Genetic diversity and structure in a collection of tulip cultivars assessed by SNP markers

Tang, Nan; Shahin, Arwa; Bijman, Paul; Liu, Jianjun; Tuyl, J.M. van; Arens, Paul

doi:10.1016/j.scienta.2013.07.016

Cited by 25 publications

(7 citation statements)

References 31 publications

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“…SNP markers were developed based on SNPs in expressed sequence tags as described by Shahin et al ( 2012 ), which have been subsequently validated in a random set of cultivars (Tang et al 2013 ). Marker names were based on the parent (KN or CA) showing the SNP variation followed by the contig number of the Tulip_All assembly as described by Shahin et al ( 2012 ).…”

Section: Methodsmentioning

confidence: 99%

Genetic mapping of resistance to Fusarium oxysporum f. sp. tulipae in tulip

et al. 2015

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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 markers on 27 linkage groups covering 1707 cM, while the map of “Cantata” comprised 300 markers on 21 linkage groups covering 1201 cM. Median distance between markers was 3.9 cM for “Kees Nelis” and 3.1 cM for “Cantata.” Six putative quantitative trait loci (QTLs) for Fusarium resistance were identified, derived from both parents. QTL2, QTL3, and QTL6 were significant in all disease tests. For the flanking markers of the QTLs, phenotypic means of the two allelic groups, segregating from a parent for such a marker, were significantly different. These markers will be useful for the development of MAS in tulip breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-015-0316-3) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Genetic mapping of resistance to Fusarium oxysporum f. sp. tulipae in tulip

et al. 2015

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“…Large-scale EST sequencing was recently conducted using NGS technology for both species from the Netherlands (Shahin et al, 2012b). The resulting data were applied for SNP discovery in lily and tulip (Shahin et al, 2012a;Tang et al, 2013).…”

Section: Lily and Tulipmentioning

confidence: 99%

Recent Progress in Genomic Analysis of Ornamental Plants, with a Focus on Carnation

Yagi

2015

The Hortic J

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Genomic analysis and marker-assisted selection have long been familiar terms. Nevertheless, compared with that on other horticultural crops, genome-related research on ornamentals has been delayed because of the polyploid nature and/or highly heterozygous genetic background of many such species. With the advent of next-generation sequencing (NGS) technology in recent years, however, the situation is changing. The acquisition of comprehensive transcriptome sequences using NGS technology has been conducted in major ornamentals, and whole-genome sequences have been generated for carnation. This review discusses recent progress in the genomic analysis of carnation, including the construction of an SSR-based reference genetic linkage map, QTL analysis of carnation bacterial wilt (CBW) resistance, and the development of tightly linked markers for CBW resistance and flower type. The current state of NGS technology-based genomic research is also summarized for other major ornamentals.

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“…Compared to traditional molecular markers, SNPs are abundant, stable, and easily detectable by sequencing technologies such as genotyping-bysequencing (GBS) even without a priori genome sequence information 13 . Thus, SNP markers have been widely used in genetic diversity assessments, molecular evolution studies, and genetic mapping for traits of interest in diverse horticultural crops such as carnation 14 , chrysanthemums 15 , roses 16 , lilies 17 , and tulips 18 .…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla

Wu¹,

Alexander

2020

Hortic Res

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Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea (Hydrangea macrophylla L.) and both are recessively inherited. Molecular marker-assisted selection (MAS) can greatly reduce the time necessary to breed cultivars with desired traits. In this study, a genome-wide association study (GWAS) using 5803 single-nucleotide polymorphisms (SNPs) was performed using a panel of 82 bigleaf hydrangea cultivars. One SNP locus (Hy_CAPS_Inflo) associated with inflorescence type was identified with general linear model (GLM) and mixed linear model (MLM) methods that explained 65.5% and 36.1% of the phenotypic variations, respectively. Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM. The SNP locus (Hy_CAPS_Inflo) was converted to a cleaved amplified polymorphic sequence (CAPS) marker that showed absolute identification accuracy (100%) of inflorescence type in a validation panel consisting of eighteen H. macrophylla cultivars. The SNP was investigated in 341 F 1 progenies using genotyping by sequencing (GBS) and co-segregated with inflorescence type (χ 2 = 0.12; P = 0.73). The SNP was subsequently used for breeding selection using kompetitive allele specific PCR (KASP) technology. Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed. The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy in H. macrophylla. The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.

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Genetic diversity and structure in a collection of tulip cultivars assessed by SNP markers

Cited by 25 publications

References 31 publications

Genetic mapping of resistance to Fusarium oxysporum f. sp. tulipae in tulip

Genetic mapping of resistance to Fusarium oxysporum f. sp. tulipae in tulip

Recent Progress in Genomic Analysis of Ornamental Plants, with a Focus on Carnation

Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla

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