Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification.
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| Title: | Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification. |
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| Authors: | Metcalfe, Cushla J.1 (AUTHOR), Li, Jingchuan1 (AUTHOR), Zheng, Bangyou1 (AUTHOR), Stiller, Jiri1 (AUTHOR), Healey, Adam2 (AUTHOR), Piperidis, Nathalie3 (AUTHOR), Aitken, Karen S.1 (AUTHOR) karen.aitken@csiro.au |
| Source: | Theoretical & Applied Genetics. Apr2022, Vol. 135 Issue 4, p1279-1292. 14p. |
| Subjects: | Chromosomes, Single nucleotide polymorphisms, Whole genome sequencing, Genomes, In situ hybridization, Wheat genetics |
| Geographic Terms: | Australia |
| Abstract: | Key message: This manuscript describes the identification, isolation and sequencing of a single chromosome containing high value resistance genes from a complex polyploid where sequencing the whole genome is too costly. The large complex genomes of many crops constrain the use of new technologies for genome-assisted selection and genetic improvement. One method to simplify a genome is to break it into individual chromosomes by flow cytometry; however, in many crop species most chromosomes cannot be isolated individually. Flow sorting of a single copy of a chromosome has been developed in wheat, and here we demonstrate its use to identify markers of interest in an Erianthus/Sacchurum hybrid. Erianthus/Saccharum hybrids are of interest because Erianthus is known to be highly resistant to soil borne diseases which cause extensive sugarcane yield losses in Australia. Sugarcane (Saccharum) cultivars are autopolyploids with a highly complex genome and over 100 chromosomes. Flow cytometry for sugarcane, as in most crops, does not resolve individual chromosomes to a karyotype peak for sorting. To isolate a single chromosome, we used genomic in situ hybridization (GISH) to identify the flow karyotype region containing the Erianthus chromosomes, flow sorted single chromosomes from this region, PCR screened for the Erianthus chromosomes and sequenced them. One Erianthus chromosome amplified and sequenced well, and from this data we could identify 57 resistant type genes and SNPs in nearly half of these genes. We developed KASP SNP assays and demonstrated that the identified SNP markers segregated as expected in a small introgression population. The pipeline we developed here to flow sort and sequence single chromosomes could be used in any crop with a large complex genome to rapidly discover and develop markers to important loci. [ABSTRACT FROM AUTHOR] |
| Copyright of Theoretical & Applied Genetics is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
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| Header | DbId: egs DbLabel: Engineering Source An: 156504198 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Metcalfe%2C+Cushla+J%2E%22">Metcalfe, Cushla J.</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Li%2C+Jingchuan%22">Li, Jingchuan</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Zheng%2C+Bangyou%22">Zheng, Bangyou</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Stiller%2C+Jiri%22">Stiller, Jiri</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Healey%2C+Adam%22">Healey, Adam</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Piperidis%2C+Nathalie%22">Piperidis, Nathalie</searchLink><relatesTo>3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Aitken%2C+Karen+S%2E%22">Aitken, Karen S.</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> karen.aitken@csiro.au</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Theoretical+%26+Applied+Genetics%22">Theoretical & Applied Genetics</searchLink>. Apr2022, Vol. 135 Issue 4, p1279-1292. 14p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Chromosomes%22">Chromosomes</searchLink><br /><searchLink fieldCode="DE" term="%22Single+nucleotide+polymorphisms%22">Single nucleotide polymorphisms</searchLink><br /><searchLink fieldCode="DE" term="%22Whole+genome+sequencing%22">Whole genome sequencing</searchLink><br /><searchLink fieldCode="DE" term="%22Genomes%22">Genomes</searchLink><br /><searchLink fieldCode="DE" term="%22In+situ+hybridization%22">In situ hybridization</searchLink><br /><searchLink fieldCode="DE" term="%22Wheat+genetics%22">Wheat genetics</searchLink> – Name: SubjectGeographic Label: Geographic Terms Group: Su Data: <searchLink fieldCode="DE" term="%22Australia%22">Australia</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Key message: This manuscript describes the identification, isolation and sequencing of a single chromosome containing high value resistance genes from a complex polyploid where sequencing the whole genome is too costly. The large complex genomes of many crops constrain the use of new technologies for genome-assisted selection and genetic improvement. One method to simplify a genome is to break it into individual chromosomes by flow cytometry; however, in many crop species most chromosomes cannot be isolated individually. Flow sorting of a single copy of a chromosome has been developed in wheat, and here we demonstrate its use to identify markers of interest in an Erianthus/Sacchurum hybrid. Erianthus/Saccharum hybrids are of interest because Erianthus is known to be highly resistant to soil borne diseases which cause extensive sugarcane yield losses in Australia. Sugarcane (Saccharum) cultivars are autopolyploids with a highly complex genome and over 100 chromosomes. Flow cytometry for sugarcane, as in most crops, does not resolve individual chromosomes to a karyotype peak for sorting. To isolate a single chromosome, we used genomic in situ hybridization (GISH) to identify the flow karyotype region containing the Erianthus chromosomes, flow sorted single chromosomes from this region, PCR screened for the Erianthus chromosomes and sequenced them. One Erianthus chromosome amplified and sequenced well, and from this data we could identify 57 resistant type genes and SNPs in nearly half of these genes. We developed KASP SNP assays and demonstrated that the identified SNP markers segregated as expected in a small introgression population. The pipeline we developed here to flow sort and sequence single chromosomes could be used in any crop with a large complex genome to rapidly discover and develop markers to important loci. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Theoretical & Applied Genetics is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
| PLink | https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=156504198 |
| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1007/s00122-022-04030-1 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 14 StartPage: 1279 Subjects: – SubjectFull: Chromosomes Type: general – SubjectFull: Single nucleotide polymorphisms Type: general – SubjectFull: Whole genome sequencing Type: general – SubjectFull: Genomes Type: general – SubjectFull: In situ hybridization Type: general – SubjectFull: Wheat genetics Type: general – SubjectFull: Australia Type: general Titles: – TitleFull: Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Metcalfe, Cushla J. – PersonEntity: Name: NameFull: Li, Jingchuan – PersonEntity: Name: NameFull: Zheng, Bangyou – PersonEntity: Name: NameFull: Stiller, Jiri – PersonEntity: Name: NameFull: Healey, Adam – PersonEntity: Name: NameFull: Piperidis, Nathalie – PersonEntity: Name: NameFull: Aitken, Karen S. IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 04 Text: Apr2022 Type: published Y: 2022 Identifiers: – Type: issn-print Value: 00405752 Numbering: – Type: volume Value: 135 – Type: issue Value: 4 Titles: – TitleFull: Theoretical & Applied Genetics Type: main |
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