scholarly journals The Selection of Gamma-Ray Irradiated Higher Yield Rice Mutants by Directed Evolution Method

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1004
Author(s):  
Hiroshi Kato ◽  
Feng Li ◽  
Akemi Shimizu
Keyword(s):  
Directed Evolution ◽  
Gamma Ray ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
High Yielding Variety ◽  
Novel Approach ◽  
Yield Trials ◽  
Selection Of ◽  
Plot Design

We have succeeded in selecting four higher yield mutants from five gamma-ray irradiated high-yielding Japanese rice varieties using a novel approach. A total of 464 M2 plants which had heavier total panicle weights per plant were first selected from 9801 irradiated M2 plants. Their higher yields were confirmed by yield trials conducted for three years with a six to ten-pairwise replicated plot design. FukuhibikiH6 and FukuhibikiH8 were selected from an irradiated high-yielding variety Fukuhibiki and showed 1.2% to 22.5% higher yield than their original significantly. YamadawaraH3 was selected from an irradiated high-yielding variety Yamadawara and its yield advantages were 2.7% to 3.9%. However, there was no difference in the genotypes of the 96 SNP (single nucleotide polymorphism) markers between the higher yield mutants and their respective original varieties. The differences in the measured phenotypical traits between each mutant and its original variety were not constant and the actual differences were marginal. Therefore, the higher yields of the selected mutants were likely to have been caused by physiological traits rather than phenotypical traits. The selection method used in this study is an application of the directed evolution method which has long been commonly used in the substantial improvements of microorganisms and their proteins.

scholarly journals Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 705
Author(s):  
John Carlos I. Ignacio ◽  
Maricris Zaidem ◽  
Carlos Casal ◽  
Shalabh Dixit ◽  
Tobias Kretzschmar ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
Genotyping Platform ◽  
Anaerobic Germination ◽  
Direct Seeded ◽  
Mapping By Sequencing ◽  
Simple Sequence

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.

scholarly journals Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers

2020 ◽  
Vol 56 (No. 2) ◽  
pp. 62-70 ◽  
Author(s):  
Shahril Ab Razak ◽  
Nor Helwa Ezzah Nor Azman ◽  
Rahiniza Kamaruzaman ◽  
Shamsul Amri Saidon ◽  
Muhammad Fairuz Mohd Yusof ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Crop Improvement ◽  
Snp Markers ◽  
Group Method ◽  
Chromosome 11 ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
K Value

Understanding genetic diversity is a main key for crop improvement and genetic resource management. In this study, we aim to evaluate the genetic diversity of the released Malaysian rice varieties using single nucleotide polymorphism (SNP) markers. A total of 46 released Malaysian rice varieties were genotyped using 1536 SNP markers to evaluate their diversity. Out of 1536 SNPs, only 932 SNPs (60.7%) represented high quality alleles, whereas the remainder either failed to amplify or had low call rates across the samples. Analysis of the 932 SNPs revealed that a total of 16 SNPs were monomorphic. The analysis of the SNPs per chromosome revealed that the average of the polymorphic information content (PIC) value ranged from 0.173 for chromosome 12 to 0.259 for chromosome 11, with an average of 0.213 per locus. The genetic analysis of the 46 released Malaysian rice varieties using an unweighted pair group method with arithmetic mean (UPGMA) dendrogram revealed the presence of two major groups. The analysis was supported by the findings from the STRUCTURE analysis which indicated the ∆K value to be at the highest peak at K = 2, followed by K = 4. The pairwise genetic distance of the shared alleles showed that the value ranged from 0.000 (MR159–MR167) to 0.723 (MRIA–Setanjung), which suggested that MR159 and MR167 were identical, and that the highest dissimilarity was detected between MRIA 1 and Setanjung. The results of the study will be very useful for the variety identification, the proper management and conservation of the genetic resources, and the exploitation and utilisation in future breeding programmes.

scholarly journals HAHap: a read-based haplotyping method using hierarchical assembly

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5852
Author(s):  
Yu-Yu Lin ◽  
Ping Chun Wu ◽  
Pei-Lung Chen ◽  
Yen-Jen Oyang ◽  
Chien-Yu Chen
Keyword(s):  
Simulated Data ◽  
Real Data ◽  
Error Rates ◽  
Lower Number ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Hierarchical Assembly ◽  
Sequencing Technologies ◽  
Error Corrections ◽  
Selection Of

Background The need for read-based phasing arises with advances in sequencing technologies. The minimum error correction (MEC) approach is the primary trend to resolve haplotypes by reducing conflicts in a single nucleotide polymorphism-fragment matrix. However, it is frequently observed that the solution with the optimal MEC might not be the real haplotypes, due to the fact that MEC methods consider all positions together and sometimes the conflicts in noisy regions might mislead the selection of corrections. To tackle this problem, we present a hierarchical assembly-based method designed to progressively resolve local conflicts. Results This study presents HAHap, a new phasing algorithm based on hierarchical assembly. HAHap leverages high-confident variant pairs to build haplotypes progressively. The phasing results by HAHap on both real and simulated data, compared to other MEC-based methods, revealed better phasing error rates for constructing haplotypes using short reads from whole-genome sequencing. We compared the number of error corrections (ECs) on real data with other methods, and it reveals the ability of HAHap to predict haplotypes with a lower number of ECs. We also used simulated data to investigate the behavior of HAHap under different sequencing conditions, highlighting the applicability of HAHap in certain situations.

Reproductive technologies and genomic selection in dairy cattle

2014 ◽  
Vol 26 (1) ◽  
pp. 12 ◽  
Author(s):  
C. Ponsart ◽  
D. Le Bourhis ◽  
H. Knijn ◽  
S. Fritz ◽  
C. Guyader-Joly ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Genomic Selection ◽  
Reproductive Technologies ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Preimplantation Stage ◽  
Genomic Tools ◽  
Dna Production ◽  
New Strategies ◽  
Selection Of

Genomic tools are now available for most livestock species and are used routinely for genomic selection (GS) in cattle. One of the most important developments resulting from the introduction of genomic testing for dairy cattle is the application of reasonably priced low-density single nucleotide polymorphism technology in the selection of females. In this context, combining genome testing and reproductive biotechnologies in young heifers enables new strategies to generate replacement and elite females in a given period of time. Moreover, multiple markers have been detected in biopsies of preimplantation stage embryos, thus paving the way to develop new strategies based on preimplantation diagnosis and the genetic screening of embryos. Based on recent advances in GS, the present review focuses on new possibilities inherent in reproductive technologies used for commercial purposes and in genetic schemes, possible side effects and beneficial impacts on reproductive efficiency. A particular focus is on the different steps allowing embryo genotyping, including embryo micromanipulation, DNA production and quality assessment.

scholarly journals Effects of single nucleotide polymorphism ascertainment on population structure inferences

2021 ◽  
Author(s):  
Kotaro Dokan ◽  
Sayu Kawamura ◽  
Kosuke M Teshima
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Natural Populations ◽  
Snp Markers ◽  
Ascertainment Bias ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Frequency Spectra ◽  
Single Nucleotide ◽  
Selection Of

Abstract Single nucleotide polymorphism (SNP) data are widely used in research on natural populations. Although they are useful, SNP genotyping data are known to contain bias, normally referred to as ascertainment bias, because they are conditioned by already confirmed variants. This bias is introduced during the genotyping process, including the selection of populations for novel SNP discovery and the number of individuals involved in the discovery panel and selection of SNP markers. It is widely recognized that ascertainment bias can cause inaccurate inferences in population genetics and several methods to address these bias issues have been proposed. However, especially in natural populations, it is not always possible to apply an ideal ascertainment scheme because natural populations tend to have complex structures and histories. In addition, it was not fully assessed if ascertainment bias has the same effect on different types of population structure. Here we examine the effects of bias produced during the selection of population for SNP discovery and consequent SNP marker selection processes under three demographic models: the island, stepping-stone, and population split models. Results show that site frequency spectra and summary statistics contain biases that depend on the joint effect of population structure and ascertainment schemes. Additionally, population structure inferences are also affected by ascertainment bias. Based on these results, it is recommended to evaluate the validity of the ascertainment strategy prior to the actual typing process because the direction and extent of ascertainment bias vary depending on several factors.

scholarly journals Single nucleotide polymorphism MTHFR677C>T and the severity of metabolic side effects of antipsychotics in patients with schizophrenia: the results of a pilot study

2018 ◽  
pp. 40-46
Author(s):  
M. A. Kosataya ◽  
A. V. Marina ◽  
A. V. Sergeeva ◽  
T. V. Zhilyaeva ◽  
A. S. Blagonravova ◽  
...  
Keyword(s):  
Side Effects ◽  
Genetic Risk ◽  
Fasting Blood Glucose ◽  
Fasting Blood Glucose Level ◽  
Nucleotide Polymorphism ◽  
Chronic Patients ◽  
Single Nucleotide ◽  
The Metabolic Syndrome ◽  
Metabolic Side Effects ◽  
Selection Of

To predict the development of side effects and personalized selection of drug therapy, it seems relevant to study the association of individual genetic risk factors with undesirable side effects of antipsychotics in chronic patients with schizophrenia. Thereby the purpose of this study was to evaluate the association between the carriage of the T-allele of the single nucleotide genetic polymorphism MTHFR677C>T and the severity of the metabolic side effects of antipsychotics. As a result of the study a greater risk of developing components of the metabolic syndrome was revealed, as well as a significantly higher fasting blood glucose level in the group of carriers of the minor T-allele of polymorphism MTHFR677C>T.

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