The PiGMaP consortium linkage map of the pig (Sus scrofa)

A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (16.5 Morgans) than the genetic map of the homogametic sex (female) (21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be 18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.     

Direction of Translation and Size of Bacteriophage phiX174 Cistrons

Translation of the bacteriophage X174 genome follows cistron order D-E-F-G-H-A-B-C. To establish this, the position of a nonsense mutation on the genetic map was compared with the physical size (molecular weight) of the appropriate protein fragment generated in nonpermissive cells. Distances on the X174 genetic map and distances on a physical map constructed from the molecular weights of X174 proteins and protein fragments are proportional over most of the genome with the exception of the high recombination region within cistron A.     

Identification of Receptor-Tyrosine-Kinase-Signaling Target Genes Reveals Receptor-Specific Activities and Pathway Branchpoints During Drosophila Development

Genetic maps provide a means to estimate the probability of the co-inheritance of linked loci as they are transmitted across generations in both experimental and natural populations. However, in the age of whole-genome sequences, physical distances measured in base pairs of DNA provide the standard coordinates for navigating the myriad features of genomes. Although genetic and physical maps are colinear, there are well-characterized and sometimes dramatic heterogeneities in the average frequency of meiotic recombination events that occur along the physical extent of chromosomes. There also are documented differences in the recombination landscape between the two sexes. We have revisited high-resolution genetic map data from a large heterogeneous mouse population and have constructed a revised genetic map of the mouse genome, incorporating 10,195 single nucleotide polymorphisms using a set of 47 families comprising 3546 meioses. The revised map provides a different picture of recombination in the mouse from that reported previously. We have further integrated the genetic and physical maps of the genome and incorporated SSLP markers from other genetic maps into this new framework. We demonstrate that utilization of the revised genetic map improves QTL mapping, partially due to the resolution of previously undetected errors in marker ordering along the chromosome.GENETIC maps exist for hundreds of different species, and genetic map construction continues to play an important role in the characterization of genomes (Tanksley et al. 1992; Kong et al. 2002; Chowdhary and Raudsepp 2006; Stapley et al. 2008). A genetic map defines the linear order and relative distances among a set of marker loci in units that correspond to the frequency of meiotic recombination between the loci. Until recently mouse genetic maps based on simple sequence length polymorphism (SSLP) markers (Lyon 1976) have been sufficient for most experimental purposes since, unlike the hundreds of thousands of markers required in human genetic association studies, a relatively small number of markers is needed to map crosses between inbred mouse strains. However, recent developments in whole-genome high-resolution mapping in the mouse (Churchill et al. 2004; Valdar et al. 2006) and interest in examining recombination rates at an ultra-fine scale (Myers et al. 2005) have reawakened the need to develop a high-resolution genetic map in the mouse.The current standard genetic map of the mouse has been compiled from a substantial body of historical data and maintained by the Mouse Genome Informatics (MGI) project at The Jackson Laboratory (Bult et al. 2008). We will refer to it as the MGI map. The primary sources of data used to construct the MGI map were two mapping panels, described here. However, the current map is based on a consensus developed by the 2000 Chromosome Committee using all available published data. The map has continued to be maintained by MGI with the addition of new genetic markers and data but, because the map is based on consensus, published errors may have been perpetuated.The Jackson Laboratory developed a genetic map based on two sets of 94 progeny obtained from reciprocal backcrosses (BSB and BSS) between the inbred strains C57BL/6J and SPRET/EiJ (Rowe et al. 1994). These strains represent two different species of mouse (Mus musculus and Mus spretus). The map provides a wealth of genetic information, but problems with male fertility restrict breeding options and thus the map is female specific. The problems with male fertility may have resulted in some multi-locus distortion in the mapping panel (Montagutelli et al. 1996). Currently, 1372 and 4913 markers have been typed on the BSB and BSS backcross panels, respectively (Broman et al. 2002). Researchers at The Whitehead Institute and the Massachusetts Institute of Technology (MIT) developed a map of 4006 SSLP markers using an intercross population of 46 mice derived from strains OB (C57BL/6J-Lep^ob/ob) and CAST (CAST/EiJ) (Dietrich et al. 1994). Both parental strains OB and CAST are derived from M. musculus, but CAST is from a distinct subspecies, M. m. castaneus. The intercross mating strategy produces observable recombination from both male and female parents, but the two cannot be distinguished. Thus the map is sex averaged and based on 92 meioses. The Whitehead/MIT map was expanded to include 7377 SSLP markers (Dietrich et al. 1996). These are denoted as, e.g., D7Mit54, where “7” indicates the chromosome to which the marker is mapped and “54” is an arbitrary index. They are commonly referred to as “Mit” markers.Map resolution is limited by the number of observable recombination events in each of these panels. With 94 meioses (in each backcross) and an average of 14 recombination events/haploid genome transmitted, limiting resolution is on the order of 1 cM. A much larger panel would be needed to achieve subcentimorgan resolution and to accurately position high-density sets of SNP markers.Here we propose a new standard genetic map of the laboratory mouse based on data from a large heterogeneous stock (HS) mouse population descended from eight inbred strains (DBA/2J, C3H/HeJ, AKR/J, A/J, BALB/cJ, CBA/J, C57BL/6J, and LP/J) representing a diverse sample of the classical inbred strains (Petkov et al. 2004). Shifman et al. (2006) calculated genetic maps based on 11,247 informative SNP markers in 2293 HS individuals. The marker set is dense with 99% of the SNP intervals <500 kb, 81.2% <250 kb, and an estimated allele inheritance-based accuracy of 99.98%. Map positions were calculated separately for male and female meioses using CRIMAP software (Green et al. 1990), and the total length of the sex-averaged map is 1630 cM, as defined by the most distal SNP markers in their panel. The MGI map is 1783 cM on the basis of the most distal available marker position for each chromosome. However, on the basis of the most distal shared markers, the original Shifman map at 1612 cM is substantially longer than the MGI map at 1445 cM. It was not immediately clear if this discrepancy was due to the nature of recombination in the HS population or to their method of map estimation.There are at least two methodological problems with the HS map reported in Shifman et al. (2006). First, the map was constructed using a sliding window of 5–15 SNPs to handle eight multi-generation families within the CRIMAP software. Ideally, one considers all markers on a chromosome simultaneously in constructing a genetic map, and we found that this could be accomplished by splitting the complex pedigrees into sibships. Although splitting the pedigree results in slightly less efficient estimates of intermarker distances, this approach should incur no bias. Maps based on the full set of markers but with the complex pedigrees split into sibships are thus arguably better than maps based on the full pedigrees but with a sliding window of 5–15 markers. Second, analysis of families with incomplete parental genotypes may have contributed to an inflated map size. Sixteen of the 72 families lack parental genotypes or have genotypes for just one parent (15 of the 72), and many of them are small (26 have six or fewer siblings). Sibships with no parental genotype data of their own can give no information about sex-specific recombination rates. In conjunction with other sibships for which parental genotypes are available, they can provide some information, but the CRIMAP software (last modified in 1990) makes some approximations that result in a large bias even in the sex-averaged genetic maps for small sibships lacking parental genotype data.For these reasons, we recomputed the mouse genetic map on the basis of the original data reported and discuss the differences between the original Shifman map and the revised Shifman map below. The revised Shifman map provides a markedly different picture of recombination in the mouse: the estimated sex-averaged chromosome lengths correspond more closely to those in the original MGI map; the sex difference in the overall recombination rate is greatly reduced; and numerous narrow regions of high recombination rate, apparent in the original Shifman map, have disappeared.We propose the revised Shifman map as a new standard genetic map for the mouse. The new genetic map represents a substantial improvement over the existing MGI map due to the large number of meioses and to the genetic diversity of strains in the HS population. We have generated male, female, and sex-averaged genetic maps with physical positions and updated locus identifiers. We have established the correspondence between physical and genetic positions of 7080 Mit markers and corrected inconsistencies in the MGI map. We provide a web-based tool for the interpolation of new marker loci into the genetic map and for converting genetic map positions to NCBI mouse build 37 coordinates. Finally, we examine the effect of changing to this revised genetic map on QTL mapping in five previously published data sets (Beamer et al. 1999, 2001; Ishimori et al. 2004, 2008; Wergedal et al. 2006).     

Direction of SPP1 DNA replication in transfected B. subtilis cells

Summary The origin and the direction of replication of the SPP1 chromosome, which has a unique, nonpermuted sequence of markers, was established by determination of the frequency distribution of various markers along the SPP1 map. For this purpose replicating DNA was isolated from transfected competent B. subtilis cells. Marker frequencies were measured by means of helper mediated transfection. In the range defined by the genetic map, replication is unidirectional, originating from a point in the left part of the map. Shearing the DNA into halves prior to transfection permits only one round of replication of that half molecule which carries the origin.     

Functionally associated molecular genetic marker map construction in perennial ryegrass (Lolium perenne L.)

A molecular marker-based map of perennial ryegrass (Lolium perenne L.) has been constructed through the use of polymorphisms associated with expressed sequence tags (ESTs). A pair-cross between genotypes from a North African ecotype and the cultivar Aurora was used to generate a two-way pseudo-testcross population. A selection of 157 cDNAs assigned to eight different functional categories associated with agronomically important biological processes was used to detect polymorphic ESTRFLP loci in the F₁(NA₆ í AU₆) population. A comprehensive set of ESTSSR markers was developed from the analysis of 14,767 unigenes, with 310 primer pairs showing efficient amplification and detecting 113 polymorphic loci. Two parental genetic maps were produced: the NA₆ genetic map contains 88 ESTRFLP and 71 ESTSSR loci with a total map length of 963 cM, while the AU₆ genetic map contains 67 ESTRFLP and 58 ESTSSR loci with a total map length of 757 cM. Bridging loci permitted the alignment of homologous chromosomes between the parental maps, and a sub-set of genomic DNA-derived SSRs was used to relate linkage groups to the perennial ryegrass reference map. Regions of segregation distortion were identified, in some instances in common with other perennial ryegrass maps. The EST-derived marker-based map provides the basis for in silico comparative genetic mapping, as well as the evaluation of co-location between QTLs and functionally associated genetic loci.An erratum to this article can be found at M.J. Faville and A.C. Vecchies contributed equally to this work.     

A first linkage map of pecan cultivars based on RAPD and AFLP markers

We report here the first genetic linkage maps of pecan [Carya illinoinensis (Wangenh.) K. Koch], using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Independent maps were constructed for the cultivars Pawnee and Elliot using the double pseudo-testcross mapping strategy and 120 F₁ seedlings from a full-sib family. A total of 477 markers, including 217 RAPD, 258 AFLP, and two morphological markers were used in linkage analysis. The Pawnee linkage map has 218 markers, comprising 176 testcross and 42 intercross markers placed in 16 major and 13 minor (doublets and triplets) linkage groups. The Pawnee linkage map covered 2,227 cM with an average map distance of 12.7 cM between adjacent markers. The Elliot linkage map has 174 markers comprising 150 testcross and 22 intercross markers placed in 17 major and nine minor linkage groups. The Elliot map covered 1,698 cM with an average map distance of 11.2 cM between adjacent markers. Segregation ratios for dichogamy type and stigma color were not significantly different from 1:1, suggesting that both traits are controlled by single loci with protogyny and green stigmas dominant to protandry and red stigmas. These loci were tightly linked (1.9 cM) and were placed in Elliot linkage group 16. These linkage maps are an important first step towards the detection of genes controlling horticulturally important traits such as nut size, nut maturity date, kernel quality, and disease resistance.     

Physical mapping of the BglI, BglII, PstI and EcoRI restriction fragments of staphylococcal phage phi 11 DNA

Summary A cleavage map of the generalized transducing staphylococcal phage 11 DNA has been constructed by reciprocal double digestion. All three BglI, the six BglII, the three PstI, and 11 out of 15 EcoRI sites have been mapped. The map is circular, with a total length of 42 kb, and has been divided into 100 map units. The phage DNA is cyclically permuted and has a terminal redundancy of about 11 kb. The preferential starting point and direction for packaging DNA lies at map unit 79 and proceeds towards higher map units.     

A genetic map of citrus based on the segregation of isozymes and RFLPs in an intergeneric cross

Summary Isozymes and restriction fragment length polymorphisms were used as markers in the construction of a genetic map of the citrus nuclear genome. The map was based on the segregation of 8 isozyme, 1 protein, and 37 RFLP loci in 60 progeny of a cross of two intergeneric hybrids, Sacaton citrumelo (Citrus paradisi Macf. x Poncirus trifoliata (L.) Raf.) and Troyer citrange (C. sinensis (L.) Osbeck x P. trifoliata), often used as rootstocks. The map contains 38 of 46 studied loci distributed on ten linkage groups. A genome size of 1,700 cM was estimated from partial linkage data. Approximately 35% of the genome should be within 10 cM and 58% within 20 cM of the mapped markers. Eight loci in three linkage groups and 1 unlinked locus deviated significantly from Mendelian segregation.     

Map location of the Escherichia coli origin of replication.

Summary Working with restriction fragments obtained directly from the Escherichia coli K12 chromosome, the EcoRI-HindIII restriction map of the section of the chromosome containing the replication origin has been extended by 14 kilobase pairs (kb) to cover 56kb. Within this newly mapped portion, the liv and rrnC cistrons have been identified by (1) hybridization of individual restriction fragmenents to the ilv-transducing phage dilv5 and (2) a comparison of the restriction map of this region with the EcoRI map of dilv5 and the HindIII map of the plasmid pJC110, a ColE1-ilv hybrid. The replication origin is located approximately 30 kb from the ilvE gene and 20 kb from the rrnC 16S rRNA cistron. This places the origin near 82.7 min on the genetic map, close to uncA.     

Detection of segregation distortions in an indica-japonica rice cross using a high-resolution molecular map

We have constructed a high-resolution rice genetic map containing 1383 DNA markers covering 1575 cM on the 12 linkage groups of rice using 186 F₂ progeny from a cross between a japonica variety, Nipponbare, and an indica variety, Kasalath. Using this high-resolution molecular linkage map, we detected segregation distortion in a single wide cross of rice. The frequencies of genotypes for 1181 markers with more than 176 genotype data were plotted along this map to detect segregation distortion. Several types of distorted segregation were observed on 6 of the chromosomes. We could detect 11 major segregation distortions at ten positions on chromosomes 1, 3, 6, 8, 9, and 10. The strongest segregation distortion was at 107.2 cM on chromosome 3 and may be the gametophyte gene 2 (ga-2). The Kasalath genotype at this position was transmitted to the progeny with about a 95% probability through the pollen gamete. At least 8 out of the 11 segregation distortions detected here are new. The use of the high-resolution molecular linkage map for improving our understanding of the genetic nature and cause of these segregation distortions is discussed.     

Organization of Methanobacterium thermoautotrophicum bacteriophage psi M1 DNA

Summary M1 is a virulent bacteriophage of Methanobacterium thermoautotrophicum strain Marburg. Restriction enzyme analysis of the linear, 30.4 kb phage DNA led to a circular map of the 27.1 kb M1 genome. M1 is thus circularly permuted and exhibits terminal redundancy of approximately 3 kb. Packaging of M1 DNA from a concatemeric precursor initiates at the pac site which was identified at coordinate 4.6 kb on the circular genome map. It proceeds clockwise for at least five packaging rounds. Headful packaging was also shown for M2, a phage variant with a 0.7 kb deletion at coordinate 23.25 on the map.     

RFLP mapping of Brassica napus using doubled haploid lines

The combined use of doubled haploid lines and molecular markers can provide new genetic information for use in breeding programs. An F₁-derived doubled haploid (DH) population of Brassica napus obtained from a cross between an annual canola cultivar (Stellar) and a biennial rapeseed (Major) was used to construct a linkage map of 132 restriction fragment length polymorphism loci. The marker loci were arranged into 22 linkage groups and six pairs of linked loci covering 1016 cM. The DH map was compared to a partial map constructed with a common set of markers for an F₂ population derived from the same F₁ plant, and the overall maps were not significantly different. Comparisons of maps in Brassica species suggest that less recombination occurs in B. napus (n = 19) than expected from the combined map distances of the two hypothesized diploid progenitors, B. oleracea (n = 9) and B. rapa (n=10). A high percentage (32%) of segregating marker loci were duplicated in the DH map, and conserved linkage arrangements of some duplicated loci indicated possible intergenome homoeology in the amphidiploid or intragenome duplications from the diploid progenitors. Deviation from Mendelian segregation ratios (P < 0.05) was observed for 30% of the marker loci in the DH population and for 24% in the F₂ population. Deviation towards each parent occurred at equal frequencies in both populations and marker loci that showed deviation clustered in specific linkage groups. The DH lines and molecular marker map generated for this study can be used to map loci for agronomic traits segregating in this population. Present address Embrapa/Cenargen, C.P. 0.2372, CEP 70.770, Brasilia DF, Brazil     

Habitat evaluation for crested ibis: A GIS-based approach

We evaluated habitat quality for crested ibis (Nipponia nippon) using a geographic information system (GIS). First, we digitized the topography map, vegetation map, river map, road map and villages/towns map by ArcInfo, and gave each map layer a suitability index based on our perceptions of the needs of crested ibis. Second, we overlayed these maps to obtain an integrated map of habitat quality. Finally, we compared the calculated habitat quality with the actual distribution of crested ibis. We found that the birds were almost always located at the site of high quality (habitat suitability index [HSI]>0.6), which indicated that the factors we selected were important for crested ibis. We also found that crested ibis were never located at some sites of high quality, thus, we assume that other factors not considered in this study limit the distribution of crested ibis. Regression analysis indicated that crested ibis preferred lower elevation habitats and tolerated higher levels of human disturbance in recent years than previously reported. These results reflected a 20-year protection program for this species.     

A genetic map of soybean (Glycine max L.) using an intraspecific cross of two cultivars: ‘Minosy’ and ‘Noir 1’

Genetic markers were mapped in segregating progeny from a cross between two soybean (Glycine max (L.) Merr.) cultivars: Minsoy (PI 27.890) and Noir 1 (PI 290.136). A genetic linkage map was constructed (LOD 3), consisting of 132 RFLP, isozyme, morphological, and biochemical markers. The map defined 1550cM of the soybean genome comprising 31 linkage groups. An additional 24 polymorphic markers remained unlinked. A family of RFLP markers, identified by a single probe (hybridizing to an interspersed repeated DNA sequence), extended the map, linking other markers and defining regions for which other markers were not available.     

A genetic linkage map of quinoa (<Emphasis Type="Italic">Chenopodium quinoa</Emphasis>) based on AFLP,RAPD, and SSR markers

Quinoa (Chenopodium quinoa Willd.) is an important seed crop for human consumption in the Andean region of South America. It is the primary staple in areas too arid or saline for the major cereal crops. The objective of this project was to build the first genetic linkage map of quinoa. Selection of the mapping population was based on a preliminary genetic similarity analysis of four potential mapping parents. Breeding lines Ku-2 and 0654, a Chilean lowland type and a Peruvian Altiplano type, respectively, showed a low similarity coefficient of 0.31 and were selected to form an F₂ mapping population. The genetic map is based on 80 F₂ individuals from this population and consists of 230 amplified length polymorphism (AFLP), 19 simple-sequence repeat (SSR), and six randomly amplified polymorphic DNA markers. The map spans 1,020 cM and contains 35 linkage groups with an average marker density of 4.0 cM per marker. Clustering of AFLP markers was not observed. Additionally, we report the primer sequences and map locations for 19 SSR markers that will be valuable tools for future quinoa genome analysis. This map provides a key starting point for genetic dissection of agronomically important characteristics of quinoa, including seed saponin content, grain yield, maturity, and resistance to disease, frost, and drought. Current efforts are geared towards the generation of more than 200 mapped SSR markers and the development of several recombinant-inbred mapping populations.     

Localization of the Laevigatum powdery mildew resistance gene to barley chromosome 2 by the use of RFLP markers

Summary The powdery mildew disease resistance gene Ml(La) was found to belong to a locus on barely chromosome 2. We suggest that this locus be designated MlLa. Linkage analysis was carried out on 72 chromosome-doubled, spring-type progeny lines from a cross between the winter var Vogelsanger Gold and the spring var Alf. A map of chromosome 2 spanning 119cM and flanked by two peroxidase gene loci was constructed. In addition to the Laevigatum resistance locus the map includes nine RFLP markers, the two peroxidase gene loci and the six-row locus in barley.     

Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.)

The availability of suitable genetic markers is essential to efficiently select and breed apple varieties of high quality and with multiple disease resistances. Microsatellites (simple sequence repeats, SSR) are very useful in this respect since they are codominant, highly polymorphic, abundant and reliably reproducible. Over 140 new SSR markers have been developed in apple and tested on a panel of 7 cultivars and 1 breeding selection. Their high level of polymorphism is expressed with an average of 6.1 alleles per locus and an average heterozygosity (H) of 0.74. Of all SSR markers, 115 have been positioned on a genetic linkage map of the cross Fiesta × Discovery. As a result, all 17 linkage groups, corresponding to the 17 chromosomes of apple, were identified. Each chromosome carries at least two SSR markers, allowing the alignment of any apple molecular marker map both with regard to identification as well as to orientation of the linkage groups. To test the degree of conservation of the SSR flanking regions and the transferability of the SSR markers to other Rosaceae species, 15 primer pairs were tested on a series of Maloideae and Amygdaloideae species. The usefulness of the newly developed microsatellites in genetic mapping is demonstrated by means of the genetic linkage map. The possibility of constructing a global apple linkage map and the impact of such a number of microsatellite markers on gene and QTL mapping is discussed.     

Analysis of molecular markers associated with powdery mildew resistance genes in peach (Prunus persica (L.) Batsch)xPrunus davidiana hybrids

A progeny of 77 hybrids issued from a cross between two heterozygous Prunus, peach [P. persica (L.) Batsch] (variety Summergrand) and a related species, P. davidiana (clone 1908), was analysed for powdery mildew resistance in five independent experiments. This population was also analysed for its genotype with isoenzyme and RAPD markers in order to map the genes responsible for resistance. A genetic linkage map was generated for each parent. The Summergrand linkage map is composed of only four linkage groups including 15 RAPD markers and covering 83.1 centiMorgans (cM) of the peach nuclear genome, whereas the P. davidiana linkage map contains 84 RAPD markers and one isoenzyme assigned to ten linkage groups and covering 536 cM. Significant associations between molecular markers and powdery mildew resistance were found in each parent. For P. davidiana, one major QTL with a very strong effect and five other QTLs with minor effects were located in different linkage groups. For Summergrand, three QTLs for powdery mildew resistance, with minor effects, were also detected. Consequently, evidence is given here that the powdery mildew resistance of P. davidiana clone 1908 and P. persica variety Summergrand is not a monogenic character but is controlled by at least one major gene and several minor genes.     

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 -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.     

The effect of genome and sex on recombination rates in Pennisetum species

The effects of homoeology and sex on recombination frequency were studied in crosses between cultivated pearl millet, Pennisetum glaucum, and two wild subspecies, P. violaceum and P. mollissimum. For the two wild x cultivated crosses, reciprocal three-way crosses were made between the F₁ hybrid and an inbred line (Tift 23DB₁). The three-way cross populations were mapped to produce a female map of each wide cross (where the F₁ was the female) and a male map (where the F₁ was the male). Total genetic map lengths of the two inter-subspecies crosses were broadly similar and around 85 % of a comparable intervarietal map. In the P. glaucumxP. mollissimum crosses, the map was further shortened by a large (40 cM) inversion in linkage group 1. Comparison of the recovered recombinants from male and female meiocytes showed an overall trend for the genetic maps to be longer in the male (10%) in both inter-subspecific crosses; however, analysis of individual linkage intervals showed no significant differences. Gametophytic selection was prevalent, and sometimes extreme, for example 121 in favour of wild alleles in the P. glaucumxP. mollissimum male recombinant population. One of the loci which determines panicle type in cultivated pearl millet and wild relatives, H, was mapped 9 cM from Xpsm812 on linkage group 7 in the P. violaceum cross.