Publications by authors named "Don C Jones"

25 Publications

  • Page 1 of 1

LCM and RNA-seq analyses revealed roles of cell cycle and translational regulation and homoeolog expression bias in cotton fiber cell initiation.

BMC Genomics 2021 Apr 29;22(1):309. Epub 2021 Apr 29.

Department of Molecular Biosciences, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.

Background: Cotton fibers provide a powerful model for studying cell differentiation and elongation. Each cotton fiber is a singular and elongated cell derived from epidermal-layer cells of a cotton seed. Efforts to understand this dramatic developmental shift have been impeded by the difficulty of separation between fiber and epidermal cells.

Results: Here we employed laser-capture microdissection (LCM) to separate these cell types. RNA-seq analysis revealed transitional differences between fiber and epidermal-layer cells at 0 or 2 days post anthesis. Specifically, down-regulation of putative cell cycle genes was coupled with upregulation of ribosome biosynthesis and translation-related genes, which may suggest their respective roles in fiber cell initiation. Indeed, the amount of fibers in cultured ovules was increased by cell cycle progression inhibitor, Roscovitine, and decreased by ribosome biosynthesis inhibitor, Rbin-1. Moreover, subfunctionalization of homoeologs was pervasive in fiber and epidermal cells, with expression bias towards 10% more D than A homoeologs of cell cycle related genes and 40-50% more D than A homoeologs of ribosomal protein subunit genes. Key cell cycle regulators were predicted to be epialleles in allotetraploid cotton. MYB-transcription factor genes displayed expression divergence between fibers and ovules. Notably, many phytohormone-related genes were upregulated in ovules and down-regulated in fibers, suggesting spatial-temporal effects on fiber cell development.

Conclusions: Fiber cell initiation is accompanied by cell cycle arrest coupled with active ribosome biosynthesis, spatial-temporal regulation of phytohormones and MYB transcription factors, and homoeolog expression bias of cell cycle and ribosome biosynthesis genes. These valuable genomic resources and molecular insights will help develop breeding and biotechnological tools to improve cotton fiber production.
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http://dx.doi.org/10.1186/s12864-021-07579-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082777PMC
April 2021

From Sequencing to Genome Editing for Cotton Improvement.

Trends Biotechnol 2021 03 28;39(3):221-224. Epub 2020 Sep 28.

Department of Biology, East Carolina University, Greenville, NC 27858, USA. Electronic address:

Traditional breeding techniques are proven, but additional knowledge learned from genome sequencing provides vast new data that might help identify gene targets for improving cotton sustainability. CRISPR/Cas9 provides a powerful tool for precision cotton breeding. Here, we discuss the opportunities and challenges of genome sequencing and editing for cotton improvement.
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http://dx.doi.org/10.1016/j.tibtech.2020.09.001DOI Listing
March 2021

Validation of QTLs for Fiber Quality Introgressed from by Selective Genotyping.

G3 (Bethesda) 2020 07 7;10(7):2377-2384. Epub 2020 Jul 7.

School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China.

Gene introgression from wild species has been shown to be a feasible approach for fiber quality improvement in Upland cotton. Previously, we developed an interspecific × advanced-backcross population and mapped over one hundred QTL for fiber quality traits. In the current study, a trait-based selective genotyping approach was utilized to prioritize a small subset of introgression lines with high phenotypic values for different fiber quality traits, to simultaneously validate multiple fiber quality QTL in a single experiment. A total of 75 QTL were detected by CIM and/or single-marker analysis, including 11 significant marker-trait associations ( < 0.001) and three putative associations ( < 0.005) also reported in earlier studies. The QTL that have been validated include three each for fiber length, micronaire, and elongation, and one each for fiber strength and uniformity. Collectively, about 10% of the QTL previously reported have been validated here, indicating that selective genotyping has the potential to validate multiple marker-trait associations for different traits, especially those with a moderate to large-effect detected simultaneously in one experimental population. The alleles contributed to improved fiber quality for all validated loci. The results from this study will lay the foundation for further fine mapping, marker-assisted selection and map-based gene cloning.
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http://dx.doi.org/10.1534/g3.120.401125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341125PMC
July 2020

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement.

Nat Genet 2020 05 20;52(5):525-533. Epub 2020 Apr 20.

Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.

Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.
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http://dx.doi.org/10.1038/s41588-020-0614-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203012PMC
May 2020

High-density linkage map construction and QTL analyses for fiber quality, yield and morphological traits using CottonSNP63K array in upland cotton (Gossypium hirsutum L.).

BMC Genomics 2019 Nov 21;20(1):889. Epub 2019 Nov 21.

Cotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA.

Background: Improving fiber quality and yield are the primary research objectives in cotton breeding for enhancing the economic viability and sustainability of Upland cotton production. Identifying the quantitative trait loci (QTL) for fiber quality and yield traits using the high-density SNP-based genetic maps allows for bridging genomics with cotton breeding through marker assisted and genomic selection. In this study, a recombinant inbred line (RIL) population, derived from cross between two parental accessions, which represent broad allele diversity in Upland cotton, was used to construct high-density SNP-based linkage maps and to map the QTLs controlling important cotton traits.

Results: Molecular genetic mapping using RIL population produced a genetic map of 3129 SNPs, mapped at a density of 1.41 cM. Genetic maps of the individual chromosomes showed good collinearity with the sequence based physical map. A total of 106 QTLs were identified which included 59 QTLs for six fiber quality traits, 38 QTLs for four yield traits and 9 QTLs for two morphological traits. Sub-genome wide, 57 QTLs were mapped in A sub-genome and 49 were mapped in D sub-genome. More than 75% of the QTLs with favorable alleles were contributed by the parental accession NC05AZ06. Forty-six mapped QTLs each explained more than 10% of the phenotypic variation. Further, we identified 21 QTL clusters where 12 QTL clusters were mapped in the A sub-genome and 9 were mapped in the D sub-genome. Candidate gene analyses of the 11 stable QTL harboring genomic regions identified 19 putative genes which had functional role in cotton fiber development.

Conclusion: We constructed a high-density genetic map of SNPs in Upland cotton. Collinearity between genetic and physical maps indicated no major structural changes in the genetic mapping populations. Most traits showed high broad-sense heritability. One hundred and six QTLs were identified for the fiber quality, yield and morphological traits. Majority of the QTLs with favorable alleles were contributed by improved parental accession. More than 70% of the mapped QTLs shared the similar map position with previously reported QTLs which suggest the genetic relatedness of Upland cotton germplasm. Identification of QTL clusters could explain the correlation among some fiber quality traits in cotton. Stable and major QTLs and QTL clusters of traits identified in the current study could be the targets for map-based cloning and marker assisted selection (MAS) in cotton breeding. The genomic region on D12 containing the major stable QTLs for micronaire, fiber strength and lint percentage could be potential targets for MAS and gene cloning of fiber quality traits in cotton.
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http://dx.doi.org/10.1186/s12864-019-6214-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6878679PMC
November 2019

Evaluation of genomic selection methods for predicting fiber quality traits in Upland cotton.

Mol Genet Genomics 2020 Jan 31;295(1):67-79. Epub 2019 Aug 31.

Cotton Incorporated, Cary, NC, 27513, USA.

The use of genomic selection (GS) has stimulated a new way to utilize molecular markers in breeding for complex traits in the absence of phenotypic data. GS can potentially decrease breeding cycle by selecting the progeny in the early stages. The objective of this study was to experimentally evaluate the potential value of genomic selection in Upland cotton breeding. Six fiber quality traits were obtained in 3 years of replicated field trials in Starkville, MS. Genotyping-by-sequencing-based genotyping was performed using 550 recombinant inbred lines of the multi-parent advanced generation inter-cross population, and 6292 molecular markers were used for the GS analysis. Several methods were compared including genomic BLUP (GBLUP), ridge regression BLUP (rrBLUP), BayesB, Bayesian LASSO, and reproducing kernel hilbert spaces (RKHS). The average heritability (h) ranged from 0.38 to 0.88 for all tested traits across the 3 years evaluated. BayesB predicted the highest accuracies among the five GS methods tested. The prediction ability (PA) and prediction accuracy (PACC) varied widely across 3 years for all tested traits and the highest PA and PACC were 0.65, and 0.69, respectively, in 2010 for fiber elongation. Marker density and training population size appeared to be very important factors for PA and PACC in GS. Results indicated that BayesB-based GS method could predict genomic estimated breeding value efficiently in Upland cotton fiber quality attributes and has great potential utility in breeding by reducing cost and time.
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http://dx.doi.org/10.1007/s00438-019-01599-zDOI Listing
January 2020

Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.).

Theor Appl Genet 2019 Apr 1;132(4):989-999. Epub 2018 Dec 1.

Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA.

Key Message: Significant associations between candidate genes and six major cotton fiber quality traits were identified in a MAGIC population using GWAS and whole genome sequencing. Upland cotton (Gossypium hirsutum L.) is the world's major renewable source of fibers for textiles. To identify causative genetic variants that influence the major agronomic measures of cotton fiber quality, which are used to set discount or premium prices on each bale of cotton in the USA, we measured six fiber phenotypes from twelve environments, across three locations and 7 years. Our 550 recombinant inbred lines were derived from a multi-parent advanced generation intercross population and were whole-genome-sequenced at 3× coverage, along with the eleven parental cultivars at 20× coverage. The segregation of 473,517 single nucleotide polymorphisms (SNPs) in this population, including 7506 non-synonymous mutations, was combined with phenotypic data to identify seven highly significant fiber quality loci. At these loci, we found fourteen genes with non-synonymous SNPs. Among these loci, some had simple additive effects, while others were only important in a subset of the population. We observed additive effects for elongation and micronaire, when the three most significant loci for each trait were examined. In an informative subset where the major multi-trait locus on chromosome A07:72-Mb was fixed, we unmasked the identity of another significant fiber strength locus in gene Gh_D13G1792 on chromosome D13. The micronaire phenotype only revealed one highly significant genetic locus at one environmental location, demonstrating a significant genetic by environment component. These loci and candidate causative variant alleles will be useful to cotton breeders for marker-assisted selection with minimal linkage drag and potential biotechnological applications.
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http://dx.doi.org/10.1007/s00122-018-3254-8DOI Listing
April 2019

Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids.

Sci Rep 2017 11 10;7(1):15274. Epub 2017 Nov 10.

Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA.

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 to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.
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http://dx.doi.org/10.1038/s41598-017-14885-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681701PMC
November 2017

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.

BMC Plant Biol 2017 02 3;17(1):37. Epub 2017 Feb 3.

Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.

Background: 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 analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits.

Results: The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content.

Conclusions: Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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http://dx.doi.org/10.1186/s12870-017-0981-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5291959PMC
February 2017

Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.).

Proc Natl Acad Sci U S A 2017 01 20;114(1):E57-E66. Epub 2016 Dec 20.

Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620;

Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D), which is responsible for the major leaf shapes in cotton. The l-D locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype.
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http://dx.doi.org/10.1073/pnas.1613593114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224360PMC
January 2017

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton.

BMC Genomics 2016 11 9;17(1):903. Epub 2016 Nov 9.

Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA.

Background: Cotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders' ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed through random-mating of multiple diverse parents has the ability to break this negative correlation. Genotyping-by-sequencing (GBS) is a method that can rapidly identify and genotype a large number of single nucleotide polymorphisms (SNP). Genotyping a MAGIC population using GBS technologies will enable us to identify marker-trait associations with high resolution.

Results: An Upland cotton MAGIC population was developed through random-mating of 11 diverse cultivars for five generations. In this study, fiber quality data obtained from four environments and 6071 SNP markers generated via GBS and 223 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS). By employing a mixed linear model, GWAS enabled us to identify markers significantly associated with fiber quantitative trait loci (QTL). We identified and validated one QTL cluster associated with four fiber quality traits [short fiber content (SFC), strength (STR), length (UHM) and uniformity (UI)] on chromosome A07. We further identified candidate genes related to fiber quality attributes in this region. Gene expression and amino acid substitution analysis suggested that a regeneration of bulb biogenesis 1 (GhRBB1_A07) gene is a candidate for superior fiber quality in Upland cotton. The DNA marker CFBid0004 designed from an 18 bp deletion in the coding sequence of GhRBB1_A07 in Acala Ultima is associated with the improved fiber quality in the MAGIC RILs and 105 additional commercial Upland cotton cultivars.

Conclusion: Using GBS and a MAGIC population enabled more precise fiber QTL mapping in Upland cotton. The fiber QTL and associated markers identified in this study can be used to improve fiber quality through marker assisted selection or genomic selection in a cotton breeding program. Target manipulation of the GhRBB1_A07 gene through biotechnology or gene editing may potentially improve cotton fiber quality.
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http://dx.doi.org/10.1186/s12864-016-3249-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103610PMC
November 2016

Genome-Wide Identification of R2R3-MYB Genes and Expression Analyses During Abiotic Stress in Gossypium raimondii.

Sci Rep 2016 Mar 24;6:22980. Epub 2016 Mar 24.

Department of Biology, East Carolina University, Greenville, NC 27858, United States of America.

The R2R3-MYB is one of the largest families of transcription factors, which have been implicated in multiple biological processes. There is great diversity in the number of R2R3-MYB genes in different plants. However, there is no report on genome-wide characterization of this gene family in cotton. In the present study, a total of 205 putative R2R3-MYB genes were identified in cotton D genome (Gossypium raimondii), that are much larger than that found in other cash crops with fully sequenced genomes. These GrMYBs were classified into 13 groups with the R2R3-MYB genes from Arabidopsis and rice. The amino acid motifs and phylogenetic tree were predicted and analyzed. The sequences of GrMYBs were distributed across 13 chromosomes at various densities. The results showed that the expansion of the G. Raimondii R2R3-MYB family was mainly attributable to whole genome duplication and segmental duplication. Moreover, the expression pattern of 52 selected GrMYBs and 46 GaMYBs were tested in roots and leaves under different abiotic stress conditions. The results revealed that the MYB genes in cotton were differentially expressed under salt and drought stress treatment. Our results will be useful for determining the precise role of the MYB genes during stress responses with crop improvement.
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http://dx.doi.org/10.1038/srep22980DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806351PMC
March 2016

Comprehensive analysis of TCP transcription factors and their expression during cotton (Gossypium arboreum) fiber early development.

Sci Rep 2016 Feb 9;6:21535. Epub 2016 Feb 9.

Department of Biology, East Carolina University, Greenville, NC 27858, USA.

TCP proteins are plant-specific transcription factors implicated to perform a variety of physiological functions during plant growth and development. In the current study, we performed for the first time the comprehensive analysis of TCP gene family in a diploid cotton species, Gossypium arboreum, including phylogenetic analysis, chromosome location, gene duplication status, gene structure and conserved motif analysis, as well as expression profiles in fiber at different developmental stages. Our results showed that G. arboreum contains 36 TCP genes, distributing across all of the thirteen chromosomes. GaTCPs within the same subclade of the phylogenetic tree shared similar exon/intron organization and motif composition. In addition, both segmental duplication and whole-genome duplication contributed significantly to the expansion of GaTCPs. Many these TCP transcription factor genes are specifically expressed in cotton fiber during different developmental stages, including cotton fiber initiation and early development. This suggests that TCP genes may play important roles in cotton fiber development.
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http://dx.doi.org/10.1038/srep21535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4746668PMC
February 2016

Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set.

J Hered 2016 05 16;107(3):274-86. Epub 2016 Jan 16.

From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones).

A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources.
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http://dx.doi.org/10.1093/jhered/esw004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4885238PMC
May 2016

Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood.

Appl Environ Microbiol 2015 Nov 4;81(22):7802-12. Epub 2015 Sep 4.

U.S. Forest Products Laboratory, Madison, Wisconsin, USA Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA

Since uncertainty remains about how white rot fungi oxidize and degrade lignin in wood, it would be useful to monitor changes in fungal gene expression during the onset of ligninolysis on a natural substrate. We grew Phanerochaete chrysosporium on solid spruce wood and included oxidant-sensing beads bearing the fluorometric dye BODIPY 581/591 in the cultures. Confocal fluorescence microscopy of the beads showed that extracellular oxidation commenced 2 to 3 days after inoculation, coincident with cessation of fungal growth. Whole transcriptome shotgun sequencing (RNA-seq) analyses based on the v.2.2 P. chrysosporium genome identified 356 genes whose transcripts accumulated to relatively high levels at 96 h and were at least four times the levels found at 40 h. Transcripts encoding some lignin peroxidases, manganese peroxidases, and auxiliary enzymes thought to support their activity showed marked apparent upregulation. The data were also consistent with the production of ligninolytic extracellular reactive oxygen species by the action of manganese peroxidase-catalyzed lipid peroxidation, cellobiose dehydrogenase-catalyzed Fe(3+) reduction, and oxidase-catalyzed H2O2 production, but the data do not support a role for iron-chelating glycopeptides. In addition, transcripts encoding a variety of proteins with possible roles in lignin fragment uptake and processing, including 27 likely transporters and 18 cytochrome P450s, became more abundant after the onset of extracellular oxidation. Genes encoding cellulases showed little apparent upregulation and thus may be expressed constitutively. Transcripts corresponding to 165 genes of unknown function accumulated more than 4-fold after oxidation commenced, and some of them may merit investigation as possible contributors to ligninolysis.
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http://dx.doi.org/10.1128/AEM.02064-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4616959PMC
November 2015

A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery.

Plant Genome 2015 Jul;8(2):eplantgenome2014.10.0068

Univ. of California-Davis, Dep. of Plant Sciences and Seed Biotechnology Center, One Shields Ave., Davis, CA, 95616.

Upland cotton (Gossypium hirsutum L.) has a narrow germplasm base, which constrains marker development and hampers intraspecific breeding. A pressing need exists for high-throughput single nucleotide polymorphism (SNP) markers that can be readily applied to germplasm in breeding and breeding-related research programs. Despite progress made in developing new sequencing technologies during the past decade, the cost of sequencing remains substantial when one is dealing with numerous samples and large genomes. Several strategies have been proposed to lower the cost of sequencing for multiple genotypes of large-genome species like cotton, such as transcriptome sequencing and reduced-representation DNA sequencing. This paper reports the development of a transcriptome assembly of the inbred line Texas Marker-1 (TM-1), a genetic standard for cotton, its usefulness as a reference for RNA sequencing (RNA-seq)-based SNP identification, and the availability of transcriptome sequences of four other cotton cultivars. An assembly of TM-1 was made using Roche 454 transcriptome reads combined with an assembly of all available public expressed sequence tag (EST) sequences of TM-1. The TM-1 assembly consists of 72,450 contigs with a total of 70 million bp. Functional predictions of the transcripts were estimated by alignment to selected protein databases. Transcriptome sequences of the five lines, including TM-1, were obtained using an Illumina Genome Analyzer-II, and the short reads were mapped to the TM-1 assembly to discover SNPs among the five lines. We identified >14,000 unfiltered allelic SNPs, of which ∼3,700 SNPs were retained for assay development after applying several rigorous filters. This paper reports availability of the reference transcriptome assembly and shows its utility in developing intraspecific SNP markers in upland cotton.
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http://dx.doi.org/10.3835/plantgenome2014.10.0068DOI Listing
July 2015

Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

G3 (Bethesda) 2015 Apr 22;5(6):1187-209. Epub 2015 Apr 22.

USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.
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http://dx.doi.org/10.1534/g3.115.018416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4478548PMC
April 2015

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.

Nat Biotechnol 2015 May 20;33(5):531-7. Epub 2015 Apr 20.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.

Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.
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http://dx.doi.org/10.1038/nbt.3207DOI Listing
May 2015

Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii.

Funct Integr Genomics 2015 Jul 26;15(4):481-93. Epub 2015 Mar 26.

Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China.

Auxin response factors (ARFs) are recently discovered transcription factors that bind with auxin response elements (AuxRE, TGTCTC) to regulate the expression of early auxin-responsive genes. To our knowledge, the ARF gene family has never been characterized in cotton, the most important fiber crop in the world. In this study, a total of 35 ARF genes, named as GrARFs, were identified in a diploid cotton species Gossypium raimondii. The 35 ARF genes were located in 12 of the 13 cotton chromosomes; the intron/exon distribution of the GrARF genes was similar among sister pairs, whereas the divergence of some GrARF genes suggests the possibility of functional diversification. Our results show that the middle domains of nine GrARF proteins rich in glutamine (Q) are activators, while 26 other GrARF proteins rich in proline (P), serine (S), and threonine (T) are repressors. Our results also show that the expression of GrARF genes is diverse in different tissues. The expression of GrARF1 was significantly higher in leaves, whereas GrARF2a had higher expression level in shoots, which implicates different roles in the tested tissues. The GrARF11 has a higher expression level in buds than that in leaves, while GrARF19.2 shows contrasting expression patterns, having higher expression in leaves than that in buds. This suggests that they play different roles in leaves and buds. During long-term evolution of G. raimondii, some ARF genes were lost and some arose. The identification and characterization of the ARF genes in G. raimondii elucidate its important role in cotton that ARF genes regulate the development of flower buds, sepals, shoots, and leaves.
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http://dx.doi.org/10.1007/s10142-015-0437-0DOI Listing
July 2015

Small RNA sequencing identifies miRNA roles in ovule and fibre development.

Plant Biotechnol J 2015 Apr 9;13(3):355-69. Epub 2015 Jan 9.

Department of Biology, East Carolina University, Greenville, NC, USA.

MicroRNAs (miRNAs) have been found to be differentially expressed during cotton fibre development. However, which specific miRNAs and how they are involved in fibre development is unclear. Here, using deep sequencing, 65 conserved miRNA families were identified and 32 families were differentially expressed between leaf and ovule. At least 40 miRNAs were either leaf or ovule specific, whereas 62 miRNAs were shared in both leaf and ovule. qRT-PCR confirmed these miRNAs were differentially expressed during fibre early development. A total of 820 genes were potentially targeted by the identified miRNAs, whose functions are involved in a series of biological processes including fibre development, metabolism and signal transduction. Many predicted miRNA-target pairs were subsequently validated by degradome sequencing analysis. GO and KEGG analyses showed that the identified miRNAs and their targets were classified to 1027 GO terms including 568 biological processes, 324 molecular functions and 135 cellular components and were enriched to 78 KEGG pathways. At least seven unique miRNAs participate in trichome regulatory interaction network. Eleven trans-acting siRNA (tasiRNA) candidate genes were also identified in cotton. One has never been found in other plant species and two of them were derived from MYB and ARF, both of which play important roles in cotton fibre development. Sixteen genes were predicted to be tasiRNA targets, including sucrose synthase and MYB2. Together, this study discovered new miRNAs in cotton and offered evidences that miRNAs play important roles in cotton ovule/fibre development. The identification of tasiRNA genes and their targets broadens our understanding of the complicated regulatory mechanism of miRNAs in cotton.
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http://dx.doi.org/10.1111/pbi.12296DOI Listing
April 2015

Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts.

BMC Genomics 2014 Oct 30;15:945. Epub 2014 Oct 30.

Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.

Background: Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection.

Results: Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3-79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays.

Conclusions: This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development.
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http://dx.doi.org/10.1186/1471-2164-15-945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298081PMC
October 2014

Genome-wide identification and expression analysis of TCP transcription factors in Gossypium raimondii.

Sci Rep 2014 Oct 16;4:6645. Epub 2014 Oct 16.

1] Department of Biology, East Carolina University, Greenville, NC 27858, USA [2] Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, P. R. China.

Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play versatile functions in multiple aspects of plant growth and development. However, no systematical study has been performed in cotton. In this study, we performed for the first time the genome-wide identification and expression analysis of the TCP transcription factor family in Gossypium raimondii. A total of 38 non-redundant cotton TCP encoding genes were identified. The TCP transcription factors were divided into eleven subgroups based on phylogenetic analysis. Most TCP genes within the same subfamily demonstrated similar exon and intron organization and the motif structures were highly conserved among the subfamilies. Additionally, the chromosomal distribution pattern revealed that TCP genes were unevenly distributed across 11 out of the 13 chromosomes; segmental duplication is a predominant duplication event for TCP genes and the major contributor to the expansion of TCP gene family in G. raimondii. Moreover, the expression profiles of TCP genes shed light on their functional divergence.
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http://dx.doi.org/10.1038/srep06645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5377578PMC
October 2014

Non-destructive high-throughput DNA extraction and genotyping methods for cotton seeds and seedlings.

Biotechniques 2015 May 1;58(5):234-43. Epub 2015 May 1.

Cotton Incorporated, Cary, NC.

Extensive use of targeted PCR-based genotyping is precluded for many plant research laboratories by the cost and time required for DNA extraction. Using cotton (Gossypium hirsutum) as a model for plants with medium-sized seeds, we report here manual procedures for inexpensive non-destructive high-throughput extraction of DNA suitable for PCR-based genotyping of large numbers of individual seeds and seedlings. By sampling only small amounts of cotyledon tissue of ungerminated seed or young seedlings, damage is minimized, and viability is not discernibly affected. The yield of DNA from each seed or seedling is typically sufficient for 1000 or 500 PCR reactions, respectively. For seeds, the tissue sampling procedure relies on a modified 96-well plate that is used subsequently for seed storage. For seeds and seedlings, the DNA is extracted in a strongly basic DNA buffer that is later neutralized and diluted. Extracts can be used directly for high-throughput PCR-based genotyping. Any laboratory can thus extract DNA from thousands of individual seeds/seedlings per person-day at a very modest cost for consumables (~$0.05 per sample). Being non-destructive, our approach enables a wide variety of time- and resource-saving applications, such as marker-assisted selection (MAS), before planting, transplanting, and flowering.
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http://dx.doi.org/10.2144/000114286DOI Listing
May 2015

RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

PLoS One 2013 6;8(12):e82634. Epub 2013 Dec 6.

USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America.

An RNA-Seq experiment was performed using field grown well-watered and naturally rain fed cotton plants to identify differentially expressed transcripts under water-deficit stress. Our work constitutes the first application of the newly published diploid D5 Gossypium raimondii sequence in the study of tetraploid AD1 upland cotton RNA-seq transcriptome analysis. A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed root tissues, in patterns that confirm the accuracy of this technique for future studies in cotton genomics. Additionally, putative sequence based genome localization of differentially expressed transcripts detected A2 genome specific gene expression under water-deficit stress. These data will facilitate efforts to understand the complex responses governing transcriptomic regulatory mechanisms and to identify candidate genes that may benefit applied plant breeding programs.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082634PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855774PMC
July 2014

Spatial mapping of extracellular oxidant production by a white rot basidiomycete on wood reveals details of ligninolytic mechanism.

Environ Microbiol 2013 Mar 4;15(3):956-66. Epub 2012 Dec 4.

US Forest Products Laboratory, Madison, WI 53726, USA.

Oxidative cleavage of the recalcitrant plant polymer lignin is a crucial step in global carbon cycling, and is accomplished most efficiently by fungi that cause white rot of wood. These basidiomycetes secrete many enzymes and metabolites with proposed ligninolytic roles, and it is not clear whether all of these agents are physiologically important during attack on natural lignocellulosic substrates. One new approach to this problem is to infer properties of ligninolytic oxidants from their spatial distribution relative to the fungus on the lignocellulose. We grew Phanerochaete chrysosporium on wood sections in the presence of oxidant-sensing beads based on the ratiometric fluorescent dye BODIPY 581/591. The beads, having fixed locations relative to the fungal hyphae, enabled spatial mapping of cumulative extracellular oxidant distributions by confocal fluorescence microscopy. The results showed that oxidation gradients occurred around the hyphae, and data analysis using a mathematical reaction-diffusion model indicated that the dominant oxidant during incipient white rot had a half-life under 0.1 s. The best available hypothesis is that this oxidant is the cation radical of the secreted P. chrysosporium metabolite veratryl alcohol.
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http://dx.doi.org/10.1111/1462-2920.12039DOI Listing
March 2013
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