locus and Gli-B1 was not found. Analogously, in the cross Bezostaya 1×Anda, no recombination was found between Gli-A1 and Glu-A3, suggesting the maximum genetic distance between these loci to be 0.97% (P=0.05). A B-type LMW GS in cv Kharkovskaya 6 was assigned to the Glu-B2 locus, with about 25% recombination from the Gli-B1 locus. The present results suggested that alleles at Gli loci may relate to dough quality and serve as genetic markers of certain LMW GS affecting breadmaking quality. Received: 9 July 1996/Accepted: 15 November 1996