AFLP-Based Genetic Linkage Maps of the Pacific Oyster Crassostrea gigas Thunberg

2004 ◽  
Vol 6 (1) ◽  
pp. 26-36 ◽  
Author(s):  
Li Li ◽  
Ximing Guo
Keyword(s):  
Crassostrea Gigas ◽  
Genetic Linkage ◽  
Pacific Oyster ◽  
Linkage Maps ◽  
The Pacific ◽  
Genetic Linkage Maps

scholarly journals High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas

2020 ◽  
Vol 10 (12) ◽  
pp. 4691-4705
Author(s):  
Xiaoshen Yin ◽  
Alberto Arias-Pérez ◽  
Tevfik Hamdi Kitapci ◽  
Dennis Hedgecock
Keyword(s):  
Genome Assembly ◽  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
Genotyping By Sequencing ◽  
Biological Knowledge ◽  
Linkage Maps ◽  
Nucleotide Polymorphisms ◽  
Linkage Groups ◽  
The Pacific ◽  
Chromosome Level

Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first genome assembly for the Pacific oyster Crassostrea gigas were chimeric, containing single nucleotide polymorphisms (SNPs) mapping to different linkage groups. Here, we merge 14 linkage maps constructed of SNPs generated from genotyping-by-sequencing (GBS) methods with five, previously constructed linkage maps, to create a compendium of nearly 69 thousand SNPs mapped with high confidence. We use this compendium to assess a recently available, chromosome-level assembly of the C. gigas genome, mapping SNPs in 275 of 301 contigs and comparing the ordering of these contigs, by linkage, to their assembly by Hi-C sequencing methods. We find that, while 26% of contigs contain chimeric blocks of SNPs, i.e., adjacent SNPs mapping to different linkage groups than the majority of SNPs in their contig, these apparent misassemblies amount to only 0.08% of the genome sequence. Furthermore, nearly 90% of 275 contigs mapped by linkage and sequencing are assembled identically; inconsistencies between the two assemblies for the remaining 10% of contigs appear to result from insufficient linkage information. Thus, our compilation of linkage maps strongly supports this chromosome-level assembly of the oyster genome. Finally, we use this assembly to estimate, for the first time in a Lophotrochozoan, genome-wide recombination rates and causes of variation in this fundamental process.

scholarly journals Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds

2015 ◽  
Vol 5 (10) ◽  
pp. 2007-2019 ◽  
Author(s):  
Dennis Hedgecock ◽  
Grace Shin ◽  
Andrew Y. Gracey ◽  
David Van Den Berg ◽  
Manoj P. Samanta
Keyword(s):  
Crassostrea Gigas ◽  
Second Generation ◽  
Pacific Oyster ◽  
Linkage Maps ◽  
The Pacific

scholarly journals VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Morad M Mokhtar ◽  
Ebtissam H A Hussein ◽  
Salah El-Din S El-Assal ◽  
Mohamed A M Atia
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Expressed Sequence Tags ◽  
Genetic Linkage ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Microrna Target ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1923-1933 ◽  
Author(s):  
Lorinda K Anderson ◽  
Naser Salameh ◽  
Hank W Bass ◽  
Lisa C Harper ◽  
W Z Cande ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Chromosome Structure ◽  
Single Copy ◽  
Chromosome 9 ◽  
Linkage Maps ◽  
Cytogenetic Map ◽  
Recombination Nodules ◽  
Novel Approach ◽  
Genetic Linkage Maps ◽  
High Degree

Abstract Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1) all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2) each RN corresponds to one crossover, and (3) the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r2 = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.

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