Table S3. Sequences flanking reliable single nucleotide polymorphisms (SNPs) in onion cDNA al_con... more Table S3. Sequences flanking reliable single nucleotide polymorphisms (SNPs) in onion cDNA al_contigs conducive for genotyping using the KASP platform. (XLSX 1413Â kb)
Table S2. Results of Blast2Go to obtain functional anotation of RF contigs containing SNPs that w... more Table S2. Results of Blast2Go to obtain functional anotation of RF contigs containing SNPs that were selected for the KASP platform. (XLSX 57Â kb)
Table S6. Positions and Chi-square values to expected segregation ratios for SNPs markers segrega... more Table S6. Positions and Chi-square values to expected segregation ratios for SNPs markers segregating in the CCxRF_new population based on RF-SNP markers. (XLSX 57Â kb)
Table S5. Positions and Chi-square values to expected segregation ratios for SNPs markers segrega... more Table S5. Positions and Chi-square values to expected segregation ratios for SNPs markers segregating in the F2(CxR) population. (XLSX 42Â kb)
Figure S1. Aligned genetic maps of the CCxRF (left) and the F2(CxR) populations (right). (DOCX 20... more Figure S1. Aligned genetic maps of the CCxRF (left) and the F2(CxR) populations (right). (DOCX 201Â kb)
Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliace... more Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
Genetic mapping in Lilium: mapping of major genes and quantitative trait loci for several ornamen... more Genetic mapping in Lilium: mapping of major genes and quantitative trait loci for several ornamental trait and disease resistances. Plant
Molecular breeding : new strategies in plant improvement
Fusarium oxysporum is a major problem in the production of tulip bulbs. Breeding for resistant cu... more Fusarium oxysporum is a major problem in the production of tulip bulbs. Breeding for resistant cultivars through a conventional approach is a slow process due to the long life cycle of tulip. Until now, marker-assisted selection (MAS) has been hampered by the large genome size and the absence of a genetic map. This study is aimed at construction of the first genetic map for tulip and at the identification of loci associated with resistance to F. oxysporum. A cross-pollinated population of 125 individuals segregating for Fusarium resistance was obtained from Tulipa gesneriana "Kees Nelis" and T. fosteriana "Cantata." Fusarium resistance of the mapping population was evaluated through a soil infection test in two consecutive years, and a spot inoculation test in which a green fluorescent protein tagged Fusarium strain was used for inoculation. The genetic maps have been constructed for the parents separately. The genetic map of "Kees Nelis" comprised 342 ...
Table S1. Sequences flanking reliable single nucleotide polymorphisms (SNPs) in RF cDNA RF_ctgs c... more Table S1. Sequences flanking reliable single nucleotide polymorphisms (SNPs) in RF cDNA RF_ctgs conducive for genotyping using the KASP platform. (XLSX 244Â kb)
Pollen fertility was assessed in 113 tulip (2n = 24) genotypes by pollen staining and germination... more Pollen fertility was assessed in 113 tulip (2n = 24) genotypes by pollen staining and germination on media. 23 genotypes were selected based on high 2n pollen percentage and will be used for crosses. Genomic in situ hybridization (GISH) was used to investigate the genome composition and the extent of intergenomic recombination in 2 F1, 24 BC1 and 2 BC2 tulip progenies. F1 comprised of 12 chromosomes of each parent without recombination and the percentage of introgressed T. fosteriana genome was 45.6%. In all BC1 (GGF) and BC2 (GGGF) hybrids recombinant chromosomes were observed and most of them had both G/F and F/G recombination. The number of T. fosteriana chromosomes as well as the number and type of recombinant chromosomes differed among progenies. In BC1, the percentage of introgressed T. fosteriana genome ranged from 16.8% to 24.7%, while in BC2 the percentage varied from 13.3% to 16.67%. The position of recombination distributed on both arms from distal to interstitial, but mo...
Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and effect... more Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and effective; however, deeper sequencing and using more tissues and stages is advisable for extended comparative Shahin et al. BMC Genomics 2012, 13:640
Lily (Lilium L.) is a perennial bulbous ornamental, belonging to subclass Monocotyledonae and fam... more Lily (Lilium L.) is a perennial bulbous ornamental, belonging to subclass Monocotyledonae and family Liliaceae. Lily, according to statistics of Dutch auctions, is the fifth most important cut flower and the second in flower bulbs based on acreage. This species has been extensively used for cytogenetic studies, but molecular genetic studies are limited. The heterogenic nature and the very complex and huge genome (36 Gb) of lily might be the reason for this. To improve the efficiency of breeding and selection in this species, and set up the basis for genetic studies in Lilium, genomic resources are needed. Next generation sequencing (NGS) technology (454 pyro-sequencing) was used to sequence the transcriptomes (RNA-seq) of four lily cultivars: ‘Connecticut King’, ‘White Fox’, ‘Star Gazer’, and Trumpet that belong to the four most important hybrid groups: Asiatic, Longiflorum, Oriental, and Trumpet respectively. Successfully, 52,172 unigenes with an average length of 555 bp were devel...
MotivationPolyploid species carry more than two copies of each chromosome, a condition found in m... more MotivationPolyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.ResultspolymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these cro...
Table S3. Sequences flanking reliable single nucleotide polymorphisms (SNPs) in onion cDNA al_con... more Table S3. Sequences flanking reliable single nucleotide polymorphisms (SNPs) in onion cDNA al_contigs conducive for genotyping using the KASP platform. (XLSX 1413Â kb)
Table S2. Results of Blast2Go to obtain functional anotation of RF contigs containing SNPs that w... more Table S2. Results of Blast2Go to obtain functional anotation of RF contigs containing SNPs that were selected for the KASP platform. (XLSX 57Â kb)
Table S6. Positions and Chi-square values to expected segregation ratios for SNPs markers segrega... more Table S6. Positions and Chi-square values to expected segregation ratios for SNPs markers segregating in the CCxRF_new population based on RF-SNP markers. (XLSX 57Â kb)
Table S5. Positions and Chi-square values to expected segregation ratios for SNPs markers segrega... more Table S5. Positions and Chi-square values to expected segregation ratios for SNPs markers segregating in the F2(CxR) population. (XLSX 42Â kb)
Figure S1. Aligned genetic maps of the CCxRF (left) and the F2(CxR) populations (right). (DOCX 20... more Figure S1. Aligned genetic maps of the CCxRF (left) and the F2(CxR) populations (right). (DOCX 201Â kb)
Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliace... more Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
Genetic mapping in Lilium: mapping of major genes and quantitative trait loci for several ornamen... more Genetic mapping in Lilium: mapping of major genes and quantitative trait loci for several ornamental trait and disease resistances. Plant
Molecular breeding : new strategies in plant improvement
Fusarium oxysporum is a major problem in the production of tulip bulbs. Breeding for resistant cu... more Fusarium oxysporum is a major problem in the production of tulip bulbs. Breeding for resistant cultivars through a conventional approach is a slow process due to the long life cycle of tulip. Until now, marker-assisted selection (MAS) has been hampered by the large genome size and the absence of a genetic map. This study is aimed at construction of the first genetic map for tulip and at the identification of loci associated with resistance to F. oxysporum. A cross-pollinated population of 125 individuals segregating for Fusarium resistance was obtained from Tulipa gesneriana "Kees Nelis" and T. fosteriana "Cantata." Fusarium resistance of the mapping population was evaluated through a soil infection test in two consecutive years, and a spot inoculation test in which a green fluorescent protein tagged Fusarium strain was used for inoculation. The genetic maps have been constructed for the parents separately. The genetic map of "Kees Nelis" comprised 342 ...
Table S1. Sequences flanking reliable single nucleotide polymorphisms (SNPs) in RF cDNA RF_ctgs c... more Table S1. Sequences flanking reliable single nucleotide polymorphisms (SNPs) in RF cDNA RF_ctgs conducive for genotyping using the KASP platform. (XLSX 244Â kb)
Pollen fertility was assessed in 113 tulip (2n = 24) genotypes by pollen staining and germination... more Pollen fertility was assessed in 113 tulip (2n = 24) genotypes by pollen staining and germination on media. 23 genotypes were selected based on high 2n pollen percentage and will be used for crosses. Genomic in situ hybridization (GISH) was used to investigate the genome composition and the extent of intergenomic recombination in 2 F1, 24 BC1 and 2 BC2 tulip progenies. F1 comprised of 12 chromosomes of each parent without recombination and the percentage of introgressed T. fosteriana genome was 45.6%. In all BC1 (GGF) and BC2 (GGGF) hybrids recombinant chromosomes were observed and most of them had both G/F and F/G recombination. The number of T. fosteriana chromosomes as well as the number and type of recombinant chromosomes differed among progenies. In BC1, the percentage of introgressed T. fosteriana genome ranged from 16.8% to 24.7%, while in BC2 the percentage varied from 13.3% to 16.67%. The position of recombination distributed on both arms from distal to interstitial, but mo...
Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and effect... more Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and effective; however, deeper sequencing and using more tissues and stages is advisable for extended comparative Shahin et al. BMC Genomics 2012, 13:640
Lily (Lilium L.) is a perennial bulbous ornamental, belonging to subclass Monocotyledonae and fam... more Lily (Lilium L.) is a perennial bulbous ornamental, belonging to subclass Monocotyledonae and family Liliaceae. Lily, according to statistics of Dutch auctions, is the fifth most important cut flower and the second in flower bulbs based on acreage. This species has been extensively used for cytogenetic studies, but molecular genetic studies are limited. The heterogenic nature and the very complex and huge genome (36 Gb) of lily might be the reason for this. To improve the efficiency of breeding and selection in this species, and set up the basis for genetic studies in Lilium, genomic resources are needed. Next generation sequencing (NGS) technology (454 pyro-sequencing) was used to sequence the transcriptomes (RNA-seq) of four lily cultivars: ‘Connecticut King’, ‘White Fox’, ‘Star Gazer’, and Trumpet that belong to the four most important hybrid groups: Asiatic, Longiflorum, Oriental, and Trumpet respectively. Successfully, 52,172 unigenes with an average length of 555 bp were devel...
MotivationPolyploid species carry more than two copies of each chromosome, a condition found in m... more MotivationPolyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.ResultspolymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these cro...
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