Construction of Genetic Linkage Maps From a Hybrid Family of Large Yellow Croaker (Larimichthys crocea)

Consensus and sex-specific genetic linkage maps for large yellow croaker (Larimichthys crocea) were constructed using samples from an F1 family produced by crossing a Daiqu female and a Mindong male. A total of 20,147 single nucleotide polymorphisms (SNPs) by restriction site associated DNA sequencing were assigned to 24 linkage groups (LGs). The total length of the consensus map was 1757.4 centimorgan (cM) with an average marker interval of 0.09 cM. The total length of female and male linkage map was 1533.1 cM and 1279.2 cM, respectively. The average female-to-male map length ratio was 1.2 ± 0.23. Collapsed markers in the genetic maps were re-ordered according to their relative positions in the ASM435267v1 genome assembly to produce integrated genetic linkage maps with 9885 SNPs distributed across the 24 LGs. The recombination pattern of most LGs showed sigmoidal patterns of recombination, with higher recombination in the middle and suppressed recombination at both ends, which corresponds with the presence of sub-telocentric and acrocentric chromosomes in the species. The average recombination rate in the integrated female and male maps was respectively 3.55 cM/Mb and 3.05 cM/Mb. In most LGs, higher recombination rates were found in the integrated female map, compared to the male map, except in LG12, LG16, LG21, LG22, and LG24. Recombination rate profiles within each LG differed between the male and the female, with distinct regions indicating potential recombination hotspots. Separate quantitative trait loci (QTL) and association analyses for growth related traits in 6 months fish were performed, however, no significant QTL was detected. The study indicates that there may be genetic differences between the two strains, which may have implications for the application of DNA-information in the further breeding schemes.

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

AoB Plants ◽

10.1093/aobpla/plaa064 ◽

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.

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Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

Peanut Science ◽

10.3146/ps13-03.1 ◽

2013 ◽

Vol 40 (2) ◽

pp. 95-106 ◽

Cited By ~ 12

Author(s):

Baozhu Guo ◽

Manish K. Pandey ◽

Guohao He ◽

Xinyou Zhang ◽

Boshou Liao ◽

...

Keyword(s):

Genetic Linkage ◽

High Density ◽

Genetic Maps ◽

Linkage Maps ◽

Consensus Map ◽

Genetic Linkage Maps ◽

Marker Loci ◽

Cultivated Peanut ◽

Peanut Genome ◽

Mapping Populations

ABSTRACT The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.

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Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps

Genome Research ◽

10.1101/gr.111252.110 ◽

2010 ◽

Vol 21 (1) ◽

pp. 114-125 ◽

Cited By ~ 50

Author(s):

B. L. Dumont ◽

M. A. White ◽

B. Steffy ◽

T. Wiltshire ◽

B. A. Payseur

Keyword(s):

House Mouse ◽

Recombination Rate ◽

Genetic Linkage ◽

Species Complex ◽

Rate Variation ◽

Linkage Maps ◽

Genetic Linkage Maps ◽

Mouse Species ◽

Recombination Rate Variation

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Development of High-Density Genetic Linkage Maps and Identification of Loci for Chestnut Gall Wasp Resistance in Castanea spp.

Plants ◽

10.3390/plants9081048 ◽

2020 ◽

Vol 9 (8) ◽

pp. 1048

Author(s):

Daniela Torello Marinoni ◽

Sogo Nishio ◽

Nadia Valentini ◽

Kenta Shirasawa ◽

Alberto Acquadro ◽

...

Keyword(s):

Genetic Linkage ◽

Castanea Sativa ◽

High Density ◽

Genetic Maps ◽

Phenotypic Variance ◽

Linkage Maps ◽

Gall Wasp ◽

Resistance Response ◽

Genetic Linkage Maps ◽

Resistance Trait

Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar ‘Bouche de Bétizac’ (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between ‘Bouche de Bétizac’ and the susceptible cultivar ‘Madonna’ (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of ‘Bouche de Bétizac’ consisted of 1459 loci and spanned 809.6 cM; the map of ‘Madonna’ consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the ‘Bouche de Bétizac’ map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes.

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Accounting for Errors in Low Coverage High-Throughput Sequencing Data when Constructing Genetic Maps using Biparental Outcrossed Populations

10.1101/249722 ◽

2018 ◽

Author(s):

Timothy P. Bilton ◽

Matthew R. Schofield ◽

Michael A. Black ◽

David Chagné ◽

Phillip L. Wilcox ◽

...

Keyword(s):

High Throughput ◽

Genetic Linkage ◽

High Throughput Sequencing ◽

Diploid Species ◽

Genotyping By Sequencing ◽

Genetic Maps ◽

Linkage Maps ◽

Sequencing Data ◽

Genetic Linkage Maps ◽

Low Coverage

ABSTRACTNext generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high density genetic linkage maps, which facilitate the development of non-model species’ genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology (e.g., genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth. If unaccounted for, these errors lead to inflated genetic maps. In addition, map construction in many species is performed using full-sib family populations derived from the outcrossing of two individuals, where unknown parental phase and varying segregation types further complicate construction. We present a new methodology for modeling low coverage sequencing data in the construction of genetic linkage maps using full-sib populations of diploid species, implemented in a package called GUSMap. Our model is based on an extension of the Lander-Green hidden Markov model that accounts for errors present in sequencing data. Results show that GUSMap was able to give accurate estimates of the recombination fractions and overall map distance, while most existing mapping packages produced inflated genetic maps in the presence of errors. Our results demonstrate the feasibility of using low coverage sequencing data to produce genetic maps without requiring extensive filtering of potentially erroneous genotypes, provided that the associated errors are correctly accounted for in the model.

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Construction of High-quality Linkage Maps in Populus with RADseq Data and their Application in QTL Mapping and Genome Assembly

10.21203/rs.2.17615/v1 ◽

2019 ◽

Author(s):

Chunfa Tong ◽

Dan Yao ◽

Hainan Wu ◽

Yuhua Chen ◽

Wenguo Yang ◽

...

Keyword(s):

Qtl Mapping ◽

Genome Assembly ◽

Genetic Linkage ◽

High Density ◽

Genetic Maps ◽

Linkage Maps ◽

Linkage Groups ◽

High Quality ◽

Populus Simonii ◽

Genetic Linkage Maps

Abstract Background: Although great efforts have been made to construct genetic linkage maps in Populus using traditional molecular markers, these maps are typically sparse, and the number of linkage groups does not match the karyotype of Populus . With the advances in high-throughput sequencing technologies and new software packages available for extracting single nucleotide polymorphisms (SNPs) across a mapping population, it is possible to construct high-quality, high-density genetic linkage maps with thousands of SNPs in such outbred species. Results: Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing (RADseq) data from an F 1 hybrid population from Populus de l toides and Populus simonii and were applied to identify growth trait loci and facilitate genome assembly. The female Populus deltoides map contained 4,018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55, perfectly matching the karyotype of Populus . The male Populus simonii map showed similar characteristics, consisting of 2,097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP genotype data for linkage analysis were confirmed to be of high quality. The SNP order of each linkage group was optimal among different ordering results from several available software platforms. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height, some of which were strongly associated with QTLs identified in previous studies. In addition, the linkage maps enabled the anchoring of 671 contigs of a draft genome assembly of Populus simonii to chromosomes, corresponding to approximately 83.6% of the genome and showing a high level of collinearity with the genetic maps. Conclusions: The two parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus as well as performance in QTL mapping and genome assembly. The adopted approaches for both extracting and ordering SNPs could be applied to other species to construct high-density, high-quality genetic maps.

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Construction of genetic linkage maps of silver birch based on AFLP markers

Hereditas (Beijing) ◽

10.3724/sp.j.1005.2009.00213 ◽

2009 ◽

Vol 31 (2) ◽

pp. 213-218 ◽

Cited By ~ 1

Author(s):

Fu-Ling GAO ◽

Ting-Bo JIANG

Keyword(s):

Genetic Linkage ◽

Silver Birch ◽

Aflp Markers ◽

Linkage Maps ◽

Genetic Linkage Maps

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Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize

Genetics ◽

10.1093/genetics/166.4.1923 ◽

2004 ◽

Vol 166 (4) ◽

pp. 1923-1933 ◽

Cited By ~ 8

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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