Cotton (Gossypium hirsutum L.) has nectar containing modified stomates called nectaries that can ... more Cotton (Gossypium hirsutum L.) has nectar containing modified stomates called nectaries that can be located on leaves, bracts or calyces. The nectar attracts some beneficial insects such as bees, but also predatory damaging insects such as heliothines and Lygus species. There is a naturally occurring mutation that eliminates the nectar containing nectaries and makes the cotton plants less attractive to insects. The nectariless (ne) trait is associated with a double recessive mutation of two genes (ne1 and ne2) on homeologous chromosomes 12 and 26. Expression of the trait can be variable and is also affected by environmental conditions. This makes accurately selecting for the trait based on phenotype difficult. This study identified SSR and SNP markers that can be used by breeders for marker assisted selection (MAS) of the nectariless trait. DNA markers associated with the genes conditioning the trait and used for MAS, will allow cotton cultivars to be easily developed that have decr...
Individual matrices with numbers of different and identical SNPs for entries with the same name. ... more Individual matrices with numbers of different and identical SNPs for entries with the same name. These values were extracted directly from Additional file 5. Values above the diagonal represent the count of homozygous differences between pairs of samples. Values below the diagonal represent the number of identical SNPs genotyped between pairs. Heterozygous SNPs within samples were not counted in the number of differences between samples. SNP numbers were determined using all SNPs on the CottonSNP63K array. Five samples are included here that were identified as outliers and not used in the diversity analysis. (XLSX 17Â kb)
Results and discussion in relation to the removal of admixed/misclassified samples. Five samples ... more Results and discussion in relation to the removal of admixed/misclassified samples. Five samples were removed from overall SNP diversity analysis, and three samples were removed from the comparison of SNP and SSR data. This file presents the original results and discusses why the samples were subsequently removed. For the original diversity analysis, this file includes the MDS figures, Venn diagrams of unique and shared SNPs, and distribution of pairwise IBS values when these samples are included. Likewise, for the comparison of SNP and SSR data, the original principal coordinate analyses and the plots comparing SNP- and SSR-based genetic similarity are shown. (DOCX 325Â kb)
List of Gossypium samples genotyped for SNP diversity analyses. The table includes information fo... more List of Gossypium samples genotyped for SNP diversity analyses. The table includes information for seed source, improved/wild classification, assigned categories for improved breeding regions, assigned categories for wild race types, availability of SSR genotypes for SNP-SSR comparison, and values for seed oil, protein, and seed index for samples used in GWAS analysis. In addition, for each sample, the coordinates of the first two MDS dimensions are listed for Figs. 3 and 4a, b. Five samples are included here that were identified as outliers and not used in the SNP analysis. Siokra 104–90 was not a cultivar developed in Australia (I. Wilson, personal communication). It may be a mislabeling of Siokra 1–4/649 which is actually just Siokra 1–4. (XLSX 97 kb)
Matrix showing numbers of different and identical SNPs for all pairwise combinations of 395 sampl... more Matrix showing numbers of different and identical SNPs for all pairwise combinations of 395 samples. Values above the diagonal represent the count of homozygous differences between pairs of samples. Values below the diagonal represent the number of identical SNPs genotyped between pairs. Heterozygous SNPs within samples were not counted in the number of differences between samples. SNP numbers were determined using all SNPs on the CottonSNP63K array. Five samples are included here that were identified as outliers and not used in the diversity analysis. (XLSX 1032Â kb)
Successful breeding programs optimize time and resources to produce elite lines. Selecting indivi... more Successful breeding programs optimize time and resources to produce elite lines. Selecting individual plants in the F2 generation is an efficient strategy if the trait is highly heritable and nondestructive methods exist to analyze the seed. Cotton (Gossypium hirsutum L.) seed has limited uses because of gossypol, a toxic compound found in the seed. Gossypol exists in two enantiomeric forms with the (+) less toxic than the (−) form. Reducing gossypol or increasing the (+) enantiomer in the seed would increase the amount that could be fed to livestock, chicken, or fish. Rapid, costeffective methods were developed to measure (+) and (−) gossypol in the cotyledon (chalazal) half of a seed by high performance liquid chromatography (HPLC) on a reduced scale. Techniques were also developed to propagate the embryo (micropylar) half of the seed. The techniques were used to develop elite lines with varied gossypol levels produced one year earlier than possible with more conventional breeding...
Gossypol is a terpenoid aldehyde found in cotton (Gossypium hirsutum L.) glands that are located ... more Gossypol is a terpenoid aldehyde found in cotton (Gossypium hirsutum L.) glands that are located throughout the plant and seed, where it serves a protective function against pests and pathogens. Cottonseed use is limited mainly to cattle feed because gossypol is toxic to most animals except ruminants. Lowering gossypol content in the seed would increase the possible uses for cottonseed. Developing new strategies to modify gossypol in cottonseed requires a better understanding of the development of gossypol containing glands. The first step is to determine when gossypol glands are initiated and filled with gossypol. Gland development was investigated using microscopic images of developing seeds from 10 glanded and two glandless cotton lines. A digital microscope with a VH-Z20R (20X to 200X) lens was used to capture developing ovule (seed) images at 14 to 22 d after flowering (DAF). One boll per plot was imaged for each DAF time point and five different sets of time intervals were col...
Nutrients, including macronutrients such as Ca, P, K, and Mg, are essential for crop production a... more Nutrients, including macronutrients such as Ca, P, K, and Mg, are essential for crop production and seed quality, and for human and animal nutrition and health. Macronutrient deficiencies in soil lead to poor crop nutritional qualities and a low level of macronutrients in cottonseed meal-based products, leading to malnutrition. Therefore, the discovery of novel germplasm with a high level of macronutrients or significant variability in the macronutrient content of crop seeds is critical. To our knowledge, there is no information available on the effects of chromosome or chromosome arm substitution on cottonseed macronutrient content. The objective of this study was to evaluate the effects of chromosome or chromosome arm substitution on the variability and content of the cottonseed macronutrients Ca, K, Mg, N, P, and S in chromosome substitution lines (CS). Nine chromosome substitution lines were grown in two-field experiments at two locations in 2013 in South Carolina, USA, and in 2...
A new technique was developed to study the cotton fiber initiation process and fiber initial dens... more A new technique was developed to study the cotton fiber initiation process and fiber initial densities. The goal was to provide an additional tool to cotton breeders and geneticists interested in fiber improvement. The objectives were to assess whether fiber initiation patterns reported for some Gossypium hirsutum L. and G. barbadense L. cultivars extend to a more diverse range of cultivars/lines; and to test if there is a relationship between fiber initials density, lint percentage, and fiber characteristics. This study was performed with 17 cultivars and experimental lines of G. hirsutum (upland cotton) and G. barbadense (Pima cotton) and one G. arboreum L. accession. The ovules were extracted from flowers at the day of anthesis and 1 and 2 d thereafter, stained with a fluorescent dye, DiOC6(3) (3,3′-dihexyloxacarbocyanine iodide), and observed under a light microscope. Staining cotton fiber initials with DiOC 6(3) enabled the evaluation of a greater number of samples than the mor...
Improved Host Plant Resistance (HPR) has long been a goal of plant breeders. Despite the fact tha... more Improved Host Plant Resistance (HPR) has long been a goal of plant breeders. Despite the fact that improvements have been made by a number of researchers over the past 50 years, chemical control of insect pests has remained the preferred method for most production systems. The introduction of Bt cotton and the pressure to decrease insecticide use has renewed interest in increasing the plants endogenous defenses against insect pests. A number of simply inherited traits have been identified that can improve the plants defenses against various insect pests. Each individual trait is not enough to provide adequate protection, but in combination, should provide a defense network that could further reduce insecticide usage. The traits being combined include semismooth leaf (t2t2t3t3) which deters some insects from feeding and inhibits egg laying, nectariless (ne1 ne1ne2 ne2) which eliminates nectaries that can be an insect attractant, high glanding (Gl3Gl s 3) which produces glands on th...
Micronutrients are essential for plant growth and development, and important for human health nut... more Micronutrients are essential for plant growth and development, and important for human health nutrition and livestock feed. Therefore, the discovery of novel germplasm with significant variability or higher micronutrients content in crop seeds is critical. Currently, there is no information available on the effects of chromosome or chromosome arm substitution in cotton on cottonseed micronutrients. Thus, the objective of this study was to evaluate the effects of chromosome or chromosome arm substitution on the variability and levels of micronutrients B, Fe, Cu, Zn, Mn, and Ni in cottonseed from chromosome substitution (CS) cotton lines. Our hypothesis was that interspecific chromosome substitution in cotton can affect cottonseed micronutrients content, resulting in significant differences and variabilities of these nutrients among CS lines and between CS lines and the controls. Nine CS lines were grown in two-field experiments at two locations (in 2013 in South Carolina, USA; and in...
Background: Whiteflies (Bemisia tabaci) are phloem sap-sucking pests that because of their broad ... more Background: Whiteflies (Bemisia tabaci) are phloem sap-sucking pests that because of their broad host range and ability to transmit viruses damage crop plants worldwide. B. tabaci are now known to be a complex of cryptic species that differ from each other in many characteristics such as mode of interaction with viruses, invasiveness, and resistance to insecticides. Asia II 1 is an indigenous species found on the Indian sub-continent and southeast Asia while the species named as Middle East Asia Minor 1 (MEAM1), likely originated from the Middle-East and has spread worldwide in recent decades. The purpose of this study is to find genomic differences between these two species. Results: Sequencing of the nuclear genome of Asia II 1 with Illumina HiSeq and MiSeq generated 198.90 million reads that covers 88% of the reference genome. The sequence comparison with MEAM1 identified 2,327,972 SNPs and 202, 479 INDELs. In Total, 1294 genes were detected with high impact variants. The functional analysis revealed that some of the genes are involved in virus transmission including 4 genes in Tomato yellow leaf curl virus (TYLCV) transmission, 96 in Tomato crinivirus (ToCV) transmission, and 14 genes in insecticide resistance. Conclusions: These genetic differences between Asia II 1 and MEAM1 may underlie the major biological differences between the two species such as virus transmission, insecticide resistance, and range of host plants. The present study provides new genomic data and information resources for Asia II 1 that will not only contribute to the species delimitation of whitefly, but also help in conceiving future research studies to develop more targeted management strategies against whitefly.
This is an open access article under the terms of the Creat ive Commo ns Attri bution License, wh... more This is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the g... more We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33Â genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following transoceanic dispersal from Africa about 6.6 Ma, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5-2.0 Ma), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands, and Peru. Comparative analyses of cpDNAversus nuclear data indicate that this history was accompanied by several clear cases of interspecific introgression. Repetitive DNAs contribute roughly half of the total 880 Mb genome, but most transposable element families are relatively old and stable among species. In the genic fraction, pairwise synonymous mutation rates average 1% per Myr, with nonsynonymous changes being about seven times less frequent. Over 1.1 million indels were detected and phylogenetically polarized, revealing a 2fold bias toward deletions over small insertions. We suggest that this genome down-sizing bias counteracts genome size growth by TE amplification and insertions, and helps explain the relatively small genomes that are restricted to this subgenus. Compared with the rate of nucleotide substitution, the rate of indel occurrence is much lower averaging about 17 nucleotide substitutions per indel event.
Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most ... more Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. While the widely cultivated cotton species Gossypium hirsutum is generally susceptible, the diploid species G. arboreum is a natural source for resistance against CLCuD. However, the influence of CLCuD on the G. arboreum transcriptome and the interaction of CLCuD with G. arboreum remains to be elucidated. Here we have used an RNA-Seq based study to analyze differential gene expression in G. arboreum under CLCuD infestation. G. arboreum plants were infested by graft inoculation using a CLCuD infected scion of G. hirsutum. CLCuD infested asymptomatic and symptomatic plants were analyzed with RNA-seq using an Illumina HiSeq. 2500. Data analysis revealed 1062 differentially expressed genes (DEGs) in G. arboreum. We selected 17 genes for qPCR to validate RNA-Seq data. We identified several genes involved in disease resistance and pathogen defense. Furthermore, ...
Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large... more Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used...
Cotton leaf curl virus disease (CLCuD) is caused by a suite of whitefly-transmitted begomovirus s... more Cotton leaf curl virus disease (CLCuD) is caused by a suite of whitefly-transmitted begomovirus species and strains, resulting in extensive losses annually in India and Pakistan. RNA-interference (RNAi) is a proven technology used for knockdown of gene expression in higher organisms and viruses. In this study, a small interfering RNA (siRNA) construct was designed to target the AC1 gene of Cotton leaf curl Kokhran virus-Burewala (CLCuKoV-Bu) and the βC1 gene and satellite conserved region of the Cotton leaf curl Multan betasatellite (CLCuMB). The AC1 gene and CLCuMB coding and non-coding regions function in replication initiation and suppression of the plant host defense pathway, respectively. The construct, Vβ, was transformed into cotton plants using the Agrobacterium-mediated embryo shoot apex cut method. Results from fluorescence in situ hybridization and karyotyping assays indicated that six of the 11 T₁ plants harbored a single copy of the Vβ transgene. Transgenic cotton plant...
The first epidemic of cotton leaf curl disease (CLCuD) in early 1990's in the Indian subconti... more The first epidemic of cotton leaf curl disease (CLCuD) in early 1990's in the Indian subcontinent was associated with several distinct begomoviruses along with a disease-specific betasatellite. Resistant cotton varieties were introduced in late 1990's but soon resistance was broken and was associated with a single recombinant begomovirus named Burewala strain of Cotton leaf curl Kokhran virus that lacks a full complement of a gene encoding a transcription activator protein (TrAP). In order to understand the ongoing changes in CLCuD complex in Pakistan, CLCuD affected plants from cotton fields at Vehari were collected. Illumina sequencing was used to assess the diversity of CLCuD complex. At least three distinct begomoviruses characterized from the first epidemic; Cotton leaf curl Multan virus, Cotton leaf curl Kokhran virus and Cotton leaf curl Alabad virus, several distinct species of alphasatellites and cotton leaf curl Multan betasatellite were found associated with CLCuD...
Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm ... more Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzi...
The whitefly Bemisia tabaci (Genn.) is a pest and vector of plant viruses to crop and ornamental ... more The whitefly Bemisia tabaci (Genn.) is a pest and vector of plant viruses to crop and ornamental plants worldwide. Using RNA interference (RNAi) to down regulate whitefly genes by expressing their homologous double stranded RNAs in plants has great potential for management of whiteflies to reduce plant virus disease spread. Using a Tobacco rattle virus-derived plasmid for in planta transient expression of double stranded RNA (dsRNA) homologous to the acetylcholinesterase (AChE) and ecdysone receptor (EcR) genes of B. tabaci, resulted in significant adult whitefly mortality. Nicotiana tabacum L. plants expressing dsRNA homologous to B. tabaci AChE and EcR were constructed by fusing sequences derived from both genes. Mortality of adult whiteflies exposed to dsRNA by feeding on N. tabacum plants, compared to non-dsRNA expressing plants, recorded at 24-hr intervals post-ingestion for three days, was >90% and 10%, respectively. Analysis of gene expression by real time quantitative PCR...
Cotton (Gossypium hirsutum L.) has nectar containing modified stomates called nectaries that can ... more Cotton (Gossypium hirsutum L.) has nectar containing modified stomates called nectaries that can be located on leaves, bracts or calyces. The nectar attracts some beneficial insects such as bees, but also predatory damaging insects such as heliothines and Lygus species. There is a naturally occurring mutation that eliminates the nectar containing nectaries and makes the cotton plants less attractive to insects. The nectariless (ne) trait is associated with a double recessive mutation of two genes (ne1 and ne2) on homeologous chromosomes 12 and 26. Expression of the trait can be variable and is also affected by environmental conditions. This makes accurately selecting for the trait based on phenotype difficult. This study identified SSR and SNP markers that can be used by breeders for marker assisted selection (MAS) of the nectariless trait. DNA markers associated with the genes conditioning the trait and used for MAS, will allow cotton cultivars to be easily developed that have decr...
Individual matrices with numbers of different and identical SNPs for entries with the same name. ... more Individual matrices with numbers of different and identical SNPs for entries with the same name. These values were extracted directly from Additional file 5. Values above the diagonal represent the count of homozygous differences between pairs of samples. Values below the diagonal represent the number of identical SNPs genotyped between pairs. Heterozygous SNPs within samples were not counted in the number of differences between samples. SNP numbers were determined using all SNPs on the CottonSNP63K array. Five samples are included here that were identified as outliers and not used in the diversity analysis. (XLSX 17Â kb)
Results and discussion in relation to the removal of admixed/misclassified samples. Five samples ... more Results and discussion in relation to the removal of admixed/misclassified samples. Five samples were removed from overall SNP diversity analysis, and three samples were removed from the comparison of SNP and SSR data. This file presents the original results and discusses why the samples were subsequently removed. For the original diversity analysis, this file includes the MDS figures, Venn diagrams of unique and shared SNPs, and distribution of pairwise IBS values when these samples are included. Likewise, for the comparison of SNP and SSR data, the original principal coordinate analyses and the plots comparing SNP- and SSR-based genetic similarity are shown. (DOCX 325Â kb)
List of Gossypium samples genotyped for SNP diversity analyses. The table includes information fo... more List of Gossypium samples genotyped for SNP diversity analyses. The table includes information for seed source, improved/wild classification, assigned categories for improved breeding regions, assigned categories for wild race types, availability of SSR genotypes for SNP-SSR comparison, and values for seed oil, protein, and seed index for samples used in GWAS analysis. In addition, for each sample, the coordinates of the first two MDS dimensions are listed for Figs. 3 and 4a, b. Five samples are included here that were identified as outliers and not used in the SNP analysis. Siokra 104–90 was not a cultivar developed in Australia (I. Wilson, personal communication). It may be a mislabeling of Siokra 1–4/649 which is actually just Siokra 1–4. (XLSX 97 kb)
Matrix showing numbers of different and identical SNPs for all pairwise combinations of 395 sampl... more Matrix showing numbers of different and identical SNPs for all pairwise combinations of 395 samples. Values above the diagonal represent the count of homozygous differences between pairs of samples. Values below the diagonal represent the number of identical SNPs genotyped between pairs. Heterozygous SNPs within samples were not counted in the number of differences between samples. SNP numbers were determined using all SNPs on the CottonSNP63K array. Five samples are included here that were identified as outliers and not used in the diversity analysis. (XLSX 1032Â kb)
Successful breeding programs optimize time and resources to produce elite lines. Selecting indivi... more Successful breeding programs optimize time and resources to produce elite lines. Selecting individual plants in the F2 generation is an efficient strategy if the trait is highly heritable and nondestructive methods exist to analyze the seed. Cotton (Gossypium hirsutum L.) seed has limited uses because of gossypol, a toxic compound found in the seed. Gossypol exists in two enantiomeric forms with the (+) less toxic than the (−) form. Reducing gossypol or increasing the (+) enantiomer in the seed would increase the amount that could be fed to livestock, chicken, or fish. Rapid, costeffective methods were developed to measure (+) and (−) gossypol in the cotyledon (chalazal) half of a seed by high performance liquid chromatography (HPLC) on a reduced scale. Techniques were also developed to propagate the embryo (micropylar) half of the seed. The techniques were used to develop elite lines with varied gossypol levels produced one year earlier than possible with more conventional breeding...
Gossypol is a terpenoid aldehyde found in cotton (Gossypium hirsutum L.) glands that are located ... more Gossypol is a terpenoid aldehyde found in cotton (Gossypium hirsutum L.) glands that are located throughout the plant and seed, where it serves a protective function against pests and pathogens. Cottonseed use is limited mainly to cattle feed because gossypol is toxic to most animals except ruminants. Lowering gossypol content in the seed would increase the possible uses for cottonseed. Developing new strategies to modify gossypol in cottonseed requires a better understanding of the development of gossypol containing glands. The first step is to determine when gossypol glands are initiated and filled with gossypol. Gland development was investigated using microscopic images of developing seeds from 10 glanded and two glandless cotton lines. A digital microscope with a VH-Z20R (20X to 200X) lens was used to capture developing ovule (seed) images at 14 to 22 d after flowering (DAF). One boll per plot was imaged for each DAF time point and five different sets of time intervals were col...
Nutrients, including macronutrients such as Ca, P, K, and Mg, are essential for crop production a... more Nutrients, including macronutrients such as Ca, P, K, and Mg, are essential for crop production and seed quality, and for human and animal nutrition and health. Macronutrient deficiencies in soil lead to poor crop nutritional qualities and a low level of macronutrients in cottonseed meal-based products, leading to malnutrition. Therefore, the discovery of novel germplasm with a high level of macronutrients or significant variability in the macronutrient content of crop seeds is critical. To our knowledge, there is no information available on the effects of chromosome or chromosome arm substitution on cottonseed macronutrient content. The objective of this study was to evaluate the effects of chromosome or chromosome arm substitution on the variability and content of the cottonseed macronutrients Ca, K, Mg, N, P, and S in chromosome substitution lines (CS). Nine chromosome substitution lines were grown in two-field experiments at two locations in 2013 in South Carolina, USA, and in 2...
A new technique was developed to study the cotton fiber initiation process and fiber initial dens... more A new technique was developed to study the cotton fiber initiation process and fiber initial densities. The goal was to provide an additional tool to cotton breeders and geneticists interested in fiber improvement. The objectives were to assess whether fiber initiation patterns reported for some Gossypium hirsutum L. and G. barbadense L. cultivars extend to a more diverse range of cultivars/lines; and to test if there is a relationship between fiber initials density, lint percentage, and fiber characteristics. This study was performed with 17 cultivars and experimental lines of G. hirsutum (upland cotton) and G. barbadense (Pima cotton) and one G. arboreum L. accession. The ovules were extracted from flowers at the day of anthesis and 1 and 2 d thereafter, stained with a fluorescent dye, DiOC6(3) (3,3′-dihexyloxacarbocyanine iodide), and observed under a light microscope. Staining cotton fiber initials with DiOC 6(3) enabled the evaluation of a greater number of samples than the mor...
Improved Host Plant Resistance (HPR) has long been a goal of plant breeders. Despite the fact tha... more Improved Host Plant Resistance (HPR) has long been a goal of plant breeders. Despite the fact that improvements have been made by a number of researchers over the past 50 years, chemical control of insect pests has remained the preferred method for most production systems. The introduction of Bt cotton and the pressure to decrease insecticide use has renewed interest in increasing the plants endogenous defenses against insect pests. A number of simply inherited traits have been identified that can improve the plants defenses against various insect pests. Each individual trait is not enough to provide adequate protection, but in combination, should provide a defense network that could further reduce insecticide usage. The traits being combined include semismooth leaf (t2t2t3t3) which deters some insects from feeding and inhibits egg laying, nectariless (ne1 ne1ne2 ne2) which eliminates nectaries that can be an insect attractant, high glanding (Gl3Gl s 3) which produces glands on th...
Micronutrients are essential for plant growth and development, and important for human health nut... more Micronutrients are essential for plant growth and development, and important for human health nutrition and livestock feed. Therefore, the discovery of novel germplasm with significant variability or higher micronutrients content in crop seeds is critical. Currently, there is no information available on the effects of chromosome or chromosome arm substitution in cotton on cottonseed micronutrients. Thus, the objective of this study was to evaluate the effects of chromosome or chromosome arm substitution on the variability and levels of micronutrients B, Fe, Cu, Zn, Mn, and Ni in cottonseed from chromosome substitution (CS) cotton lines. Our hypothesis was that interspecific chromosome substitution in cotton can affect cottonseed micronutrients content, resulting in significant differences and variabilities of these nutrients among CS lines and between CS lines and the controls. Nine CS lines were grown in two-field experiments at two locations (in 2013 in South Carolina, USA; and in...
Background: Whiteflies (Bemisia tabaci) are phloem sap-sucking pests that because of their broad ... more Background: Whiteflies (Bemisia tabaci) are phloem sap-sucking pests that because of their broad host range and ability to transmit viruses damage crop plants worldwide. B. tabaci are now known to be a complex of cryptic species that differ from each other in many characteristics such as mode of interaction with viruses, invasiveness, and resistance to insecticides. Asia II 1 is an indigenous species found on the Indian sub-continent and southeast Asia while the species named as Middle East Asia Minor 1 (MEAM1), likely originated from the Middle-East and has spread worldwide in recent decades. The purpose of this study is to find genomic differences between these two species. Results: Sequencing of the nuclear genome of Asia II 1 with Illumina HiSeq and MiSeq generated 198.90 million reads that covers 88% of the reference genome. The sequence comparison with MEAM1 identified 2,327,972 SNPs and 202, 479 INDELs. In Total, 1294 genes were detected with high impact variants. The functional analysis revealed that some of the genes are involved in virus transmission including 4 genes in Tomato yellow leaf curl virus (TYLCV) transmission, 96 in Tomato crinivirus (ToCV) transmission, and 14 genes in insecticide resistance. Conclusions: These genetic differences between Asia II 1 and MEAM1 may underlie the major biological differences between the two species such as virus transmission, insecticide resistance, and range of host plants. The present study provides new genomic data and information resources for Asia II 1 that will not only contribute to the species delimitation of whitefly, but also help in conceiving future research studies to develop more targeted management strategies against whitefly.
This is an open access article under the terms of the Creat ive Commo ns Attri bution License, wh... more This is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the g... more We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33Â genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following transoceanic dispersal from Africa about 6.6 Ma, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5-2.0 Ma), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands, and Peru. Comparative analyses of cpDNAversus nuclear data indicate that this history was accompanied by several clear cases of interspecific introgression. Repetitive DNAs contribute roughly half of the total 880 Mb genome, but most transposable element families are relatively old and stable among species. In the genic fraction, pairwise synonymous mutation rates average 1% per Myr, with nonsynonymous changes being about seven times less frequent. Over 1.1 million indels were detected and phylogenetically polarized, revealing a 2fold bias toward deletions over small insertions. We suggest that this genome down-sizing bias counteracts genome size growth by TE amplification and insertions, and helps explain the relatively small genomes that are restricted to this subgenus. Compared with the rate of nucleotide substitution, the rate of indel occurrence is much lower averaging about 17 nucleotide substitutions per indel event.
Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most ... more Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. While the widely cultivated cotton species Gossypium hirsutum is generally susceptible, the diploid species G. arboreum is a natural source for resistance against CLCuD. However, the influence of CLCuD on the G. arboreum transcriptome and the interaction of CLCuD with G. arboreum remains to be elucidated. Here we have used an RNA-Seq based study to analyze differential gene expression in G. arboreum under CLCuD infestation. G. arboreum plants were infested by graft inoculation using a CLCuD infected scion of G. hirsutum. CLCuD infested asymptomatic and symptomatic plants were analyzed with RNA-seq using an Illumina HiSeq. 2500. Data analysis revealed 1062 differentially expressed genes (DEGs) in G. arboreum. We selected 17 genes for qPCR to validate RNA-Seq data. We identified several genes involved in disease resistance and pathogen defense. Furthermore, ...
Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large... more Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used...
Cotton leaf curl virus disease (CLCuD) is caused by a suite of whitefly-transmitted begomovirus s... more Cotton leaf curl virus disease (CLCuD) is caused by a suite of whitefly-transmitted begomovirus species and strains, resulting in extensive losses annually in India and Pakistan. RNA-interference (RNAi) is a proven technology used for knockdown of gene expression in higher organisms and viruses. In this study, a small interfering RNA (siRNA) construct was designed to target the AC1 gene of Cotton leaf curl Kokhran virus-Burewala (CLCuKoV-Bu) and the βC1 gene and satellite conserved region of the Cotton leaf curl Multan betasatellite (CLCuMB). The AC1 gene and CLCuMB coding and non-coding regions function in replication initiation and suppression of the plant host defense pathway, respectively. The construct, Vβ, was transformed into cotton plants using the Agrobacterium-mediated embryo shoot apex cut method. Results from fluorescence in situ hybridization and karyotyping assays indicated that six of the 11 T₁ plants harbored a single copy of the Vβ transgene. Transgenic cotton plant...
The first epidemic of cotton leaf curl disease (CLCuD) in early 1990's in the Indian subconti... more The first epidemic of cotton leaf curl disease (CLCuD) in early 1990's in the Indian subcontinent was associated with several distinct begomoviruses along with a disease-specific betasatellite. Resistant cotton varieties were introduced in late 1990's but soon resistance was broken and was associated with a single recombinant begomovirus named Burewala strain of Cotton leaf curl Kokhran virus that lacks a full complement of a gene encoding a transcription activator protein (TrAP). In order to understand the ongoing changes in CLCuD complex in Pakistan, CLCuD affected plants from cotton fields at Vehari were collected. Illumina sequencing was used to assess the diversity of CLCuD complex. At least three distinct begomoviruses characterized from the first epidemic; Cotton leaf curl Multan virus, Cotton leaf curl Kokhran virus and Cotton leaf curl Alabad virus, several distinct species of alphasatellites and cotton leaf curl Multan betasatellite were found associated with CLCuD...
Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm ... more Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzi...
The whitefly Bemisia tabaci (Genn.) is a pest and vector of plant viruses to crop and ornamental ... more The whitefly Bemisia tabaci (Genn.) is a pest and vector of plant viruses to crop and ornamental plants worldwide. Using RNA interference (RNAi) to down regulate whitefly genes by expressing their homologous double stranded RNAs in plants has great potential for management of whiteflies to reduce plant virus disease spread. Using a Tobacco rattle virus-derived plasmid for in planta transient expression of double stranded RNA (dsRNA) homologous to the acetylcholinesterase (AChE) and ecdysone receptor (EcR) genes of B. tabaci, resulted in significant adult whitefly mortality. Nicotiana tabacum L. plants expressing dsRNA homologous to B. tabaci AChE and EcR were constructed by fusing sequences derived from both genes. Mortality of adult whiteflies exposed to dsRNA by feeding on N. tabacum plants, compared to non-dsRNA expressing plants, recorded at 24-hr intervals post-ingestion for three days, was >90% and 10%, respectively. Analysis of gene expression by real time quantitative PCR...
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Papers by Jodi Scheffler