Genomic Variation in Korean <i>japonica</i> Rice Varieties

Next-generation sequencing technologies have enabled the discovery of numerous sequence variations among closely related crop varieties. We analyzed genome resequencing data from 24 Korean temperate <i>japonica</i> rice varieties and discovered 954,233 sequence variations, including 791,...

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Autores principales:	Hyeonso Ji, Yunji Shin, Chaewon Lee, Hyoja Oh, In Sun Yoon, Jeongho Baek, Young-Soon Cha, Gang-Seob Lee, Song Lim Kim, Kyung-Hwan Kim
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>japonica</i> InDel marker resequencing rice SNP Genetics QH426-470
Acceso en línea:	https://doaj.org/article/aa80d5f7dcab4c5c876187a59724c868
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spelling	oai:doaj.org-article:aa80d5f7dcab4c5c876187a59724c8682021-11-25T17:41:30ZGenomic Variation in Korean <i>japonica</i> Rice Varieties10.3390/genes121117492073-4425https://doaj.org/article/aa80d5f7dcab4c5c876187a59724c8682021-10-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1749https://doaj.org/toc/2073-4425Next-generation sequencing technologies have enabled the discovery of numerous sequence variations among closely related crop varieties. We analyzed genome resequencing data from 24 Korean temperate <i>japonica</i> rice varieties and discovered 954,233 sequence variations, including 791,121 single nucleotide polymorphisms (SNPs) and 163,112 insertions/deletions (InDels). On average, there was one variant per 391 base-pairs (bp), a variant density of 2.6 per 1 kbp. Of the InDels, 10,860 were longer than 20 bp, which enabled conversion to markers resolvable on an agarose gel. The effect of each variant on gene function was predicted using the SnpEff program. The variants were categorized into four groups according to their impact: high, moderate, low, and modifier. These groups contained 3524 (0.4%), 27,656 (2.9%), 24,875 (2.6%), and 898,178 (94.1%) variants, respectively. To test the accuracy of these data, eight InDels from a pre-harvest sprouting resistance QTL (<i>qPHS11</i>) target region, four highly polymorphic InDels, and four functional sequence variations in known agronomically important genes were selected and successfully developed into markers. These results will be useful to develop markers for marker-assisted selection, to select candidate genes in map-based cloning, and to produce efficient high-throughput genome-wide genotyping systems for Korean temperate <i>japonica</i> rice varieties.Hyeonso JiYunji ShinChaewon LeeHyoja OhIn Sun YoonJeongho BaekYoung-Soon ChaGang-Seob LeeSong Lim KimKyung-Hwan KimMDPI AGarticle<i>japonica</i>InDelmarkerresequencingriceSNPGeneticsQH426-470ENGenes, Vol 12, Iss 1749, p 1749 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>japonica</i> InDel marker resequencing rice SNP Genetics QH426-470
spellingShingle	<i>japonica</i> InDel marker resequencing rice SNP Genetics QH426-470 Hyeonso Ji Yunji Shin Chaewon Lee Hyoja Oh In Sun Yoon Jeongho Baek Young-Soon Cha Gang-Seob Lee Song Lim Kim Kyung-Hwan Kim Genomic Variation in Korean <i>japonica</i> Rice Varieties
description	Next-generation sequencing technologies have enabled the discovery of numerous sequence variations among closely related crop varieties. We analyzed genome resequencing data from 24 Korean temperate <i>japonica</i> rice varieties and discovered 954,233 sequence variations, including 791,121 single nucleotide polymorphisms (SNPs) and 163,112 insertions/deletions (InDels). On average, there was one variant per 391 base-pairs (bp), a variant density of 2.6 per 1 kbp. Of the InDels, 10,860 were longer than 20 bp, which enabled conversion to markers resolvable on an agarose gel. The effect of each variant on gene function was predicted using the SnpEff program. The variants were categorized into four groups according to their impact: high, moderate, low, and modifier. These groups contained 3524 (0.4%), 27,656 (2.9%), 24,875 (2.6%), and 898,178 (94.1%) variants, respectively. To test the accuracy of these data, eight InDels from a pre-harvest sprouting resistance QTL (<i>qPHS11</i>) target region, four highly polymorphic InDels, and four functional sequence variations in known agronomically important genes were selected and successfully developed into markers. These results will be useful to develop markers for marker-assisted selection, to select candidate genes in map-based cloning, and to produce efficient high-throughput genome-wide genotyping systems for Korean temperate <i>japonica</i> rice varieties.
format	article
author	Hyeonso Ji Yunji Shin Chaewon Lee Hyoja Oh In Sun Yoon Jeongho Baek Young-Soon Cha Gang-Seob Lee Song Lim Kim Kyung-Hwan Kim
author_facet	Hyeonso Ji Yunji Shin Chaewon Lee Hyoja Oh In Sun Yoon Jeongho Baek Young-Soon Cha Gang-Seob Lee Song Lim Kim Kyung-Hwan Kim
author_sort	Hyeonso Ji
title	Genomic Variation in Korean <i>japonica</i> Rice Varieties
title_short	Genomic Variation in Korean <i>japonica</i> Rice Varieties
title_full	Genomic Variation in Korean <i>japonica</i> Rice Varieties
title_fullStr	Genomic Variation in Korean <i>japonica</i> Rice Varieties
title_full_unstemmed	Genomic Variation in Korean <i>japonica</i> Rice Varieties
title_sort	genomic variation in korean <i>japonica</i> rice varieties
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/aa80d5f7dcab4c5c876187a59724c868
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Genomic Variation in Korean <i>japonica</i> Rice Varieties

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