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.

Short-term salt tolerance mechanisms in differentially salt tolerant tomato species

1999 ◽  
Vol 37 (1) ◽  
pp. 65-71 ◽  
Author(s):  
Ana Santa-Cruz ◽  
Manuel Acosta ◽  
Ana Rus ◽  
Maria C. Bolarin
Keyword(s):  
Salt Tolerance ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Short Term ◽  
Tomato Species

148 Multiple Dysregulated Novel Pathways and Genes in Aleutian Mink Disease Revealed by Selection Signatures and Gene Network Analyses Using Whole-genome Sequence Data

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 76-76
Author(s):  
Seyed Milad Vahedi ◽  
Karim Karimi ◽  
Siavash Salek Ardestani ◽  
Younes Miar
Keyword(s):  
Sequence Data ◽  
American Mink ◽  
Enrichment Analysis ◽  
Whole Genome Sequence ◽  
Fixation Index ◽  
Pathway Enrichment Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Network Analyses ◽  
Genome Level

Abstract Aleutian disease (AD) is a chronic persistent infection in domestic mink caused by Aleutian mink disease virus (AMDV). Female mink’s fertility and pelt quality depression are the main reasons for the AD’s negative economic impacts on the mink industry. A total number of 79 American mink from the Canadian Center for Fur Animal Research at Dalhousie University (Truro, NS, Canada) were classified based on the results of counter immunoelectrophoresis (CIEP) tests into two groups of positive (n = 48) and negative (n = 31). Whole-genome sequences comprising 4,176 scaffolds and 8,039,737 single nucleotide polymorphisms (SNPs) were used to trace the selection footprints for response to AMDV infection at the genome level. Window-based fixation index (Fst) and nucleotide diversity (θπ) statistics were estimated to compare positive and negative animals’ genomes. The overlapped top 1% genomic windows between two statistics were considered as potential regions underlying selection pressures. A total of 98 genomic regions harboring 33 candidate genes were detected as selective signals. Most of the identified genes were involved in the development and functions of immune system (PPP3CA, SMAP2, TNFRSF21, SKIL, and AKIRIN2), musculoskeletal system (COL9A2, PPP1R9A, ANK2, AKAP9, and STRIT1), nervous system (ASCL1, ZFP69B, SLC25A27, MCF2, and SLC7A14), reproductive system (CAMK2D, GJB7, SSMEM1, C6orf163), liver (PAH and DPYD), and lung (SLC35A1). Gene-expression network analysis showed the interactions among 27 identified genes. Moreover, pathway enrichment analysis of the constructed genes network revealed significant oxytocin (KEGG: hsa04921) and GnRH signaling (KEGG: hsa04912) pathways, which are likely to be impaired by AMDV leading to dams’ fecundity reduction. These results provided a perspective to the genetic architecture of response to AD in American mink and novel insight into the pathogenesis of AMDV.

scholarly journals Molecular response of canola to salt stress: insights on tolerance mechanisms

2018 ◽  
Author(s):  
Reza Shokri-Gharelo ◽  
Pouya Motie-Noparvar
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Edible Oils ◽  
Biodiesel Fuel ◽  
Molecular Response ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Brassica Napus L ◽  
Salt Response ◽  
The Many

Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests where researchers should focus future studies.

scholarly journals Advances and Challenges in the Breeding of Salt-Tolerant Rice

2020 ◽  
Vol 21 (21) ◽  
pp. 8385
Author(s):  
Hua Qin ◽  
Yuxiang Li ◽  
Rongfeng Huang
Keyword(s):  
Food Security ◽  
Salt Tolerance ◽  
Quantitative Trait ◽  
Molecular Mechanisms ◽  
Soil Salinization ◽  
Ecological Environment ◽  
Salt Tolerant ◽  
Salt Stress Tolerance ◽  
Rice Varieties ◽  
Salt Susceptible

Soil salinization and a degraded ecological environment are challenging agricultural productivity and food security. Rice (Oryza sativa), the staple food of much of the world’s population, is categorized as a salt-susceptible crop. Improving the salt tolerance of rice would increase the potential of saline-alkali land and ensure food security. Salt tolerance is a complex quantitative trait. Biotechnological efforts to improve the salt tolerance of rice hinge on a detailed understanding of the molecular mechanisms underlying salt stress tolerance. In this review, we summarize progress in the breeding of salt-tolerant rice and in the mapping and cloning of genes and quantitative trait loci (QTLs) associated with salt tolerance in rice. Furthermore, we describe biotechnological tools that can be used to cultivate salt-tolerant rice, providing a reference for efforts aimed at rapidly and precisely cultivating salt-tolerance rice varieties.

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

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 Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies potential targets of allele-specific immunity to clinical malaria

2020 ◽  
Author(s):  
Zalak Shah ◽  
Myo T Naung ◽  
Kara A Moser ◽  
Matthew Adams ◽  
Andrea G Buchwald ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Sequence Data ◽  
Clinical Malaria ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Multiple Alleles ◽  
Vaccine Candidates ◽  
Genome Wide ◽  
Allele Specific

Individuals acquire immunity to clinical malaria after repeated Plasmodium falciparum infections. This immunity to disease is thought to reflect the acquisition of a repertoire of responses to multiple alleles in diverse parasite antigens. In previous studies, we identified polymorphic sites within individual antigens that are associated with parasite immune evasion by examining antigen allele dynamics in individuals followed longitudinally. Here we expand this approach by analyzing genome-wide polymorphisms using whole genome sequence data from 140 parasite isolates representing malaria cases from a longitudinal study in Malawi and identify 25 genes that encode likely targets of naturally acquired immunity and that should be further characterized for their potential as vaccine candidates.

scholarly journals Population-level genome-wide STR typing in Plasmodium species reveals higher resolution population structure and genetic diversity relative to SNP typing

2021 ◽  
Author(s):  
Jiru Han ◽  
Jacob E Munro ◽  
Anthony Kocoski ◽  
Alyssa E Barry ◽  
Melanie Bahlo
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
Tandem Repeats ◽  
Plasmodium Species ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genome Wide ◽  
Field Samples

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been made available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).

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