Genome-wide DNA polymorphisms of Citrus unshiu Marc. cv. Miyagawa-wase cultivated in different regions based on whole-genome re-sequencing

2021 ◽  
Author(s):  
Chang-Ho Eun ◽  
In-Jung Kim
Keyword(s):  
Dna Polymorphisms ◽  
Citrus Unshiu ◽  
Whole Genome ◽  
Genome Wide

scholarly journals Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Prasanta K. Subudhi ◽  
Rama Shankar ◽  
Mukesh Jain
Keyword(s):  
Salt Tolerance ◽  
Dna Polymorphisms ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Rice Varieties ◽  
Genome Wide ◽  
Rice Genotypes ◽  
Genome Level

AbstractSalinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. Since few studies focused on the genome level variation in rice genotypes with contrasting response to salt stress, genomic resequencing in diverse genetic materials is needed to elucidate the molecular basis of salt tolerance mechanisms. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt sensitive (Bengal, Cocodrie, and IR64) rice genotypes were analyzed. A total of 413 million reads were generated with a mean genome coverage of 93% and mean sequencing depth of 18X. Analysis of the DNA polymorphisms revealed that 2347 nonsynonymous SNPs and 51 frameshift mutations could differentiate the salt tolerant from the salt sensitive genotypes. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions. These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. The genome-wide DNA polymorphisms and the promising candidate genes identified in this study represent a valuable resource for molecular breeding of salt tolerant rice varieties.

Genome-wide DNA polymorphisms in eliteindicarice inbreds discovered by whole-genome sequencing

2012 ◽  
Vol 10 (6) ◽  
pp. 623-634 ◽  
Author(s):  
Gopala K. Subbaiyan ◽  
Daniel L. E. Waters ◽  
Sanjay K. Katiyar ◽  
Ajanahalli R. Sadananda ◽  
Satyadev Vaddadi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Dna Polymorphisms ◽  
Whole Genome ◽  
Genome Wide

scholarly journals Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing

2019 ◽  
Author(s):  
Miaomiao Lin ◽  
Jinbao Fang ◽  
Chungen Hu ◽  
Xiujuan Qi ◽  
Shihang Sun ◽  
...  
Keyword(s):  
Cold Resistance ◽  
Genomic Variation ◽  
Dna Polymorphisms ◽  
Future Research ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Sucrose Transport ◽  
Actinidia Arguta ◽  
Genome Wide ◽  
Insight Into

AbstractAmong 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 ‘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.

scholarly journals Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing

PLoS ONE ◽  
2020 ◽  
Vol 15 (4) ◽  
pp. e0219884
Author(s):  
Miaomiao Lin ◽  
Jinbao Fang ◽  
Chungen Hu ◽  
Xiujuan Qi ◽  
Shihang Sun ◽  
...  
Keyword(s):  
Dna Polymorphisms ◽  
Whole Genome ◽  
Actinidia Arguta ◽  
Genome Wide

scholarly journals Discovery of Genome-Wide DNA Polymorphisms in a Landrace Cultivar of Japonica Rice by Whole-Genome Sequencing

2011 ◽  
Vol 52 (2) ◽  
pp. 274-282 ◽  
Author(s):  
Yuko Arai-Kichise ◽  
Yuh Shiwa ◽  
Hideki Nagasaki ◽  
Kaworu Ebana ◽  
Hirofumi Yoshikawa ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Dna Polymorphisms ◽  
Japonica Rice ◽  
Whole Genome ◽  
Genome Wide

scholarly journals A curated dataset of modern and ancient high-coverage shotgun human genomes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Pierpaolo Maisano Delser ◽  
Eppie R. Jones ◽  
Anahit Hovhannisyan ◽  
Lara Cassidy ◽  
Ron Pinhasi ◽  
...  
Keyword(s):  
Sequence Data ◽  
Whole Genome ◽  
Reference Dataset ◽  
High Coverage ◽  
Sample Distribution ◽  
Human Samples ◽  
Human Genomes ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Computationally Intensive

AbstractOver the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10–18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.

scholarly journals Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Gabriel Costa Monteiro Moreira ◽  
Clarissa Boschiero ◽  
Aline Silva Mello Cesar ◽  
James M. Reecy ◽  
Thaís Fernanda Godoy ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Association Studies ◽  
Fat Deposition ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Genome Wide
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