Huma Saleem | University of Agriculture, Faisalabad, Pakistan (original) (raw)

Papers by Huma Saleem

Research paper thumbnail of Wild Cotton Genepool: An Unopened Treasure

Wild Germplasm for Genetic Improvement in Crop Plants, 2021

Abstract The genus Gossypium is comprised of more than 50 genetically diverse species with differ... more Abstract The genus Gossypium is comprised of more than 50 genetically diverse species with different origins and ploidy levels. Each of cultivated and wild species is a source of unique alleles to improve cotton crop under ever increasing fiber demand and rapidly evolving climatic factors. Formerly, most of the improvement has been made in cotton germplasm by utilizing the genetic diversity of only cultivated types of species. The plenty of examples are reported for the utilization of wild cotton species in plant breeding despite of the fact of proven to be a novel genetic resource. The major hindrance was the transfer of genetic material which is now easier as compared to past due to advancement of gene transfer methods and technologies. Therefore, the conservation and utilization of cotton wild germplasm have gained much importance and is now become imperative to sustain the yield and quality of cotton fibers. This chapter highlights the background and potential of wild species of cotton to improve yield, quality, and adaptability of modern cultivars.

Research paper thumbnail of Morphological Differences and Molecular Characterization of Begomoviruses in Progeny to Row Trials of Okra (Abelmoschusesculentus L.)

Journal of Environmental and Agricultural Sciences, 2014

Ninety five okra genotypes were evaluated for morphological differences and yellow vein mosaic vi... more Ninety five okra genotypes were evaluated for morphological differences and yellow vein mosaic virus (YVMV) occurrence in progeny to row trials. Principal component analysis (PCA) was executed to obtain more reliable information. A high degree of diversity was found among okra genotypes for qualitative and quantitative characters. Distance of each variable with respect to PC1 and PC2 showed the contribution of this variable in the variation of germplasm. PCA analysis showed that inter-nodal distance, plant height at maturity, days to first flowering and 100-seed weight are the most important descriptors for variation. For the identification of Begomovirus, the putative viruses were cloned in plasmid and the respective plasmids were restricted by appropriate restriction enzyme. The phylogenetic analysis established that the partial DNA-A resemble to the CLCuMuV-[PK:Fai:Okra:13]. Which is actually a cotton infecting virus and closely resemble to the BYVMV-[IN:Har:05].

Research paper thumbnail of Identification of the Viral Determinant of Hypovirulence and Host Range in Sclerotiniaceae of a Genomovirus Reconstructed from the Plant Metagenome

Journal of Virology, 2021

Little is known about the exact host range of widespread genomoviruses. The genome of soybean lea... more Little is known about the exact host range of widespread genomoviruses. The genome of soybean leaf-associated gemygorvirus-1 (SlaGemV-1) was originally assembled from a metagenomic/metatranscriptomic study without known hosts.

Research paper thumbnail of Molecular Screening of Cotton Germplasm for Cotton Leaf Curl Disease Causedby Viral Strains

International Journal of Agriculture and Biology, 2017

Cotton crop is infected by single stranded DNA viruses (Family, Geminiviridae) in Pakistan. Due t... more Cotton crop is infected by single stranded DNA viruses (Family, Geminiviridae) in Pakistan. Due to changing global climate, which favors the whitefly (insect vector) growth and reproduction, the spread of cotton leaf curl disease is increasing at an alarming rate. Various approaches are being used to diagnose the ssDNA viruses in cotton. One step PCR protocol was established to identify the three viruses, namely cotton leaf curl Multan virus (CLCuMuV), Burewala strain of Kokhran virus (CLCuKo-Bur) and cotton leaf curl Kokhran virus (CLCuKoV). Thirty eight genotypes were screened on the basis of symptoms and molecular diagnosis. Out of 38 genotypes, 13 were positive for CLCuMuV, 24 were positive for Burewala strain and one was positive for both CLCuMuV and CLCuKoV-Bur strain. However, none of the samples was positives for cotton leaf curl Kokhran virus. Our experiments have established one step guide PCR for screening of cotton germplasm for major cotton infecting viruses. This diagnostic assay will promote the breeding programs for the development of resistant cotton varieties against cotton leaf curl disease (CLCuD) in Pakistan.

Research paper thumbnail of Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses

PLOS ONE, 2016

The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analy... more The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analysis of available sequence data determined that there is a substantial diversity of cotton-infecting geminiviruses in Pakistan. Phylogenetic analyses indicated that recombination between two major groups of viruses, cotton leaf curl Multan virus (CLCuMuV) and cotton leaf curl Kokhran virus (CLCuKoV), led to the emergence of several new viruses. Recombination detection programs and phylogenetic analyses showed that CLCuMuV and CLCu-KoV are highly recombinant viruses. Indeed, CLCuKoV appeared to be a major donor virus for the coat protein (CP) gene, while CLCuMuV donated the Rep gene in the majority of recombination events. Using recombination free nucleotide datasets the substitution rates for CP and Rep genes were determined. We inferred similar nucleotide substitution rates for the CLCuMuV-Rep gene (4.96X10-4) and CLCuKoV-CP gene (2.706X10-4), whereas relatively higher substitution rates were observed for CLCuMuV-CP and CLCuKoV-Rep genes. The combination of sequences with equal and relatively low substitution rates, seemed to result in the emergence of viral isolates that caused epidemics in Pakistan and India. Our findings also suggest that CLCuMuV is spreading at an alarming rate, which can potentially be a threat to cotton production in the Indian subcontinent.

Research paper thumbnail of Roles of Argonautes and Dicers on Sclerotinia sclerotiorum Antiviral RNA Silencing

Frontiers in Plant Science

RNA silencing or RNA interference (RNAi) is an essential mechanism in animals, fungi, and plants ... more RNA silencing or RNA interference (RNAi) is an essential mechanism in animals, fungi, and plants that functions in gene regulation and defense against foreign nucleic acids. In fungi, RNA silencing has been shown to function primarily in defense against invasive nucleic acids. We previously determined that mycoviruses are triggers and targets of RNA silencing in Sclerotinia sclerotiorum. However, recent progresses in RNAi or dsRNA-based pest control requires more detailed characterization of the RNA silencing pathways in S. sclerotiorum to investigate the utility of dsRNA-based strategy for white mold control. This study elucidates the roles of argonaute enzymes, agl-2 and agl-4, in small RNA metabolism in S. sclerotiorum. Gene disruption mutants of agl-2 and agl-4 were compared for changes in phenotype, virulence, viral susceptibility, and small RNA profiles. The agl-2 mutant but not the agl-4 mutant had significantly slower growth and virulence prior to virus infection. Similarly, the agl-2 mutant but not the agl-4 mutant, showed greater debilitation under virus infection compared to uninfected strains. The responses were confirmed in complementation studies and revealed the antiviral role of agl-2. Gene disruption mutants of agl-2, agl-4, Dicer-like (dcl)-1, and dcl-2 did not change the stability of the most abundant endogenous small RNAs, which suggests the existence of alternative enzymes/pathways for small RNA biogenesis in S. sclerotiorum. Furthermore, in vitro synthesized dsRNA targeting agl-2 showed a significantly reduced average lesion diameter (P < 0.05) on canola leaves with agl-2 down-regulated compared to controls. This is the first report describing the effectiveness of RNA pesticides targeting S. sclerotiorum RNA silencing pathway for the control of the economically important pathogen.

Research paper thumbnail of A Sequence-Independent, Unstructured IRES is Responsible for Internal Expression of the Coat Protein of Turnip Crinkle Virus

Journal of virology, Apr 8, 2017

To maximize the coding potential of viral genomes, internal ribosome entry sites (IRES) can be us... more To maximize the coding potential of viral genomes, internal ribosome entry sites (IRES) can be used to bypass the traditional requirement of a 5' cap and some/all of the associated translation initiation factors. Although viral IRES typically contain higher order RNA structure, an unstructured sequence of about 84-nt immediately upstream of the Turnip crinkle virus (TCV) coat protein (CP) ORF has been found to promote internal expression of the CP from the genomic (g)RNA both in vitro and in vivo Absence of extensive RNA structure was predicted using RNA folding algorithms and confirmed by SHAPE structure probing. Analysis of the IRES region in vitro using both the TCV gRNA and reporter constructs did not reveal any sequence-specific elements but rather suggested that overall lack of structure was an important feature for IRES activity. The CP IRES is A-rich, independent of orientation, and is strongly conserved among viruses in the same genus. The IRES was dependent on eIF4G, b...

Research paper thumbnail of Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses

PLOS ONE, 2016

The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analy... more The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analysis of available sequence data determined that there is a substantial diversity of cotton-infecting geminiviruses in Pakistan. Phylogenetic analyses indicated that recombination between two major groups of viruses, cotton leaf curl Multan virus (CLCuMuV) and cotton leaf curl Kokhran virus (CLCuKoV), led to the emergence of several new viruses. Recombination detection programs and phylogenetic analyses showed that CLCuMuV and CLCuKoV are highly recombinant viruses. Indeed, CLCuKoV appeared to be a major donor virus for the coat protein (CP) gene, while CLCuMuV donated the Rep gene in the majority of recombination events. Using recombination free nucleotide datasets the substitution rates for CP and Rep genes were determined. We inferred similar nucleotide substitution rates for the CLCuMuV-Rep gene (4.96X10-4) and CLCuKoV-CP gene (2.706X10-4), whereas relatively higher substitution rates were observed for CLCuMuV-CP and CLCuKoV-Rep genes. The combination of sequences with equal and relatively low substitution rates, seemed to result in the emergence of viral isolates that caused epidemics in Pakistan and India. Our findings also suggest that CLCuMuV is spreading at an alarming rate, which can potentially be a threat to cotton production in the Indian subcontinent.

Research paper thumbnail of Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses

The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analy... more The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analysis of available sequence data determined that there is a substantial diversity of cotton infecting geminiviruses in Pakistan. Phylogenetic analyses indicated that recombination between two major groups of viruses, cotton leaf curl Multan virus (CLCuMuV) and cotton leaf curl Kokhran virus (CLCuKoV), led to the emergence of several new viruses. Recombi-nation detection programs and phylogenetic analyses showed that CLCuMuV and CLCu-KoV are highly recombinant viruses. Indeed, CLCuKoV appeared to be a major donor virus for the coat protein (CP) gene, while CLCuMuV donated the Rep gene in the majority of recombination events. Using recombination free nucleotide datasets the substitution rates for CP and Rep genes were determined. We inferred similar nucleotide substitution rates for the CLCuMuV-Rep gene (4.96X10-4) and CLCuKoV-CP gene (2.706X10-4), whereas relatively higher substitution rates were observed for CLCuMuV-CP and CLCuKoV-Rep genes. The combination of sequences with equal and relatively low substitution rates, seemed to result in the emergence of viral isolates that caused epidemics in Pakistan and India. Our findings also suggest that CLCuMuV is spreading at an alarming rate, which can potentially be a threat to cotton production in the Indian subcontinent.

Research paper thumbnail of Wild Cotton Genepool: An Unopened Treasure

Wild Germplasm for Genetic Improvement in Crop Plants, 2021

Abstract The genus Gossypium is comprised of more than 50 genetically diverse species with differ... more Abstract The genus Gossypium is comprised of more than 50 genetically diverse species with different origins and ploidy levels. Each of cultivated and wild species is a source of unique alleles to improve cotton crop under ever increasing fiber demand and rapidly evolving climatic factors. Formerly, most of the improvement has been made in cotton germplasm by utilizing the genetic diversity of only cultivated types of species. The plenty of examples are reported for the utilization of wild cotton species in plant breeding despite of the fact of proven to be a novel genetic resource. The major hindrance was the transfer of genetic material which is now easier as compared to past due to advancement of gene transfer methods and technologies. Therefore, the conservation and utilization of cotton wild germplasm have gained much importance and is now become imperative to sustain the yield and quality of cotton fibers. This chapter highlights the background and potential of wild species of cotton to improve yield, quality, and adaptability of modern cultivars.

Research paper thumbnail of Morphological Differences and Molecular Characterization of Begomoviruses in Progeny to Row Trials of Okra (Abelmoschusesculentus L.)

Journal of Environmental and Agricultural Sciences, 2014

Ninety five okra genotypes were evaluated for morphological differences and yellow vein mosaic vi... more Ninety five okra genotypes were evaluated for morphological differences and yellow vein mosaic virus (YVMV) occurrence in progeny to row trials. Principal component analysis (PCA) was executed to obtain more reliable information. A high degree of diversity was found among okra genotypes for qualitative and quantitative characters. Distance of each variable with respect to PC1 and PC2 showed the contribution of this variable in the variation of germplasm. PCA analysis showed that inter-nodal distance, plant height at maturity, days to first flowering and 100-seed weight are the most important descriptors for variation. For the identification of Begomovirus, the putative viruses were cloned in plasmid and the respective plasmids were restricted by appropriate restriction enzyme. The phylogenetic analysis established that the partial DNA-A resemble to the CLCuMuV-[PK:Fai:Okra:13]. Which is actually a cotton infecting virus and closely resemble to the BYVMV-[IN:Har:05].

Research paper thumbnail of Identification of the Viral Determinant of Hypovirulence and Host Range in Sclerotiniaceae of a Genomovirus Reconstructed from the Plant Metagenome

Journal of Virology, 2021

Little is known about the exact host range of widespread genomoviruses. The genome of soybean lea... more Little is known about the exact host range of widespread genomoviruses. The genome of soybean leaf-associated gemygorvirus-1 (SlaGemV-1) was originally assembled from a metagenomic/metatranscriptomic study without known hosts.

Research paper thumbnail of Molecular Screening of Cotton Germplasm for Cotton Leaf Curl Disease Causedby Viral Strains

International Journal of Agriculture and Biology, 2017

Cotton crop is infected by single stranded DNA viruses (Family, Geminiviridae) in Pakistan. Due t... more Cotton crop is infected by single stranded DNA viruses (Family, Geminiviridae) in Pakistan. Due to changing global climate, which favors the whitefly (insect vector) growth and reproduction, the spread of cotton leaf curl disease is increasing at an alarming rate. Various approaches are being used to diagnose the ssDNA viruses in cotton. One step PCR protocol was established to identify the three viruses, namely cotton leaf curl Multan virus (CLCuMuV), Burewala strain of Kokhran virus (CLCuKo-Bur) and cotton leaf curl Kokhran virus (CLCuKoV). Thirty eight genotypes were screened on the basis of symptoms and molecular diagnosis. Out of 38 genotypes, 13 were positive for CLCuMuV, 24 were positive for Burewala strain and one was positive for both CLCuMuV and CLCuKoV-Bur strain. However, none of the samples was positives for cotton leaf curl Kokhran virus. Our experiments have established one step guide PCR for screening of cotton germplasm for major cotton infecting viruses. This diagnostic assay will promote the breeding programs for the development of resistant cotton varieties against cotton leaf curl disease (CLCuD) in Pakistan.

Research paper thumbnail of Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses

PLOS ONE, 2016

The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analy... more The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analysis of available sequence data determined that there is a substantial diversity of cotton-infecting geminiviruses in Pakistan. Phylogenetic analyses indicated that recombination between two major groups of viruses, cotton leaf curl Multan virus (CLCuMuV) and cotton leaf curl Kokhran virus (CLCuKoV), led to the emergence of several new viruses. Recombination detection programs and phylogenetic analyses showed that CLCuMuV and CLCu-KoV are highly recombinant viruses. Indeed, CLCuKoV appeared to be a major donor virus for the coat protein (CP) gene, while CLCuMuV donated the Rep gene in the majority of recombination events. Using recombination free nucleotide datasets the substitution rates for CP and Rep genes were determined. We inferred similar nucleotide substitution rates for the CLCuMuV-Rep gene (4.96X10-4) and CLCuKoV-CP gene (2.706X10-4), whereas relatively higher substitution rates were observed for CLCuMuV-CP and CLCuKoV-Rep genes. The combination of sequences with equal and relatively low substitution rates, seemed to result in the emergence of viral isolates that caused epidemics in Pakistan and India. Our findings also suggest that CLCuMuV is spreading at an alarming rate, which can potentially be a threat to cotton production in the Indian subcontinent.

Research paper thumbnail of Roles of Argonautes and Dicers on Sclerotinia sclerotiorum Antiviral RNA Silencing

Frontiers in Plant Science

RNA silencing or RNA interference (RNAi) is an essential mechanism in animals, fungi, and plants ... more RNA silencing or RNA interference (RNAi) is an essential mechanism in animals, fungi, and plants that functions in gene regulation and defense against foreign nucleic acids. In fungi, RNA silencing has been shown to function primarily in defense against invasive nucleic acids. We previously determined that mycoviruses are triggers and targets of RNA silencing in Sclerotinia sclerotiorum. However, recent progresses in RNAi or dsRNA-based pest control requires more detailed characterization of the RNA silencing pathways in S. sclerotiorum to investigate the utility of dsRNA-based strategy for white mold control. This study elucidates the roles of argonaute enzymes, agl-2 and agl-4, in small RNA metabolism in S. sclerotiorum. Gene disruption mutants of agl-2 and agl-4 were compared for changes in phenotype, virulence, viral susceptibility, and small RNA profiles. The agl-2 mutant but not the agl-4 mutant had significantly slower growth and virulence prior to virus infection. Similarly, the agl-2 mutant but not the agl-4 mutant, showed greater debilitation under virus infection compared to uninfected strains. The responses were confirmed in complementation studies and revealed the antiviral role of agl-2. Gene disruption mutants of agl-2, agl-4, Dicer-like (dcl)-1, and dcl-2 did not change the stability of the most abundant endogenous small RNAs, which suggests the existence of alternative enzymes/pathways for small RNA biogenesis in S. sclerotiorum. Furthermore, in vitro synthesized dsRNA targeting agl-2 showed a significantly reduced average lesion diameter (P < 0.05) on canola leaves with agl-2 down-regulated compared to controls. This is the first report describing the effectiveness of RNA pesticides targeting S. sclerotiorum RNA silencing pathway for the control of the economically important pathogen.

Research paper thumbnail of A Sequence-Independent, Unstructured IRES is Responsible for Internal Expression of the Coat Protein of Turnip Crinkle Virus

Journal of virology, Apr 8, 2017

To maximize the coding potential of viral genomes, internal ribosome entry sites (IRES) can be us... more To maximize the coding potential of viral genomes, internal ribosome entry sites (IRES) can be used to bypass the traditional requirement of a 5' cap and some/all of the associated translation initiation factors. Although viral IRES typically contain higher order RNA structure, an unstructured sequence of about 84-nt immediately upstream of the Turnip crinkle virus (TCV) coat protein (CP) ORF has been found to promote internal expression of the CP from the genomic (g)RNA both in vitro and in vivo Absence of extensive RNA structure was predicted using RNA folding algorithms and confirmed by SHAPE structure probing. Analysis of the IRES region in vitro using both the TCV gRNA and reporter constructs did not reveal any sequence-specific elements but rather suggested that overall lack of structure was an important feature for IRES activity. The CP IRES is A-rich, independent of orientation, and is strongly conserved among viruses in the same genus. The IRES was dependent on eIF4G, b...

Research paper thumbnail of Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses

PLOS ONE, 2016

The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analy... more The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analysis of available sequence data determined that there is a substantial diversity of cotton-infecting geminiviruses in Pakistan. Phylogenetic analyses indicated that recombination between two major groups of viruses, cotton leaf curl Multan virus (CLCuMuV) and cotton leaf curl Kokhran virus (CLCuKoV), led to the emergence of several new viruses. Recombination detection programs and phylogenetic analyses showed that CLCuMuV and CLCuKoV are highly recombinant viruses. Indeed, CLCuKoV appeared to be a major donor virus for the coat protein (CP) gene, while CLCuMuV donated the Rep gene in the majority of recombination events. Using recombination free nucleotide datasets the substitution rates for CP and Rep genes were determined. We inferred similar nucleotide substitution rates for the CLCuMuV-Rep gene (4.96X10-4) and CLCuKoV-CP gene (2.706X10-4), whereas relatively higher substitution rates were observed for CLCuMuV-CP and CLCuKoV-Rep genes. The combination of sequences with equal and relatively low substitution rates, seemed to result in the emergence of viral isolates that caused epidemics in Pakistan and India. Our findings also suggest that CLCuMuV is spreading at an alarming rate, which can potentially be a threat to cotton production in the Indian subcontinent.

Research paper thumbnail of Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses

The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analy... more The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analysis of available sequence data determined that there is a substantial diversity of cotton infecting geminiviruses in Pakistan. Phylogenetic analyses indicated that recombination between two major groups of viruses, cotton leaf curl Multan virus (CLCuMuV) and cotton leaf curl Kokhran virus (CLCuKoV), led to the emergence of several new viruses. Recombi-nation detection programs and phylogenetic analyses showed that CLCuMuV and CLCu-KoV are highly recombinant viruses. Indeed, CLCuKoV appeared to be a major donor virus for the coat protein (CP) gene, while CLCuMuV donated the Rep gene in the majority of recombination events. Using recombination free nucleotide datasets the substitution rates for CP and Rep genes were determined. We inferred similar nucleotide substitution rates for the CLCuMuV-Rep gene (4.96X10-4) and CLCuKoV-CP gene (2.706X10-4), whereas relatively higher substitution rates were observed for CLCuMuV-CP and CLCuKoV-Rep genes. The combination of sequences with equal and relatively low substitution rates, seemed to result in the emergence of viral isolates that caused epidemics in Pakistan and India. Our findings also suggest that CLCuMuV is spreading at an alarming rate, which can potentially be a threat to cotton production in the Indian subcontinent.