scholarly journals Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

2019 ◽  
Author(s):  
Yongfu Tao ◽  
Barbara George-Jaeggli ◽  
Marie Bouteille-Pallas ◽  
Shuaishuai Tai ◽  
Alan Cruickshank ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Gene Family ◽  
Sequence Data ◽  
Allelic Variation ◽  
Balancing Selection ◽  
Allelic Diversity ◽  
Gene Families ◽  
Photosynthetic Pathway ◽  
Sorghum Bicolor L

Abstract Background C 4 photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C 4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C 3 and C 4 species have elucidated the genetic diversity underpinning the C 4 photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C 4 crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Results Here, we present the first genetic diversity survey of 8 known C 4 gene families in an important C 4 crop, Sorghum bicolor (L.) Moench using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C 4 gene families varied more than 20-fold from the NADP-MDH gene family (θπ =0.2×10 -3 ) to the PPDK gene family (θπ = 5.21×10 -3 ). Genetic diversity of C 4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C 4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C 4 PPDK and CA genes, and balancing selection signals on C 4 PPDK-RP and PEPC genes. Allelic distribution of these C 4 genes was consistent with selection signals detected. Conclusions Domestication of sorghum has reshaped diversity of C 4 pathway. A better understanding of the genetic diversity of this pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.

scholarly journals Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

2019 ◽  
Author(s):  
Yongfu Tao ◽  
Barbara George-Jaeggli ◽  
Marie Bouteille-Pallas ◽  
Shuaishuai Tai ◽  
Alan Cruickshank ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Gene Family ◽  
C4 Photosynthesis ◽  
Allelic Variation ◽  
Balancing Selection ◽  
Allelic Diversity ◽  
Gene Families ◽  
Photosynthetic Pathway ◽  
Sorghum Bicolor L

Abstract Background C4 photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C3 and C4 species have elucidated the genetic diversity underpinning the C4 photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C4 crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Results Here, we present the first genetic diversity survey of 8 known C4 gene families in an important C4 crop, Sorghum bicolor (L.) Moench using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C4 gene families varied more than 20-fold from the NADP-MDH gene family (θπ =0.2×10-3) to the PPDK gene family (θπ = 5.21×10-3). Genetic diversity of C4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C4 PPDK and CA genes, and balancing selection signals on C4 PPDK-RP and PEPC genes. Allelic distribution of these C4 genes was consistent with selection signals detected.Conclusions Domestication of sorghum has reshaped diversity of C4 pathway. A better understanding of the genetic diversity of this pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.

scholarly journals Genetic Diversity of C4 Photosynthesis Pathway Genes in Sorghum bicolor (L.)

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 806
Author(s):  
Yongfu Tao ◽  
Barbara George-Jaeggli ◽  
Marie Bouteillé-Pallas ◽  
Shuaishuai Tai ◽  
Alan Cruickshank ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Gene Family ◽  
C4 Photosynthesis ◽  
Balancing Selection ◽  
Regulatory Protein ◽  
Allelic Diversity ◽  
Gene Families ◽  
Photosynthetic Pathway ◽  
Sorghum Bicolor L

C4 photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C3 and C4 species have elucidated the genetic diversity underpinning the C4 photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C4 crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Here, we present the first genetic diversity survey of 8 known C4 gene families in an important C4 crop, Sorghum bicolor (L.) Moench, using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C4 gene families varied more than 20-fold from the NADP-malate dehydrogenase (MDH) gene family (θπ = 0.2 × 10−3) to the pyruvate orthophosphate dikinase (PPDK) gene family (θπ = 5.21 × 10−3). Genetic diversity of C4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C4 PPDK and carbonic anhydrase (CA) genes, and balancing selection signals on C4 PPDK-regulatory protein (RP) and phosphoenolpyruvate carboxylase (PEPC) genes. Allelic distribution of these C4 genes was consistent with selection signals detected. A better understanding of the genetic diversity of C4 pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.

RFLP-based assay of Sorghum bicolor (L.) Moench genetic diversity

1995 ◽  
Vol 90 (6) ◽  
pp. 787-796 ◽  
Author(s):  
Y. X. Cui ◽  
G. W. Xu ◽  
C. W. Magill ◽  
K. F. Schertz ◽  
G. E. Hart
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Sorghum Bicolor L

scholarly journals Genetic diversity in sorghum (Sorghum bicolor L. Moench)

2006 ◽  
Vol 2 (2) ◽  
pp. 6
Author(s):  
K. Mohanraj ◽  
A. Gopalan ◽  
M. Shanmuganathan
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Sorghum Bicolor L

scholarly journals Genetic diversity in some Ghanaian and Malian sorghum [Sorghum bicolor (L) Moench] accessions using SSR markers

2019 ◽  
Vol 18 (27) ◽  
pp. 591-602
Author(s):  
Danquah Andrews ◽  
K. A. Galyuon Isaac ◽  
P. Otwe Emmanuel ◽  
K. A. Asante Daniel
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Ssr Markers ◽  
Sorghum Bicolor L

scholarly journals Population genetic analysis of the Plasmodium falciparum circumsporozoite protein in two distinct ecological regions in Ghana

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Elikplim A. Amegashie ◽  
Lucas Amenga-Etego ◽  
Courage Adobor ◽  
Peter Ogoti ◽  
Kevin Mbogo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Sequence Data ◽  
Balancing Selection ◽  
Population Expansion ◽  
Circumsporozoite Protein ◽  
Cape Coast ◽  
Population Genetic Analysis ◽  
Coastal Belt ◽  
Tajima’S D

Abstract Background Extensive genetic diversity in the Plasmodium falciparum circumsporozoite protein (PfCSP) is a major contributing factor to the moderate efficacy of the RTS,S/AS01 vaccine. The transmission intensity and rates of recombination within and between populations influence the extent of its genetic diversity. Understanding the extent and dynamics of PfCSP genetic diversity in different transmission settings will help to interpret the results of current RTS,S efficacy and Phase IV implementation trials conducted within and between populations in malaria-endemic areas such as Ghana. Methods Pfcsp sequences were retrieved from the Illumina-generated paired-end short-read sequences of 101 and 131 malaria samples from children aged 6–59 months presenting with clinical malaria at health facilities in Cape Coast (in the coastal belt) and Navrongo (Guinea savannah region), respectively, in Ghana. The sequences were mapped onto the 3D7 reference strain genome to yield high-quality genome-wide coding sequence data. Following data filtering and quality checks to remove missing data, 220 sequences were retained and analysed for the allele frequency spectrum, genetic diversity both within the host and between populations and signatures of selection. Population genetics tools were used to determine the extent and dynamics of Pfcsp diversity in P. falciparum from the two geographically distinct locations in Ghana. Results Pfcsp showed extensive diversity at the two sites, with the higher transmission site, Navrongo, exhibiting higher within-host and population-level diversity. The vaccine strain C-terminal epitope of Pfcsp was found in only 5.9% and 45.7% of the Navrongo and Cape Coast sequences, respectively. Between 1 and 6 amino acid variations were observed in the TH2R and TH3R epitope regions of PfCSP. Tajima’s D was negatively skewed, especially for the population from Cape Coast, given the expected historical population expansion. In contrast, a positive Tajima’s D was observed for the Navrongo P. falciparum population, consistent with balancing selection acting on the immuno-dominant TH2R and TH3R vaccine epitopes. Conclusion The low frequencies of the Pfcsp vaccine haplotype in the analysed populations indicate a need for additional molecular and immuno-epidemiological studies with broader temporal and geographic sampling in endemic populations targeted for RTS,S application. These results have implications for the efficacy of the vaccine in Ghana and will inform the choice of alleles to be included in future multivalent or chimeric vaccines.

Genetic Diversity and Heritability Characters Associated in Sweet Sorghum [Sorghum bicolor (L.) Moench]

Sugar Tech ◽  
2013 ◽  
Vol 16 (2) ◽  
pp. 200-210 ◽  
Author(s):  
M. Elangovan ◽  
P. Kiran babu ◽  
N. Seetharama ◽  
J. V. Patil
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Sweet Sorghum ◽  
Sorghum Bicolor L

scholarly journals Population Genetic Analysis of Plasmodium falciparum Circumsporozoite Protein in Two Distinct Ecological Regions in Ghana

2020 ◽  
Author(s):  
Elikplim A Amegashie ◽  
Lucas Amenga-Etego ◽  
Courage Adobor ◽  
Peter Ogoti ◽  
Kevin Mbogo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Sequence Data ◽  
Balancing Selection ◽  
Population Expansion ◽  
Circumsporozoite Protein ◽  
Cape Coast ◽  
Population Genetic Analysis ◽  
Coastal Belt ◽  
Tajima’S D

Abstract Background Extensive genetic diversity in the Plasmodium falciparum circumsporozoite protein (PfCSP) is a major contributing factor to the moderate efficacy of the RTS,S/AS01 vaccine. The transmission intensity and rates of recombination within and between populations influence the extent of its genetic diversity. Understanding the extent and dynamics of PfCSP genetic diversity in different transmission settings will help to interpret the results of current RTS,S efficacy and Phase IV implementation trials conducted within and between populations in malaria-endemic areas such as Ghana. Methods Pfcsp sequences were retrieved from the Illumina-generated paired-end short-read sequences of 101 and 131 malaria samples from children aged 6-59 months presenting with clinical malaria at health facilities in Cape Coast (in the coastal belt) and Navrongo (Guinea savannah region), respectively, in Ghana. The sequences were mapped onto the 3D7 reference strain genome to yield high-quality genome-wide coding sequence data. Following data filtering and quality checks to remove missing data, 220 sequences were retained and analysed for the allele frequency spectrum, genetic diversity both within the host and between populations and signatures of selection. Population genetics tools were used to determine the extent and dynamics of Pfcsp diversity in P. falciparum from the two geographically distinct locations in Ghana. Results Pfcsp showed extensive diversity at the two sites, with the higher transmission site, Navrongo, exhibiting higher within-host and population-level diversity. The vaccine strain C-terminal epitope of Pfcsp was found in only 5.9% and 45.7% of the Navrongo and Cape Coast sequences, respectively. Between 1 and 6 amino acid variations were observed in the TH2R and TH3R epitope regions of PfCSP. Tajima’s D was negatively skewed, especially for the population from Cape Coast, given the expected historical population expansion. In contrast, a positive Tajima’s D was observed for the Navrongo P. falciparum population, consistent with balancing selection acting on the immuno-dominant TH2R and TH3R vaccine epitopes. Conclusion The low frequencies of the Pfcsp vaccine haplotype in the analysed populations indicate a need for additional molecular and immuno-epidemiological studies with broader temporal and geographic sampling in endemic populations targeted for RTS,S application. These results have implications for the efficacy of the vaccine in Ghana and will inform the choice of alleles to be included in future multivalent or chimeric vaccines.

A CRISPR/Cas9-based strategy to simultaneously inactivate the entire ALS gene family in Candida orthopsilosis

2019 ◽  
Vol 14 (16) ◽  
pp. 1383-1396 ◽  
Author(s):  
Marina Zoppo ◽  
Mariagrazia Di Luca ◽  
Santiago N Villarreal ◽  
Noemi Poma ◽  
M Inmaculada Barrasa ◽  
...  
Keyword(s):  
Gene Family ◽  
Sequence Data ◽  
Gene Families ◽  
Opportunistic Pathogen ◽  
Phenotypic Characterization ◽  
Nucleotide Sequence Data ◽  
Solid Media ◽  
One Step ◽  
Repair Template ◽  
Candida Orthopsilosis

Aim: In this study, the CRISPR gene-editing approach was used to simultaneously inactivate all three members of the ALS gene family in the opportunistic pathogen Candida orthopsilosis. Materials & methods: Using a single gRNA and repair template, CRISPR-edited clones were successfully generated in a one-step process in both C. orthopsilosis reference and clinical strains. Results: The phenotypic characterization of the ALS triple-edited strains revealed no impact on growth in liquid or solid media. However, pseudohyphal formation and the ability to adhere to human buccal epithelial cells were significantly decreased in triple-edited clones. Conclusion: Our CRISPR/Cas9 system is a powerful tool for simultaneous editing of fungal gene families, which greatly accelerates the generation of multiple gene-edited Candida strains. Data deposition: Nucleotide sequence data are available in the GenBank databases under the accession numbers MK875971, MK875972, MK875973, MK875974, MK875975, MK875976, MK875977.

Sign in / Sign up

Export Citation Format

Share Document