scholarly journals Genome-wide DNA polymorphisms in low Phosphate tolerant and sensitive rice genotypes

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Poonam Mehra ◽  
Bipin K. Pandey ◽  
Jitender Giri
Keyword(s):  
Dna Polymorphisms ◽  
Genome Wide ◽  
Rice Genotypes

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.

scholarly journals Identification of genome-wide single-nucleotide polymorphisms among geographically diverse radish accessions

DNA Research ◽  
2020 ◽  
Vol 27 (1) ◽  
Author(s):  
Hiroto Kobayashi ◽  
Kenta Shirasawa ◽  
Nobuko Fukino ◽  
Hideki Hirakawa ◽  
Takashi Akanuma ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Southeast Asia ◽  
East Asia ◽  
Near East ◽  
Dna Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
South And Southeast Asia ◽  
Snp Data ◽  
Genome Wide

Abstract Radish (Raphanus sativus L.) is cultivated around the world as a vegetable crop and exhibits diverse morphological and physiological features. DNA polymorphisms are responsible for differences in traits among cultivars. In this study, we determined genome-wide single-nucleotide polymorphisms (SNPs) among geographically diverse radish accessions using the double-digest restriction site-associated DNA sequencing (ddRAD-Seq) method. A total of 52,559 SNPs was identified in a collection of over 500 radish accessions (cultivated and wild) from East Asia, South and Southeast Asia, and the Occident and Near East. In addition, 2,624 SNP sites without missing data (referred to as common SNP sites) were identified among 510 accessions. Genetic diversity analyses, based on the common SNP sites, divided the cultivated radish accessions into four main groups, each derived from four geographical areas (Japan, East Asia, South and Southeast Asia, and the Occident and Near East). Furthermore, we discuss the origin of cultivated radish and its migration from the West to East Asia. SNP data generated in this work will facilitate further genetic studies on the radish breeding and production of DNA markers.

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 two cultivars of mei (Prunus mume sieb. et zucc.)

BMC Genetics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 98 ◽  
Author(s):  
Lidan Sun ◽  
Qixiang Zhang ◽  
Zongda Xu ◽  
Weiru Yang ◽  
Yu Guo ◽  
...  
Keyword(s):  
Dna Polymorphisms ◽  
Prunus Mume ◽  
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.

Studying genome-wide DNA polymorphisms to understand Magnaporthe-rice interactions

2011 ◽  
Vol 40 (4) ◽  
pp. 328-334 ◽  
Author(s):  
Ryohei Terauchi ◽  
Kentaro Yoshida ◽  
Hiromasa Saitoh ◽  
Hiroyuki Kanzaki ◽  
Yudai Okuyama ◽  
...  
Keyword(s):  
Dna Polymorphisms ◽  
Genome Wide
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