A comparison of RFLP maps based on anther culture derived, selfed, and hybrid progenies of Solanum chacoense

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 611-621 ◽  
Author(s):  
Sylvain R. Rivard ◽  
Mario Cappadocia ◽  
Benoit S. Landry
Keyword(s):  
Anther Culture ◽  
Solanum Chacoense ◽  
Hybrid Population ◽  
Cdna Clones ◽  
Mendelian Segregation ◽  
Male Gametes ◽  
Genome Wide ◽  
Skewed Segregation ◽  
Two Populations ◽  
Group 1

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.

scholarly journals NIMG-46. RADIOGENOMIC FEATURES PREDICT CLINICALLY RELEVANT GENOME-WIDE ALTERATION SIGNATURES IN GLIOBLASTOMA

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii158-ii158
Author(s):  
Nicholas Nuechterlein ◽  
Beibin Li ◽  
James Fink ◽  
David Haynor ◽  
Eric Holland ◽  
...  
Keyword(s):  
Machine Learning ◽  
Feature Selection ◽  
Molecular Subtypes ◽  
Feature Selection Method ◽  
Selection Method ◽  
Versus Group ◽  
Mri Features ◽  
Genome Wide ◽  
Group 2 ◽  
Group 1

Abstract BACKGROUND Previously, we have shown that combined whole-exome sequencing (WES) and genome-wide somatic copy number alteration (SCNA) information can separate IDH1/2-wildtype glioblastoma into two prognostic molecular subtypes (Group 1 and Group 2) and that these subtypes cannot be distinguished by epigenetic or clinical features. However, the potential for radiographic features to discriminate between these molecular subtypes has not been established. METHODS Radiogenomic features (n=35,400) were extracted from 46 multiparametric, pre-operative magnetic resonance imaging (MRI) of IDH1/2-wildtype glioblastoma patients from The Cancer Imaging Archive, all of whom have corresponding WES and SCNA data in The Cancer Genome Atlas. We developed a novel feature selection method that leverages the structure of extracted radiogenomic MRI features to mitigate the dimensionality challenge posed by the disparity between the number of features and patients in our cohort. Seven traditional machine learning classifiers were trained to distinguish Group 1 versus Group 2 using our feature selection method. Our feature selection was compared to lasso feature selection, recursive feature elimination, and variance thresholding. RESULTS We are able to classify Group 1 versus Group 2 glioblastomas with a cross-validated area under the curve (AUC) score of 0.82 using ridge logistic regression and our proposed feature selection method, which reduces the size of our feature set from 35,400 to 288. An interrogation of the selected features suggests that features describing contours in the T2 abnormality region on the FLAIR MRI modality may best distinguish these two groups from one another. CONCLUSIONS We successfully trained a machine learning model that allows for relevant targeted feature extraction from standard MRI to accurately predict molecularly-defined risk-stratifying IDH1/2-wildtype glioblastoma patient groups. This algorithm may be applied to future prospective studies to assess the utility of MRI as a surrogate for costly prognostic genomic studies.

Molecular Mapping of Segregation Distortion Loci in Aegilops tauschii

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 319-327 ◽  
Author(s):  
J D Faris ◽  
B Laddomada ◽  
B S Gill
Keyword(s):  
Segregation Distortion ◽  
Molecular Mapping ◽  
Aegilops Tauschii ◽  
Distorted Segregation ◽  
F2 Population ◽  
Male Gametes ◽  
Skewed Segregation ◽  
Segregation Ratios ◽  
Backcross Populations ◽  
Intraspecific Hybrids

Abstract Distorted segregation ratios of genetic markers are often observed in progeny of inter- and intraspecific hybrids and may result from competition among gametes or from abortion of the gamete or zygote. In this study, 194 markers mapped in an Aegilops tauschii F2 population were surveyed for distorted segregation ratios. Region(s) with skewed segregation ratios were detected on chromosomes 1D, 3D, 4D, and 7D. These distorter loci are designated as QSd.ksu-1D, QSd.ksu-3D, QSd.ksu-4D, and QSd.ksu-7D. Three regions of segregation distortion identified on chromosome 5D were analyzed in two sets of reciprocal backcross populations to analyze the effect of sex and cytoplasm on segregation distortion. Extreme distortion of marker segregation ratios was observed in populations in which the F1 was used as the male parent, and ratios were skewed in favor of TA1691 alleles. There was some evidence of differential transmission caused by nucleo-cytoplasmic interactions. Our results agree with other studies stating that loci affecting gametophyte competition in male gametes are located on 5DL. The distorter loci on 5DL are designated as QSd.ksu-5D.1, QSd.ksu-5D.2, and QSd.ksu-5D.3.

scholarly journals A Genome-wide Scan of Loci Linked to Serum Adiponectin in Two Populations of African Descent*

Obesity ◽  
2007 ◽  
Vol 15 (5) ◽  
pp. 1207-1214 ◽  
Author(s):  
Chindo Hicks ◽  
Xiaofeng Zhu ◽  
Amy Luke ◽  
Donghui Kan ◽  
Adebowale Adeyemo ◽  
...  
Keyword(s):  
African Descent ◽  
Serum Adiponectin ◽  
Genome Wide ◽  
A Genome ◽  
Two Populations ◽  
Genome Wide Scan

13q14 Chromosome Deletion Size and Number of Deleted Cells Influence Prognosis In Chronic Lymphocytic Leukemia

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3578-3578
Author(s):  
Francesca Maria Rossi ◽  
Davide Rossi ◽  
Clara Deambrogi ◽  
Francesco Bertoni ◽  
Michele Dal Bo ◽  
...  
Keyword(s):  
Clinical Course ◽  
Lymphocytic Leukemia ◽  
Single Institution ◽  
Group 4 ◽  
Median Size ◽  
Mutational Status ◽  
Genome Wide ◽  
Group 3 ◽  
Group 2 ◽  
Group 1

Abstract Abstract 3578 Introduction: Chronic lymphocytic leukemia (CLL) patients bearing 13q14 deletion are known to experience a more favorable clinical course. Recent studies, focusing on patients with loss of 13q as the sole cytogenetic aberration at diagnosis (del13q-only cases), showed that the number of malignant cells carrying this genetic lesion correlates with a more aggressive clinical behavior. However, whether the size of the 13q deletion may also influence the clinical outcome remains to be elucidated. Patients and Methods: Probes for chromosome 13q (LSI-RB1, LSI-D13S319), 11q (LSI-ATM), 17p (LSI-p53) and chromosome 12 (CEP12) were utilized on nuclei collected at diagnosis from: i) a multi-institutional CLL cohort (342 del13q-only cases) and ii) a consecutive unselected single-institution cohort of 265 cases. RB1 deleted cases (delRB1) were defined as having at least 5% of deleted nuclei. Time to treatment (TTT) intervals, as well as Rai staging, IGHV mutational status, CD38 and ZAP70 expression, B2-microglobulin levels, all evaluated at diagnosis, were also available for all cases that entered the study. Genome wide DNA profile was performed in a pilot series of 90 CLL samples using Affymetrix GeneChip Human SNP6 arrays. Results: According to genome wide DNA analysis, delRB1 occurred in a proportion of del13q-only cases (36/90; 40%), always comprising the deleted region detected with the LSI-D13S319 probe (that covers the miR-15a/16-1 cluster and the DLEU2 gene) and characterized by a larger chromosome loss (median size 2.07 Mb vs. a median size of 0.86 Mb for the canonical del13S319). Maximally selected log-rank statistics identified the 70% of nuclei bearing del13S319 as the most appropriate cut-off value capable of separating del13q-only cases into two subgroups with different TTT distributions. Consistently, del13q-only cases with at least 70% of nuclei bearing del13S319 showed a significantly shorter TTT than del13q-only cases with less than 70% deleted nuclei (p=0.0001). Del13q-only cases were then divided in four subsets according to the percentage of nuclei bearing del13S319 with or without a concomitant delRB1: del13S319 <70% (group 1), 144 cases; del13S319 <70% + delRB1 (group 2), 95 cases; del13S319 >70% (group 3), 64 cases; del13S319 >70% + delRB1 (group 4), 39 cases. The median TTT of group 1 (not reached) was significantly longer than the median TTT of group 2 (92 months, p=0.012), group 3 (68 months, p<0.0001), and group 4 (82 months, p=0.0025; see Fig. 1A). Multivariate Cox proportional hazard analyses selected the presence of delRB1 (p=0.029), along with the IGHV mutational status (p<0.0001), as an independent negative prognosticator in the context of del13q-only cases with low/intermediate Rai risk (Rai stage of 0/I at diagnosis) and <70% of del13S319. Cases belonging to the consecutive unselected single-institution CLL cohort were divided into subsets according to the classification proposed by Döhner et al (NEJM, 2000). Notably, the presence of del13S319 in <70% of cells in the absence of delRB1 identified a patient subset with particularly stable and benign clinical course (group A in Fig. 1B, 48 cases; median TTT not reached). Conversely, patients characterized by del13S319 in <70% of cells but with a larger deletion, as determined by concomitant delRB1 (group B, 24 cases), or del13S319 in >70% of cells (with or without delRB1, group C, 25 cases) or a normal karyotype (group D, 75 cases) had shorter median TTT intervals (ranging from 105 to 129 months, p<0.01 in all the comparisons). Finally, patients affected by CLL bearing trisomy 12 (group E, 48 cases) and del11q or del17p (group F, 45 cases) experienced the worst clinical courses (p<0.0001). Conclusion: In the context of del13q-only cases, different clinical outcomes were associated to the percentage of 13q14 deleted cells, as well as to the size of the 13q14 deletion, as detected by the LSI-RB1 probe. Moreover, the presence of delRB1 emerged as a feature capable of refining the prognostic assessment in the context of CLL cases with <70% del13S319. The underlying genetic mechanisms correlated with the different clinical outcomes and associated with the size of the 13q deletion are presently under investigation. Disclosures: No relevant conflicts of interest to declare.

Reproductive Success of Two Eucalyptus Hybrid Populations. I. Generalized Seed Output Model and Comparison of Fruit Parameters

1981 ◽  
Vol 29 (1) ◽  
pp. 25 ◽  
Author(s):  
DW Drake
Keyword(s):  
Reproductive Success ◽  
Reproductive Effort ◽  
Significant Loss ◽  
Hybrid Population ◽  
Subsequent Paper ◽  
Species Trees ◽  
Seed Output ◽  
Eucalyptus Hybrid ◽  
Canopy Size ◽  
Two Populations

The dynamics of the reproductive success of two interspecific Eucalyptus hybrid populations are examined here and in a subsequent paper in relation to a generalized model of seed output of a single plant. The model describes a structural system of seed output per plant under both physiological and physical regulation. It can readily be extended to a population model and to postdispersal reproductive stages. Fruit loss, output and damage in the two populations are presented. The E. melanophloia × E. crebra hybrids are considerably less fertile than their parent species. Significant loss of reproductive structures during maturation and low reproductive effort, together with variable canopy size and proportion of canopy bearing fruits, result in the fruit output per average hybrid tree being 10% of either of the average species trees. Biotic damage to surviving hybrid fruits by an insect and a fungus is individually significantly greater than levels suffered by the species and together account for an average of 56% of fruits compared with 16% for either species. Damage and loss levels to these hybrids are more or less constant in space and time and constitute a strong selective force against these hybrids. In contrast, fruit loss parameters are low and differences between the taxa are non-significant throughout the E.populnea × E. crebra hybrid system, resulting in hybrid fertility about equal to the fertilities of the parents. These contrasting results are discussed in relation to hybrid frequencies in the ecotone and levels of hybrid population development.

scholarly journals Genome-Wide Association Study of Actinidia Chinensis

2020 ◽  
Author(s):  
Yu Zhang ◽  
Yuexing Wang ◽  
Shimao Zheng ◽  
Wanying Zhou ◽  
Wenhui Zhang ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Haplotype Analysis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Actinidia Chinensis ◽  
Analysis Of Molecular Variance ◽  
Growth Environment ◽  
Molecular Variance ◽  
Genome Wide ◽  
Two Populations

Abstract Background: A total of 74,936 SNPs were employed to carry out GWAS and post-GWAS of the fifty-six accessions, representing the two most valuable varieties of Actinidia chinensis, namely, A. chinensis var. chinensis and A. chinensis var. deliciosa, are mainly distributed in China. The percentage of heterozygous sites of A. chinensis var. deliciosa is higher than that of A. chinensis var. chinensis, which could be one of the reasons for A. chinensis var. deliciosa high disease resistance. LD decay distance of male plants is shorter than that of female plants. Results: Fifty-six accessions were divided into two subgroups. Analysis of molecular variance shows that the frequency of genetic variations within the population is 83.53% and 16.47% between populations. Fst between the two populations is 0.14, and Nm is 1.60. Set at α ≤ 0.05, a total of 327 SNPs and 260 haplotypes were related to the hispidus. A total of 246 proteins were annotated using GO and KEGG analyses, which indicated the membrane-related genes and stress-resistant metabolic pathways are related to the hispidus condition of leaves, stems, and peels of kiwifruit, which is also the result of the adaptation of A. chinensis var. deliciosa to its growth environment. Conclusions: Haplotype analysis showed that the evolution of is A. chinensis var. deliciosa later than that of A. chinensis var. chinensis.

scholarly journals Molecular Analysis by SSR of Genes Associated with Alkaloid Synthesis in a Segregating Monoploid Potato Family

1994 ◽  
Author(s):  
Richard E. Veilleux ◽  
Jossi Hillel ◽  
A. Raymond Miller ◽  
David Levy
Keyword(s):  
Genomic Library ◽  
Solanum Chacoense ◽  
Enriched Library ◽  
Backcross Population ◽  
Ssr Analysis ◽  
Natural Defense ◽  
Alkaloid Synthesis ◽  
Regenerated Plants ◽  
Skewed Segregation ◽  
Putative Marker

More than 15,000 anthers of an interspecific hybrid (CP2) between two diploid (2n=2x=24) potato species, Solanum chacoense (weedy) and S. phureja (cultivated), were cultured to generate a family of monoploid (haploid, 2n-1x=12) plants. Of 260 regenerated plants, 34 were monoploid, 210 diploid and 16 tetraploid. SSR analysis revealed that six monoploids were genetically identical and 14 diploids were homozygous, thus limiting the population to 42 (28 monoploids and 14 homozygous diploids). New microsatellite loci were developed for potato from database sequences (15), a conventional genomic library (6), an enriched library (18) and tomato (11). Of these, 13 were polymorphic in the CP2 family and 11 were used to study genetic segregatin. Four of 11 exhibited skewed segregation in the monoploid family. Seven of 18 microsatellite markers were polymorphic and informative on a set of 12 tetraploid potato cultivars. Acetylleptinidine (ALD) is the aglycone of leptines, a natural defense against insects, especially the highly destructuve Colorado potato beetle. ALD is absend in S. phureja but highly expressed in the S. chacoense parent of CP2. A backcross population between CP2 and tis S. phureja parent was used to examine segregation for ALD. Bulks of 10 backcross individuals that expressed ALD and 10 that did not were used to identify putative RAPD markers associatd with the trait. Of 80 primers tested, one putative marker amplified by OPQ02 was present in eight of ten individuals comprising the high bulk and absent in all 10 individuals comprising the low bulk. This is a putative marker for ALD expression in potato.

scholarly journals Tracing the Origin of the RSPO2 Long-Hair Allele and Epistatic Interaction between FGF5 and RSPO2 in Sapsaree Dog

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 102
Author(s):  
Mingue Kang ◽  
Byeongyong Ahn ◽  
Seungyeon Youk ◽  
Yun-Mi Lee ◽  
Jong-Joo Kim ◽  
...  
Keyword(s):  
Epistatic Interaction ◽  
Genome Wide Association Study ◽  
Dominant Mode ◽  
Causative Mutation ◽  
Entire Body ◽  
Hair Length ◽  
Mendelian Segregation ◽  
Selection Signature ◽  
Genome Wide ◽  
History Of

Genetic analysis of the hair-length of Sapsaree dogs, a Korean native dog breed, showed a dominant mode of inheritance for long hair. Genome-Wide Association Study (GWAS) analysis and subsequent Mendelian segregation analysis revealed an association between OXR1, RSPO2, and PKHD1L1 on chromosome 13 (CFA13). We identified the previously reported 167 bp insertion in RSPO2 3’ untranslated region as a causative mutation for hair length variations. The analysis of 118 dog breeds and wolves revealed the selection signature on CFA13 in long-haired breeds. Haplotype analysis showed the association of only a few specific haplotypes to the breeds carrying the 167 bp insertion. The genetic diversity in the neighboring region linked to the insertion was higher in Sapsarees than in other Asian and European dog breeds carrying the same variation, suggesting an older history of its insertion in the Sapsaree genome than in that of the other breeds analyzed in this study. Our results show that the RSPO2 3’ UTR insertion is responsible for not only the furnishing phenotype but also determining the hair length of the entire body depending on the genetic background, suggesting an epistatic interaction between FGF5 and RSPO2 influencing the hair-length phenotype in dogs.

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