Genome resequencing, improvement of variant calling, and population genomic analyses provide insights into the seedlessness in the genus Vitis = 유전체 재분석, 변이 호출의 개선, 및 집단유전분석은 포도속에서 무핵성에 대한 통찰력을 제공한다

Cited 3 time in scopus
Metadata Downloads

Full metadata record

DC FieldValueLanguage
dc.contributor.authorMyung-Shin Kim-
dc.contributor.authorY Y Hur-
dc.contributor.authorJi Hong Kim-
dc.contributor.authorSoon-Chun Jeong-
dc.date.accessioned2020-09-24T04:09:49Z-
dc.date.available2020-09-24T04:09:49Z-
dc.date.issued2020-
dc.identifier.issn2160-1836-
dc.identifier.urihttps://oak.kribb.re.kr/handle/201005/22807-
dc.description.abstractThe seedlessness of grape derived from stenospermocarpy is one of the most prized traits of table or raisin grapes. It is controlled by a complex genetic system containing one dominant gene and multiple recessive genes. Here, we collected dense variation data from high-depth resequencing data of seeded, seedless, and wild relative grape genomes sequenced to > 37x mean depth. Variant calls were made using a modified variant calling pipeline that was suitable for highly diverse interspecific grape accessions. The modified pipeline enabled us to call several million more variants than the commonly recommended pipeline. The quality was validated by Sanger sequencing data and subsequently supported by the genetic population structure and the phylogenetic tree constructed using the obtained variation data, results of which were generally consistent with known pedigree and taxonomic classifications. Variation data enabled us to confirm a dominant gene and identify recessive loci for seedlessness. Incidentally, we found that grape cultivar Rizamat contains an ancestral chromosomal region of the dominant gene in Sultanina, a predominant seedlessness donor cultivar. Furthermore, we predicted new candidate causal genes including Vitvi01g00455, Vitvi08g01528, and Vitvi18g01237 associated with the recessive seedless-regulating loci, which showed high homology with genes that regulate seed development in Arabidopsis This study provides fundamental insights relevant to variant calling from genome resequencing data of diverse interspecific hybrid germplasms such as grape and will accelerate future efforts aimed at crop improvement.-
dc.publisherGenetics Society America-
dc.titleGenome resequencing, improvement of variant calling, and population genomic analyses provide insights into the seedlessness in the genus Vitis = 유전체 재분석, 변이 호출의 개선, 및 집단유전분석은 포도속에서 무핵성에 대한 통찰력을 제공한다-
dc.title.alternativeGenome resequencing, improvement of variant calling, and population genomic analyses provide insights into the seedlessness in the genus Vitis-
dc.typeArticle-
dc.citation.titleG3-Genes Genomes Genetics-
dc.citation.number9-
dc.citation.endPage3377-
dc.citation.startPage3365-
dc.citation.volume10-
dc.contributor.affiliatedAuthorMyung-Shin Kim-
dc.contributor.affiliatedAuthorJi Hong Kim-
dc.contributor.affiliatedAuthorSoon-Chun Jeong-
dc.contributor.alternativeName김명신-
dc.contributor.alternativeName허윤영-
dc.contributor.alternativeName김지홍-
dc.contributor.alternativeName정순천-
dc.identifier.bibliographicCitationG3-Genes Genomes Genetics, vol. 10, no. 9, pp. 3365-3377-
dc.identifier.doi10.1534/g3.120.401521-
dc.subject.keywordGrape-
dc.subject.keywordresequencing-
dc.subject.keywordseedless-
dc.subject.keywordvariant calling-
dc.subject.keywordVitis vinifera-
dc.subject.localGrape-
dc.subject.localgrape-
dc.subject.localResequencing-
dc.subject.localresequencing-
dc.subject.localRe-sequencing-
dc.subject.localre-sequencing-
dc.subject.localseedless-
dc.subject.localvariant calling-
dc.subject.localVitis vinifera-
dc.description.journalClassY-
Appears in Collections:
Division of Bio Technology Innovation > Bio-Evaluation Center > 1. Journal Articles
Ochang Branch Institute > 1. Journal Articles
Files in This Item:
  • There are no files associated with this item.


Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.