Enrichment of a papaya high-density genetic map with AFLP markers

A high-density genetic linkage map of papaya, previously developed using an F2 mapping population derived from the intraspecific cross AU9 × SunUp, was enriched with AFLP markers. The comprehensive genetic map presented here spans 945.2 cM and covers 9 major and 5 minor linkage groups containing 712 SSR, 277 AFLP, and 1 morphological markers. The average marker density for the 9 major linkage groups is 0.9 cM between adjacent markers, and the total number of gaps >5 cM was reduced from 48 to 27 in the current map. AFLPs generated by EcoRI/MseI primer combinations were distributed throughout the 14 linkage groups and resulted in several large locus order rearrangements within the 9 major linkage groups. Integration of AFLP markers provided tighter linkage association between loci, leading to a reduction in map distance on LGs 1, 2, and 4, which were inflated in the previous map, and correction of the marker order on LG8. Suppression of recombination in the male-specific Y region (MSY) of LG1 is further validated by the addition of 27 sex co-segregating AFLP markers. A large region of distorted segregation surrounding the MSY spans 54.4 cM and represents ∼71% of the linkage group. This comprehensive high-density genetic map provides a framework for mapping quantitative trait loci and for fine mapping as well as for comparative genomic studies of crop plant development and evolution.

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High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata

International Journal of Molecular Sciences ◽

10.3390/ijms22115723 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5723

Author(s):

Yuan-Yuan Xu ◽

Sheng-Rui Liu ◽

Zhi-Meng Gan ◽

Ren-Fang Zeng ◽

Jin-Zhi Zhang ◽

...

Keyword(s):

Qtl Mapping ◽

Linkage Map ◽

Genetic Map ◽

Expression Patterns ◽

High Density ◽

Poncirus Trifoliata ◽

Leaf Abscission ◽

Comparative Genomic ◽

Map Comparison ◽

Genomic Studies

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.

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A Molecular Genetic Map and Electrophoretic Karyotype of the Plant Pathogenic Fungus Cochliobolus sativus

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2002.15.5.481 ◽

2002 ◽

Vol 15 (5) ◽

pp. 481-492 ◽

Cited By ~ 48

Author(s):

Shaobin Zhong ◽

Brian J. Steffenson ◽

J. Patrick Martinez ◽

Lynda M. Ciuffetti

Keyword(s):

Genetic Map ◽

Length Polymorphism ◽

Fragment Length Polymorphism ◽

Molecular Genetic ◽

Aflp Markers ◽

Cochliobolus Sativus ◽

Electrophoretic Karyotype ◽

Linkage Groups ◽

Molecular Genetic Map ◽

Map Distance

A molecular genetic map was constructed and an electrophoretic karyotype was resolved for Cochliobolus sativus, the causal agent of spot blotch of barley and wheat. The genetic map consists of 27 linkage groups with 97 amplified fragment length polymorphism (AFLP) markers, 31 restriction fragment length polymorphism (RFLP) markers, two polymerase chain reaction amplified markers, the mating type locus (CsMAT), and a gene (VHv1) conditioning high virulence on barley cv. Bowman. These linkage groups covered a map distance of 849 cM. The virulence gene VHv1 cosegregated with six AFLP markers and was mapped on one of the major linkage groups. Fifteen chromosome-sized DNAs were resolved in C. sativus isolates ND93-1 and ND90Pr with contour-clamped homogeneous electric field (CHEF) electrophoresis combined with telo-mere probe analysis of comigrating chromosome-sized DNAs. The chromosome sizes ranged from 1.25 to 3.80 Mbp, and the genome size of the fungus was estimated to be approximately 33 Mbp. By hybridizing genetically mapped RFLP and AFLP markers to CHEF blots, 25 of the 27 linkage groups were assigned to specific chromosomes. The barley-specific virulence locus VHv1 was localized on a chromosome of 2.80 Mbp from isolate ND90Pr in the CHEF gel. The total map length of the fungus was estimated to be at least 1,329 cM based on the map distance covered by the linked markers and the estimated gaps. Therefore, the physical to genetic distance ratio is approximately 25 kb/cM. Construction of a high-resolution map around target loci will facilitate the cloning of the genes conferring virulence and other characters in C. sativus by a map-based cloning strategy.

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A High‐Density Soybean Genetic Map Based on AFLP Markers

Crop Science ◽

10.2135/cropsci1997.0011183x003700020038x ◽

1997 ◽

Vol 37 (2) ◽

pp. 537-543 ◽

Cited By ~ 118

Author(s):

Paul Keim ◽

James M. Schupp ◽

Steven E. Travis ◽

Kathryn Clayton ◽

Tong Zhu ◽

...

Keyword(s):

Genetic Map ◽

High Density ◽

Aflp Markers

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Genetic map of triticale compiling DArT, SSR, and AFLP markers

Genome ◽

10.1139/g11-009 ◽

2011 ◽

Vol 54 (5) ◽

pp. 391-401 ◽

Cited By ~ 40

Author(s):

M. Tyrka ◽

P.T. Bednarek ◽

A. Kilian ◽

M. Wędzony ◽

T. Hura ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Genetic Linkage Map ◽

Fragment Length Polymorphism ◽

Aflp Markers ◽

Structural Rearrangements ◽

Linkage Groups ◽

Array Technology ◽

Dh Lines ◽

Simple Sequence

A set of 90 doubled haploid (DH) lines derived from F1plants that originated from a cross between × Triticosecale Wittm. ‘Saka3006’ and ×Triticosecale Wittm. ‘Modus’, via wide crossing with maize, were used to create a genetic linkage map of triticale. The map has 21 linkage groups assigned to the A, B, and R genomes including 155 simple sequence repeat (SSR), 1385 diversity array technology (DArT), and 28 amplified fragment length polymorphism (AFLP) markers covering 2397 cM with a mean distance between two markers of 4.1 cM. Comparative analysis with wheat consensus maps revealed that triticale chromosomes of the A and B genomes were represented by 15 chromosomes, including combinations of 2AS.2AL#, 2AL#2BL, 6AS.6AL#, and 2BS.6AL# instead of 2A, 2B, and 6A. In respect to published maps of rye, substantial rearrangements were found also for chromosomes 1R, 2R, and 3R of the rye genome. Chromosomes 1R and 2R were truncated and the latter was linked with 3R. A nonhomogeneous distribution of markers across the triticale genome was observed with evident bias (48%) towards the rye genome. This genetic map may serve as a reference linkage map of triticale for efficient studies of structural rearrangements, gene mapping, and marker-assisted selection.

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A Genetic Linkage Map of the Model Legume Lotus japonicus and Strategies for Fast Mapping of New Loci

Genetics ◽

10.1093/genetics/161.4.1673 ◽

2002 ◽

Vol 161 (4) ◽

pp. 1673-1683 ◽

Cited By ~ 3

Author(s):

Niels Sandal ◽

Lene Krusell ◽

Simona Radutoiu ◽

Magdalena Olbryt ◽

Andrea Pedrosa ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Lotus Japonicus ◽

Aflp Markers ◽

Linkage Groups ◽

Model Legume ◽

Group I

Abstract A genetic map for the model legume Lotus japonicus has been developed. The F2 mapping population was established from an interspecific cross between L. japonicus and L. filicaulis. A high level of DNA polymorphism between these parents was the source of markers for linkage analysis and the map is based on a framework of amplified fragment length polymorphism (AFLP) markers. Additional markers were generated by restriction fragment length polymorphism (RFLP) and sequence-specific PCR. A total of 524 AFLP markers, 3 RAPD markers, 39 gene-specific markers, 33 microsatellite markers, and six recessive symbiotic mutant loci were mapped. This genetic map consists of six linkage groups corresponding to the six chromosomes in L. japonicus. Fluorescent in situ hybridization (FISH) with selected markers aligned the linkage groups to chromosomes as described in the accompanying article by Pedrosa et al. (2002, this issue). The length of the linkage map is 367 cM and the average marker distance is 0.6 cM. Distorted segregation of markers was found in certain sections of the map and linkage group I could be assembled only by combining colormapping and cytogenetics (FISH). A fast method to position genetic loci employing three AFLP primer combinations yielding 89 markers was developed and evaluated by mapping three symbiotic loci, Ljsym1, Ljsym5, and Ljhar1-3.

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A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander

BMC Genomics ◽

10.1186/s12864-021-07550-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Qiaomu Hu ◽

Yang Liu ◽

Xiaolin Liao ◽

Haifeng Tian ◽

Xiangshan Ji ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Economic Value ◽

Genetic Research ◽

High Density ◽

Amphibian Species ◽

Genomic Studies ◽

Chinese Giant Salamander

Abstract Background The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci. Results In this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes of A. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively. Conclusion We constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.

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Genomic distribution of MITEs in barley determined by MITE-AFLP mapping

Genome ◽

10.1139/g06-115 ◽

2006 ◽

Vol 49 (12) ◽

pp. 1616-1620 ◽

Cited By ~ 8

Author(s):

H. Takahashi ◽

H. Akagi ◽

K. Mori ◽

K. Sato ◽

K. Takeda

Keyword(s):

Fragment Length Polymorphism ◽

Linkage Groups ◽

Entire Genome ◽

Ssr Loci ◽

Plant Genes ◽

Flanking Sequences ◽

Average Marker Density ◽

Simple Sequence ◽

Map Distance ◽

Hordeum Vulgare Ssp

Miniature inverted-repeat transposable elements (MITEs) represent a large superfamily of transposons that are moderately to highly repetitive and frequently found near or within plant genes. To elucidate the organization of MITEs in the barley genome, MITEs were integrated into the genetic map of barley. In this report, we describe the use of MITEs in amplified fragment length polymorphism (AFLP) mapping, and demonstrate their superiority over conventional AFLP mapping. Barley MITEs include members of the Stowaway, Barfly, and Pangrangja families. By amplifying the flanking sequences of these MITEs, a total of 214 loci were mapped from a population of 93 doubled-haploid segregating individuals between Hordeum vulgare ssp. vulgare and H. vulgare ssp. spontaneum. The 214 MITE-AFLP and 40 anchor simple sequence repeat (SSR) loci were distributed on 7 linkage groups, covering a total map distance of 1 165 cM. The average marker density on each chromosome ranged between 3.4 and 9.6 cM per locus. Only 1 MITE-based locus was frequently found to be associated with MITE loci from the same family, resulting in clusters in chromosomal subregions. In barley, it will be possible to cover the entire genome with a limited set of MITE-based primers and to build highly dense maps of specific regions.

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QTL Mapping for Kernel Related Traits Based on a High-Density Genetic Map

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2015.01510 ◽

2015 ◽

Vol 41 (10) ◽

pp. 1510 ◽

Cited By ~ 1

Author(s):

Wei-Wei QIN ◽

Yong-Xiang LI ◽

Chun-Hui LI ◽

Lin CHEN ◽

Xun WU ◽

...

Keyword(s):

Qtl Mapping ◽

Genetic Map ◽

High Density

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The Diversity and Evolution of Sex Chromosomes in Frogs

Genes ◽

10.3390/genes12040483 ◽

2021 ◽

Vol 12 (4) ◽

pp. 483

Author(s):

Wen-Juan Ma ◽

Paris Veltsos

Keyword(s):

Sex Determination ◽

Sex Chromosomes ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Comparative Genomic ◽

Ancestral State ◽

Heteromorphic Sex Chromosomes ◽

Genomic Studies ◽

Evolutionary Trajectories ◽

Heterogametic Sex

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

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