Genetic linkage map of a wheat×spelt cross

 We constructed a genetic map of a cross between the Swiss winter wheat (Triticum aestivum L.) variety Forno and the Swiss winter spelt (Triticum spelta L.) variety Oberkulmer. For the linkage analysis,176 polymorphic RFLP probes and nine microsatellites were tested on 204 F₅ recombinant inbred lines (RILs) of Forno×Oberkulmer revealing 242 segregating marker loci. Thirty five percent of these loci showed significant (P>0.05) deviation from a 1 : 1 segregation, and the percentage of Forno alleles ranged from 21% to 83% for individual marker loci. Linkage analysis was performed with the program MAPMAKER using the Haldane mapping function. Using a LOD threshold of 10, we obtained 37 linkage groups. After finding the best order of marker loci within linkage groups by multi-point analysis we assembled the linkage groups into 23 larger units by lowering the LOD threshold. All except one of the 23 new linkage groups could be assigned to physical chromosomes or chromosome arms according to hybridisation patterns of nulli-tetrasomic lines of Chinese Spring and published wheat maps. This resulted in a genetic map comprising 230 marker loci and spanning 2469 cM. Since the analysed population is segregating for a wide range of agronomically important traits, this genetic map is an ideal basis for the identification of quantitative trait loci (QTLs) for these traits. Received: 3 August 1998 / Accepted: 28 November 1998     

Genetic linkage map of the interspecific grape rootstock cross Ramsey (Vitis champinii) × Riparia Gloire (Vitis riparia)

The first genetic linkage map of grape derived from rootstock parents was constructed using 188 progeny from a cross of Ramsey (Vitis champinii) × Riparia Gloire (V. riparia). Of 354 simple sequence repeat markers tested, 205 were polymorphic for at least one parent, and 57.6% were fully informative. Maps of Ramsey, Riparia Gloire, and the F1 population were created using JoinMap software, following a pseudotestcross strategy. The set of 205 SSRs allowed for the identification of all 19 Vitis linkage groups (2n=38), with a total combined map length of 1,304.7 cM, averaging 6.8 cM between markers. The maternal map consists of 172 markers aligned into 19 linkage groups (1,244.9 cM) while 126 markers on the paternal map cover 18 linkage groups (1,095.5 cM). The expected genome coverage is over 92%. Segregation distortion occurred in the Ramsey, Riparia Gloire, and consensus maps for 10, 13, and 16% of the markers, respectively. These distorted markers clustered primarily on the linkage groups 3, 5, 14 and 17. No genome-wide difference in recombination rate was observed between Ramsey and Riparia Gloire based on 315 common marker intervals. Fifty-four new Vitis-EST-derived SSR markers were mapped, and were distributed evenly across the genome on 16 of the 19 linkage groups. These dense linkage maps of two phenotypically diverse North American Vitis species are valuable tools for studying the genetics of many rootstock traits including nematode resistance, lime and salt tolerance, and ability to induce vigor.     

Genetic analysis of a two-row × six-row cross of barley using doubled-haploid lines

 A study was conducted on a two-row/six-row cross of barley to (1) determine the yield potential, (2) detect epistasis and genetic correlations, (3) estimate the heritabilities of six agronomic traits, and (4) study the effect of the V locus on the agronomic traits in the barley cross. The effects of five other marker loci (Re2, s, R, Est1, and Est5) on the six agronomic traits were also studied. One hundred and ninety doubled-haploid (DH) lines were derived from a ‘Leger’/CI9831 cross using the bulbosum method. The DH lines and the two parents were tested for grain yield, test weight, seed weight, plant height, lodging, and heading/maturity at two locations in Eastern Canada in 1993. Additive×additive epistasis and genetic correlations were detected for some of the agronomic traits. Many of the heritability estimates were high; however, significant progress in yield improvement would be difficult to achieve because of a low mean yield of the DH lines. Under the growing conditions in Eastern Canada, six-row lines outyielded two-row by 20–27%. Six-row lines, however, were associated with low test weight, low seed weight, and severe lodging. Some two-row lines yielded higher than the two-row parent CI9831, but none of the six-row lines yielded higher than the six-row parent ‘Leger’. The R, s, and Est5 loci were associated with the six agronomic traits, but the Est1 locus was apparently not associated with the agronomic traits. The effect of the Re2 locus was probably due to its close linkage with the V locus. Further studies are needed to determine if superior six-row lines can be developed from two-row/six-row crosses. Received: 19 September 1996 / Accepted: 18 October 1996     

Genetic linkage mapping of an annual × perennial ryegrass population

Annual (Lolium multiflorum Lam.) and perennial (L. perenne L.) ryegrass are two common forage and turfgrass species grown throughout the world. Perennial ryegrass is most commonly used for turfgrass purposes, and contamination by annual ryegrass, through physical seed mixing or gene flow, can result in a significant reduction in turfgrass quality. Seed certifying agencies in the United States currently use a test called seedling root fluorescence (SRF) to detect contamination between these species. The SRF test, however, can be inaccurate and therefore, the development of additional markers for species separation is needed. Male and female molecular-marker linkage maps of an interspecific annual × perennial ryegrass mapping population were developed to determine the map location of the SRF character and to identify additional genomic regions useful for species separation. A total of 235 AFLP markers, 81 RAPD markers, 16 comparative grass RFLPs, 106 SSR markers, 2 isozyme loci and 2 morphological characteristics, 8-h flowering, and SRF were used to construct the maps. RFLP markers from oat and barley and SSR markers from tall fescue and other grasses allowed the linkage groups to be numbered, relative to the Triticeae and the International Lolium Genome Initative reference population P150/112. The three-generation population structure allowed both male and female maps to be constructed. The male and female maps each have seven linkage groups, but differ in map length with the male map being 537 cm long and the female map 712 cm long. Regions of skewed segregation were identified in both maps with linkage groups 1, 3, and 6 of the male map showing the highest percentage of skewed markers. The (SRF) character mapped to linkage group 1 in both the male and female maps, and the 8-h flowering character was also localized to this linkage group on the female map. In addition, the Sod-1 isozyme marker, which can separate annual and perennial ryegrasses, mapped to linkage group 7. These results indicate that Lolium linkage groups 1 and 7 may provide additional markers and candidate genes for use in ryegrass species separation.Communicated by C. Möllers     

Constructing a linkage–linkage disequilibrium map using dominant-segregating markers

The relationship between linkage disequilibrium (LD) and recombination fraction can be used to infer the pattern of genetic variation and evolutionary process in humans and other systems. We described a computational framework to construct a linkage–LD map from commonly used biallelic, single-nucleotide polymorphism (SNP) markers for outcrossing plants by which the decline of LD is visualized with genetic distance. The framework was derived from an open-pollinated (OP) design composed of plants randomly sampled from a natural population and seeds from each sampled plant, enabling simultaneous estimation of the LD in the natural population and recombination fraction due to allelic co-segregation during meiosis. We modified the framework to infer evolutionary pasts of natural populations using those marker types that are segregating in a dominant manner, given their role in creating and maintaining population genetic diversity. A sophisticated two-level EM algorithm was implemented to estimate and retrieve the missing information of segregation characterized by dominant-segregating markers such as single methylation polymorphisms. The model was applied to study the relationship between linkage and LD for a non-model outcrossing species, a gymnosperm species, Torreya grandis, naturally distributed in mountains of the southeastern China. The linkage–LD map constructed from various types of molecular markers opens a powerful gateway for studying the history of plant evolution.     

Construction of a saturated linkage map for Prunus using an almond×peach F2 progeny

 A map with 246 markers (11 isozymes and 235 RFLPs) was constructed using an interspecific F₂ population between almond (cv Texas) and peach (cv Earlygold). RFLPs were obtained using 213 probes from the genomic and cDNA libraries of different species (almond, peach, P. ferganensis, cherry, plum and apple), including 16 almond probes which correspond to known genes. All markers were distributed in eight linkage groups, the same as the basic chromosome number of the genus, covering a total distance of 491 cM. The average map density was 2.0 cM/marker and only four gaps of 10 cM or more were found; the two largest gaps were 12cM each. This map was compared with one constructed previously with an intraspecific almond population sharing 67 anchor loci. Locus order was nearly identical and distances were not significantly different. A large proportion of the mapped loci (46%) had skewed segregations; in approximately half of them, the distortion was due to an excess of heterozygotes. One of the distorted regions could be associated with the position of the self-incompatibility gene of almond. Received: 6 November 1997 / Accepted: 26 May 1998     

Generation and exploration of a dense genetic map in a region of a QTL affecting corpora lutea in a Meishan × Yorkshire cross

Previously genomic scans revealed quantitative trait loci (QTL) on porcine Chromosome 8 (SSC8) as significantly affecting the number of corpora lutea (CL) in swine. In one study, statistical evidence for the putative QTL was found in the chromosomal region defined by the microsatellites (MS) SW205, SW444, SW206, and SW29. A Yeast Artificial Chromosome library was screened by using the corresponding primers for clones containing these MS by PCR. From five positive YAC clones, 10 additional MS were isolated and mapped to SSC8 with the INRA-University of Minnesota porcine Radiation Hybrid (IMpRH) panel. The genetic map position of the QTL has been refined by addition of these 10 markers. The QTL evaluation included pedigrees of F₂-intercross Meishan × Yorkshire design, with phenotypic data of 108 F₂ female offspring and genotypic data for 29 MS markers on SSC8. The analysis was performed by using the least squares regression method. The calculated QTL effect for CL obtained by the multilocus least squares method showed a maximum test statistic (F value = 13.98) at position 99 cM between three MS derived from YACs containing SW205 and SW1843 spanning an interval of 7.1 cM. The point-wise (nominal) P-value was 5.21 × 10⁻⁶ corresponding to a genome-wide P-value of 0.009. The additive QTL effect explained 17.4% of the phenotypic variance. Received: 23 December 2000 / Accepted: 07 May 2001     

A molecular linkage map with associated QTLs from a hulless × covered spring oat population

In spring-type oat (Avena sativa L.), quantitative trait loci (QTLs) detected in adapted populations may have the greatest potential for improving germplasm via marker-assisted selection. An F₆ recombinant inbred (RI) population was developed from a cross between two Canadian spring oat varieties: Terra, a hulless line, and Marion, an elite covered-seeded line. A molecular linkage map was generated using 430 AFLP, RFLP, RAPD, SCAR, and phenotypic markers scored on 101 RI lines. This map was refined by selecting a robust set of 124 framework markers that mapped to 35 linkage groups and contained 35 unlinked loci. One hundred one lines grown in up to 13 field environments in Canada and the United States between 1992 and 1997 were evaluated for 16 agronomic, kernel, and chemical composition traits. QTLs were localized using three detection methods with an experiment-wide error rate of approximately 0.05 for each trait. In total, 34 main-effect QTLs affecting the following traits were identified: heading date, plant height, lodging, visual score, grain yield, kernel weight, milling yield, test weight, thin and plump kernels, groat -glucan concentration, oil concentration, and protein. Several of these correspond to QTLs in homologous or homoeologous regions reported in other oat QTL studies. Twenty-four QTL-by-environment interactions and three epistatic interactions were also detected. The locus controlling the covered/hulless character (N1) affected most of the traits measured in this study. Additive QTL models with N1 as a covariate were superior to models based on separate covered and hulless sub-populations. This approach is recommended for other populations segregating for major genes. Marker-trait associations identified in this study have considerable potential for use in marker-assisted selection strategies to improve traits within spring oat breeding programs.Communicated by P. Langridge     

Genetic dissection of top three leaf traits in rice using progenies from a japonica × indica cross

The size of the top three leaves of rice plants is strongly associated with yield; thus, it is important to consider quantitative traits representing leaf size(e.g.,length and width) when breeding novel rice varieties.It is challenging to measure such traits on a large scale in the field, and little is known about the genetic factors that determine the size of the top three leaves. In the present study, a population of recombinant inbred lines(RILs) and reciprocal single chromosomal segment substitution lines(SSSLs) derived from the progeny of a japonica Asominori ? indica IR24 cross were grown under four diverse environmental conditions. Six morphological traits associated with leaf size were measured,namely length and width of the flag, second and third leaves. In the RIL population, 49 QTLs were identified that clustered in 30 genomic region. Twenty-three of these QTLs were confirmed in the SSSL population. A comparison with previously reported genes/QTLs revealed eight novel genomic regions that contained uncharacterized ORFs associated with leaf size. The QTLs identified in this study can be used for markerassisted breeding and for fine mapping of novel genetic elements controlling leaf size in rice.     

Localization of Müllerian mimicry genes on a dense linkage map of Heliconius erato

We report a dense genetic linkage map of Heliconius erato, a neotropical butterfly that has undergone a remarkable adaptive radiation in warningly colored mimetic wing patterns. Our study exploited natural variation segregating in a cross between H. erato etylus and H. himera to localize wing color pattern loci on a dense linkage map containing amplified fragment length polymorphisms (AFLP), microsatellites, and single-copy nuclear loci. We unambiguously identified all 20 autosomal linkage groups and the sex chromosome (Z). The map spanned a total of 1430 Haldane cM and linkage groups varied in size from 26.3 to 97.8 cM. The average distance between markers was 5.1 cM. Within this framework, we localized two major color pattern loci to narrow regions of the genome. The first gene, D, responsible for red/orange elements, had a most likely placement in a 6.7-cM region flanked by two AFLP markers on the end of a large 87.5-cM linkage group. The second locus, Sd, affects the melanic pattern on the forewing and was found within a 6.3-cM interval between flanking AFLP loci. This study complements recent linkage analysis of H. erato's comimic, H. melpomene, and forms the basis for marker-assisted physical mapping and for studies into the comparative genetic architecture of wing-pattern mimicry in Heliconius.     

Constructing a high-density linkage map for Gossypium hirsutum × Gossypium barbadense and identifying QTLs for lint percentage

To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high-density simple sequence repeat(SSR) genetic linkage map was developed from a BC1F1 population of Gossypium hirsutum×Gossypium barbadense. The map comprised 2,292 loci and covered 5115.16 centi Morgan(c M) of the cotton AD genome, with an average marker interval of 2.23 c M. Of the marker order for 1,577 common loci on this new map, 90.36% agrees well with the marker order on the D genome sequence genetic map. Compared with five published high-density SSR genetic maps, 53.14% of marker loci were newly discovered in this map. Twenty-six quantitative trait loci(QTLs) for lint percentage(LP) were identified on nine chromosomes. Nine stable or common QTLs could be used for marker-assisted selection. Fifty percent of the QTLs were from G. barbadense and increased LP by 1.07%–2.41%. These results indicated that the map could be used for screening chromosome substitution segments from G. barbadense in the Upland cotton background, identifying QTLs or genes from G. barbadense, and further developing the gene pyramiding effect for improving fiber yield and quality.     

Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map

Key message

Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement.

Abstract

Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today’s fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.     

Genetic linkage studies of the human glycosphingolipid β-galactosidases

The genetic linkage relationships of the human glycosphingolipid beta-galactosidases were determined using human--mouse somatic cell hybrids. A new method was devised for the estimation of human galactosylceramide, lactosylceramide, and GMI-ganglioside beta-galactosidase activities in the presence of their mouse counterparts, which takes advantage of the reproducible specific activity of lysosomal hydrolases under a given set of culture conditions and is based on differences in both pH optima and sensitivity to chloride ion. Human and mouse chromosomes were identified by their characteristic banding patterns obtained after quinacrine staining, and the optimum glycolipid beta-galactosidase activity was determined for three different substrates. A ratio was defined for each activity which was the specific activity at the human pH optimum divided by the specific activity at the mouse pH optimum. Linear regression analysis was used to test for concordant segregation between pH ratios for each enzyme and the frequency of occurrence of different human chromosomes in the man--mouse somatic hybrid clones. The results obtained from two independent series of hybrid clones indicated that human beta-galactosidase activities consistently segregated with human chromosome 12 in these somatic cell hybrids.     

A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid

Genetic maps provide an important genomic resource of basic and applied significance. Spruce (Picea) has a very large genome size (between 0.85 × 1010 and 2.4 × 1010 bp; 8.5-24.0 pg/1C, a mean of 17.7 pg/1C ). We have constructed a near-saturated genetic linkage map for an interspecific backcross (BC1) hybrid of black spruce (BS; Picea mariana (Mill.) B.S.P.) and red spruce (RS; Picea rubens Sarg.), using selectively amplified microsatellite polymorphic loci (SAMPL) markers. A total of 2284 SAMPL markers were resolved using 31 SAMPL-MseI selective nucleotide primer combinations. Of these, 1216 SAMPL markers showing Mendelian segregation were mapped, whereas 1068 (46.8%) SAMPL fragments showed segregation distortion at α = 0.05. Maternal, paternal, and consensus maps consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal BS map consisted of 814 markers distributed over 12 linkage groups, covering 1670 cM, with a mean map distance of 2.1 cM between adjacent markers. The paternal BS × RS map consisted of 773 markers distributed over 12 linkage groups, covering 1563 cM, with a mean map distance of 2.0 cM between adjacent markers. The consensus interspecific hybrid BC1 map consisted of 1216 markers distributed over 12 linkage groups, covering 1865 cM (98% genome coverage), with a mean map distance of 1.5 cM between adjacent markers. The genetic map reported here provides an important genomic resource in Picea, Pinaceae, and conifers.     

Exploitation of pepper EST–SSRs and an SSR-based linkage map

As genome and cDNA sequencing projects progress, a tremendous amount of sequence information is becoming publicly available. These sequence resources can be exploited for gene discovery and marker development. Simple sequence repeat (SSR) markers are among the most useful because of their great variability, abundance, and ease of analysis. By in silico analysis of 10,232 non-redundant expressed sequence tags (ESTs) in pepper as a source of SSR markers, 1,201 SSRs were found, corresponding to one SSR in every 3.8 kb of the ESTs. Eighteen percent of the SSR–ESTs were dinucleotide repeats, 66.0% were trinucleotide, 7.7% tetranucleotide, and 8.2% pentanucleotide; AAG (14%) and AG (12.4%) motifs were the most abundant repeat types. Based on the flanking sequences of these 1,201 SSRs, 812 primer pairs that satisfied melting temperature conditions and PCR product sizes were designed. 513 SSRs (63.1%) were successfully amplified and 150 of them (29.2%) showed polymorphism between Capsicum annuum ‘TF68’ and C. chinense ‘Habanero’. Dinucleotide SSRs and EST–SSR markers containing AC-motifs were the most polymorphic. Polymorphism increased with repeat length and repeat number. The polymorphic EST–SSRs were mapped onto the previously generated pepper linkage map, using 107 F₂ individuals from an interspecific cross of TF68 × Habanero. One-hundred and thirtynine EST–SSRs were located on the linkage map in addition to 41 previous SSRs and 63 RFLP markers, forming 14 linkage groups (LGs) and spanning 2,201.5 cM. The EST–SSR markers were distributed over all the LGs. This SSR-based map will be useful as a reference map in Capsicum and should facilitate the use of molecular markers in pepper breeding.Gibum Yi and Je Min Lee equally contributed to this work.     

Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

The construction of the first genetic map in autotetraploid blueberry has been made possible by the development of new SNP markers developed using genotyping by sequencing in a mapping population created from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum). The novel SNP markers were supplemented with existing SSR markers to enable the alignment of parental maps.  In total, 1794 single nucleotide polymorphic (SNP) markers and 233 simple sequence repeat (SSR) markers exhibited segregation patterns consistent with a random chromosomal segregation model for meiosis in an autotetraploid. Of these, 700 SNPs and 85 SSRs were utilized for construction of the ‘Draper’ genetic map, and 450 SNPs and 86 SSRs for the ‘Jewel’ map.  The ‘Draper’ map comprises 12  linkage groups (LG), associated with the haploid chromosome number for blueberry, and totals 1621 cM while the ‘Jewel’ map comprises 20 linkage groups totalling 1610 cM. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents.     

Advanced backcross QTL analysis of a Lycopersicon esculentum ×Lycopersicon parviflorum cross

Lycopersicon parviflorum is a sexually compatible, wild tomato species which has been largely unutilized in tomato breeding. The Advanced Backcross QTL (AB-QTL) strategy was used to explore this genome for QTLs affecting traits of agronomic importance in an interspecific cross between a tomato elite processing inbred, Lycopersicon esculentum E6203, and the wild species L. parviflorum (LA2133). A total of 170 BC2 plants were genotyped by means of 133 genetic markers (131 RFLPs; one PCR-based marker, I-2, and one morphological marker, u, uniform ripening). Approximately 170 BC3 families were grown in replicated field trials, in California, Spain and Israel, and were scored for 30 horticultural traits. Significant putative QTLs were identified for all traits, for a total of 199 QTLs, ranging from 1 to 19 QTLs detected for each trait. For 19 (70%) traits (excluding traits for which effects of either direction are not necessarily favourable or unfavourable) at least one QTL was identified for which the L. parviflorum allele was associated with an agronomically favourable effect, despite the overall inferior phenotype of the wild species. Received: 14 September 1999 / Accepted: 7 October 1999