Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing
Among the genus Actinidia, Actinidia arguta possesses the strongest cold resistance and produces fresh fruit with an intense flavor. To investigate genomic variation that may contribute to variation in phenotypic traits, we performed whole-genome re-sequencing of four A. arguta genotypes originating...
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| creator | Lin, Miaomiao Fang, Jinbao Hu, Chungen Qi, Xiujuan Sun, Shihang Chen, Jinyong Sun, Leiming Zhong, Yunpeng |
| description | Among the genus Actinidia, Actinidia arguta possesses the strongest cold resistance and produces fresh fruit with an intense flavor. To investigate genomic variation that may contribute to variation in phenotypic traits, we performed whole-genome re-sequencing of four A. arguta genotypes originating from different regions in China and identified the polymorphisms using InDel markers. In total, 4,710,650, 4,787,750, 4,646,026, and 4,590,616 SNPs and 1,481,002, 1,534,198, 1,471,304, and 1,425,393 InDels were detected in the 'Ruby-3', 'Yongfeng male', 'Kuilv male', and 'Hongbei male' genomes, respectively, compared with the reference genome sequence of cv 'Hongyang'. A subset of 120 InDels were selected for re-sequencing validation. Additionally, genes related to non-synonymous SNPs and InDels in coding domain sequences were screened for functional analysis. The analysis of GO and KEGG showed that genes involved in cellular responses to water deprivation, sucrose transport, decreased oxygen levels and plant hormone signal transduction were significantly enriched in A. arguta. The results of this study provide insight into the genomic variation of kiwifruit and can inform future research on molecular breeding to improve cold resistance in kiwifruit. |
| doi_str_mv | 10.1371/journal.pone.0219884 |
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To investigate genomic variation that may contribute to variation in phenotypic traits, we performed whole-genome re-sequencing of four A. arguta genotypes originating from different regions in China and identified the polymorphisms using InDel markers. In total, 4,710,650, 4,787,750, 4,646,026, and 4,590,616 SNPs and 1,481,002, 1,534,198, 1,471,304, and 1,425,393 InDels were detected in the 'Ruby-3', 'Yongfeng male', 'Kuilv male', and 'Hongbei male' genomes, respectively, compared with the reference genome sequence of cv 'Hongyang'. A subset of 120 InDels were selected for re-sequencing validation. Additionally, genes related to non-synonymous SNPs and InDels in coding domain sequences were screened for functional analysis. The analysis of GO and KEGG showed that genes involved in cellular responses to water deprivation, sucrose transport, decreased oxygen levels and plant hormone signal transduction were significantly enriched in A. arguta. The results of this study provide insight into the genomic variation of kiwifruit and can inform future research on molecular breeding to improve cold resistance in kiwifruit.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0219884</identifier><identifier>PMID: 32275655</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Actinidia ; Actinidia arguta ; Biology and Life Sciences ; Breeding ; Cold ; Cold resistance ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Electrolytes ; Engineering and Technology ; Flavor ; Fruits ; Functional analysis ; Gene sequencing ; Genes ; Genomes ; Genotype & phenotype ; Genotypes ; Germplasm ; Horticulture ; Kiwifruit ; Low temperature resistance ; MicroRNAs ; Nucleotide sequence ; Oxygen ; Oxygen enrichment ; Phenotypic variations ; Plant hormones ; Research and Analysis Methods ; Signal transduction ; Single-nucleotide polymorphism ; Sucrose ; Sugar ; Water deprivation</subject><ispartof>PloS one, 2020-04, Vol.15 (4), p.e0219884-e0219884</ispartof><rights>2020 Lin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020 Lin et al 2020 Lin et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-d6ac591c7df898c3cda9bf15d88dc8c07b0725c78cdb788fbacca98e1c0e6ffb3</citedby><cites>FETCH-LOGICAL-c526t-d6ac591c7df898c3cda9bf15d88dc8c07b0725c78cdb788fbacca98e1c0e6ffb3</cites><orcidid>0000-0002-5318-7476</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147731/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147731/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32275655$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Causse, Mathilde</contributor><creatorcontrib>Lin, Miaomiao</creatorcontrib><creatorcontrib>Fang, Jinbao</creatorcontrib><creatorcontrib>Hu, Chungen</creatorcontrib><creatorcontrib>Qi, Xiujuan</creatorcontrib><creatorcontrib>Sun, Shihang</creatorcontrib><creatorcontrib>Chen, Jinyong</creatorcontrib><creatorcontrib>Sun, Leiming</creatorcontrib><creatorcontrib>Zhong, Yunpeng</creatorcontrib><title>Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Among the genus Actinidia, Actinidia arguta possesses the strongest cold resistance and produces fresh fruit with an intense flavor. To investigate genomic variation that may contribute to variation in phenotypic traits, we performed whole-genome re-sequencing of four A. arguta genotypes originating from different regions in China and identified the polymorphisms using InDel markers. In total, 4,710,650, 4,787,750, 4,646,026, and 4,590,616 SNPs and 1,481,002, 1,534,198, 1,471,304, and 1,425,393 InDels were detected in the 'Ruby-3', 'Yongfeng male', 'Kuilv male', and 'Hongbei male' genomes, respectively, compared with the reference genome sequence of cv 'Hongyang'. A subset of 120 InDels were selected for re-sequencing validation. Additionally, genes related to non-synonymous SNPs and InDels in coding domain sequences were screened for functional analysis. The analysis of GO and KEGG showed that genes involved in cellular responses to water deprivation, sucrose transport, decreased oxygen levels and plant hormone signal transduction were significantly enriched in A. arguta. The results of this study provide insight into the genomic variation of kiwifruit and can inform future research on molecular breeding to improve cold resistance in kiwifruit.</description><subject>Actinidia</subject><subject>Actinidia arguta</subject><subject>Biology and Life Sciences</subject><subject>Breeding</subject><subject>Cold</subject><subject>Cold resistance</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Electrolytes</subject><subject>Engineering and Technology</subject><subject>Flavor</subject><subject>Fruits</subject><subject>Functional analysis</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Germplasm</subject><subject>Horticulture</subject><subject>Kiwifruit</subject><subject>Low temperature resistance</subject><subject>MicroRNAs</subject><subject>Nucleotide sequence</subject><subject>Oxygen</subject><subject>Oxygen enrichment</subject><subject>Phenotypic variations</subject><subject>Plant hormones</subject><subject>Research and Analysis Methods</subject><subject>Signal transduction</subject><subject>Single-nucleotide polymorphism</subject><subject>Sucrose</subject><subject>Sugar</subject><subject>Water 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DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing</title><author>Lin, Miaomiao ; Fang, Jinbao ; Hu, Chungen ; Qi, Xiujuan ; Sun, Shihang ; Chen, Jinyong ; Sun, Leiming ; Zhong, Yunpeng</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-d6ac591c7df898c3cda9bf15d88dc8c07b0725c78cdb788fbacca98e1c0e6ffb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Actinidia</topic><topic>Actinidia arguta</topic><topic>Biology and Life Sciences</topic><topic>Breeding</topic><topic>Cold</topic><topic>Cold resistance</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>Electrolytes</topic><topic>Engineering and Technology</topic><topic>Flavor</topic><topic>Fruits</topic><topic>Functional analysis</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genomes</topic><topic>Genotype & phenotype</topic><topic>Genotypes</topic><topic>Germplasm</topic><topic>Horticulture</topic><topic>Kiwifruit</topic><topic>Low temperature resistance</topic><topic>MicroRNAs</topic><topic>Nucleotide sequence</topic><topic>Oxygen</topic><topic>Oxygen enrichment</topic><topic>Phenotypic variations</topic><topic>Plant hormones</topic><topic>Research and Analysis Methods</topic><topic>Signal transduction</topic><topic>Single-nucleotide polymorphism</topic><topic>Sucrose</topic><topic>Sugar</topic><topic>Water deprivation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lin, Miaomiao</creatorcontrib><creatorcontrib>Fang, Jinbao</creatorcontrib><creatorcontrib>Hu, Chungen</creatorcontrib><creatorcontrib>Qi, Xiujuan</creatorcontrib><creatorcontrib>Sun, Shihang</creatorcontrib><creatorcontrib>Chen, Jinyong</creatorcontrib><creatorcontrib>Sun, Leiming</creatorcontrib><creatorcontrib>Zhong, 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One</addtitle><date>2020-04-10</date><risdate>2020</risdate><volume>15</volume><issue>4</issue><spage>e0219884</spage><epage>e0219884</epage><pages>e0219884-e0219884</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Among the genus Actinidia, Actinidia arguta possesses the strongest cold resistance and produces fresh fruit with an intense flavor. To investigate genomic variation that may contribute to variation in phenotypic traits, we performed whole-genome re-sequencing of four A. arguta genotypes originating from different regions in China and identified the polymorphisms using InDel markers. In total, 4,710,650, 4,787,750, 4,646,026, and 4,590,616 SNPs and 1,481,002, 1,534,198, 1,471,304, and 1,425,393 InDels were detected in the 'Ruby-3', 'Yongfeng male', 'Kuilv male', and 'Hongbei male' genomes, respectively, compared with the reference genome sequence of cv 'Hongyang'. A subset of 120 InDels were selected for re-sequencing validation. Additionally, genes related to non-synonymous SNPs and InDels in coding domain sequences were screened for functional analysis. The analysis of GO and KEGG showed that genes involved in cellular responses to water deprivation, sucrose transport, decreased oxygen levels and plant hormone signal transduction were significantly enriched in A. arguta. The results of this study provide insight into the genomic variation of kiwifruit and can inform future research on molecular breeding to improve cold resistance in kiwifruit.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>32275655</pmid><doi>10.1371/journal.pone.0219884</doi><orcidid>https://orcid.org/0000-0002-5318-7476</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Actinidia Actinidia arguta Biology and Life Sciences Breeding Cold Cold resistance Deoxyribonucleic acid DNA DNA sequencing Electrolytes Engineering and Technology Flavor Fruits Functional analysis Gene sequencing Genes Genomes Genotype & phenotype Genotypes Germplasm Horticulture Kiwifruit Low temperature resistance MicroRNAs Nucleotide sequence Oxygen Oxygen enrichment Phenotypic variations Plant hormones Research and Analysis Methods Signal transduction Single-nucleotide polymorphism Sucrose Sugar Water deprivation |
| title | Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing |
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