scholarly journals Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome

2017 ◽  
Vol 26 (17) ◽  
pp. 4509-4522 ◽  
Author(s):  
Morten T. Limborg ◽  
Wesley A. Larson ◽  
Lisa W. Seeb ◽  
James E. Seeb
Keyword(s):  
Duplicated Loci

Secondary Tetrasomic Segregation of MDH-B and Preferential Pairing of Homeologues in Rainbow Trout

Genetics ◽  
1997 ◽  
Vol 145 (4) ◽  
pp. 1083-1092 ◽  
Author(s):  
Fred W Allendorf ◽  
Roy G Danzmann
Keyword(s):  
Allelic Variation ◽  
Male Meiosis ◽  
Proximal Region ◽  
Stage Model ◽  
Preferential Pairing ◽  
Homologous Chromosomes ◽  
Tetrasomic Inheritance ◽  
Segregation Ratios ◽  
Homeologous Chromosomes ◽  
Duplicated Loci

We examined the inheritance of allelic variation at an isozyme locus, MDH-B, duplicated by ancestral polyploidy in salmonid fishes. We detected only disomic segregation in females. Segregation ratios in males were best explained by a mixture of disomic and tetrasomic inheritance. We propose a two-stage model of pairing in male meiosis in which, first, homologous chromosomes pair and recombine in the proximal region of the chromosome. Next, homeologous chromosomes pair and recombine distally. We suggest that this type of tetrasomic inheritance in which centromeres segregate disomically should be referred to as “secondary tetrasomy” to distinguish it from tetrasomy involving entire chromosomes (i.e., “primary tetrasomy”). Differences in segregation ratios between males indicate differences between individuals in the amount of recombination between homeologous chromosomes. We also consider the implication of these results for estimation of allele frequencies at duplicated loci in salmonid populations.

Assigning alleles to different loci in amplifications of duplicated loci

2019 ◽  
Vol 19 (5) ◽  
pp. 1240-1253 ◽  
Author(s):  
Kang Huang ◽  
Pei Zhang ◽  
Derek W. Dunn ◽  
Tongcheng Wang ◽  
Rui Mi ◽  
...  
Keyword(s):  
Duplicated Loci

scholarly journals Genetic Mapping in Onion: Insight to the Evolution of a Large Diploid Genome

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 596d-596
Author(s):  
Joseph J. King ◽  
Michael J. Havey
Keyword(s):  
Mapping Population ◽  
Nuclear Genome ◽  
Restriction Enzymes ◽  
Cdna Libraries ◽  
Rflp Markers ◽  
Structural Rearrangements ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Duplicated Loci ◽  
Bulb Color

The bulb onion (Allium cepa L.) is a diploid with an very large nuclear genome of 15300 Mbp/1C (107× arabidopsis, 16× tomato, 6× maize). We developed a low-density genetic map with morphological, RAPD, and RFLP markers to examine genome organization and to study QTL controlling phenotypically correlated bulb quality traits. A mapping population of 58 F3 families was derived from a cross of the inbreds Brigham Yellow Globe 15-23 (BYG) × Alisa Craig 43 (AC). These inbreds are distinct in solids, storability, pungency, and bulb shape. Analysis of 580 RAPD primers detected 53 (9%) polymorphisms between BYG and AC, but only 12 (2%) segregated at expected ratios among F3 families. Using probes from onion cDNA libraries and four restriction enzymes, 214 RFLPs were identified between mapping parents. A 112-point map includes 96 RFLPs, 13 RAPDs, a locus controlling complementary red bulb color, and two loci hybridizing with a clone of the enzyme alliinase (EC 4.4.1.4), which produces the flavors characteristic of Allium species. Duplicated loci were detected by ≈25% of RFLP probes and were unlinked, loosely linked (2 to 30 cM), or tightly linked (<2 cM). This frequency of duplication was comparable to species with polyploid ancestors (paleopolyploids) and was higher than that found in most true diploids. However, the distribution of duplicated loci suggests that, in contrast to whole genome duplications typical of paleopolyploids, the contemporary size and structure of the onion genome may be a product of intrachromosomal duplications (cryptopolyploidy) and subsequent structural rearrangements.

scholarly journals Detailed Alignment of Saccharum and Sorghum Chromosomes: Comparative Organization of Closely Related Diploid and Polyploid Genomes

Genetics ◽  
1998 ◽  
Vol 150 (4) ◽  
pp. 1663-1682 ◽  
Author(s):  
R Ming ◽  
S-C Liu ◽  
Y-R Lin ◽  
J da Silva ◽  
W Wilson ◽  
...  
Keyword(s):  
Molecular Analysis ◽  
Saccharum Officinarum ◽  
Dna Probes ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Structural Polymorphism ◽  
Sorghum Genome ◽  
F1 Progeny ◽  
Duplicated Loci ◽  
Intrachromosomal Rearrangements

Abstract The complex polyploid genomes of three Saccharum species have been aligned with the compact diploid genome of Sorghum (2n = 2x = 20). A set of 428 DNA probes from different Poaceae (grasses) detected 2460 loci in F1 progeny of the crosses Saccharum officinarum Green German × S. spontaneum IND 81-146, and S. spontaneum PIN 84-1 × S. officinarum Muntok Java. Thirty-one DNA probes detected 226 loci in S. officinarum LA Purple × S. robustum Molokai 5829. Genetic maps of the six Saccharum genotypes, including up to 72 linkage groups, were assembled into “homologous groups” based on parallel arrangements of duplicated loci. About 84% of the loci mapped by 242 common probes were homologous between Saccharum and Sorghum. Only one interchromosomal and two intrachromosomal rearrangements differentiated both S. officinarum and S. spontaneum from Sorghum, but 11 additional cases of chromosome structural polymorphism were found within Saccharum. Diploidization was advanced in S. robustum, incipient in S. officinarum, and absent in S. spontaneum, consistent with biogeographic data suggesting that S. robustum is the ancestor of S. officinarum, but raising new questions about the antiquity of S. spontaneum. The densely mapped Sorghum genome will be a valuable tool in ongoing molecular analysis of the complex Saccharum genome.

New evidence from Sinapis alba L. for ancestral triplication in a crucifer genome

Genome ◽  
2006 ◽  
Vol 49 (3) ◽  
pp. 230-238 ◽  
Author(s):  
Matthew N Nelson ◽  
Derek J Lydiate
Keyword(s):  
Large Scale ◽  
Brassica Species ◽  
Sinapis Alba ◽  
Close Relative ◽  
Yellow Mustard ◽  
Brassica Hirta ◽  
Rflp Probe ◽  
Duplicated Loci ◽  
New Evidence

We present clear evidence of ancestral genome triplication in Sinapis alba, a close relative of the cultivated Brassica species. Exceptionally high levels of heterozygosity in the parents of an F1 intercross permitted the mapping of an estimated 87% of all detected restriction fragment length polymorphism (RFLP) loci, with each RFLP probe typically detecting 2 or 3 loci. These duplicated loci were arranged in 8 triplicated homologous linkage blocks and 2 small, duplicated, homologous linkage blocks covering the majority of the S. alba genome. Several large-scale inversions and translocations appear to have rearranged the order of loci within homologous blocks. The role of successive polyploidization events on the evolution of crucifer species is discussed.Key words: polyploidy, yellow mustard, Brassica hirta, genome duplication, hexaploid ancestor, paralogous loci.

scholarly journals CNVmap: A Method and Software To Detect and Map Copy Number Variants from Segregation Data

Genetics ◽  
2019 ◽  
Vol 214 (3) ◽  
pp. 561-576
Author(s):  
Matthieu Falque ◽  
Kamel Jebreen ◽  
Etienne Paux ◽  
Carsten Knaak ◽  
Sofiane Mezmouk ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Variants ◽  
Original Method ◽  
Nucleotide Polymorphisms ◽  
Extra Copy ◽  
Segregation Data ◽  
Wheat Population ◽  
Causal Variants ◽  
Duplicated Loci ◽  
Additional Value

Single nucleotide polymorphisms (SNPs) are used widely for detecting quantitative trait loci, or for searching for causal variants of diseases. Nevertheless, structural variations such as copy-number variants (CNVs) represent a large part of natural genetic diversity, and contribute significantly to trait variation. Numerous methods and softwares based on different technologies (amplicons, CGH, tiling, or SNP arrays, or sequencing) have already been developed to detect CNVs, but they bypass a wealth of information such as genotyping data from segregating populations, produced, e.g., for QTL mapping. Here, we propose an original method to both detect and genetically map CNVs using mapping panels. Specifically, we exploit the apparent heterozygous state of duplicated loci: peaks in appropriately defined genome-wide allelic profiles provide highly specific signatures that identify the nature and position of the CNVs. Our original method and software can detect and map automatically up to 33 different predefined types of CNVs based on segregation data only. We validate this approach on simulated and experimental biparental mapping panels in two maize populations and one wheat population. Most of the events found correspond to having just one extra copy in one of the parental lines, but the corresponding allelic value can be that of either parent. We also find cases with two or more additional copies, especially in wheat, where these copies locate to homeologues. More generally, our computational tool can be used to give additional value, at no cost, to many datasets produced over the past decade from genetic mapping panels.

scholarly journals Functionally Divergent Alleles and Duplicated Loci Encoding an Acyltransferase Contribute to Acylsugar Metabolite Diversity in Solanum Trichomes

2015 ◽  
Vol 27 (4) ◽  
pp. 1002-1017 ◽  
Author(s):  
Anthony L. Schilmiller ◽  
Gaurav D. Moghe ◽  
Pengxiang Fan ◽  
Banibrata Ghosh ◽  
Jing Ning ◽  
...  
Keyword(s):  
Metabolite Diversity ◽  
Duplicated Loci

scholarly journals Physical Mapping of Duplicated Genomic Regions of Two Chromosome Ends in Rice

Genetics ◽  
1998 ◽  
Vol 150 (4) ◽  
pp. 1595-1603 ◽  
Author(s):  
Jianzhong Wu ◽  
Nori Kurata ◽  
Hiroshi Tanoue ◽  
Takanori Shimokawa ◽  
Yosuke Umehara ◽  
...  
Keyword(s):  
Recombination Frequency ◽  
Oryza Sativa L ◽  
Genetic Distances ◽  
Cdna Clones ◽  
Physical Size ◽  
Physical Maps ◽  
Expected Length ◽  
Duplicated Loci ◽  
Genomic Regions ◽  
Rice Cdna

Abstract Two genomic regions duplicated in distal ends of the short arms of chromosomes 11 and 12 in rice (Oryza sativa L.) were characterized by YAC ordering with 46 genetic markers. Physical maps covering most of the duplicated regions were generated. Thirty-five markers, including 21 rice cDNA clones, showed the duplicated loci arrayed strictly in the same order along the two specific genomic regions. Regardless of their different genetic distances, the two duplicated segments may have a similar and minimum physical size with an expected length of about 2.5 Mb. However, differences of RFLP frequency for the duplicated DNA copies and recombination frequency for a given homoeologous area between the two regions were observed, indicating that these changes in genome organization occurred after the duplication. Our results establish a good model system for resolving the relationships between gene duplication, expression of duplicated genes, and the frequency of meiotic recombination in small chromosomal regions.

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