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Liebao Han - One of the best experts on this subject based on the ideXlab platform.
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analysis of transcripts and splice isoforms in Red Clover trifolium pratense l by single molecule long read sequencing
BMC Plant Biology, 2018Co-Authors: Yuehui Chao, Jianbo Yuan, Siqiao Jia, Liebao HanAbstract:Red Clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. Although a draft genome sequence was published already, the sequences and completed structure of mRNA transcripts remain unclear, which limit further explore on Red Clover. In this study, the Red Clover transcriptome was sequenced using single-molecule long-read sequencing to identify full-length splice isoforms, and 29,730 novel isoforms from known genes and 2194 novel isoforms from novel genes were identified. A total of 5492 alternative splicing events was identified and the majority of alter spliced events in Red Clover was corrected as intron retention. In addition, of the 15,229 genes detected by SMRT, 8719 including 186,517 transcripts have at least one poly(A) site. Furthermore, we identified 4333 long non-coding RNAs and 3762 fusion transcripts. We analyzed full-length transcriptome of Red Clover with PacBio SMRT. Those new findings provided important information for improving Red Clover draft genome annotation and fully characterization of Red Clover transcriptome.
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analysis of transcripts and splice isoforms in Red Clover trifolium pratense l by single molecule long read sequencing
bioRxiv, 2018Co-Authors: Yuehui Chao, Jianbo Yuan, Siqiao Jia, Liebao HanAbstract:Abstract Red Clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. Although a draft genome sequence was published already, the sequences and completed structure of mRNA transcripts remain unclear, which limit further explore on Red Clover. In this study, the Red Clover transcriptome was sequenced using single-molecule long-read sequencing to identify full-length splice isoforms, and 29,730 novel isoforms from known genes and 2,194 novel isoforms from novel genes were identified. A total of 5,492 alternative splicing events was identified and the majority of alter spliced events in Red Clover was corrected as intron retention. In addition, of the 15,229 genes detected by SMRT, 8,719 including 1,86,517 transcripts have at least one poly(A) site. Furthermore, we identified 4,333 long non-coding RNAs and 3,762 fusion transcripts. Our results show the feasibility of deep sequencing full-length RNA from Red Clover transcriptome on a single-molecule level.
Satoshi Tabata - One of the best experts on this subject based on the ideXlab platform.
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integration of linkage and chromosome maps of Red Clover trifolium pratense l
Cytogenetic and Genome Research, 2012Co-Authors: Ryohei Kataoka, Sachiko Isobe, Satoshi Tabata, Masaki Hara, S Kato, Shusei Sato, Nobuko OhmidoAbstract:Red Clover (Trifolium pratense L.) is a forage legume and an allogamous diploid plant (2n = 14; 440 Mb). Here, we examine the 7 prometaphase chromosomes of Red Clover using fluorescence in situ hybridization (FISH) with ribosomal RNA sequences, pericentromeric and telomeric repeats, as well as bacterial artificial chromosome (BAC) clones. Position of hybridization signals and chromosome condensation patterns were quantified by the help of the chromosome image analysis system ver. 4.0 (CHIAS IV). Fourteen BAC clones belonging to linkage groups (LG) 1-7 hybridized to individual chromosomes 4, 2, 6, 5, 1, 7, and 3, respectively. Quantitative analysis of FISH mapping and chromosome analysis using CHIAS IV allowed us to construct a quantitative idiogram that constitutes the comprehensive chromosome map of Red Clover. Chromosomal positions of the 26S rDNA locus were detected at a heterozygous locus on chromosome 6 in the variety HR, and polymorphisms of rDNA loci were observed in other varieties, although chromosomal positions of some BAC clones did not vary among HR and other varieties. These results demonstrate chromosomal collinearity among allogamous Red Clover varieties. This integration of genetic linkage and quantitative chromosome maps should provide valuable insight into allogamous legume genetics.
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construction of a consensus linkage map for Red Clover trifolium pratense l
BMC Plant Biology, 2009Co-Authors: Sachiko Isobe, Roland Kolliker, Hiroshi Hisano, Shigemi Sasamoto, Tshyuko Wada, Irina Klimenko, Kenji Okumura, Satoshi TabataAbstract:Background Red Clover (Trifolium pratense L.) is a major forage legume that has a strong self-incompatibility system and exhibits high genetic diversity within populations. For several crop species, integrated consensus linkage maps that combine information from multiple mapping populations have been developed. For Red Clover, three genetic linkage maps have been published, but the information in these existing maps has not been integrated.
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construction of a consensus linkage map for Red Clover trifolium pratense l
BMC Plant Biology, 2009Co-Authors: Sachiko Isobe, Roland Kolliker, Hiroshi Hisano, Shigemi Sasamoto, Tshyuko Wada, Irina Klimenko, Kenji Okumura, Satoshi TabataAbstract:Red Clover (Trifolium pratense L.) is a major forage legume that has a strong self-incompatibility system and exhibits high genetic diversity within populations. For several crop species, integrated consensus linkage maps that combine information from multiple mapping populations have been developed. For Red Clover, three genetic linkage maps have been published, but the information in these existing maps has not been integrated. A consensus linkage map was constructed using six mapping populations originating from eight parental accessions. Three of the six mapping populations were established for this study. The integrated Red Clover map was composed of 1804 loci, including 1414 microsatellite loci, 181 amplified fragment length polymorphism (AFLP) loci and 204 restriction fragment length polymorphism (RFLP) loci, in seven linkage groups. The average distance between loci and the total length of the consensus map were 0.46 cM and 836.6 cM, respectively. The locus order on the consensus map correlated highly with that of accession-specific maps. Segregation distortion was observed across linkage groups. We investigated genome-wide allele frequency in 1144 Red Clover individuals using 462 microsatellite loci randomly chosen from the consensus map. The average number of alleles and polymorphism information content (PIC) were 9.17 and 0.69, respectively. A consensus genetic linkage map for Red Clover was constructed for the first time based on six mapping populations. The locus order on the consensus map was highly conserved among linkage maps and was sufficiently reliable for use as a reference for genetic analysis of random Red Clover germplasms.
Sachiko Isobe - One of the best experts on this subject based on the ideXlab platform.
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integration of linkage and chromosome maps of Red Clover trifolium pratense l
Cytogenetic and Genome Research, 2012Co-Authors: Ryohei Kataoka, Sachiko Isobe, Satoshi Tabata, Masaki Hara, S Kato, Shusei Sato, Nobuko OhmidoAbstract:Red Clover (Trifolium pratense L.) is a forage legume and an allogamous diploid plant (2n = 14; 440 Mb). Here, we examine the 7 prometaphase chromosomes of Red Clover using fluorescence in situ hybridization (FISH) with ribosomal RNA sequences, pericentromeric and telomeric repeats, as well as bacterial artificial chromosome (BAC) clones. Position of hybridization signals and chromosome condensation patterns were quantified by the help of the chromosome image analysis system ver. 4.0 (CHIAS IV). Fourteen BAC clones belonging to linkage groups (LG) 1-7 hybridized to individual chromosomes 4, 2, 6, 5, 1, 7, and 3, respectively. Quantitative analysis of FISH mapping and chromosome analysis using CHIAS IV allowed us to construct a quantitative idiogram that constitutes the comprehensive chromosome map of Red Clover. Chromosomal positions of the 26S rDNA locus were detected at a heterozygous locus on chromosome 6 in the variety HR, and polymorphisms of rDNA loci were observed in other varieties, although chromosomal positions of some BAC clones did not vary among HR and other varieties. These results demonstrate chromosomal collinearity among allogamous Red Clover varieties. This integration of genetic linkage and quantitative chromosome maps should provide valuable insight into allogamous legume genetics.
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construction of a consensus linkage map for Red Clover trifolium pratense l
BMC Plant Biology, 2009Co-Authors: Sachiko Isobe, Roland Kolliker, Hiroshi Hisano, Shigemi Sasamoto, Tshyuko Wada, Irina Klimenko, Kenji Okumura, Satoshi TabataAbstract:Background Red Clover (Trifolium pratense L.) is a major forage legume that has a strong self-incompatibility system and exhibits high genetic diversity within populations. For several crop species, integrated consensus linkage maps that combine information from multiple mapping populations have been developed. For Red Clover, three genetic linkage maps have been published, but the information in these existing maps has not been integrated.
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construction of a consensus linkage map for Red Clover trifolium pratense l
BMC Plant Biology, 2009Co-Authors: Sachiko Isobe, Roland Kolliker, Hiroshi Hisano, Shigemi Sasamoto, Tshyuko Wada, Irina Klimenko, Kenji Okumura, Satoshi TabataAbstract:Red Clover (Trifolium pratense L.) is a major forage legume that has a strong self-incompatibility system and exhibits high genetic diversity within populations. For several crop species, integrated consensus linkage maps that combine information from multiple mapping populations have been developed. For Red Clover, three genetic linkage maps have been published, but the information in these existing maps has not been integrated. A consensus linkage map was constructed using six mapping populations originating from eight parental accessions. Three of the six mapping populations were established for this study. The integrated Red Clover map was composed of 1804 loci, including 1414 microsatellite loci, 181 amplified fragment length polymorphism (AFLP) loci and 204 restriction fragment length polymorphism (RFLP) loci, in seven linkage groups. The average distance between loci and the total length of the consensus map were 0.46 cM and 836.6 cM, respectively. The locus order on the consensus map correlated highly with that of accession-specific maps. Segregation distortion was observed across linkage groups. We investigated genome-wide allele frequency in 1144 Red Clover individuals using 462 microsatellite loci randomly chosen from the consensus map. The average number of alleles and polymorphism information content (PIC) were 9.17 and 0.69, respectively. A consensus genetic linkage map for Red Clover was constructed for the first time based on six mapping populations. The locus order on the consensus map was highly conserved among linkage maps and was sufficiently reliable for use as a reference for genetic analysis of random Red Clover germplasms.
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comprehensive structural analysis of the genome of Red Clover trifolium pratense l
DNA Research, 2005Co-Authors: Shusei Sato, Sachiko Isobe, Kenji Okumura, Ryohei Kataoka, Erika Asamizu, Yasukazu Nakamura, Takakazu Kaneko, Nozomi Sakurai, Irina KlimenkoAbstract:With the aim of establishing the basic knowledge and resources needed for applied genetics, we investigated the genome structure of Red Clover Trifolium pratense L. by a combination of cytological, genomic and genetic approaches. The deduced genome size was approximately 440 Mb, as estimated by measuring the nuclear DNA content by flow cytometry. Seven chromosomes could be distinguished by microscopic observation of DAPI stained prometaphase chromosomes and fluorescence in situ hybridization using 28S and 5S rDNA probes and bacterial artificial chromosome probes containing microsatellite markers with known positions on a genetic linkage map. The average GC content of the genomes of chloroplast, mitochondrion and nucleus were shown to be 33.8, 42.9 and 34.2%, respectively, by the analysis of 1.4 Mb of random genomic sequences. A total of 26,356 expressed sequence tags (ESTs) that were grouped into 9339 non-Redundant sequences were collected, and 78% of the ESTs showed sequence similarity to registeRed genes, mainly of Arabidopsis thaliana and rice. To facilitate basic and applied genetics in Red Clover, we generated a high-density genetic linkage map with gene-associated microsatellite markers. A total of 7159 primer pairs were designed to amplify simple sequence repeats (SSRs) identified in four different types of libraries. Based on sequence similarity, 82% of the SSRs were likely to be associated with genes. Polymorphism was examined using two parent plants, HR and R130, and 10 F(1) progeny by agarose gel electrophoresis, followed by genotyping for the primer pairs showing polymorphisms using 188 F(1) plants from the mapping population. The selected 1305 microsatellite markers as well as the previously developed 167 restriction fragment length polymorphism markers were subjected to linkage analysis. A total of 1434 loci detected by 1399 markers were successfully mapped onto seven linkage groups totaling 868.7 cM in length; 405 loci (28%) were bi-parental, 611 (43%) were specific to HR and 418 (29%) were specific to R130. Each genetic linkage group was linked to a corresponding chromosome by FISH analysis using seven microsatellite markers specific to each of the linkage groups as probes. Transferability of the developed microsatellite markers to other germplasms was confirmed by testing 268 selected markers on 88 Red Clover germplasms. Macrosynteny at the segmental level was observed between the genomes of Red Clover and two model legumes, Lotus japonicus and Medicago truncatula, strongly suggesting that the genome information for the model legumes is transferable to Red Clover for genetic investigations and experimental breeding.
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first rflp linkage map of Red Clover trifolium pratense l based on cdna probes and its transferability to other Red Clover germplasm
Theoretical and Applied Genetics, 2003Co-Authors: Sachiko Isobe, Irina Klimenko, Sergey I Ivashuta, Mitsuru Gau, N N KozlovAbstract:We constructed a genetic linkage map of Red Clover (Trifolium pratense L., 2n=2x=14) using RFLP markers from cDNA probes of a backcrossed mapping population, and investigated the transferability of the markers to other Red Clover germplasm. The map contains 157 RFLP markers and one morphological marker on seven linkage groups. The total map distance was 535.7 cM and the average distance between two markers was 3.4 cM. All of the cDNA probes of the map were hybridized to the fragments of genomic DNA from 12 plants derived from three varieties, and 87% of the cDNA probes detected polymorphic bands that corresponded to those of mapping parents. This result indicated that RFLP markers on the present map were transferable to the genome analysis of other Red Clover germplasm. This is the first report to construct a linkage map of Trifolium species; it should provide fundamental and useful genetic information relevant to the breeding of Red Clover and genus Trifolium.
Aila Vanhatalo - One of the best experts on this subject based on the ideXlab platform.
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equol in milk of dairy cows is derived from forage legumes such as Red Clover
British Journal of Nutrition, 2009Co-Authors: Eeva Mustonen, Kristiina Wähälä, Ilkka Saastamoinen, Juhani Taponen, Hannu Saloniemi, Mikko Tuori, Aila VanhataloAbstract:The intake of isoflavones and the resulting equol contents of both plasma and milk of the same Red Clover-fed cows are reported for the first time in cyclic change-over design study. Cows were fed four different Red Clover silages and two timothy-meadow fescue silages as controls. The Red Clover silages contained daidzein, formononetin, biochanin A and genistein, whereas the timothy-meadow fescue silages contained no isoflavones. We found a strong association (y = 0.071x+2.75, R 2 0.71) between the formononetin intake (x) and equol concentration (y) in the plasma, while the formononetin intake and milk equol concentration were weakly associated (y = 0.0035x+0.358, R 2 0.20). This means that a small part of the total formononetin in the silage is secreted into milk as equol. The mean equol contents in plasma and milk of cows fed Red Clover silage diets were in the range of 4.6-8.4 mg/l and 458-643 microg/l, respectively, while the respective values for the control diets were in the range of 0.8-1.5 mg/l and 171-287 microg/l. We showed that shorter growing periods of Red Clover resulted in higher silage formononetin contents and plasma and milk equol contents, suggesting that the equol content of milk can be manipulated by varying the harvesting strategy of Red Clover. We conclude that milk equol is derived from the formononetin of Red Clover silage and that milk from Red Clover-fed cows can be consideRed as a source of equol in human nutrition.
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equol in milk of dairy cows is derived from forage legumes such as Red Clover
British Journal of Nutrition, 2009Co-Authors: Eeva Mustonen, Kristiina Wähälä, Ilkka Saastamoinen, Juhani Taponen, Hannu Saloniemi, Mikko Tuori, Aila VanhataloAbstract:The intake of isoflavones and the resulting equol contents of both plasma and milk of the same Red Clover-fed cows are reported for the first time in cyclic change-over design study. Cows were fed four different Red Clover silages and two timothy – meadow fescue silages as controls. The Red Clover silages contained daidzein, formononetin, biochanin A and genistein, whereas the timothy – meadow fescue silages contained no isoflavones. We found a strong association (y ¼ 0·071x þ 2·75, R 2 0·71) between the formononetin intake (x) and equol concentration (y) in the plasma, while the formononetin intake and milk equol concentration were weakly associated (y ¼ 0·0035x þ 0·358, R 2 0·20). This means that a small part of the total formononetin in the silage is secreted into milk as equol. The mean equol contents in plasma and milk of cows fed Red Clover silage diets were in the range of 4·6 –8·4 mg/l and 458–643mg/l, respectively, while the respective values for the control diets were in the range of 0·8 –1·5 mg/l and 171–287mg/l. We showed that shorter growing periods of Red Clover resulted in higher silage formononetin contents and plasma and milk equol contents, suggesting that the equol content of milk can be manipulated by varying the harvesting strategy of Red Clover. We conclude that milk equol is derived from the formononetin of Red Clover silage and that milk from Red Clover-fed cows can be consideRed as a source of equol in human nutrition. Equol: Formononetin: Bovine milk: Isoflavones: Phyto-oestrogens: Red Clover
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effects of feeding grass or Red Clover silage cut at two maturity stages in dairy cows 1 nitrogen metabolism and supply of amino acids
Journal of Dairy Science, 2009Co-Authors: Aila Vanhatalo, Kaisa Kuoppala, Seppo Ahvenjarvi, Marketta RinneAbstract:This study investigated the effects of plant species (Red Clover vs. timothy-meadow fescue) and forage maturity at primary harvest (early vs. late cut silage) on rumen fermentation, nutrient digestion, and nitrogen metabolism including omasal canal AA flow and plasma AA concentration in lactating cows. Five dairy cows equipped with rumen cannulas were used in a study designed as a 5 x 5 Latin square with 21-d periods. The diets consisted of early-cut and late-cut grass and Red Clover silage, respectively, and a mixture of late-cut grass and early-cut Red Clover silages given ad libitum with 9 kg/d of a standard concentrate. Grass silage dry matter intake tended to decrease but that of Red Clover silages tended to increase with advancing maturity. Milk yields were unchanged among treatments, milk protein and fat concentrations being lower for Red Clover than for grass silage diets. Rumen fluid pH was unchanged but volatile fatty acid and ammonia concentrations were higher for Red Clover than for grass silage diets. Intake of N, and omasal canal flows of total nonammonia N (NAN), microbial NAN, and dietary NAN were higher for Red Clover than for grass silage diets but were not affected by forage maturity. However, microbial NAN flow and amount of N excreted in the feces decreased with advancing maturity for grass diets but increased for Red Clover diets. Apparent ruminal N degradability of the diets was unchanged, but true ruminal N degradability decreased and efficiency of microbial synthesis increased with Red Clover diets compaRed with grass silage diets. Omasal canal flows of AA, except those for Met and Cys, were on average 20% higher for Red Clover than grass silage diets. Omasal canal digesta concentrations of Leu, Phe, branched-chain, and essential AA were higher but those of Met lower for Red Clover than for grass silage diets. Plasma AA concentrations, except for His (unchanged) and Met (lower), were higher for Red Clover than for grass diets. However, none of these AA-related variables were affected by forage maturity. Total digestibility of N and excretion of N in the urine were higher for Red Clover than for grass diets and decreased with advancing maturity. It was concluded that despite the higher total AA supply of cows fed Red Clover versus grass silage diets, further milk production responses on Red Clover diets were compromised by an inadequate supply of Met as evidenced by lower Met concentration in the AA profile of omasal digesta and plasma.
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effects of feeding grass or Red Clover silage cut at two maturity stages in dairy cows 2 dry matter intake and cell wall digestion kinetics
Journal of Dairy Science, 2009Co-Authors: Kaisa Kuoppala, Marketta Rinne, Seppo Ahvenjarvi, Aila VanhataloAbstract:Abstract This study examined the effects of Red Clover or grass silages cut at 2 stages of growth on feed intake, cell wall digestion, and ruminal passage kinetics in lactating dairy cows. Five dairy cows equipped with rumen cannulas were used in a study designed as a 5×5 Latin square with 21-d periods. Diets consisted of early-cut and late-cut grass and Red Clover silages and a mixture of late-cut grass and early-cut Red Clover silages offeRed ad libitum. All diets were supplemented with 9 kg/d of concentrate. Ruminal digestion and passage kinetics were assessed by the rumen evacuation technique. Apparent total-tract digestibility was determined by total fecal collection. The silage dry matter intake was highest when the mixed forage diet was fed and lowest with the early-cut Red Clover diet. Delaying the harvest tended to decrease DMI of grass and increase that of Red Clover. The intake of neutral detergent fiber (NDF) and potentially digestible NDF (pdNDF) was lower but the intake of indigestible NDF (iNDF) was higher for Red Clover diets than for grass diets. The rumen pool size of iNDF and the ratio of iNDF to pdNDF in the rumen contents were larger, and pool sizes of NDF and pdNDF were smaller for Red Clover than for grass silage diets. Outflow of iNDF and the ratio of iNDF to pdNDF in digesta entering the omasal canal were larger, and the outflow of pdNDF was smaller for Red Clover than for grass silage diets. The digestion rate (k d ) of pdNDF was faster for Red Clover diets than for grass silage diets. Delaying the harvest decreased k d for grass but increased it for Red Clover silage diets. Observed differences in fiber characteristics of Red Clover and grass silages were reflected in ruminal digestion and passage kinetics of these forages. The low intake of early-cut Red Clover silage could not be explained by silage digestibility, fermentation quality, or rumen fill, but was most likely related to nutritionally suboptimal composition because inclusion of moderate quality grass silage improved silage intake. Increasing the maturity of ensiled Red Clover does not seem to affect silage dry matter intake as consistently as that of grasses.
Roland Kolliker - One of the best experts on this subject based on the ideXlab platform.
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construction of a consensus linkage map for Red Clover trifolium pratense l
BMC Plant Biology, 2009Co-Authors: Sachiko Isobe, Roland Kolliker, Hiroshi Hisano, Shigemi Sasamoto, Tshyuko Wada, Irina Klimenko, Kenji Okumura, Satoshi TabataAbstract:Red Clover (Trifolium pratense L.) is a major forage legume that has a strong self-incompatibility system and exhibits high genetic diversity within populations. For several crop species, integrated consensus linkage maps that combine information from multiple mapping populations have been developed. For Red Clover, three genetic linkage maps have been published, but the information in these existing maps has not been integrated. A consensus linkage map was constructed using six mapping populations originating from eight parental accessions. Three of the six mapping populations were established for this study. The integrated Red Clover map was composed of 1804 loci, including 1414 microsatellite loci, 181 amplified fragment length polymorphism (AFLP) loci and 204 restriction fragment length polymorphism (RFLP) loci, in seven linkage groups. The average distance between loci and the total length of the consensus map were 0.46 cM and 836.6 cM, respectively. The locus order on the consensus map correlated highly with that of accession-specific maps. Segregation distortion was observed across linkage groups. We investigated genome-wide allele frequency in 1144 Red Clover individuals using 462 microsatellite loci randomly chosen from the consensus map. The average number of alleles and polymorphism information content (PIC) were 9.17 and 0.69, respectively. A consensus genetic linkage map for Red Clover was constructed for the first time based on six mapping populations. The locus order on the consensus map was highly conserved among linkage maps and was sufficiently reliable for use as a reference for genetic analysis of random Red Clover germplasms.
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construction of a consensus linkage map for Red Clover trifolium pratense l
BMC Plant Biology, 2009Co-Authors: Sachiko Isobe, Roland Kolliker, Hiroshi Hisano, Shigemi Sasamoto, Tshyuko Wada, Irina Klimenko, Kenji Okumura, Satoshi TabataAbstract:Background Red Clover (Trifolium pratense L.) is a major forage legume that has a strong self-incompatibility system and exhibits high genetic diversity within populations. For several crop species, integrated consensus linkage maps that combine information from multiple mapping populations have been developed. For Red Clover, three genetic linkage maps have been published, but the information in these existing maps has not been integrated.
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characterization of novel microsatellite loci for Red Clover trifolium pratense l from enriched genomic libraries
Molecular Ecology Notes, 2006Co-Authors: Roland Kolliker, Jurg Enkerli, Franco WidmerAbstract:Twenty-seven polymorphic microsatellite markers were isolated from Red Clover (Trifolium pratense). Allelic variability and cross-species amplification were assessed on 24 Red Clover and eight white Clover (Trifolium repens) genotypes. The number of alleles detected in Red Clover ranged from two to 25. Observed and expected heterozygosities were high with average values of 0.71 and 0.88, respectively. Five of the 27 loci were also successfully amplified from white Clover, where two to 13 alleles were detected. These highly polymorphic microsatellite loci provide powerful tools for population genetic studies as well as for marker-assisted selection in this important forage legume species.
