QTL examination of a bi-parental mapping population segregating for “short-stature” in hop (Humulus lupulus L.)

Henning, Jimmy C.; Hill, Steven T.; Darby, Peter; Hendrix, David A.

doi:10.1007/s10681-017-1848-x

Cited by 11 publications

(11 citation statements)

References 27 publications

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“…Plant material, DNA extraction, library prep, sequencing, and identification of SNP markers for developing a linkage map were previously reported (Henning, Hill, Darby, & Hendrix, 2017b) except for using the draft haplotype‐phased assembly as reference genome. Over one million SNPs were identified across 660 unique genotypes, including both cultivars and USDA experimental varieties.…”

Section: Methodsmentioning

confidence: 99%

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A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome

et al. 2021

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Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing and contain compounds of therapeutic interest including xanthohumol. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large (2.8 Gb), repetitive, and heterozygous genome of hop. We present a draft haplotype‐phased assembly of the Cascade cultivar genome. Our draft assembly and annotation of the Cascade genome is the most extensive representation of the hop genome to date. PacBio long‐read sequences from hop were assembled with FALCON and partially phased with FALCON‐Unzip. Comparative analysis of haplotype sequences provides insight into selective pressures that have driven evolution in hop. We discovered genes with greater sequence divergence enriched for stress‐response, growth, and flowering functions in the draft phased assembly. With improved resolution of long terminal retrotransposons (LTRs) due to long‐read sequencing, we found that hop is over 70% repetitive. We identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze the draft phased assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

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Section: Methodsmentioning

confidence: 99%

“…Estimation of a linkage map for a dwarf mapping population followed the same process as previously reported (Henning et al., 2017b). Approximately 13,000 highly‐filtered markers were identified.…”

Section: Methodsmentioning

confidence: 99%

A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome

et al. 2021

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“…We estimated a linkage map using dwarf mapping population [52] containing 2,871 SNP markers across 10 linkage groups (Figure 3a). Using the linkage groups, we mapped associate contigs, heterozygosity, SNP, gene, and LTR density to ordered primary contigs to visualize large-scale structural patterns and variation (Figure 3b).…”

Section: Resultsmentioning

confidence: 99%

“…Plant material, DNA extraction, library prep, sequencing, and identification of SNP markers for developing a linkage map were previously reported [52] except for using the haplotype-phased assembly as reference genome. Over one million SNPs were identified across 660 unique genotypes, including both cultivars and USDA experimental varieties.…”

Section: Methodsmentioning

confidence: 99%

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A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

Padgitt-Cobb

Kingan

Wells

et al. 2019

Preprint

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Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing, and around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

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The 4R QTLs pollen fertility restoration in triticale with CMS Triticum timopheevii

et al. 2022

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The Triticum timopheevii Zhuk. (Tt) cytoplasm is the most exploited cytoplasmic male sterility (CMS) type used in triticale in commercial seed production of hybrid varieties. The present study established a recombinant inbred line (RIL) mapping population to identify genetic loci controlling fertility restoration in triticale with CMS Tt. The trait was evaluated via phenotyping the BC 1 F 1 materials originating from a backcross of maternal line MS 112(15)-2-1 (on CMS Tt) and RILs. A genetic map spanning 2293 cM over 21 linkage groups was constructed using 1,170 single nucleotide polymorphisms and silico diversity array technology (DArT) markers generated through DArTseq genotyping. Two quantitative trait loci (QTL) controlling fertility restoration were localized at the 4RL chromosome. They were stable during two vegetative seasons and, depending on the year, explained 17.8 to 37.5 (QRft-4R.1) and 17.8 to 27.1% (QRft-4R.2) of phenotypic variance. Bioinformatic analysis was performed to predict genes potentially responsible for the trait. Four markers linked to the trait were successfully converted into a polymerase chain reaction-based assay to select the pollen fertility QTLs easily. The exact position of QTLs detected previously in the rye and here in the triticale suggests that the same loci might control the trait.

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QTL examination of a bi-parental mapping population segregating for “short-stature” in hop (Humulus lupulus L.)

Cited by 11 publications

References 27 publications

A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome

A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome

A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

The 4R QTLs pollen fertility restoration in triticale with CMS Triticum timopheevii

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