DEVELOPING GENETIC LINKAGE MAP AND CDNA SUBTRACTION LIBRARY FOR WATERMELON

Genetic linkage map is being constructed for watermelon based on a testcross population and an F2 population. The testcross map comprises 262 markers (RAPD, ISSR, AFLP, SSR and ASRP markers) and covers 1,350 cM. The map comprises 11 large linkage groups (50.7–155.2 cM), 5 medium-size linkage groups (37.5–46.2 cM), and 16 small linkage groups (4.2–31.4 cM). Most AFLP markers are clustered on two linkage regions, while all other marker types are randomly dispersed on the genome. Many of the markers in this study are skewed from the classical (Mendelian) segregation ratio of1:1 in the testcross or the 3:1 ratio in the F2 population. Although the skewed segregation, marker order appeared to be consistent in linkage groups of the testcross and F2 population. A cDNA library was constructed using RNA isolated from watermelon flesh 1 week (rapid cell division stage), 2 weeks (cell growth and storage deposition stage, 4 weeks (maturation stage), and 5 weeks (postmaturation stage) post pollination. Over 1,020 cDNA clones were sequenced, and were analyzed using the Basic Local Alignment Search Tool (BLAST). The sequenced cDNA clones were designated as expressed sequenced tag (EST) markers and will be used in mapping analysis of watermelon genome.

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(259) A Genetic Linkage Map and a cDNA Library for Watermelon

HortScience ◽

10.21273/hortsci.40.4.1089d ◽

2005 ◽

Vol 40 (4) ◽

pp. 1089D-1089

Author(s):

Amnon Levi ◽

C.E. Thomas ◽

Angela Davis ◽

O.U.K. Reddy ◽

Y. Xu ◽

...

Keyword(s):

Linkage Map ◽

Cdna Library ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Local Alignment ◽

Maturation Stage ◽

Cdna Clones ◽

Linkage Groups ◽

Mendelian Segregation ◽

Mapping Populations

A genetic linkage map was constructed for watermelon based on a testcross population and an F2 population. The testcross map includes 312 markers (RAPD, ISSR, AFLP, SSR, and ASRP). This map covered a genetic distance of 1385 cM, and identified 11 large (50.7-155.2 cm), five intermediate (37.5-46.2 cm), and 16 small linkage groups (4.2-31.4 cm). Most AFLP markers are clustered in two linkage regions, while all other markers are randomly dispersed throughout the genome. Many of the markers in this study were skewed from the classical (Mendelian) segregation ratio of 1:1 in the testcross or 3:1 in the F2 population. The order of the markers within linkage groups was similar in the testcross and F2 populations. Additionally, a cDNA library was constructed using RNA isolated from watermelon flesh 1 week (rapid cell division stage), 2 weeks (cell growth and storage deposition stage), 4 weeks (maturation stage), and 5 weeks (mature fruit) after pollination. More than 1020 cDNA clones were sequenced, and analyzed using the basic local alignment search Tool (BLAST). The sequenced cDNA clones were designated as expressed sequenced tag (EST). The ESTs were searched for simple sequence repeats. About 7% of the ESTs contained SSR motifs. The ESTs containing SSRs are being used to design PCR primers and the putative markers are being tested for polymorphism among the parental lines of the mapping populations. Polymorphic markers will then be mapped using the mapping populations.

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GENETIC LINKAGE MAP FOR WATERMELON: SEGREGATION AND DISTRIBUTION OF DNA MARKERS

HortScience ◽

10.21273/hortsci.40.3.872a ◽

2005 ◽

Vol 40 (3) ◽

pp. 872a-872

Author(s):

A. Levi ◽

C. E. Thomas ◽

J. Thies ◽

A. Simmons ◽

Y. Xu ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Rapd Markers ◽

Genetic Linkage Map ◽

Genetic Distances ◽

Aflp Markers ◽

F2 Population ◽

Skewed Segregation ◽

Linkage Distance ◽

Map Distance

Genetic linkage map is being constructed for watermelon based on a testcross population and an F2 population. About 51.0% and 31.8% of the markers in the testcross and F2 populations are skewed form the expected segregation ratios. AFLP markers appeared to be clustered on linkage regions, while ISSR and RAPD markers are randomly dispersed on the genome. AFLP markers also have greater genetic distances as compared with ISSR and RAPD markers, resulting in significant increase of map distance. An initial genetic map (based on the testcross population) that contains 27 ISSR and 141 RAPD markers has a total linkage distance of 1,166.2 cM. The addition of 2 ISSR, 8 RAPD and 77 AFLP markers increased the genetic distance of the map to 2,509.9 cM. Similar results with AFLP markers were also shown in mapping experiments with an F2S7 recombinant inbred line (RIL) population that was recently constructed for watermelon. Although the skewed segregation, marker order appeared to be consistent in linkage groups of the testcross and the F2 population. Experiments with SSR, and EST markers are being conducted to saturate the linkage map of watermelon genome.

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Genetic Linkage Map of the Edible BasidiomycetePleurotus ostreatus

Applied and Environmental Microbiology ◽

10.1128/aem.66.12.5290-5300.2000 ◽

2000 ◽

Vol 66 (12) ◽

pp. 5290-5300 ◽

Cited By ~ 61

Author(s):

Luis M. Larraya ◽

GÃ¯Â¿Â½mer PÃ¯Â¿Â½rez ◽

Enrique Ritter ◽

Antonio G. Pisabarro ◽

Lucı́a Ramı́rez

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Gene Sequence ◽

Genetic Linkage Map ◽

Fragment Length Polymorphism ◽

Individual Cell ◽

Random Amplified Polymorphic Dna ◽

Rrna Gene ◽

Linkage Groups ◽

Rrna Gene Sequence

ABSTRACT We have constructed a genetic linkage map of the edible basidiomycete Pleurotus ostreatus (var. Florida). The map is based on the segregation of 178 random amplified polymorphic DNA and 23 restriction fragment length polymorphism markers; four hydrophobin, two laccase, and two manganese peroxidase genes; both mating type loci; one isozyme locus (est1); the rRNA gene sequence; and a repetitive DNA sequence in a population of 80 sibling monokaryons. The map identifies 11 linkage groups corresponding to the chromosomes ofP. ostreatus, and it has a total length of 1,000.7 centimorgans (cM) with an average of 35.1 kbp/cM. The map shows a high correlation (0.76) between physical and genetic chromosome sizes. The number of crossovers observed per chromosome per individual cell is 0.89. This map covers nearly the whole genome of P. ostreatus.

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A genetic linkage map for Stevia rebaudiana

Genome ◽

10.1139/g98-161 ◽

1999 ◽

Vol 42 (4) ◽

pp. 657-661 ◽

Cited By ~ 7

Author(s):

Y Yao ◽

M Ban ◽

J Brandle

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Rapd Markers ◽

Genetic Linkage Map ◽

Average Distance ◽

Stevia Rebaudiana ◽

Linkage Groups ◽

Genome Map ◽

High Level ◽

Map Distance

To lay a foundation for molecular breeding efforts, the first genetic linkage map for Stevia rebaudiana has been constructed using segregation data from a pseudo test-cross F1 population. A total of 183 randomly amplified polymorphic DNA (RAPD) markers were analysed and assembled into 21 linkage groups covering a total distance of 1389 cM, with an average distance between markers of of 7.6 cM. The 11 largest linkage groups consisted of 4-19 loci, ranged in length from 56 to 174 cM, and accounted for 75% of the total map distance. Fifteen RAPD loci were found to be unlinked. From the 521 primers showing amplification products, 185 (35.5%) produced a total of 293 polymorphic fragments, indicating a high level of genetic diversity in stevia. Most of the RAPD markers in stevia segregated in normal Mendelian fashion.Key words: stevia, open-pollinated, genome map, RAPD.

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Mapping of quantitative trait loci underlying resistance to cassava anthracnose disease

The Journal of Agricultural Science ◽

10.1017/s0021859615001057 ◽

2015 ◽

Vol 154 (7) ◽

pp. 1209-1217 ◽

Cited By ~ 3

Author(s):

A. BOONCHANAWIWAT ◽

S. SRAPHET ◽

S. WHANKAEW ◽

O. BOONSENG ◽

D. R. SMITH ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Linkage Map ◽

Dna Markers ◽

Quantitative Trait ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Gene Annotation ◽

Linkage Groups ◽

Anthracnose Disease ◽

Trait Loci

SUMMARYCassava (Manihot esculenta Crantz) is an economically important root crop in Thailand, which is ranked the world's top cassava exporting country. Production of cassava can be hampered by several pathogens and pests. Cassava anthracnose disease (CAD) is an important disease caused by the fungus Colletotrichum gloeosporioides f. sp. manihotis. The pathogen causes severe stem damage resulting in yield reductions and lack of stem cuttings available for planting. Molecular studies of cassava response to CAD will provide useful information for cassava breeders to develop new varieties with resistance to the disease. The current study aimed to identify quantitative trait loci (QTL) and DNA markers associated with resistance to CAD. A total of 200 lines of two F1 mapping populations were generated by reciprocal crosses between the varieties Huabong60 and Hanatee. The F1 samples were genotyped based on simple sequence repeat (SSR) and expressed sequence tag-SSR markers and a genetic linkage map was constructed using the JoinMap®/version3·0 program. The results showed that the map consisted of 512 marker loci distributed on 24 linkage groups with a map length of 1771·9 centimorgan (cM) and a mean interval between markers of 5·7 cM. The genetic linkage map was integrated with phenotypic data for the response to CAD infection generated by a detached leaf assay test. A total of three QTL underlying the trait were identified on three linkage groups using the MapQTL®/version4·0 program. Those DNA markers linked to the QTL that showed high statistically significant values with the CAD resistance trait were identified for gene annotation analysis and 23 candidate resistance genes to CAD infection were identified.

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Development of a genetic linkage map for Sharon goatgrass (Aegilops sharonensis) and mapping of a leaf rust resistance gene

Genome ◽

10.1139/gen-2013-0065 ◽

2013 ◽

Vol 56 (7) ◽

pp. 367-376 ◽

Cited By ~ 8

Author(s):

P.D. Olivera ◽

A. Kilian ◽

P. Wenzl ◽

B.J. Steffenson

Keyword(s):

Linkage Map ◽

Leaf Rust ◽

Resistance Genes ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Chromosomal Location ◽

Dominant Gene ◽

Leaf Rust Resistance Gene ◽

Linkage Groups ◽

Aegilops Sharonensis

Aegilops sharonensis (Sharon goatgrass), a diploid wheat relative, is known to be a rich source of disease resistance genes for wheat improvement. To facilitate the transfer of these genes into wheat, information on their chromosomal location is important. A genetic linkage map of Ae. sharonensis was constructed based on 179 F2 plants derived from a cross between accessions resistant (1644) and susceptible (1193) to wheat leaf rust. The linkage map was based on 389 markers (377 Diversity Arrays Technology (DArT) and 12 simple sequence repeat (SSR) loci) and was comprised of 10 linkage groups, ranging from 2.3 to 124.6 cM. The total genetic length of the map was 818.0 cM, with an average interval distance between markers of 3.63 cM. Based on the chromosomal location of 115 markers previously mapped in wheat, the four linkage groups of A, B, C, and E were assigned to Ae. sharonensis (Ssh) and homoeologous wheat chromosomes 6, 1, 3, and 2. The single dominant gene (designated LrAeSh1644) conferring resistance to leaf rust race THBJ in accession 1644 was positioned on linkage group A (chromosome 6Ssh) and was flanked by DArT markers wpt-9881 (at 1.9 cM distal from the gene) and wpt-6925 (4.5 cM proximal). This study clearly demonstrates the utility of DArT for genotyping uncharacterized species and tagging resistance genes where pertinent genomic information is lacking.

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A genetic linkage map of tetraploid orchardgrass (Dactylis glomerata L.) and quantitative trait loci for heading date

Genome ◽

10.1139/g2012-026 ◽

2012 ◽

Vol 55 (5) ◽

pp. 360-369 ◽

Cited By ~ 17

Author(s):

Wengang Xie ◽

Joseph G. Robins ◽

B. Shaun Bushman

Keyword(s):

Quantitative Trait Loci ◽

Linkage Map ◽

Quantitative Trait ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Heading Date ◽

Dactylis Glomerata ◽

Linkage Groups ◽

Trait Loci ◽

Dactylis Glomerata L

Orchardgrass ( Dactylis glomerata L.), or cocksfoot, is indigenous to Eurasia and northern Africa, but has been naturalized on nearly every continent and is one of the top perennial forage grasses grown worldwide. To improve the understanding of genetic architecture of orchardgrass and provide a template for heading date candidate gene search in this species, the goals of the present study were to construct a tetraploid orchardgrass genetic linkage map and identify quantitative trait loci associated with heading date. A combination of SSR markers derived from an orchardgrass EST library and AFLP markers were used to genotype an F1 population of 284 individuals derived from a very late heading Dactylis glomerata subsp. himalayensis parent and an early to mid-heading Dactylis glomerata subsp. aschersoniana parent. Two parental maps were constructed with 28 cosegregation groups and seven consensus linkage groups each, and homologous linkage groups were tied together by 38 bridging markers. Linkage group lengths varied from 98 to 187 cM, with an average distance between markers of 5.5 cM. All but two mapped SSR markers had homologies to physically mapped rice (Oryza sativa L.) genes, and six of the seven orchardgrass linkage groups were assigned based on this putative synteny with rice. Quantitative trait loci were detected for heading date on linkage groups 2, 5, and 6 in both parental maps, explaining between 12% and 24% of the variation.

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Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades

10.1101/486175 ◽

2018 ◽

Author(s):

linbin huang ◽

Xing-hong Yan

Keyword(s):

Growth Rate ◽

Specific Growth Rate ◽

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Specific Growth ◽

Pyropia Yezoensis ◽

Economic Traits ◽

Fresh Weight ◽

Skewed Segregation

Pyropia yezoensis is an important economic seaweed, to construct a genetic linkage map and analyze the quantitative trait loci (QTLs) of blades, a doubled haploid (DH) population containing 148 DH strains established from the intraspecific hybridization between two strains with different colors was used in the present study and genotyped using 79 pairs of polymorphic sequence-related amplified polymorphism (SRAP) markers labeled with 5'-HEX and capillary electrophoresis. A chi-square test for significance of deviations from the expected ratio (1:1) on the loci which were polymorphic between parents and segregated in mapping population identified 301 loci with normal segregation (P ≥ 0.01) and 96 loci (24.18%) with low-level skewed segregation (0.001 ≤ P < 0.01). The map was constructed using JoinMap software after a total of 92 loci were assembled into three linkage groups. The map spanned 557.36 cM covering 93.71% of the estimated genome, with a mean interlocus space of 6.23 cM. Kolmogorov-Smirnov test (α=5%) of the marker positions along each LG showed a uniform distribution. After that, 10 QTLs associated with five economic traits of blades were detected, among which one QTL was for length, one for width, two for fresh weight, two for specific growth rate of length and four for specific growth rate of fresh weight. These QTLs could explain 2.29-7.87% of the trait variations, indicating that their effects were all minor. The results will serve as a framework for future marker-assisted breeding in P. yezoensis.

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Linkage of random amplified polymorphic DNA, isozyme and morphological markers in grasspea (Lathyrus sativus)

The Journal of Agricultural Science ◽

10.1017/s0021859699007108 ◽

1999 ◽

Vol 133 (4) ◽

pp. 389-395 ◽

Cited By ~ 13

Author(s):

M. A. CHOWDHURY ◽

A. E. SLINKARD

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Rapd Markers ◽

Genetic Linkage Map ◽

Average Distance ◽

Random Amplified Polymorphic Dna ◽

Lathyrus Sativus ◽

Morphological Markers ◽

Linkage Studies ◽

Linkage Groups

We constructed a genetic linkage map of grasspea (Lathyrus sativus L.; 2n = 14) from 100 F2 individuals derived from a cross between PI 426891.1.3 and PI 283564c.3.2. A total of 71 RAPD, three isozyme and one morphological markers segregated in the F2 progeny. A small fraction of markers (12%) deviated significantly from the expected Mendelian ratio (1[ratio ]2[ratio ]1 or 3[ratio ]1). Out of 75 markers, 69 (one morphological, three isozyme and 65 RAPD markers) were assigned to 14 linkage groups comprising 898 cM. The average distance between two adjacent markers was 17·2 cM. The present linkage map will serve as a reference point for further linkage studies in grasspea.

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A molecular genetic linkage map identifying the St and H subgenomes of Elymus (Poaceae: Triticeae) wheatgrass

Genome ◽

10.1139/g11-045 ◽

2011 ◽

Vol 54 (10) ◽

pp. 819-828 ◽

Cited By ~ 8

Author(s):

Ivan W. Mott ◽

Steven R. Larson ◽

Thomas A. Jones ◽

Joseph G. Robins ◽

Kevin B. Jensen ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Molecular Genetic ◽

Perennial Grass ◽

Rice Genome ◽

Backcross Progeny ◽

Linkage Groups ◽

Sts Markers ◽

Snake River Wheatgrass

Elymus L. is the largest and most complex genus in the Triticeae tribe of grasses with approximately 150 polyploid perennial species occurring worldwide. We report here the first genetic linkage map for Elymus. Backcross mapping populations were created by crossing caespitose Elymus wawawaiensis (EW) (Snake River wheatgrass) and rhizomatous Elymus lanceolatus (EL) (thickspike wheatgrass) to produce F1 interspecific hybrids that were then backcrossed to the same EL male to generate progeny with segregating phenotypes. EW and EL are both allotetraploid species (n = 14) containing the St (Pseudoroegneria) and H (Hordeum) genomes. A total of 387 backcross progeny from four populations were genotyped using 399 AFLP and 116 EST-based SSR and STS markers. The resulting consensus map was 2574 cM in length apportioned among the expected number of 14 linkage groups. EST-based SSR and STS markers with homology to rice genome sequences were used to identify Elymus linkage groups homoeologous to chromosomes 1–7 of wheat. The frequency of St-derived genome markers on each linkage group was used to assign genome designations to all linkage groups, resulting in the identification of the seven St and seven H linkage groups of Elymus. This map also confirms the alloploidy and disomic chromosome pairing and segregation of Elymus and will be useful in identifying QTLs controlling perennial grass traits in this genus.

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