Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley

Genome ◽  
2014 ◽  
Vol 57 (4) ◽  
pp. 239-244 ◽  
Author(s):  
Xifeng Ren ◽  
Yonggang Wang ◽  
Songxian Yan ◽  
Dongfa Sun ◽  
Genlou Sun
Keyword(s):  
Population Genetics ◽  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Hordeum Vulgare ◽  
Nucleotide Diversity ◽  
Wild Barley ◽  
Haplotype Diversity ◽  
Lateral Spikelet ◽  
Cultivated Barley ◽  
Barley Population

Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.

scholarly journals Genetic Variation and Population Genetics ofTaenia saginatain North and Northeast Thailand in relation toTaenia asiatica

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Malinee Anantaphruti ◽  
Urusa Thaenkham ◽  
Teera Kusolsuk ◽  
Wanna Maipanich ◽  
Surapol Saguankiat ◽  
...  
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Endangered Species ◽  
Selective Sweep ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
World Population ◽  
Taenia Saginata ◽  
Northeast Thailand ◽  
Haplotype A

Taenia saginatais the most common humanTaeniain Thailand. Bycox1sequences, 73 isolates from four localities in north and northeast were differentiated into 14 haplotypes, 11 variation sites and haplotype diversity of 0.683. Among 14 haplotypes, haplotype A was the major (52.1%), followed by haplotype B (21.9%). Clustering diagram of Thai and GenBank sequences indicated mixed phylogeny among localities. By MJ analysis, haplotype clustering relationships showed paired-stars-like network, having two main cores surrounded by minor haplotypes. Tajima’sDvalues were significantly negative inT. saginataworld population, suggesting population expansion. Significant Fu’sFsvalues in Thai, as well as world population, also indicate that population is expanding and may be hitchhiking as part of selective sweep. Haplotype B and its dispersion were only found in populations from Thailand. Haplotype B may evolve and ultimately become an ancestor of future populations in Thailand. Haplotype A seems to be dispersion haplotype, not just in Thailand, but worldwide. High geneticT. saginataintraspecies divergence was found, in contrast to its sister species,T. asiatica; among 30 samples from seven countries, its haplotype diversity was 0.067, while only 2 haplotypes were revealed. This extremely low intraspecific variation suggests thatT. asiaticacould be an endangered species.

A comparative analysis of genetic polymorphism in wild and cultivated barley from Tibet using isozyme and ribosomal DNA markers

Genome ◽  
1994 ◽  
Vol 37 (4) ◽  
pp. 631-638 ◽  
Author(s):  
Qifa Zhang ◽  
G. P. Yang ◽  
Xiankai Dai ◽  
J. Z. Sun
Keyword(s):  
Genetic Variation ◽  
Ribosomal Dna ◽  
Wild Barley ◽  
Length Variation ◽  
Spacer Length ◽  
Origin And Evolution ◽  
Centre Of Diversity ◽  
Esterase Loci ◽  
Cultivated Barley ◽  
Comparison Of The Results

This study was conducted to address some of the issues concerning the possible significance of Tibet in the origin and evolution of cultivated barley. A total of 1757 barley accessions from Tibet, including 1496 entries of Hordeum vulgare ssp. vulgare (HV), 229 entries of the six-rowed wild barley H. vulgare ssp. agriocrithon (HA), and 32 entries of the two-rowed wild barley H. vulgare ssp. spontaneum (HS), were assayed for allozymes at four esterase loci. A subsample of 491 accessions was surveyed for spacer-length polymorphism at two ribosomal DNA loci. Genetic variation is extensive in these barley groups, and the amount of genetic diversity in cultivated barley of this region is comparable with that of cultivated barley worldwide. The level of genetic variation of HA is significantly lower than the other two barley groups, and there is also substantial heterogeneity in the level of polymorphism among different agrigeographical subregions. However, little genetic differentiation was detected among the three barley groups (HV, HA, and HS), as well as among different agrigeographical subregions. Comparison of the results from this and previous studies indicated a strong differentiation between Oriental and Occidental barley, thus favoring the hypothesis of a diphyletic origin of cultivated barley.Key words: Hordeum, allozyme, rDNA spacer-length variation, centre of diversity, phylogeny.

scholarly journals Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

2018 ◽  
Vol 20 (1) ◽  
pp. 17-22
Author(s):  
TETY HARTATIK ◽  
DWI NUR HAPPY HARIYONO ◽  
YUDI ADINATA
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Cytochrome B Gene ◽  
Cyt B ◽  
Gene Sequences ◽  
Cattle Breeds ◽  
Cyt B Gene

Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22. Genetic diversity and phylogenetic relationships of two Indonesian local cattle breeds (Pasundan and Pacitan cattle) were investigated using mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene analysis. Partial sequences of cyt b gene, 404 bp in length, were determined for 21 individuals from the two breeds. Genetic diversity of the breeds was assessed based on the number of polymorphic sites, number of haplotypes, haplotype diversity, nucleotide diversity and average number of differences. In addition, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura’s two-parameter model. Among the two breeds, haplotype and nucleotide diversity of Pacitan cattle were the highest with values of 0.3778 and 0.00099, respectively. In contrast, Pasundan cattle had the lowest value for haplotype (0.1818) and nucleotide (0.00045) diversity. Four haplotypes (Hap_16, Hap_17, Hap_18 and Hap_19) were found across the two breeds and around 85.71% of investigated individuals were classified as Hap_16. Phylogenetic analysis with the inclusion of the cyt b sequences from 39 cattle breeds from Genbank database, showed that Indonesian cattle made a separated lineage together with Bos javanicus, B. bison, and B. bonasus. Pasundan and Pacitan cattle were considered from the same lineage based on haplotype distribution as well as phylogenetic analysis. This study may help the future researchers and livestock breeders for designing a breeding program based on a better understanding of the genetic diversity and history of local breeds.

Leaf scald resistance genes in Hordeum vulgare and Hordeum vulgare ssp. spontaneum: parallels between cultivated and wild barley

2003 ◽  
Vol 54 (12) ◽  
pp. 1335 ◽  
Author(s):  
R. K. Genger ◽  
K. J. Williams ◽  
H. Raman ◽  
B. J. Read ◽  
H. Wallwork ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Hordeum Vulgare ◽  
Wild Barley ◽  
Infection Type ◽  
Field Trials ◽  
Field Resistance ◽  
Adult Plant ◽  
Sources Of Resistance ◽  
Ssr Loci ◽  
Cultivated Barley

The prerequisite for breeding barley varieties with durable scald resistance is a diversity of genes each with molecular markers for their manipulation in crosses. Here we compare the outcomes of genetic analysis of scald resistance in 5 doubled haploid mapping populations of cultivated barley with 9 third-backcross families that derive from a set of diverse wild barley populations. In all cases, resistance was assessed as seedling infection type responses, but the Sloop/Halcyon population was also tested for adult plant resistance in field trials at two sites. In the latter case, the major quantitative trait locus for field resistance was coincident with that for seedling response on chromosome 3H. Most of the other cultivated barley sources of resistance in this study (1 cultivar and 3 breeders populations synthesised for resistance) also resolved to markers in the region of this 3H locus. In contrast, the genetic basis of resistance in wild barley populations resolved to at least 5 chromosome locations (1HS, 3H, 6HS, 7HL, and 7HS). Useful markers were of several kinds including proteins, isozymes, PCR based on RFLPs, AFLP, and SSR loci. Thus, wild barley increases the range of options for pyramid breeding and provides linked molecular markers that will be useful in manipulating those genes, or in the analysis of resistance in new sources.

scholarly journals Genetic diversity, haplotype analysis, and risk factor assessment of hepatitis a virus (HAV) isolates from the West Bank, Palestine during the period between 2014 and 2016

2020 ◽  
Author(s):  
Kamal Dumaidi ◽  
Hayah Qaraqe ◽  
Amer Al-Jawabreh ◽  
Rasmi Abu-Helu ◽  
Fekri Samarah ◽  
...  
Keyword(s):  
Risk Factors ◽  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Network Analysis ◽  
Nucleotide Diversity ◽  
Hepatitis A Virus ◽  
West Bank ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
The West

AbstractBackgroundHAV genotypes and its genetic diversity is rarely investigated in our region as well as worldwide.Aimsthe aims of the present study were to determine the HAV genotypes and its risk factors and to investigate the genetic diversity of the HAV isolates in the West bank, Palestine.Study designa cohort of 161 clinically and laboratory confirmed HAV (IgM-positive) cases and 170 IgM negative individuals from all the districts of the West Bank, Palestine during the period of 2014-2016 were tested for VP3/VP1 junction of the HAV genome using RT-PCR and sequence analysis. Phylogenetic analysis, genetic diversity and haplotypes analysis were used to characterize the VP3/VP1 sequences.ResultsOverall, all the 34 sequences of the HAV was found to be HAV-IB sub-genotype. The phylogenetic analysis showed four main clusters with cluster III exclusively consisting of 18 Palestinian isolates (18/23-78%) with weak bootstrap values. A high haplotype diversity (Hd) and low nucleotide diversity (π) were observed. Cluster III showed high number of haplotypes (h=8), but low haplotype (gene) diversity (Hd=0.69). A total of 28 active haplotypes with some consisting of more than one sequence were observed using haplotype network analysis. The Palestinian haplotypes are characterized by closely related viral haplotypes with one SNV away from each other which ran parallel to cluster III in the phylogenetic tree. A smaller Palestinian haplotype (4 isolates) was three SNVs away from the major haplotype cluster (n=10) and closer to haplotypes from Iran, Spain, and South Africa. Young age, low level of parent’s education, poor hand washing and drinking of un-treated water was considered the major HAV risk factors in the present study.ConclusionHAV-IB subgentype is endemic in Palestine. HAV showed low genetic variation and nucleotide diversity. Furthermore, haplotype network analysis revealed haplotype variation among the Palestinian sequences.

scholarly journals Transcriptome and Metabolite Insights Into Domestication Process of Cultivated Barley in China

2021 ◽  
Author(s):  
Yu Zhou ◽  
Guang Lu ◽  
Genlou Sun ◽  
Daokun Sun ◽  
Xifeng Ren
Keyword(s):  
Wild Barley ◽  
Near East ◽  
Tibetan Wild Barley ◽  
Fertile Crescent ◽  
Important Intermediate ◽  
Domestication Process ◽  
Cultivated Barley ◽  
Two Stages ◽  
Barley Population ◽  
Comprehensive Study

Abstract Background Barley is one of the earliest domesticated crops and regarded as one of the founder of Neolithic transition in the Near East Fertile Crescent. Domestication process of cultivated barley (especially east-Asian cultivated barley) has been under debate because of the controversial origin centers of barley, which caused by widely dispersal of wild barley. What’s more, no comprehensive study regarding alteration in metabolism during domestication has been delineated in barley so far. Results Transcriptomic and non-targeted metabolic analyses were performed for two wild barley populations (wild barley of Near East Fertile Crescent (Wb-NE), and wild barley of Tibetan Plateau (Wb-T)), and one cultivated barley population (cultivated barley of China (Cb-C)), the results revealed two stages of the domestication process of Cb-C, first from Wb-NE to Wb-T, and then from Wb-T to Cb-C. The Wb-T played an important intermediate role in the domestication from Wb-NE to Cb-C, and had made more genetic contribution than Wb-NE to Cb-C. Meanwhile, we found continuous gene flow, a large number of selective genes and metabolites during domestication. Divergent metabolites of alkaloids and phenylpropanoids were specific targeted in stages from Wb-NE to Wb-T and from Wb-T to Cb-C, respectively. The key missense SNPs in genes HORVU6Hr1G027650 and HORVU4Hr1G072150 might be related to the divergence of metabolites of alkaloids and phenylpropanoids during domestication. Conclusions Our results revealed that two stages of the domestication process of Cb-C, and distinct sets of metabolites were targeted by selection during the evolution from wild barley of the Near East Fertile Crescent to Tibetan wild barley to cultivated barley of China. Our findings not only provided genetic and metabolic insights into domestication process of barley but also highlighted the power of combining omics data for trait dissection.

scholarly journals Single Nucleotide Polymorphisms in the Promoter of CYP19 Gene in Cattle Bred in Iraq

2020 ◽  
Vol 33 (1) ◽  
pp. 89-97
Author(s):  
Salah H. Faraj ◽  
Asaad Y. Ayied ◽  
Khalaf A. H. Al-Rishdy
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Diversity ◽  
Animal Species ◽  
Haplotype Diversity ◽  
Evolutionary Relationship ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cyp19 Gene

The present study was undertaken to characterize the genetic diversity of the aromatase cytochrome P450 (CYP19) gene in 34 cows (15 local, 14 Holstein, and 5 Crosses) in Iraq. The objectives of the present study are to detect SNPs (mutations) in promoter p1.1 of the CYP19 gene in cattle bred in Iraq using sequencing techniques. We identified five single-nucleotide polymorphisms (SNP) loci of the CYP19 gene that were detected, namely G933T, G994C, A1044G, A1062T, and C1468A. The results showed the presence of 3, 4, and 2 polymorphic sites leading to the construction of 4, 5, and 3 different haplotypes for Holstein, local, and crosses respectively. Haplotype diversity were 0.791, 0.752, and 0.700 respectively. While nucleotide diversity was 0.0017, 0.0022, and 0.0013 respectively. Besides, we carried out a phylogenetic analysis of these sequences to address the evolutionary relationship between the animal species. These fragments were assigned in the GenBank database under the accession numbers: LC490756, LC490757, LC491437, LC491438, LC491439, LC491588, and LC491589.

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