Segregation distortion and linkage analysis in eggplant (Solanum melongena L.)

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 805-815 ◽  
Author(s):  
Lorenzo Barchi ◽  
Sergio Lanteri ◽  
Ezio Portis ◽  
Anikò Stàgel ◽  
Giampiero Valè ◽  
...  
Keyword(s):  
Segregation Distortion ◽  
Mapping Population ◽  
Full Range ◽  
Solanum Melongena ◽  
Linkage Groups ◽  
Caps Marker ◽  
Dh Population ◽  
Breeding Lines ◽  
Introgressed Segment ◽  
Intraspecific Hybrid

An anther-derived doubled haploid (DH) population and an F2 mapping population were developed from an intraspecific hybrid between the eggplant breeding lines 305E40 and 67/3. The former incorporates an introgressed segment from Solanum aethiopicum Gilo Group carrying the gene Rfo-sa1, which confers resistance to Fusarium oxysporum ; the latter is a selection from an intraspecific cross involving two conventional eggplant varieties and lacks Rfo-sa1. Initially, 28 AFLP primer combinations (PCs) were applied to a sample of 93 F2 individuals and 93 DH individuals, from which 170 polymorphic AFLP fragments were identified. In the DH population, the segregation of 117 of these AFLPs as well as markers closely linked to Rfo-sa1 was substantially distorted, while in the F2 population, segregation distortion was restricted to just 10 markers, and thus the latter was chosen for map development. A set of 141 F2 individuals was genotyped with 73 AFLP PCs (generating 406 informative markers), 32 SSRs, 4 tomato RFLPs, and 3 CAPS markers linked to Rfo-sa1. This resulted in the assignment of 348 markers to 12 major linkage groups. The framework map covered 718.7 cM, comprising 238 markers (212 AFLPs, 22 SSRs, 1 RFLP, and the Rfo-sa1 CAPS). Marker order and inter-marker distances in this eggplant map were largely consistent with those reported in a recently published SSR-based map. From an eggplant breeding perspective, DH populations produced by anther culture appear to be subject to massive segregation distortion and thus may not be very efficient in capturing the full range of genetic variation present in the parental lines.

scholarly journals QTL analysis of seed germination traits in tobacco (Nicotiana tabacum L.)

2021 ◽  
Author(s):  
Monika Agacka-Mołdoch ◽  
Mian Abdur Rehman Arif ◽  
Ulrike Lohwasser ◽  
Teresa Doroszewska ◽  
Ramsey S. Lewis ◽  
...  
Keyword(s):  
Nicotiana Tabacum ◽  
Seed Germination ◽  
Doubled Haploid ◽  
Mapping Population ◽  
Area Under The Curve ◽  
Linkage Groups ◽  
Polygenic Control ◽  
Nicotiana Tabacum L ◽  
Controlled Deterioration ◽  
Germination Traits

AbstractGenetic mapping of seed germination traits has been performed with many plant species. In tobacco, however, investigations are rare. In the present study, a bi-parental mapping population consisting of 118 doubled haploid lines and derived from a cross between ‘Beinhart-1000’ and ‘Hicks’ was investigated. Four germination-related traits, total germination (TG), normal germination (NG), time to reach 50% of total germination (T50), and the area under the curve after 200 h of germination (AUC) were considered by examining seeds either untreated or after a moderate controlled deterioration (CD). Quantitative trait loci were found for all traits distributed on 11 out of the 24 linkage groups. It was demonstrated that, as in many other species, germination-related traits are very complex and under polygenic control.

Two genetic linkage maps of mungbean using RFLP and RAPD markers

2000 ◽  
Vol 51 (4) ◽  
pp. 415 ◽  
Author(s):  
C. J. Lambrides ◽  
R. J. Lawn ◽  
I. D. Godwin ◽  
J. Manners ◽  
B. C. Imrie
Keyword(s):  
Linkage Map ◽  
Segregation Distortion ◽  
Recombinant Inbred ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Rflp Markers ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genetic Linkage Maps ◽  
Map Distance

Two genetic linkage maps of mungbean derived from the cross Berken ACC 41 are reported. The F2 map constructed from 67 individuals consisted of 110 markers (52 RFLP and 56 RAPD) that grouped into 12 linkage groups. The linked markers spanned a total map distance of 758.3 cM. A recombinant inbred (RI) population derived from the 67 F2 individuals was used for the generation of an additional linkage map. The RI map, composed entirely of RAPD markers, consisted of 115 markers in 12 linkage groups. The linked markers spanned a total map distance of 691.7 cM. Using a framework set of RFLP markers, the F2 map was compared with another F2 mungbean map constructed in Minnesota. In general, the order of these markers was consistent between maps. Segregation distortion was observed for some markers. 14.5% (16/110) of mapped F2 markers and 24% (28/115) of mapped RI markers segregated with distorted ratios. Segregation distortion occurred in each successive generation after the F2 . The regions of distortion identified in the Australian maps did not coincide with regions of the Minnesota map.

scholarly journals An application of Bayesian QTL mapping to early development in double haploid lines of rainbow trout including environmental effects

2005 ◽  
Vol 86 (3) ◽  
pp. 209-221 ◽  
Author(s):  
VICTOR MARTINEZ ◽  
GARY THORGAARD ◽  
BARRIE ROBISON ◽  
MIKKO J. SILLANPÄÄ
Keyword(s):  
Rainbow Trout ◽  
Early Development ◽  
Life History Traits ◽  
Bayesian Method ◽  
Mapping Population ◽  
Linkage Groups ◽  
Dimensional Parameter ◽  
Posterior Expectation ◽  
Clonal Lines ◽  
Main Effects

A Bayesian model and variable dimensional parameter estimation based on Markov chain Monte Carlo was applied to map quantitative trait loci (QTLs) in a doubled haploid mapping population of rainbow trout. To increase power, the analysis was performed using the multiple-QTL model, which simultaneously accounted for all the environmental and genetic main effects that influence the expression of early development life history traits. By doing so we obtained the posterior estimated effects for the environmental factors as well as the number, positions, and the effects for the QTLs. The analyses revealed QTLs for time at hatching, embryonic length and weight at swim-up stage. The posterior expectation of the number of QTLs in different linkage groups shows that at least four QTLs are needed to explain the observed differences in early development between the clonal lines. The Bayesian method effectively combined all the information available to accurately position these QTLs in the rainbow trout genome.

Development of random amplified polymorphic DNA markers for genetic mapping in Pacific yew (Taxusbrevifolia)

1996 ◽  
Vol 26 (3) ◽  
pp. 497-503 ◽  
Author(s):  
B. Göçmen ◽  
Z. Kaya ◽  
K.D. Jermstad ◽  
D.B. Neale
Keyword(s):  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
Polymorphic Locus ◽  
Single Mother ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Arbitrary Sequence ◽  
Linkage Groups ◽  
Polymerase Chain

A genetic linkage map was constructed for Pacific yew (Taxusbrevifolia Nutt.) based on random amplified polymorphic DNA (RAPD) markers. A series of optimization experiments were conducted to develop a highly repeatable protocol for Pacific yew. In these experiments, a high MgCl2 concentration (5.5 mM) together with a low primer concentration (0.2 μm) in the polymerase chain reaction (PCR) mixture yielded the best amplification products. PCR amplification products were further improved by treating the template DNAs with RNase. Experiments showed that bovine serum albumine had the same effect as RNase on PCR amplification. The segregating mapping population consisted of 39 haploid megagametophytes from a single mother tree. DNA extracted from a subset of 6 megagametophytes was screened with 345 ten-base oligonucleotide primers of arbitrary sequence. Of the screened primers, 28% revealed at least one polymorphic locus. Eighty-six of these primers revealed at least one polymorphic locus and were used with the entire set of megagametophyte DNAs. One-hundred-two loci were scored and segregated in the expected 1:1 ratio (1.19 locus per primer). Linkage analysis was conducted using MAPMAKER. Forty-one of 102 markers were distributed into 17 linkage groups and covered 305.8 centimorgans. The remaining 61 unlinked markers should be assigned to linkage groups as more markers are added to the map.

A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae)

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1037-1051 ◽  
Author(s):  
Roy G Danzmann ◽  
Margaret Cairney ◽  
William S Davidson ◽  
Moira M Ferguson ◽  
Karim Gharbi ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Linkage Group ◽  
Atlantic Salmon ◽  
Segregation Distortion ◽  
Recombination Rate ◽  
Chromosome Structure ◽  
Arctic Charr ◽  
Salmonid Fishes ◽  
Linkage Groups ◽  
Recombination Rates

We updated the genetic map of rainbow trout (Oncorhynchus mykiss) for 2 outcrossed mapping panels, and used this map to assess the putative chromosome structure and recombination rate differences among linkage groups. We then used the rainbow trout sex-specific maps to make comparisons with 2 other ancestrally polyploid species of salmonid fishes, Arctic charr (Salvelinus alpinus) and Atlantic salmon (Salmo salar) to identify homeologous chromosome affinities within each species and ascertain homologous chromosome relationships among the species. Salmonid fishes exhibit a wide range of sex-specific differences in recombination rate, with some species having the largest differences for any vertebrate species studied to date. Our current estimate of female:male recombination rates in rainbow trout is 4.31:1. Chromosome structure and (or) size is associated with recombination rate differences between the sexes in rainbow trout. Linkage groups derived from presumptive acrocentric type chromosomes were observed to have much lower sex-specific differences in recombination rate than metacentric type linkage groups. Arctic charr is karyotypically the least derived species (i.e., possessing a high number of acrocentric chromosomes) and Atlantic salmon is the most derived (i.e., possessing a number of whole-arm fusions). Atlantic salmon have the largest female:male recombination ratio difference (i.e., 16.81:1) compared with rainbow trout, and Arctic charr (1.69:1). Comparisons of recombination rates between homologous segments of linkage groups among species indicated that when significant experiment-wise differences were detected (7/24 tests), recombination rates were generally higher in the species with a less-derived chromosome structure (6/7 significant comparisons). Greater similarity in linkage group syntenies were observed between Atlantic salmon and rainbow trout, suggesting their closer phylogenetic affinities, and most interspecific linkage group comparisons support a model that suggests whole chromosome arm translocations have occurred in the evolution of this group. However, some possible exceptions were detected and these findings are discussed in relation to their influence on segregation distortion patterns. We also report unusual meiotic segregation patterns in a female parent involving the duplicated (homeologous) linkage group pair 12/16 and discuss several models that may account for these patterns.Key words: linkage analysis, genetic markers, polyploidy, tetrasomic inheritance, segregation distortion, recombination rate.

Assessment of genetic diversity in advanced breeding lines derived from intraspecific crosses of garden pea (Pisum sativum L.)

2018 ◽  
Author(s):  
Bhallan Singh Sekhon ◽  
Akhilesh Sharma ◽  
Viveka Katoch . ◽  
Rakesh K. Kapila ◽  
V. K. Sood
Keyword(s):  
Genetic Diversity ◽  
Hybrid Breeding ◽  
Internodal Length ◽  
Garden Pea ◽  
Breeding Lines ◽  
Pisum Sativum L ◽  
Breeding Programmes ◽  
Pedigree Selection ◽  
Direct Use ◽  
Intraspecific Hybrid

An intraspecific hybrid breeding program involving six crosses, Palam Sumool (PS) × Palam Priya, PS × Pb-89, PS × Azad P-1, PS × Palam Triloki and VRPMR10 × Sugar Giant, Green Pearl × DPP-9411 was initiated in 2006 onwards followed by pedigree selection, resulted in isolation of 45 genotypes with desirable attributes. These progenies along with five recommended varieties were evaluated during 2014-15 to assess degree of divergence. A considerable genetic diversity was observed among genotypes, dispersed in 18 diverse clusters. Of these, 17 were monogenotypic while cluster I had maximum genotypes. Internodal length contributed maximum towards total genetic divergence followed by nodes per plant, protein content and average pod weight. Superior performing genotypes viz., ‘DPP-2011-SP-7’, ‘DPP-2011-SP-17’, and ‘DPP-2011-SP-24’ from cluster I and ‘DPP-2011-SP-6’, ‘DPP-2011-SP-22’ ‘DPPMR-09-1’, ‘DPPMR-09-2’, ‘DPP-2011-SN-5’ and ‘Palam Triloki’ from monogenotypic clusters offer promise for their direct use as varieties and as potential parents in future breeding programmes.

A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers

Genome ◽  
2012 ◽  
Vol 55 (4) ◽  
pp. 327-335 ◽  
Author(s):  
Xiaoxia Yu ◽  
Xiaolei Li ◽  
Yanhong Ma ◽  
Zhuo Yu ◽  
Zaozhe Li
Keyword(s):  
Molecular Markers ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
Gene Localization ◽  
Linkage Groups ◽  
Crested Wheatgrass ◽  
Map Distance

Using a population of 105 interspecific F2 hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. ‘Fairway’ as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future.

Genetic Analysis of Sunflower Domestication

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1257-1267 ◽  
Author(s):  
John M Burke ◽  
Shunxue Tang ◽  
Steven J Knapp ◽  
Loren H Rieseberg
Keyword(s):  
Quantitative Traits ◽  
Mapping Population ◽  
Interval Mapping ◽  
Phenotypic Variance ◽  
Linkage Groups ◽  
Multiple Traits ◽  
Wild Progenitor ◽  
Phenotypic Differences ◽  
Selection For ◽  
Major Qtl

Abstract Quantitative trait loci (QTL) controlling phenotypic differences between cultivated sunflower and its wild progenitor were investigated in an F3 mapping population. Composite interval mapping revealed the presence of 78 QTL affecting the 18 quantitative traits of interest, with 2–10 QTL per trait. Each QTL explained 3.0–68.0% of the phenotypic variance, although only 4 (corresponding to 3 of 18 traits) had effects >25%. Overall, 51 of the 78 QTL produced phenotypic effects in the expected direction, and for 13 of 18 traits the majority of QTL had the expected effect. Despite being distributed across 15 of the 17 linkage groups, there was a substantial amount of clustering among QTL controlling different traits. In several cases, regions influencing multiple traits harbored QTL with antagonistic effects, producing a cultivar-like phenotype for some traits and a wild-like phenotype for others. On the basis of the directionality of QTL, strong directional selection for increased achene size appears to have played a central role in sunflower domestication. None of the other traits show similar evidence of selection. The occurrence of numerous wild alleles with cultivar-like effects, combined with the lack of major QTL, suggests that sunflower was readily domesticated.

Gametophytic selection in a winter × spring barley cross

Genome ◽  
1991 ◽  
Vol 34 (6) ◽  
pp. 918-922 ◽  
Author(s):  
C. C. Schön ◽  
P. M. Hayes ◽  
T. K. Blake ◽  
S. J. Knapp
Keyword(s):  
Segregation Distortion ◽  
Doubled Haploid ◽  
Doubled Haploids ◽  
Spring Barley ◽  
Population Based ◽  
Doubled Haploid Population ◽  
Dh Population ◽  
Gametophytic Selection ◽  
Segregation Ratios ◽  
Haploid Population

Segregation distortion and the consequences of gametophytic selection were assessed in a winter × spring barley cross by comparing segregation of enzyme, storage protein, DNA, and morphological markers in three populations derived from the same cross: a control F2 (F2C), a doubled-haploid (DH) population, and an F2 derived from F1 plants self-pollinated at 10 °C (F2T). Segregation distortion was present in the F2T and the doubled-haploid population. Based on a comparison of the F2C and the F2T, gametophytic selection as a consequence of self-pollination at 10 °C was operative on chromosome 7 in regions linked to Rrn2. Segregation distortion in favor of the winter parent was found in the doubled-haploid population. There were significant deviations from expected segregation ratios at two loci, but only at one of the loci was the gene number significantly different from the F2C. Despite segregation distortion, the doubled-haploid population should be suitable for linkage analyses, as estimates of recombination based on F2 and doubled-haploid data were in close agreement.Key words: Hordeum vulgare, segregation distortion, doubled haploids, gametophytic selection, cold tolerance.

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