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1
Echt, C. S., K. K. Kidwell, S. J. Knapp, T. C. Osborn, and T. J. McCoy. "Linkage mapping in diploid alfalfa (Medicago sativa)." Genome 37, no. 1 (February 1, 1994): 61–71. http://dx.doi.org/10.1139/g94-008.
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A genome map of cultivated alfalfa was constructed using segregating restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNAs (RAPDs) in a diploid backcross population generated from noninbred parents. Among the 153 loci scored in 87 progeny, four segregation ratios were observed for codominant and dominant markers: 1:1, 1:2:1, 1:1:1:1, and 3:1. Deviations from expected Mendelian ratios (p < 0.05) were observed for 34% of the loci studied. A genome map was assembled from two separate linkage maps, each constructed from a subset of the segregation data. One linkage map was constructed from 46 RFLP and 40 RAPD markers segregating 1:1 from the F1 parent of the backcross and the other linkage map was constructed from 33 RFLP and 28 RAPD markers segregating 1:1 from the recurrent parent. Sixteen loci with alleles segregating 1:1 from both parents were used as locus bridges to align individual linkage groups between the two maps. The combined use of RFLPs and RAPDs was an effective method for developing an alfalfa genome map.Key words: genome mapping, RAPD, RFLP, locus bridges.
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Verhaegen, Daniel, and Christophe Plomion. "Genetic mapping in Eucalyptus urophylla and Eucalyptus grandis using RAPD markers." Genome 39, no. 6 (December 1, 1996): 1051–61. http://dx.doi.org/10.1139/g96-132.
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Two single-tree linkage maps were constructed for Eucalyptus urophylla and Eucalyptus grandis, based on the segregation of 480 random amplified polymorphic DNA (RAPD) markers in a F1 interspecific progeny. A mixture of three types of single-locus segregations were observed: 244 1:1 female, 211 1:1 male, and 25 markers common to both, segregating 3:1. Markers segregating in the 1:1 ratio (testcross loci) were used to establish separate maternal and paternal maps, while markers segregating in the 3:1 ratio were used to identify homology between linkage groups of the two species maps. An average of 2.8 polymorphic loci were mapped for each arbitrary decamer primer used in the polymerase chain reaction. The mean interval size beween framework markers on the maps was 14 cM. The maps comprised 269 markers covering 1331 cM and 236 markers covering 1415 cM, in 11 linkage groups, for E. urophylla (2n = 2x = 22) and E. grandis (2n = 2x = 22), respectively. A comparative mapping analysis with two other E. urophylla and E. grandis linkage maps showed that RAPDs could be reliable markers for establishing a consensus species map. RAPD markers were automatically and quantitatively scored with an imaging analyzer. They were classified into four categories based on their optical density. A fragment intensity threshold is proposed to optimize the selection of reliable RAPD markers for future mapping experiments. Key words : genetic linkage map, Eucalyptus urophylla, Eucalyptus grandis, random amplified polymorphic DNA, RAPD, automated data collection.
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Wang, Xindan, and David J. Sherratt. "Independent Segregation of the Two Arms of the Escherichia coli ori Region Requires neither RNA Synthesis nor MreB Dynamics." Journal of Bacteriology 192, no. 23 (October 1, 2010): 6143–53. http://dx.doi.org/10.1128/jb.00861-10.
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ABSTRACT The mechanism of Escherichia coli chromosome segregation remains elusive. We present results on the simultaneous tracking of segregation of multiple loci in the ori region of the chromosome in cells growing under conditions in which a single round of replication is initiated and completed in the same generation. Loci segregated as expected for progressive replication-segregation from oriC, with markers placed symmetrically on either side of oriC segregating to opposite cell halves at the same time, showing that sister locus cohesion in the origin region is local rather than extensive. We were unable to observe any influence on segregation of the proposed centromeric site, migS, or indeed any other potential cis-acting element on either replication arm (replichore) in the AB1157 genetic background. Site-specific inhibition of replication close to oriC on one replichore did not prevent segregation of loci on the other replichore. Inhibition of RNA synthesis and inhibition of the dynamic polymerization of the actin homolog MreB did not affect ori and bulk chromosome segregation.
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Foolad, M. R. "Unilateral Incompatibility as a Major Cause of Skewed Segregation in the Cross between Lycopersicon esculentum and L. pennellii." HortScience 31, no. 4 (August 1996): 625d—625. http://dx.doi.org/10.21273/hortsci.31.4.625d.
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Skewed segregations are frequent events in segregating populations derived from different interspecific crosses in tomato. To determine a basis for skewed segregations in the progeny of the cross between Lycopersicon esculentum and L. pennellii, monogenic segregations of 16 isozyme loci were analyzed in an F2 and two backcross populations of this cross. In the F2, nine loci mapping to chromosomes 1, 2, 4, 9, 10, and 12 exhibited skewed segregations and in all cases there was an excess of L. pennellii homozygotes. The genotypic frequencies at all but one locus were at Hardy–Weinberg equilibria. In the backcross populations, all except two loci exhibited normal Mendelian segregations. No postzygotic selection model could statistically or biologically explain the observed segregation patterns. A prezygotic selection model, assuming selective elimination of the male gametophytes during pollen function (i.e., from pollination to karyogamy) adequately explained the observed segregations in all three populations. The direction of the skewed segregations in the F2 was consistent with that expected based on the effects of unilateral incompatibility reactions between the two species. In addition, the chromosomal locations of five of the nine markers that exhibited skewed segregations coincided with the locations of several known compatibility-related genes in tomato. Multigenic unilateral incompatibility reactions between L. esculentum pollen and the stigma or style of L. pennellii (or its hybrid derivatives) are suggested to be the major cause of the skewed segregations in the F2 progeny of this cross.
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Groover, A., M. Devey, T. Fiddler, J. Lee, R. Megraw, T. Mitchel-Olds, B. Sherman, S. Vujcic, C. Williams, and D. Neale. "Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine." Genetics 138, no. 4 (December 1, 1994): 1293–300. http://dx.doi.org/10.1093/genetics/138.4.1293.
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Abstract We report the identification of quantitative trait loci (QTL) influencing wood specific gravity (WSG) in an outbred pedigree of loblolly pine (Pinus taeda L.). QTL mapping in an outcrossing species is complicated by the presence of multiple alleles (> 2) at QTL and marker loci. Multiple alleles at QTL allow the examination of interaction among alleles at QTL (deviation from additive gene action). Restriction fragment length polymorphism (RFLP) marker genotypes and wood specific gravity phenotypes were determined for 177 progeny. Two RFLP linkage maps were constructed, representing maternal and paternal parent gamete segregations as inferred from diploid progeny RFLP genotypes. RFLP loci segregating for multiple alleles were vital for aligning the two maps. Each RFLP locus was assayed for cosegregation with WSG QTL using analysis of variance (ANOVA). Five regions of the genome contained one or more RFLP loci showing differences in mean WSG at or below the P = 0.05 level for progeny as grouped by RFLP genotype. One region contained a marker locus (S6a) whose QTL-associated effects were highly significant (P > 0.0002). Marker S6a segregated for multiple alleles, a prerequisite for determining the number of alleles segregating at the linked QTL and analyzing the interactions among QTL alleles. The QTL associated with marker S6a appeared to be segregating for multiple alleles which interacted with each other and with environments. No evidence for digenic epistasis was found among the five QTL.
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Kianian, Shahryar F., and Carlos F. Quiros. "Genetic analysis of major multigene families in Brassica oleracea and related species." Genome 35, no. 3 (June 1, 1992): 516–27. http://dx.doi.org/10.1139/g92-076.
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Sequences homologous to rRNA, napin, cruciferin, self-incompatibility, isocitrate lyase, and malate synthase were mapped to the Brassica oleracea genome. Four segregating populations were used to disclose possible distortions in segregation and linkage ratios while maximizing detectable polymorphism. rRNA mapped to three unlinked loci, which reside on different chromosomes. Certain restriction fragment length polymorphism variations detected by the rDNA probe reflect changes in the number of intergenic spacer subrepeats, the size of which was estimated to be about 300 base pairs. All five napin, three self-incompatibility, and two isocitrate lyase loci mapped in linkage clusters, while those of cruciferin and malate synthase (two loci each) were independent.Key words: Brassica oleracea, RFLP analysis, linkage analysis, multigene family.
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Jarrell, David C., and Mikeal L. Roose. "A GENETIC MAP OF CITRUS BASED ON ISOZYMES AND RFLPS." HortScience 25, no. 9 (September 1990): 1154b—1154. http://dx.doi.org/10.21273/hortsci.25.9.1154b.
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We report a preliminary genetic map of citrus based on segregation of 8 isozyme and at least 33 RFLP loci. The segregating population consisted of 60 plants from a cross of two citrus rootstock, `Sacaton' citrumelo × `Troyer' citrange. This cross represents an intergeneric F2 since `Sacaton' is Citrus paradisi (grapefruit) × Poncirus trifoliata (trifoliate orange) and `Troyer' is C. sinensis (sweet orange) × P. trifoliata. RFLPs were identified using anonymous probes from both cDNA and genomic DNA libraries of citrus. About 20% of the loci deviated significantly from Mendelian segregation. Two-point linkage analysis identified 8 linkage groups in which pairs of loci were within 30 centimorgans. This suggests that we have markers on most of the 9 chromosomes of Citrus. A map based on multipoint linkage estimates will be reported. Evidence for structural rearrangements between Citrus and Poncirus and extension of the map to additional marker and disease resistance loci will be discussed.
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Beaver, J. A., and A. F. Iezzoni. "Allozyme Inheritance in Tetraploid Sour Cherry (Prunus cerasus L.)." Journal of the American Society for Horticultural Science 118, no. 6 (November 1993): 873–77. http://dx.doi.org/10.21273/jashs.118.6.873.
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Inheritance for seven enzyme loci was determined in seeds produced from crosses and self-pollinations involving four sour cherry parents and one open-pollinated ground cherry (P. fruticosa Pall.) parent. Segregation data were used to identify allozymes and determine whether sour cherry is a naturally occurring allo- or autotetraploid. Three allozymes were identified at the 6-Pgd-1 locus, and two were identified at each of the following loci: Pgi-2, Lap-1, Adh-1, Idh-2, Pgm-2, and 6-Pgd-2. Segregating allozyme patterns for the diagnostic loci Idh-2, Pgm-2, 6-Pgd-1, and 6-Pgd-2 tit disomic inheritance models and thus confirmed the allotetraploid hypothesis for sour cherry. Chi-square tests of independence between loci indicated that Pgi-2, Adh-1, Idh-2, 6-Pgd-1, and 6-Pgd-2 were not linked.
9
Landry, Benoit S., Rick V. Kesseli, Barry Farrara, and Richard W. Michelmore. "A Genetic Map of Lettuce (Lactuca sativa L.) With Restriction Fragment Length Polymorphism, Isozyme, Disease Resistance and Morphological Markers." Genetics 116, no. 2 (June 1, 1987): 331–37. http://dx.doi.org/10.1093/genetics/116.2.331.
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ABSTRACT A detailed linkage map of lettuce was constructed using 53 genetic markers including 41 restriction fragment length polymorphism (RFLP) loci, five downy mildew resistance genes, four isozyme loci and three morphological markers. The genetic markers were distributed into nine linkage groups and cover 404 cM which may be 25-30% of the lettuce genome. The majority (31 of 34) of the RFLP probes detected single segregating loci, although seven of these may have been homologous to further monomorphic loci. When several loci were detected by a single probe, the loci were generally linked, suggesting tandem duplications. One probe, however, detected loci in three linkage groups suggesting translocations. The five downy mildew resistance genes (Dm1, Dm3, Dm4, Dm5/8 and Dm13), segregating in the Calmar × Kordaat cross, represented each of the four resistance gene linkage groups. Dm5/8 is flanked by two cDNA loci, each located 10 cM away. These flanking markers will be used to study the source of variation in downy mildew genes and are also part our strategy to clone resistance genes.
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Ritter, E., C. Gebhardt, and F. Salamini. "Estimation of recombination frequencies and construction of RFLP linkage maps in plants from crosses between heterozygous parents." Genetics 125, no. 3 (July 1, 1990): 645–54. http://dx.doi.org/10.1093/genetics/125.3.645.
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Abstract The construction of a restriction fragment length polymorphism (RFLP) linkage map is based on the estimation of recombination frequencies between genetic loci and on the determination of the linear order of loci in linkage groups. RFLP loci can be identified as segregations of singular or allelic DNA-restriction fragments. From crosses between heterozygous individuals several allele (fragment) configurations are possible, and this leads to a set of formulas for the evaluation of p, the recombination frequency between two loci. Tables and figures are presented illustrating a general outline of gene mapping using heterozygous populations. The method encompasses as special cases the mapping of loci from segregating populations of pure lines. Formulas for deriving the recombination frequencies and information functions are given for different fragment configurations. Information functions derived for relevant configurations are also compared. A procedure for map construction is presented, as it has been applied to RFLP mapping in an allogamous crop.
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Rubino, David B. "Inheritance of Esterase, Diaphorase, and Glucose-6-phosphate Isomerase in Lisianthus." HortScience 28, no. 6 (June 1993): 661–63. http://dx.doi.org/10.21273/hortsci.28.6.661.
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Segregating lisianthus [Eustoma grandiflorum (Griseb.) Shinn.] progeny were evaluated to determine the inheritance of esterase (EST), diaphorase (DIA), and glucose-6-phosphate isomerase (GPI) isozymes. Phenotypic data supported the hypotheses that EST is monomeric and controlled by one locus (Est1) with at least three alleles, DIA is tetrameric and controlled by one locus (Dia2) with at least two alleles, and GPI is controlled by one locus (Gpil) with at least two alleles. The structure of the GPI isozyme could not be inferred from banding patterns. Joint segregation analyses indicated that the three loci segregate independently. These three isozymes are the first simply inherited, unlinked biochemical markers identified in lisianthus. These marker loci will be useful for genetic studies, breeding, and germplasm characterization.
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Lashermes, P., M. C. Combes, N. S. Prakash, P. Trouslot, M. Lorieux, and A. Charrier. "Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meioses." Genome 44, no. 4 (August 1, 2001): 589–95. http://dx.doi.org/10.1139/g01-041.
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Two complementary segregating plant populations of Coffea canephora were produced from the same clone. One population (DH) comprised 92 doubled haploids derived from female gametes, while the other population (TC) was a test cross consisting of 44 individuals derived from male gametes. Based on the DH population, a genetic linkage map comprising 160 loci was constructed. Eleven linkage groups that putatively correspond to the 11 gametic chromosomes of C. canephora were identified. The mapped loci included more than 40 specific sequence-tagged site markers, either single-copy RFLP probes or microsatellites, that could serve as standard landmarks in coffee-genome analyses. Furthermore, comparisons for segregation distortion and recombination frequency between the two populations were performed. Although segregation distortions were observed in both populations, the frequency of loci exhibiting a very pronounced degree of distortion was especially high in the DH population. This observation is consistent with the hypothesis of strong zygotic selection among the DH population. The recombination frequencies in both populations were found to be almost indistinguishable. These results offer evidence in favour of the lack of significant sex differences in recombination in C. canephora.Key words: coffee, mapping, sex differences, segregation distortion, recombination frequency.
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Sibov, S. T., M. Gaspar, M. J. Silva, LMM Ottoboni, P. Arruda, and A. P. Souza. "Two genes control aluminum tolerance in maize: Genetic and molecular mapping analyses." Genome 42, no. 3 (June 1, 1999): 475–82. http://dx.doi.org/10.1139/g98-146.
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We have identified two loci linked to aluminum (Al) tolerance in the maize inbred line Cat-100-6 by means of restriction fragment length polymorphism (RFLP) and bulked segregant analysis (BSA). A segregating population F2 was obtained from a cross between Cat-100-6 (Al tolerant) × S1587-17 (Al sensitive) parents. Subsequently two DNA bulks of individuals, displaying a contrasting Al tolerance trait were generated from F2. From a total of 158 markers used, 30 markers were identified showing polymorphism between parents and bulks. The segregation results derived from the hybridization from these 30 markers and 56 individuals from F2 revealed 10 markers cosegregating with the Al tolerance which were located in two linkage groups. The linkage groups were composed of 6 and 4 markers, and they were mapped on the short arm of chromosomes 6 and 10, respectively. From these observations, we deduce that two loci are involved in this trait in Cat-100-6 line. QGENE software was used to study the correlation between these two loci and the trait for aluminum tolerance. The results indicate that the locus on chromosome 10 has the stronger effect, and it is responsible for the major part of the variability of the trait.Key words: maize, aluminum tolerance, molecular mapping, somaclonal variation.
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Jiang, C., M. E. Lewis, and K. C. Sink. "Combined RAPD and RFLP molecular linkage map of asparagus." Genome 40, no. 1 (February 1, 1997): 69–76. http://dx.doi.org/10.1139/g97-009.
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Two linkage maps of asparagus (Asparagus officinalis L.) were constructed using a double pseudotestcross mapping strategy with restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), and allozymes as markers in a population generated from crossing MW25 × A19, two heterozygous parents. All data were inverted and combined with the natural data to detect linkages in repulsion phase. Two sets of data, one for each parent, were formed according to the inheritance patterns of the markers. The maternal MW25 map has a total of 163 marker loci placed in 13 linkage groups covering 1281 cM, with an average and a maximum distance between adjacent loci of 7.9 and 29 cM, respectively. The paternal A19 map has 183 marker loci covering 1324 cM in 9 linkage groups, with an average and a maximum distance between two adjacent loci of 7.7 and 29 cM, respectively. Six multiallelic RFLPs segregating in the pattern a/c × b/c and eight heterozygous loci (four RAPDs, and four RFLPs segregating in the pattern a/b × a/b (HZ loci)) were common to both maps. These 14 loci were used as bridges to align homologous groups between the two maps. In this case, RFLPs were more frequent and informative than RAPDs. Nine linkage groups in the MW25 map were homologous to six groups in the A19 map. In two cases, two or more bridge loci were common to a group; thus, the orientation of homologous linkage groups was also determined. In four other cases, only one locus was common to the two homologous groups and the orientation was unknown. Mdh, four RFLPs, and 14 RAPDs were assigned to chromosome L5, which also has the sex locus M.Key words: asparagus, bridge loci, pseudotestcross, RAPD, RFLP, sex expression.
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Cousineau, Johanne C., and Danielle J. Donnelly. "Genetic Analysis of Isoenzymes in Raspberry." Journal of the American Society for Horticultural Science 117, no. 6 (November 1992): 996–99. http://dx.doi.org/10.21273/jashs.117.6.996.
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The inheritance of five isoenzymes was studied in red and purple raspberry F1 progenies (Rubus idaeus L. and Rubus × neglectus Peck). Isocitrate dehydrogenase (IDH; EC 1.1.1.42) was a dimeric enzyme present in the cytosol and coded for by one locus (Idh-1). Three of the four crosses analyzed at this locus had deviations from expected ratios, possibly caused by its linkage to a recessive lethal gene. Malate dehydrogenase (MDH; EC 1.1.1.37), phosphoglucoisomerase (PGI; EC 5.3.1.9), and triose phosphate isomerase (TPI; EC 5.3.1.1) were dimeric enzymes with two loci. Each of these three enzymes was present in an organelle and in the cytosol for locus 1 and 2, respectively. Phosphoglucomutase (PGM; EC 2.7.5.1) was monomeric with two loci, Pgm-1 and Pgm-2, located in an organelle and the cytosol, respectively. Each allele at Pgm-1 resulted in the formation of two bands. Although most progenies analyzed supported Mendelian inheritance of polymorphic loci (except for Idh-1), there was a higher than expected number of aberrant segregation ratios observed (18.4%). Analysis of 85 pairs of jointly segregating loci revealed a possible linkage group consisting of Mdh-2, Tpi-2, and Pgm-1.
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Noyes, Richard D., and Loren H. Rieseberg. "Two Independent Loci Control Agamospermy (Apomixis) in the Triploid Flowering Plant Erigeron annuus." Genetics 155, no. 1 (May 1, 2000): 379–90. http://dx.doi.org/10.1093/genetics/155.1.379.
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Abstract Asexual seed production (agamospermy) via gametophytic apomixis in flowering plants typically involves the formation of an unreduced megagametophyte (via apospory or diplospory) and the parthenogenetic development of the unreduced egg cell into an embryo. Agamospermy is almost exclusively restricted to polyploids. In this study, the genetic basis of agamospermy was investigated in a segregating population of 130 F1's from a cross between triploid (2n = 27) agamospermous Erigeron annuus and sexual diploid (2n = 18) E. strigosus. Correlations between markers and phenotypes and linkage analysis were performed on 387 segregating amplified fragment length polymorphisms (AFLPs). Results show that four closely linked markers with polysomic inheritance are significantly associated with parthenogenesis and that 11 cosegregating markers with univalent inheritance are completely associated with diplospory. This indicates that diplospory and parthenogenesis are unlinked and inherited independently. Further, the absence of agamospermy in diploid F1's appears to be best explained by a combination of recessive-lethal gametophytic selection against the parthenogenetic locus and univalent inheritance of the region bearing diplospory. These results may have major implications for attempts to manipulate agamospermy for agricultural purposes and for interpreting the evolution of the trait.
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Hyun, Jung O., Om P. Rajora, and Louis Zsuffa. "Inheritance and linkage of isozymes in Populus tremuloides (Michx.)." Genome 29, no. 2 (April 1, 1987): 384–88. http://dx.doi.org/10.1139/g87-066.
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Progenies of four controlled crosses were assayed electrophoretically to determine the inheritance of isozymes of 10 loci coding for six enzymes, aconitase (ACO), glutamate oxaloacetate transaminase (GOT), isocitrate dehydrogenase (IDH), phosphoglucomutase (PGM), 6-phosphogluconate dehydrogenase (6-PGD), and phosphoglucose isomerase (PGI), in roots of Populus tremuloides. Chi-square goodness of fit tests verified a single-gene Mendelian control of the segregating allozyme variants at each of five loci: Aco-1, Got, Pgm-2, 6-Pgd-2, and Pgi-2. Evidence was also obtained for a single-gene control of each of the remaining five loci (Aco-2, Idh, Pgm-1, 6-Pgd-1, and Pgi-1). ACO and PGM showed monomeric, while GOT, IDH, 6-PGD, and PGI had dimeric, banding patterns. The results of joint two-locus segregation tests indicated no linkage between 6-Pgd-2 and Pgi-2. Key words: Populus species, electrophoresis, allozymes, inheritance, linkage.
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Perry, D. J., and P. Knowles. "Inheritance and linkage relationships of allozymes of eastern white cedar (Thuja occidentalis) in northwestern Ontario." Genome 32, no. 2 (April 1, 1989): 245–50. http://dx.doi.org/10.1139/g89-435.
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Allozyme variants of 12 enzyme systems were examined in seed tissues of eastern white cedar (Thuja occidentalis L.), using starch gel electrophoresis. Nine loci were polymorphic and deviation from a 1:1 segregation ratio was observed between two of three alleles at one locus (Mdh-1). Of the possible 36 locus-pair combinations, 23 could be tested for linkage. Significant linkage was detected for three pairs of loci (Aat-1/Mdh-1, Aat-1/Pgm, and Idh-2/Me). Trees jointly segregating for Aat-1 and Pgm fell into two classes, one with a low recombination frequency (9.1%) and the other with a higher recombination frequency (26.6%). An inversion polymorphism is a possible cause of this linkage heterogeneity observed among trees.Key words: allozymes, isozymes, inheritance, linkage, eastern white cedar, northern white cedar, Thuja occidentalis L., Cupressaceae.
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Arús, Pere, Carmen Olarte, Miguel Romero, and Francisco Vargas. "Linkage Analysis of Ten Isozyme Genes in F1 Segregating Almond Progenies." Journal of the American Society for Horticultural Science 119, no. 2 (March 1994): 339–44. http://dx.doi.org/10.21273/jashs.119.2.339.
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Ten isozyme genes were studied after analyzing the variability of eight enzyme systems—glucose phosphate isomerase (GPI), phosphoglucomutase (PGM), aspartate aminotransferase (AAT), leucine aminopeptidase (LAP), 6-phosphogluconate dehydrogenase (6PGD), isocitrate dehydrogenase (IDH), shikimate dehydrogenase (SDH), and aconitase (ACO)—in the progeny of five crosses among almond [Prunus amygdalus Batsch, syn. P. dulcis (Miller) D. A. Webb] cultivars. Six of these loci were found to be located in two linkage groups, one containing four loci (Pgm-2, Gpi-2, Aat-2, and Lap-1) and two more in the other (Idh-2 and Aat-1). Genetic configurations of pairs of loci specific to segregating F1 progeny of crosses between heterozygous parents were found in our data, for which we derived the estimate of the recombination fraction and its variance. Linkage data for the gene pairs that could be estimated in various crosses were used to obtain a joint estimation of the recombination fraction.
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Summerbell, R. C., A. J. Castle, P. A. Horgen, and J. B. Anderson. "Inheritance of restriction fragment length polymorphisms in Agaricus brunnescens." Genetics 123, no. 2 (October 1, 1989): 293–300. http://dx.doi.org/10.1093/genetics/123.2.293.
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Abstract The cultivated mushroom, Agaricus brunnescens, is secondarily homothallic; most basidia produce only two basidiospores, each of which receives two of the four post meiotic nuclei. The segregation of restriction fragment length polymorphisms (RFLPs) detected by four plasmid probes carrying single-copy nuclear DNA of Agaricus was followed in seven parental strains including commercial, wild-collected, and artificially synthesized heterokaryons. Of a total of 367 single-spore progeny examined, 351 (95.6%) were heteroallelic at all RFLP loci heteroallelic in the respective parents. Of the 16 segregant isolates, ten (2.7% of the total) were homoallelic at all segregating loci assayed, suggesting that these isolates were most probably derived from rare spores that had received only a single postmeiotic nucleus. Some of these ten isolates had recombinant genotypes. Only five isolates (1.4% of the total) showed homoallelism at one of the loci heteroallelic in the parent, while remaining heteroallelic at other loci. These five genotypes suggest that a crossover had occurred between a marker locus and its respective centromere. Taken together, the results suggest that meiosis in A. brunnescens is accompanied by low levels of recombination and that nonsister nuclei are preferentially incorporated into basidiospores after meiosis II.
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Lawson, Darlene M., Minou Hemmat, and Norman F. Weeden. "The Use of Molecular Markers to Analyze the Inheritance of Morphological and Developmental Traits in Apple." Journal of the American Society for Horticultural Science 120, no. 3 (May 1995): 532–37. http://dx.doi.org/10.21273/jashs.120.3.532.
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Five morphological and developmental traits (branching habit, vegetative budbreak, reproductive budbreak, bloom time, and root suckering) were analyzed in a family obtained from the apple (Malus domestica Borkh) cross `Rome Beauty' × `White Angel'. The phenotypic variation in these traits was compared with a selected set of marker loci covering the known genome of each of the parents to locate genes with major effects on the traits. The contrasting branching habits of the two parents appeared to be controlled by at least two loci. One of these, Tb, governed the presence or absence of lateral branches, particularly on the lower half of shoots. The locus was heterozygous in `White Angel' and was mapped to a 5 CM interval on linkage group 6. At least one other locus conditioning spur-type branching appeared to be segregating, but the locus or loci could not be linked to segregating markers. The timing of initial vegetative growth was tightly associated with the chromosomal region in which the Tb gene is located and maybe a pleiotropic effect of this gene. Time of reproductive budbreak correlated with segregation at the isozyme marker, Prx-c, on linkage group 5. Variation in time of bloom and later stages in flower development appeared to be controlled by different genes not linked to Prx-c. The tendency to produce root suckers cosegregated with a marker on `White Angel' linkage group 1, suggesting control by a single locus, Rs. Data from a `Rome Beauty' x `Robusta 5' family provided additional information on the inheritance of these traits.
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KEIGHTLEY, PETER D., and SARA A. KNOTT. "Testing the correspondence between map positions of quantitative trait loci." Genetical Research 74, no. 3 (December 1999): 323–28. http://dx.doi.org/10.1017/s0016672399004176.
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There are several instances in which quantitative trait locus (QTL) mapping experiments have been independently carried out for similar traits in different laboratories. We develop a permutation test of the correspondence between the test statistics obtained from genome-wide QTL scans in two such experiments to test whether the same QTLs are segregating in the experimental pair. In simulations, we show that the permutation test has the desired properties if chromosomes are of equal length, but bias can occur if chromosomes are of unequal length, a problem connected with autocorrelation of test statistic values. We apply the test to data from three recent mouse body weight QTL mapping experiments. The results from the test are non-significant, and imply a lack of overall concordance between the QTLs that were segregating in these experiments.
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Dettori, Maria Teresa, Roberta Quarta, and Ignazio Verde. "A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers." Genome 44, no. 5 (October 1, 2001): 783–90. http://dx.doi.org/10.1139/g01-065.
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A linkage map was obtained using a BC1 progeny (Prunus persica × (P. persica × P. ferganensis)). The map is composed of 109 loci (74 RFLPs, 17 SSRs, 16 RAPDs, and two morphological traits) distributed in 10 linkage groups. Loci, segregating in five different ratios, were integrated in the map with JoinMap 2.0 software. The map covers 521 cM of the peach genome. The average distance between adjacent loci is 4.8 cM. Two monogenic traits, flesh adhesion (F/f) and leaf glands (E/e), were placed on the map. Thirty-two loci in common with a saturated linkage map of Prunus allowed a comparative analysis to be made between the two maps. Homologies were found among the respective linkage groups. No relevant differences were observed in the linear order of the common loci.Key words: peach, linkage map, Prunus persica, Prunus ferganensis, molecular markers.
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Evans, G. J., E. Giuffra, A. Sanchez, S. Kerje, G. Davalos, O. Vidal, S. Illán, et al. "Identification of Quantitative Trait Loci for Production Traits in Commercial Pig Populations." Genetics 164, no. 2 (June 1, 2003): 621–27. http://dx.doi.org/10.1093/genetics/164.2.621.
Full textAbstract:
Abstract The aim of this study was to investigate methods for detecting QTL in outbred commercial pig populations. Several QTL for back fat and growth rate, previously detected in experimental resource populations, were examined for segregation in 10 different populations. Two hundred trait-by-population-by-chromosome tests were performed, resulting in 20 tests being significant at the 5% level. In addition, 53 QTL tests for 11 meat quality traits were declared significant, using a subset of the populations. These results show that a considerable amount of phenotypic variance observed in these populations can be explained by major alleles segregating at several of the loci described. Thus, despite a relatively strong selection pressure for growth and back fat traits in these populations, these alleles have not yet reached fixation. The approaches used here demonstrate that it is possible to verify segregation of QTL in commercial populations by limited genotyping of a selection of informative animals. Such verified QTL may be directly exploited in marker-assisted selection (MAS) programs in commercial populations and their molecular basis may be revealed by positional candidate cloning.
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Leung, Maria C. Y., and Kimberly M. Cheng. "Genetic variability of the Cascade mantled ground squirrel (Spermophilus saturates) in British Columbia." Canadian Journal of Zoology 72, no. 2 (February 1, 1994): 371–74. http://dx.doi.org/10.1139/z94-052.
Full textAbstract:
The rare Cascade mantled ground squirrel (Spermophilus saturatus) occurs only in southwestern British Columbia, Canada, and Washington State, U.S.A. Genetic variation in the British Columbia population was assessed using allele frequencies of blood enzymes encoded by a total of 24 presumptive gene loci. All 24 loci were fixed for the same alleles in 48 specimens of S. saturatus collected, but 8 of these 24 loci were segregating in 46 specimens from neighbouring S. lateralis populations examined. The apparent genetic uniformity of S. saturatus may be due to founder effects because of recent northern extensions of the range of the species. In S. saturatus, two loci were fixed for alleles that were absent in S. lateralis.
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Weller, Joel Ira, Jiu Zhou Song, David W. Heyen, Harris A. Lewin, and Micha Ron. "A New Approach to the Problem of Multiple Comparisons in the Genetic Dissection of Complex Traits." Genetics 150, no. 4 (December 1, 1998): 1699–706. http://dx.doi.org/10.1093/genetics/150.4.1699.
Full textAbstract:
Abstract Saturated genetic marker maps are being used to map individual genes affecting quantitative traits. Controlling the “experimentwise” type-I error severely lowers power to detect segregating loci. For preliminary genome scans, we propose controlling the “false discovery rate,” that is, the expected proportion of true null hypotheses within the class of rejected null hypotheses. Examples are given based on a granddaughter design analysis of dairy cattle and simulated backcross populations. By controlling the false discovery rate, power to detect true effects is not dependent on the number of tests performed. If no detectable genes are segregating, controlling the false discovery rate is equivalent to controlling the experimentwise error rate. If quantitative loci are segregating in the population, statistical power is increased as compared to control of the experimentwise type-I error. The difference between the two criteria increases with the increase in the number of false null hypotheses. The false discovery rate can be controlled at the same level whether the complete genome or only part of it has been analyzed. Additional levels of contrasts, such as multiple traits or pedigrees, can be handled without the necessity of a proportional decrease in the critical test probability.
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Kam-Morgan, L. N. W., B. S. Gill, and S. Muthukrishnan. "DNA restriction fragment length polymorphisms: a strategy for genetic mapping of D genome of wheat." Genome 32, no. 4 (August 1, 1989): 724–32. http://dx.doi.org/10.1139/g89-503.
Full textAbstract:
The use of restriction fragment length polymorphisms (RFLPs) as genetic markers in bread wheat, Triticum aestivum, and a wild wheat progenitor, Aegilops squarrosa, was investigated. The objectives were (i) to identify RFLP loci; (ii) to assign cDNA sequences onto specific chromosomes and chromosome arms; and (iii) to determine linkage relationships between RFLP loci. A low level of polymorphism was found, utilizing barley cDNA clones as probes, in hexaploid cultivated wheats. However, accessions of A. squarrosa revealed greater polymorphism. Wheat–barley alien addition lines were used to assign 17 cDNA sequences to specific chromosome groups and ditelosomic and nullisomic–tetrasomic wheat stocks were used to assign these sequences to specific chromosome arms. Of 16 sets of RFLP loci, excluding α-Amy-1 and α-Amy-2, 14 are new sets of loci marking 6 of the 7 homoeologous groups of wheat. The construction of a linkage map of chromosome 5D was initiated by analyzing a segregating F2 population between two homozygous accessions of A. squarrosa. A strategy using wheat aneuploids for chromosome arm location and a segregating A. squarrosa population for linkage measurement was demonstrated for mapping the D-genome chromosomes of wheat.Key words: genetic map, restriction fragment length polymorphisms, Triticum aestivum, Aegilops squarrosa, polyploidy.
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van den Boogaart, Tom, Fuijang Wen, Jeffrey W. Davies, and George P. Lomonossoff. "Replicase-Derived Resistance Against Pea early browning virus in Nicotiana benthamiana Is an Unstable Resistance Based upon Posttranscriptional Gene Silencing." Molecular Plant-Microbe Interactions® 14, no. 2 (February 2001): 196–203. http://dx.doi.org/10.1094/mpmi.2001.14.2.196.
Full textAbstract:
Virus resistance in Nicotiana benthamiana plants containing a translatable Pea early browning virus (PEBV) 54K sequence from the 201K replicase gene has been reported previously. Resistant plants contain multiple transgene copies divided between two loci. Analysis of a genetic series containing the two loci in separate homozygous or heterozygous condition suggest that only one of the loci is necessary to induce the resistance. The resistance observed in R2 and R3 generations of lines containing both transgene loci in homozygous condition became less consistent in R4 and R5 generations. This inversely correlated with steady-state transgene transcript levels of the segregating populations. The use of recombinant Potato virus X vectors carrying PEBV 54K sequences showed that the resistance is based upon posttranscriptional gene silencing, is non-strand specific, and recognizes 3′ located sequences within the PEBV 54K sequence.
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Hill, William G. "Selection with Recurrent Backcrossing to Develop Congenic Lines for Quantitative Trait Loci Analysis." Genetics 148, no. 3 (March 1, 1998): 1341–52. http://dx.doi.org/10.1093/genetics/148.3.1341.
Full textAbstract:
Abstract Sewall Wright suggested that genes of large effect on a quantitative trait could be isolated by recurrent backcrossing with selection on the trait. Loci [quantitative trait loci (QTL)] at which the recurrent and nonrecurrent lines have genes of different large effect on the trait would remain segregating, while other loci would become fixed for the gene carried by the recurrent parent. If the recurrent line is inbred and the backcrossing and selection is conducted in a series of replicate lines, in each of which only one backcross parent is selected for each generation, the lines will become congenic to the recurrent parent except for the QTL of large effect and closely linked regions of the genome, and these regions can be identified using a dense set of markers that differ between the parental lines. Such lines would be particularly valuable for subsequent fine-scale mapping and gene cloning; but by chance, even QTL of large effect will be lost from some lines. The probability that QTL of specified effect remain segregating is computed as a function of its effect on the trait, the intensity of selection, and the number of generations of backcrossing. Analytical formulas are given for one or two loci, and simulation is used for more. It is shown that the method could have substantial discriminating ability and thus potential practical value.
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Goldman, I. L., and Diane Austin. "039 The Blotchy Gene, bl, is Linked to the R and Y Loci in Table Beet." HortScience 34, no. 3 (June 1999): 447F—448. http://dx.doi.org/10.21273/hortsci.34.3.447f.
Full textAbstract:
The primary pigments in red beet are the betalains, which are comprised of the red-violet betacyanins and the yellow betaxanthins. Modification of betalain content and distribution in table beet has been practiced by breeders for many years, although little is known about the genetic control of these traits. The presence of dominant alleles at two linked loci (R and Y) condition production of betalain pigment in the beet plant. Red-pigmented roots are observed only in the presence of dominant alleles at the R and Y loci, while white roots are conditioned by recessive alleles at both loci and yellow roots by the genotype rrY-. A newly described gene, `blotchy' (bl), conditions a blotchy or irregular pigment patterning in either red or yellow roots. The objective of this investigation was to characterize the linkage relationships between the R and Y loci and the bl gene by evaluating segregating progenies developed from a series of matings of colored and white table beets. Segregation data indicate the bl gene is independent from R and Y and that this locus is linked to R and Y. The two-point linkage estimate between the R and Y loci pooled over eight crosses was 7.4 (1.7 cM) Linkage between R and Bl was estimated from a pooled sample of four crosses at 16.7 (10.8 cM). The most likely gene order was R-Y-Bl. These data suggest the RYBl genomic region plays a critical role in the genetic control of betalain biosynthesis in table beet.
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SCHAEFFER, STEPHEN W. "Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura." Genetical Research 80, no. 3 (December 2002): 163–75. http://dx.doi.org/10.1017/s0016672302005955.
Full textAbstract:
Positive and negative selection on indel variation may explain the correlation between intron length and recombination levels in natural populations of Drosophila. A nucleotide sequence analysis of the 3·5 kilobase sequence of the alcohol dehydrogenase (Adh) region from 139 Drosophila pseudoobscura strains and one D. miranda strain was used to determine whether positive or negative selection acts on indel variation in a gene that experiences high levels of recombination. A total of 30 deletion and 36 insertion polymorphisms were segregating within D. pseudoobscura populations and no indels were fixed between D. pseudoobscura and its two sibling species D. miranda and D. persimilis. The ratio of Tajima's D to its theoretical minimum value (Dmin) was proposed as a metric to assess the heterogeneity in D among D. pseudoobscura loci when the number of segregating sites differs among loci. The magnitude of the D/Dmin ratio was found to increase as the rate of population expansion increases, allowing one to assess which loci have an excess of rare variants due to population expansion versus purifying selection. D. pseudoobscura populations appear to have had modest increases in size accounting for some of the observed excess of rare variants. The D/Dmin ratio rejected a neutral model for deletion polymorphisms. Linkage disequilibrium among pairs of indels was greater than between pairs of segregating nucleotides. These results suggest that purifying selection removes deletion variation from intron sequences, but not insertion polymorphisms. Genome rearrangement and size-dependent intron evolution are proposed as mechanisms that limit runaway intron expansion.
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Fetch, T., P. A. Johnston, and R. Pickering. "Chromosomal Location and Inheritance of Stem Rust Resistance Transferred from Hordeum bulbosum into Cultivated Barley (H. vulgare)." Phytopathology® 99, no. 4 (April 2009): 339–43. http://dx.doi.org/10.1094/phyto-99-4-0339.
Full textAbstract:
Stem rust, caused by Puccinia graminis f. sp. tritici, is an important disease on barley (Hordeum vulgare). Host resistance has effectively controlled stem rust, primarily through use of gene Rpg1. However, virulence to Rpg1 is present in North America, and a new race (TTKSK, or Ug99) from eastern Africa threatens barley production. A search for novel resistance was previously conducted, and an interspecific barley breeding line (212Y1) with introgressed chromatin from H. bulbosum was identified as carrying resistance to races MCCF and QCCJ. This study evaluated the inheritance of resistance in 212Y1 using populations from crosses to Morex (Rpg1 donor) and Q21861 (rpg4 donor) and the pathogen races MCCF (avirulent on Rpg1 and rpg4) and QCCJ (virulent on Rpg1 and avirulent on rpg4), and determined the chromosomal position of the introgression using genomic in situ hybridization (GISH) and chromosome-specific polymerase chain reaction (PCR)-based markers. Progeny from the 212Y1/Q21861 F2 population segregated for resistant and susceptible plants, indicating different gene loci. Genetic analyses of Morex/212Y1 F3 families fit a 7 homozygous resistant (HR):8 segregating:1 homozygous susceptible (HS) family segregation ratio to race MCCF, indicating that two genes controlled resistance. Plants in segregating families were in 3R:1S (Rpg1), 13R:3S (Rpg1+212Y1), and 1R:3S (212Y1) ratios. Genetic analyses of the same F3 families fit a 1HR:2 segregating:1HS family segregation ratio to race QCCJ, indicating monogenic inheritance. Plants in segregating families were in a 1R: 3S ratio, indicating recessive inheritance in 212Y1. The introgression from H. bulbosum into H. vulgare was positioned on chromosome 6HS based on GISH and the PCR-based markers. No known stem rust resistance gene has previously been mapped to that region. Thus, it is proposed to name this novel gene from H. bulbosum as rpg6.
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Bian, X. Y., A. Friedrich, J. R. Bai, U. Baumann, D. L. Hayman, S. J. Barker, and P. Langridge. "High-resolution mapping of the S and Z loci of Phalaris coerulescens." Genome 47, no. 5 (October 1, 2004): 918–30. http://dx.doi.org/10.1139/g04-017.
Full textAbstract:
Self incompatibility (SI) in Phalaris coerulescens is gametophytically determined by two unlinked multi allelic loci (S and Z). Neither the S nor Z genes have yet been cloned. As part of a map-based cloning strategy, high-resolution maps of the S and Z regions were generated from distorted segregating populations using RFLP probes from wheat, barley, oat, and Phalaris. The S locus was delimited to 0.26 cM with two boundary markers (Xwg811 and Xpsr168) and cosegregated with Xbm2 and Xbcd762. Xbcd266 was the closest marker linked to Z (0.9 cM). A high level of colinearity in the S and Z regions was found in both self-incompatible and -compatible species. The S locus was localized to the subcentromere region of chromosome 1 and the Z locus to the long arm end of chromosome 2. Several rice BAC clones orthologous to the S and Z locus regions were identified. This opens the possibility of using the rice genome sequence data to generate more closely linked markers and identify SI candidate genes. These results add further support to the conservation of gene order in the S and Z regions of the grass genomes.Key words: Phalaris coerulescens, self-incompatibility, distorted segregation, mapping, map-based cloning, synteny mapping.
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Echt, C. S., P. May-Marquardt, M. Hseih, and R. Zahorchak. "Characterization of microsatellite markers in eastern white pine." Genome 39, no. 6 (December 1, 1996): 1102–8. http://dx.doi.org/10.1139/g96-138.
Full textAbstract:
An enrichment cloning method was evaluated for the isolation of microsatellite loci from eastern white pine and the resulting markers were examined for polymorphisms. A 200-fold enrichment was achieved for highly abundant (AC)n repeats, but for much less abundant (ACAG)n repeats an enrichment of only 20-fold was obtained. Using a single set of PCR conditions, 19 microsatellite loci were identified from 77 primer pairs evaluated. Genotyping of 16 (AC)n loci in 16 unrelated white pines from the north-central United States revealed an average of 5.4 alleles per locus and an average observed heterozygosity of 0.515. Five loci were scored among megagametophytes from a single pine to obtain a haploid genotype of the segregating female meiotic products. All loci segregated according to Mendelian expectations and linkage was established for two of the loci. It was concluded that (AC)n loci are highly variable in this species and that SSR (simple sequence repeat) markers can be efficiently developed for genome mapping and population genetics studies. Key words : Pinus strobus, forest genetics, simple sequence repeat, SSR, allelic diversity.
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Schäfer-Pregl, R., F. Salamini, and C. Gebhardt. "Models for mapping quantitative trait loci (QTL) in progeny of non-inbred parents and their behaviour in presence of distorted segregation ratios." Genetical Research 67, no. 1 (February 1996): 43–54. http://dx.doi.org/10.1017/s0016672300033462.
Full textAbstract:
SummaryIn plants, models for mapping quantitative trait loci (QTL) based on flanking markers have been mainly developed for progenies of inbred lines. We propose twoflanking marker models for QTL mapping in F1 progenies of non-inbred parents. The first is based on the segregation of four different scorable alleles at a marker locus (the four-allele model) and the second (the commonallele model) on one scorable allele per marker locus segregating in both parents. These models are suitable for the majority of the allelic configurations which may occur in crosses between heterozygous parents. For both cases, when four scorable or one common-allele per marker locus segregate, additional algorithms were developed to estimate the recombination frequency between two marker loci. Tests carried out with simulated populations of various sizes indicate that the models provide a good estimate of QTL genotypic means and of recombination frequencies between flanking markers and between the marker loci and the QTL.The estimates of QTL genotypic means have a higher precision than the estimates of recombination frequencies. The four-allele model shows a higher ability to detect QTLs than the common-allele model. If segregation ratios are distorted, the power of both models and the precision of the estimates of recombination frequencies are reduced, whereas the accuracy of estimates of QTL genotype means is not affected by distorted segregation ratios. The power of the common-allele model is substantially reduced if QTL genotypic means depend on additive allelic interactions, whereas the four-allele model is less affected by the non-additive behaviour of QTL alleles.
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Jake, Jernej, Katja Kindlhofer, and Branka Javornik. "Assessment of genetic variation and differentiation of hop genotypes by microsatellite and AFLP markers." Genome 44, no. 5 (October 1, 2001): 773–82. http://dx.doi.org/10.1139/g01-071.
Full textAbstract:
Microsatellites have many desirable marker properties and have been increasingly used in crop plants in genetic diversity studies. Here we report on the characterisation of microsatellite markers and on their use for the determination of genetic identities and the assessment of genetic variability among accessions from a germplasm collection of hop. Thirty-two polymorphic alleles were found in the 55 diploid genotypes, with an average number of eight alleles (3.4 effective alleles) for four microsatellite loci. Calculated polymorphic information content values classified three loci as informative markers and two loci as suitable for mapping. The average observed heterozygosity was 0.7 and the common probability of identical genotypes was 3.271 × 104. An additional locus, amplified by one primer pair, was confirmed by segregation analysis of two crosses. The locus discovered was heterozygous, with a null allele in the segregating population. The same range of alleles was detected in nine triploid and five tetraploid hop genotypes. Cultivar heterozygosity varied among all 69 accessions, with only one cultivar being homozygous at four loci. Microsatellite allele polymorphisms distinguished 81% of all genotypes; the same allelic profile was found mainly in clonally selected cultivars. Cultivar-specific alleles were found in some genotypes, as well as a specific distribution of alleles in geographically distinct hop germplasms. The genetic relationship among 41 hop accessions was compared on the basis of microsatellite and AFLP polymorphisms. Genetic similarity dendrograms showed low correlation between the two marker systems. The microsatellite dendrogram grouped genetically related accessions reasonably well, while the AFLP dendrogram showed good clustering of closely related accessions and, additionally, separated two geographically distinct hop germplasms. The results of microsatellite and AFLP analysis are discussed from the point of view of the applicability of the two marker systems for different aspects of germplasm evaluation.Key words: Humulus lupulus L., germplasm collection, molecular markers, genetic diversity.
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Saifert, Luciano, Fernando David Sánchez-Mora, Wilson Taybar Assumpção, Jean Alberto Zanghelini, Renan Giacometti, Eduardo Irineu Novak, Lírio Luiz Dal Vesco, Rubens Onofre Nodari, Rudolf Eibach, and Leocir José Welter. "Marker-assisted pyramiding of resistance loci to grape downy mildew." Pesquisa Agropecuária Brasileira 53, no. 5 (May 2018): 602–10. http://dx.doi.org/10.1590/s0100-204x2018000500009.
Full textAbstract:
Abstract: The objective of this work was to use a marker-assisted selection for pyramiding the resistance loci Rpv1 and Rpv3.1 in grapevine (Vitis vinifera), and to evaluate their conferred resistance against Brazilian downy mildew (Plasmopara viticola) isolates. A progeny of 23 plants, segregating for the two resistance loci, was obtained by the cross between the Gf 2000-305-122 and Gf.Ga-52-42 genotypes. The progeny was genotyped with four microsatellite markers and phenotyped for resistance to P. viticola using a bioassay with leaf discs. Six plants containing the Rpv1 and Rpv3.1 pyramided loci were identified by the molecular analysis. Plants harboring the Rpv1 + Rpv3.1, Rpv3.1, and Rpv1 loci showed 12.8, 30.0, and 33.1 sporangiophores per leaf disc, respectively. Plants with no resistance loci showed a dense sporulation. The phenotypic analysis of the expression of the two pyramided loci was only confirmed for four plants that showed the highest resistance level, i.e., mean value of 1.8 sporangiophores. A high-throughput method for pyramiding the Rpv1 and Rpv3.1 loci was developed, which confirmed the increased resistance to P. viticola. The selected elite genetic material shows a high resistance to downy mildew and elevated enological potential for grapevine breeding in Brazil.
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Rivard, Sylvain R., Mario Cappadocia, and Benoit S. Landry. "A comparison of RFLP maps based on anther culture derived, selfed, and hybrid progenies of Solanum chacoense." Genome 39, no. 4 (August 1, 1996): 611–21. http://dx.doi.org/10.1139/g96-078.
Full textAbstract:
Comparative RFLP linkage maps were constructed using five segregating populations derived from two self-incompatible lines (termed PI 230582 and PI 458314) of diploid tuber-bearing Solanum chacoense Bitt. The analysis was based on 84 RFLP loci identified by 73 different cDNA clones. Distortion of expected Mendelian segregation ratios was observed; less than 10% of the markers showed a skewed segregation in the gametes forming the F1, hybrid population compared with 30% in the selfed population and 46 and 70% in the two populations produced by anther culture. For the anther culture derived populations, most of the skewed loci were scattered throughout the genome, whereas in the populations derived from selfing, they were found primarily in linkage group 1, around the S locus. In this study, we also found that the rate of meiotic recombination could differ between the male and female gametes produced by our parental lines. Thus, male gametes of line PI 458314 showed significantly less recombination as assessed by the total length of the map (206 cM for male gametes vs. 375 cM for female gametes) and the phenomenon was genome-wide. In contrast, the maps from the gametes of PI 230582 had about the same length, but some linkage groups were longer in the female gametes, while others were longer in the male gametes. Key words : Solanum chacoense, RFLP, anther culture, skewed segregation, self-incompatibility, sex differences in recombination.
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Causse, Mathilde, Sylvain Santoni, Catherine Damerval, Alexandrine Maurice, Alain Charcosset, Janet Deatrick, and Dominique de Vienne. "A composite map of expressed sequences in maize." Genome 39, no. 2 (April 1, 1996): 418–32. http://dx.doi.org/10.1139/g96-053.
Full textAbstract:
A maize genetic map based mainly on expressed sequences has been constructed. The map incorporates data from four segregating populations. Three recombinant inbred line populations were derived from the nonreciprocal crosses between three inbred lines. A map derived from an independent F2 progeny from one of the crosses was also used. With a total of 521 genotyped individuals, accuracy in gene order is expected. Five sources of markers were used: (i) 109 loci corresponding to 69 genes of known function, (ii) 39 loci controlling protein position shifts revealed by two-dimensional electrophoresis, (iii) 8 isozyme loci, (iv) 17 loci corresponding to 14 sequenced cDNAs for which no homology was found in gene banks, and (v) 102 loci corresponding to 81 anonymous probes. As many loci were common to all maps, we tested heterogeneity between recombination fractions. The comparison of recombination fractions revealed: (i) a good correspondence between the maps derived from the same cross, (ii) few significant differences in interval distances, and (iii) global differences, which can reach 20% of the total map length. A composite map of 275 loci covering 1765 cM has been constructed. Key words : Zea mays L., RFLP, genetic map, molecular markers, proteins.
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Ron, Micha, David Kliger, Esther Feldmesser, Eyal Seroussi, Ephraim Ezra, and Joel Ira Weller. "Multiple Quantitative Trait Locus Analysis of Bovine Chromosome 6 in the Israeli Holstein Population by a Daughter Design." Genetics 159, no. 2 (October 1, 2001): 727–35. http://dx.doi.org/10.1093/genetics/159.2.727.
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Abstract Nine Israeli Holstein sire families with 2978 daughters were analyzed for quantitative trait loci effects on chromosome 6 for five milk production traits by a daughter design. All animals were genotyped for 2 markers. The three families with significant effects were genotyped for up to 10 additional markers spanning positions 0–122 cM of BTA6. Two sires were segregating for a locus affecting protein and fat percentage near position 55 cM with an estimated substitution effect of 0.18% protein, which is equivalent to one phenotypic standard deviation. This locus was localized to a confidence interval of 4 cM. One of these sires was also heterozygous for a locus affecting milk, fat, and protein production near the centromere. The hypothesis of two segregating loci was verified by multiple regression analysis. A third sire was heterozygous for a locus affecting milk and protein percentage near the telomeric end of the chromosome. Possible candidates for the major quantitative gene near position 55 cM were determined by comparative mapping. IBSP and SSP1 were used as anchors for the orthologous region on human chromosome 4. Twelve genes were detected within a 2-Mbp sequence. None of these genes have been previously associated with lactogenesis.
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Yuan, J., V. N. Njiti, K. Meksem, M. J. Iqbal, K. Triwitayakorn, My A. Kassem, G. T. Davis, M. E. Schmidt, and D. A. Lightfoot. "Quantitative trait loci in Two Soybean Recombinant Inbred Line Populations Segregating for Yield and Disease Resistance." Crop Science 42, no. 1 (2002): 271. http://dx.doi.org/10.2135/cropsci2002.0271.
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Yuan, J., V. N. Njiti, K. Meksem, M. J. Iqbal, K. Triwitayakorn, My A. Kassem, G. T. Davis, M. E. Schmidt, and D. A. Lightfoot. "Quantitative trait loci in Two Soybean Recombinant Inbred Line Populations Segregating for Yield and Disease Resistance." Crop Science 42, no. 1 (January 2002): 271–77. http://dx.doi.org/10.2135/cropsci2002.2710.
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Cardinal, Andrea J., Joseph W. Burton, Ana María Camacho-Roger, Rebecca Whetten, Andrew S. Chappell, Kristin D. Bilyeu, Jéròme Auclair, and Ralph E. Dewey. "Molecular Analysis of GmFAD3A in Two Soybean Populations Segregating for the fan , fap1 , and fapnc Loci." Crop Science 51, no. 5 (September 2011): 2104–12. http://dx.doi.org/10.2135/cropsci2010.08.0500.
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Ming, Ray, Terrye A. Del Monte, Eduardo Hernandez, Paul H. Moore, James E. Irvine, and Andrew H. Paterson. "Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes." Genome 45, no. 5 (October 1, 2002): 794–803. http://dx.doi.org/10.1139/g02-042.
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Quantitative trait loci (QTLs) affecting plant height and flowering were studied in the two Saccharum species from which modern sugarcane cultivars are derived. Two segregating populations derived from interspecific crosses between Saccharum officinarum and Saccharum spontaneum were genotyped with 735 DNA markers. Among the 65 significant associations found between these two traits and DNA markers, 35 of the loci were linked to sugarcane genetic maps and 30 were unlinked DNA markers. Twenty-one of the 35 mapped QTLs were clustered in eight genomic regions of six sugarcane homologous groups. Some of these could be divergent alleles at homologous loci, making the actual number of genes implicated in these traits much less than 35. Four QTL clusters controlling plant height in sugarcane corresponded closely to four of the six plant-height QTLs previously mapped in sorghum. One QTL controlling flowering in sugarcane corresponded to one of three flowering QTLs mapped in sorghum. The correspondence in locations of QTLs affecting plant height and flowering in sugarcane and sorghum reinforce the notion that the simple sorghum genome is a valuable "template" for molecular dissection of the much more complex sugarcane genome.Key words: DNA markers, genetic map, quantitative trait loci, Saccharum.
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Juvik, John A., Gad G. Yousef, Tae-Ho Han, Yaacov Tadmor, Fermin Azanza, William F. Tracy, Avri Barzur, and Torbert R. Rocheford. "QTL Influencing Kernel Chemical Composition and Seedling Stand Establishment in Sweet Corn with the shrunken2 and sugary enhancer1 Endosperm Mutations." Journal of the American Society for Horticultural Science 128, no. 6 (November 2003): 864–75. http://dx.doi.org/10.21273/jashs.128.6.0864.
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This study was conducted to identify the chromosomal location and magnitude of effect of quantitative trait loci (QTL) controlling sweet corn (Zea mays L.) stand establishment and investigate the impact of dry kernel characteristics on seedling emergence under field conditions. Genetic and chemical analysis was performed on two F2:3 populations (one homozygous for su1 and segregating for se1, the other homozygous for sh2 endosperm carbohydrate mutations) derived from crosses between parental inbreds that differed in field emergence and kernel chemical composition. A series of restriction fragment-length polymorphism (RFLP) and phenotypic markers distributed throughout the sweet corn genome were used to construct a genetic linkage map for each population. F2:3 families from the two populations were evaluated for seedling emergence and growth rate at four locations. Mature dry kernels of each family were assayed for kernel chemical and physiological parameters. Composite interval analysis revealed significant QTL associations with emergence and kernel chemical and physiological variables. Improved emergence was positively correlated with lower seed leachate conductivity, greater embryo dry weight, and higher kernel starch content. QTL affecting both field emergence and kernel characteristics were detected in both populations. In the su1 se1 population genomic regions significantly influencing emergence across all four environments were found associated with the se1 gene on chromosome 2 and the RFLP loci php200020 on chromosome 7 and umc160 on chromosome 8. In the sh2 population the RFLP loci umc131 on chromosome 2 and bnl9.08 on chromosome 8 were linked to QTL significantly affecting emergence. Since seedling emergence and kernel sugar content have been shown to be negatively correlated, undesirable effects on sweet corn eating quality associated with each emergence QTL is discussed. Segregating QTL linked to RFLP loci in these populations that exert significant effects on the studied traits are candidates for molecular marker-assisted selection to improve sweet corn seed quality.
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Pereira, Gabriella Santos, Lilian Padilha, Edila Vilela Resende Von Pinho, Rita de Kássia Siqueira Teixeira, Carlos Henrique Siqueira de Carvalho, Mirian Peres Maluf, and Bruna Line de Carvalho. "Microsatellite markers in analysis of resistance to coffee leaf miner in Arabica coffee." Pesquisa Agropecuária Brasileira 46, no. 12 (December 2011): 1650–56. http://dx.doi.org/10.1590/s0100-204x2011001200010.
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The objective of this work was to analyze coffee (Coffea arabica) genotypes resistant to the coffee leaf miner (Leucoptera coffeella) using microsatellite markers. Sixty-six loci were evaluated, of which 63 were obtained from the Brazilian Coffee Expressed Sequence Tag (EST) database. These loci were amplified in bulks of individuals from F5 progenies of 'Siriema' (C. arabica x C. racemosa) resistant and susceptible to the insect, in eight samples of C. racemosa, and in a F6 population of 'Siriema' with 91 individuals segregating for resistance to the leaf miner. Polymorphisms were verified for two simple sequence repeat (SSR) loci in bulks of the susceptible progenies. The two polymorphic alleles were present in around 70% of the susceptible genotypes in F5 and in approximately 90% of the susceptible individuals in F6. However, the polymorphic EST-SSR markers among populations contrasting for resistance to leaf miner were not correlated to the evaluated characteristics. SSR markers show inter- and intraspecific polymorphism in C. arabica and C. racemosa.
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Pettersson, Mats E., and Patric Jern. "Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups." Genes 10, no. 2 (February 20, 2019): 162. http://dx.doi.org/10.3390/genes10020162.
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Retroviruses have invaded vertebrate hosts for millions of years and left an extensive endogenous retrovirus (ERV) record in the host genomes, which provides a remarkable source for an evolutionary perspective on retrovirus-host associations. Here we identified ERV variation across whole-genomes from two chicken lines, derived from a common founder population subjected to 50 years of bi-directional selection on body weight, and a distantly related domestic chicken line as a comparison outgroup. Candidate ERV loci, where at least one of the chicken lines indicated distinct differences, were analyzed for adjacent host genomic landscapes, selective sweeps, and compared by sequence associations to reference assembly ERVs in phylogenetic analyses. Current data does not support selection acting on specific ERV loci in the domestic chicken lines, as determined by presence inside selective sweeps or composition of adjacent host genes. The varying ERV records among the domestic chicken lines associated broadly across the assembly ERV phylogeny, indicating that the observed insertion differences result from pre-existing and segregating ERV loci in the host populations. Thus, data suggest that the observed differences between the host lineages are best explained by substantial standing ERV variation within host populations, and indicates that even truncated, presumably old, ERVs have not yet become fixed in the host population.
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Nagamine, Yoshitaka, Chris S. Haley, Asheber Sewalem, and Peter M. Visscher. "Quantitative Trait Loci Variation for Growth and Obesity Between and Within Lines of Pigs (Sus scrofa)." Genetics 164, no. 2 (June 1, 2003): 629–35. http://dx.doi.org/10.1093/genetics/164.2.629.
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Abstract The hypothesis that quantitative trait loci (QTL) that explain variation between divergent populations also account for genetic variation within populations was tested using pig populations. Two regions of the porcine genome that had previously been reported to harbor QTL with allelic effects that differed between the modern pig and its wild-type ancestor and between the modern pig and a more distantly related population of Asian pigs were studied. QTL for growth and obesity traits were mapped using selectively genotyped half-sib families from five domesticated modern populations. Strong support was found for at least one QTL segregating in each population. For all five populations there was evidence of a segregating QTL affecting fatness in a region on chromosome 7. These findings confirm that QTL can be detected in highly selected commercial populations and are consistent with the hypothesis that the same chromosome locations that account for variation between populations also explain genetic variation within populations.
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Mehlenbacher, Shawn A., and Maxine M. Thompson. "Inheritance of a Chlorophyll Deficiency in Hazelnut." HortScience 26, no. 11 (November 1991): 1414–16. http://dx.doi.org/10.21273/hortsci.26.11.1414.
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A chlorophyll deficiency expressed as yellowing of leaves was observed in hazelnut (Corylus avellana L.) progenies. Segregation ratios approximated 3 green: 1 yellow, indicating control by a single recessive gene designated chlorophyll deficient #1, for which the symbol c, is proposed. `Barcelona', `Butler', `Compton', `Lansing', Willamette', and the ornamental selection `Redleaf #3' are heterozygous. Pedigree analysis strongly suggests that all heteroxygotes inherited the recessive allele from `Barcelona'. A cross of `Barcelona' with the yellow-leafed ornamental Corylus avellana L. var. aurea Kirchn. produced no yellow-leafed seedlings, indicating that the chlorophyll deficiencies from these two sources are controlled by different loci. Progenies segregating simultaneously for this trait and the gene controlling presence of anthocyanin indicated that the two traits are inherited independently. Seedlings deficient in chlorophyll but with anthocyanin were able to survive under field conditions, while leaves of yellow-leafed seedlings lacking anthocyanin became scorched and the trees died.
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Cruz-Requena, M., C. N. Aguilar-González, J. Espinoza-Velázquez, M. H. Reyes-Valdés, and R. Rodríguez-Herrera. "AFLPs loci associated with polyembryonic maize using selective genotyping analysis." Israel Journal of Plant Sciences 61, no. 1-4 (May 18, 2013): 46–50. http://dx.doi.org/10.1080/07929978.2014.950045.
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Polyembryony is a trait widely distributed in nature which occurs in different plant species including maize. This trait has been studied at the genetic level with various molecular markers. In the present study we analyzed two monoembryonic and polyembryonic maize groups, derived from the F2population of a cross between plants from a high polyembryonic brachytic (BAP) population and a monoembryonic commercial variety (PUMA). Polymorphism was analyzed among and between these two F2maize groups with AFLPs (amplified fragment length polymorphisms). A total of 16 polymorphic bands were obtained, which were recorded as binary code (1 for band presence and 0 for absence). The data were analyzed using the InfoGen software. Contingency of AFLP against polyembryony was determined using the Chi square association. The results suggest a low genetic diversity between the F2groups. This result was corroborated with the Chi square test which indicated that two markers (13 and 15) may be related to polyembryony. The present study is the first report using segregating populations to identify more than one locus associated with PE in maize by marker techniques.