Articles related to genetics 03/18
Mar 12, 2018

Breeding & Genetic improvement Biotechnology

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Ishwarappa KATAGERI

Genetic Analysis of Gossypium Fiber Quality Traits in Reciprocal Advanced Backcross Populations
Chandnani R et al.
Plant Genome. 2018 Mar; 11(1). doi: 10.3835/plantgenome2017.06.0057
Corresponding author:

In mapping populations segregating for many loci, the large amount of variation among genotypes often masks small-effect quantitative trait loci (QTL). This problem can be reduced by development of populations with fewer chromosome segments segregating. Here, we report early QTL detection in reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum L. 'Acala Maxxa' (GH) and G. barbadense L. 'Pima S6' (GB). A total of 297 BCF and BCF progeny rows-127 segregating for GB chromosome segments in GH background and 170 segregating for GH chromosome segments in GB background-were evaluated in three environments. Totals of 3186 and 3026 polymorphic single-nucleotide polymorphisms (SNPs) in GH and GB backgrounds, respectively, were identified and used for trait mapping. Small-effect QTL (<10% variance explained) made up 87 and 100% of QTL in GH and GB backgrounds, respectively

 Genetic Map Construction and Fiber Quality QTL Mapping Using the Cotton SNP80K Array in Upland Cotton
Zhaoyun Tan et al.
Front. Plant Sci. 9:225. (2018)
Corresponding author:

Cotton fiber quality traits are controlled by multiple quantitative trait loci (QTL), and the improvement of these traits requires extensive germplasm. Herein, an Upland cotton cultivar from America, Acala Maxxa, was crossed with a local high fiber quality cultivar, Yumian 1, and 180 recombinant inbred lines (RILs) were obtained. In order to dissect the genetic basis of fiber quality differences between these parents, a genetic map containing12116 SNP markers was constructed using the CottonSNP80K assay, which covered 3741.81 cM with an average distance of 0.31 cM between markers. Based on the genetic map and grow outs in three environments, we detected a total of 104 QTL controlling fiber quality traits. Among these QTL, 25 were detected in all three environments and35 in two environments.

Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton.
unji Su et al.
Theor Appl Genet. 2018 Mar 1. doi: 10.1007/s00122-018-3079-5
Corresponding author:

A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block.

Expression of cry2Ah1 and two domain II mutants in transgenic tobacco confers high resistance to susceptible and Cry1Ac-resistant cotton bollworm
Li S et al.Sci Rep. 2018 Jan 11;8(1):508.
doi: 10.1038/s41598-017-19064-5.
Corresponding author:

To improve the novel Bacillus thuringiensis insecticidal gene cry2Ah1 toxicity, two mutants cry2Ah1-vp (V354VP) and cry2Ah1-sp (V354SP) were performed. SWISS-MODEL analysis showed two mutants had a longer loop located between β-4 and β-5 of domain II, resulting in higher binding affinity with brush border membrane vesicles (BBMV) of Helicoverpa armigera comparing with Cry2Ah1

Genetic dissection of the fuzzless seed trait in Gossypium barbadense.
Zhu QH et al.
J Exp Bot. 2018 Jan 17. doi: 10.1093/jxb/erx459.
Corresponding author: and

Cotton fibres are single-celled trichomes arising from the epidermal cells of the seed coat and may be either long (lint) or very short (fuzz). The dominant fuzzless N1 of Gossypium hirsutum is a defective allele of the At-subgenome homoeolog of MYB25-like, but the genetic components underlying the recessive fuzzless trait from G. barbadense (Gb) are unknown. We have identified five genetic loci, including a major contributing locus containing MYB25-like_Dt, associated with Gb fuzzless seeds based on genotyping of fuzzy and fuzzless near isogenic lines (NILs) from an interspecies cross (G. barbadense × G. hirsutum).

Genome-Wide Characterisation of DNA Methylation in an Invasive Lepidopteran Pest, the Cotton Bollworm Helicoverpa armigera
Jones CM, Lim KS, Chapman JW, Bass C
G3 (Bethesda). 2018 Mar 2;8(3):779-787.
doi: 10.1534/g3.117.1112.
Corresponding author:

The genes and genomes of insect pests are shaped by the wide array of selective forces encountered in their environments. While the molecular adaptations that evolve are beginning to be understood at the genomic and transcriptomic level they have been less well characterised at an epigenetic level. Here, we present a genome-wide map of DNA methylation, at single-nucleotide resolution for the cotton bollworm moth, Helicoverpa armigera; a globally invasive pest of agriculture. We show that methylation is almost identical in the larvae and adults of H. armigera and that, through whole genome bisulfite sequencing, at the most ~0.9% of CpG sites in this species are methylated.


Inducement and identification of chromosome introgression and translocation of Gossypium australe on Gossypium hirsutum.
Wang Y et al.
BMC Genomics. 2018 Jan 4; 19(1):15.
doi: 10.1186/s12864-017-4398-7.
Corresponding author:

We previously reported the development of a set of Gossypium hirsutum-G. australe alien chromosome addition lines. Naturally, however, G. hirsutum-G. australe chromosome exchanges were very limited, impeding the stable transference of useful genes from G. australe (G2G2 genome) into the most cultivated cotton, G. hirsutum (AADD)

In-field High Throughput Phenotyping and Cotton Plant Growth Analysis Using LiDAR
Sun S et al.
Front Plant Sci. 2018 Jan 22; 9: 6.
doi: 10.3389/fpls.2018.00016. eCollection 2018
Corresponding author:

Plant breeding programs and a wide range of plant science applications would greatly benefit from the development of in-field high throughput phenotyping technologies. In this study, a terrestrial LiDAR-based high throughput phenotyping system was developed. A 2D LiDAR was applied to scan plants from overhead in the field, and an RTK-GPS was used to provide spatial coordinates. Precise 3D models of scanned plants were reconstructed based on the LiDAR and RTK-GPS data. The ground plane of the 3D model was separated by RANSAC algorithm and a Euclidean clustering algorithm was applied to remove noise generated by weeds. After that, clean 3D surface models of cotton plants were obtained, from which three plot-level morphologic traits including canopy height, projected canopy area, and plant volume were derived. Canopy height ranging from 85th percentile to the maximum height were computed based on the histogram of the z coordinate for all measured points; projected canopy area was derived by projecting all points on a ground plane; and a Trapezoidal rule based algorithm was proposed to estimate plant volume

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum).
Wen T et al.
Plant Biotechnol J. 2018 Feb 24. doi: 10.1111/pbi.12902.
Corresponding author: and

Brown fibre cotton is an environmental-friendly resource that plays a key role in the textile industry. However, the fibre quality and yield of natural brown cotton are poor, and fundamental research on brown cotton is relatively scarce. To understand the genetic basis of brown fibre cotton, we constructed linkage and association populations to systematically examine brown fibre accessions. We fine-mapped the brown fibre region, Lc1, and dissected it into two loci, qBF-A07-1 and qBF-A07-2.

Physical mapping and candidate gene prediction of fertility restorer gene of cytoplasmic male sterility in cotton.
Zhao C et al.
BMC Genomics. 2018 Jan 2; 19(1):6. doi: 10.1186/s12864-017-4406-y.
Corresponding author:  And

Cytoplasmic male sterility (CMS) is a maternally inherited trait failing to produce functional pollen. It plays a pivotal role in the exploitation of crop heterosis. The specific locus amplified fragment sequencing (SLAF-seq) as a high-resolution strategy for the identification of new SNPs on a large-scale is gradually applied for functional gene mining. The current study combined the bulked segregant analysis (BSA) with SLAF-seq to identify the candidate genes associated with fertility restorer gene (Rf) in CMS cotton.

QTL delineation for five fiber quality traits based on an intra-specific Gossypium hirsutum L. recombinant inbred line population.
Jia X et al.
Mol Genet Genomics. 2018 Feb 8. doi: 10.1007/s00438-018-1424-7.
Corresponding author:

Gossypium hirsutum L. is the most important fiber crop worldwide and contributes to more than 95% of global cotton production. Marker-assisted selection (MAS) is an effective approach for improving fiber quality, and quantitative trait loci (QTL) mapping of fiber quality traits is important for cotton breeding. In this study, a permanent intra-specific recombinant inbred line (RIL) population containing 137 families was used for fiber quality testing. Based on a previously reported high-density genetic map with an average marker distance of 0.63 cM, 186 additive QTLs were obtained for five fiber quality traits over five consecutive years, including 39 for fiber length (FL), 36 for fiber strength (FS), 50 for fiber uniformity (FU), 33 for micronaire (MC) and 28 for fiber elongation (FE). Three stable QTLs, qMC-A4-1, qMC-D2-3 and qFS-D9-1, were detected in four datasets, and another eight stable QTLs, qMC-A4-2, qMC-D11-2, qFU-A9-1, qFU-A10-4, qFS-D11-1, qFL-D9-2, qFL-D11-1 and qFE-A3-2, were detected in three datasets

QTL Mapping for Fiber Quality and Yield Traits Based on Introgression Lines Derived from Gossypium hirsutum × G. tomentosum
Keerio AA et al.
Int J Mol Sci. 2018 Jan 14; 19 (1). pii: E243. doi: 10.3390/ijms19010243
Corresponding author:

The tetraploid species Gossypium hirsutum is cultivated widely throughout the world with high yield and moderate fiber quality, but its genetic basis is narrow. A set of 107 introgression lines (ILs) was developed with an interspecific cross using G. hirsutumacc. 4105 as the recurrent parent and G. tomentosum as the donor parent. A specific locus amplified fragment sequencing (SLAF-seq) strategy was used to obtain high-throughput single nucleotide polymorphism (SNP) markers. In total, 3157 high-quality SNP markers were obtained and further used for identification of quantitative trait loci (QTLs) for fiber quality and yield traits evaluated in multiple environments. In total, 74 QTLs were detected that were associated with five fiber quality traits (30 QTLs) and eight yield traits (44 QTLs), with 2.02-30.15% of the phenotypic variance explained (PVE), and 69 markers were found to be associated with these thirteen traits

Pollen-mediated gene flow from transgenic cotton is constrained by physical isolation measures
Yan Set al.
Sci Rep. 2018 Feb 12;8(1):2862. doi: 10.1038/s41598-018-21312-1.
Corresponding author:

The public concern about pollen-mediated gene flow (PGF) from genetically modified (GM) crops to non-GM crops heats up in recent years over China. In the current study, we conducted greenhouse and field experiments to measure PGF with various physical isolation measures, including 90, 80, 60 and 40 holes/cm2 separation nets and Sorghum bicolor, Zea mays and Lycopersicon esculentum separation crops between GM cotton and non-GM line (Shiyuan321) by seed DNA test during 2013 to 2015, and pollen grain dyeing was also conducted to assess the pollen flow in greenhouse during 2013. Our results revealed that (1) PGF varied depending on the physical isolation measures. PGF was the lowest with 90 holes/cm2 separation net and S. bicolor separation crop, and the highest with 40 holes/cm2 separation net and no isolation measure. (2) Similar to PGF results, 90 holes/cm2 separation net and S. bicolor separation crop could minimize the pollen dispersal. (3) PGF declined exponentially with increasing distance between GM cotton and Shiyuan321. Because of the production mode of farm household (limited cultivated area) in China, our study is particularly important, which is not only benefit for constraining PGF, but also has potential application value in practical production and the scientific researches.

RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii.
Zhu G, Li W, Zhang F, Guo W
BMC Genomics. 2018 Jan 23;19(1):73. doi: 10.1186/s12864-018-4449-8.
Corresponding author:

Using a diploid D genome wild salinity-tolerant cotton species, Gossypium davidsonii, we analyzed alternative splicing (AS) of genes related to salt stress by comparing high-throughput transcriptomes from salt-treated and well-watered roots and leaves. A total of 14,172 AS events were identified involving 6798 genes, of which intron retention (35.73%) was the most frequent, being detected in 3492 genes. Under salt stress, 1287 and 1228 differential alternative splicing (DAS) events were identified in roots and leaves, respectively. These DAS genes were associated with specific functional pathways, such as "responses to stress", "metabolic process" and "RNA splicing", implying that AS represents an important pathway of gene regulation in response to salt stress. Several salt response genes, such as pyrroline-5-carboxylate synthase (P5CS), K+ channel outward (KCO1), plasma membrane intrinsic protein (PIP) and WRKY33 which were involved in osmotic balance, ion homeostasis, water transportation and transcriptional regulation, respectively, were identified with differential alternative splicing under salt stress. Moreover, we revealed that 13 genes encoding Ser/Arg-rich (SR) proteins related to AS regulation were differentially alternatively spliced under salt stres.

Simple Sequence Repeat (SSR) Genetic Linkage Map of D Genome Diploid Cotton Derived from an Interspecific Cross between Gossypium davidsonii and Gossypium klotzschianum.
Kirungu JN et al.
Int J Mol Sci. 2018 Jan 11;19(1). pii: E204. doi: 10.3390/ijms19010204.
Corresponding author: And

The challenge in tetraploid cotton cultivars is the narrow genetic base and therefore, the bottleneck is how to obtain interspecific hybrids and introduce the germplasm directly from wild cotton to elite cultivars. Construction of genetic maps has provided insight into understanding the genome structure, interrelationships between organisms in relation to evolution, and discovery of genes that carry important agronomic traits in plants. In this study, we generated an interspecific hybrid between two wild diploid cottons, Gossypium davidsonii and Gossypium klotzschianum, and genotyped 188 F2:3 populations in order to develop a genetic map. We screened 12,560 SWU Simple Sequence Repeat (SSR) primers and obtained 1000 polymorphic markers which accounted for only 8%. A total of 928 polymorphic primers were successfully scored and only 728 were effectively linked across the 13 chromosomes, but with an asymmetrical distribution. The map length was 1480.23 cM, with an average length of 2.182 cM between adjacent markers.

SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population
Huang C et al.
Mol Genet Genomics. 2018 Feb 1. doi: 10.1007/s00438-018-1419-4.
Corresponding author:

The quality of fiber is significant in the upland cotton industry. As complex quantitative traits, fiber quality traits are worth studying at a genetic level. To investigate the genetic architecture of fiber quality traits, we conducted an association analysis using a multi-parent advanced generation inter-cross (MAGIC) population developed from eight parents and comprised of 960 lines. The reliable phenotypic data for six major fiber traits of the MAGIC population were collected from five environments in three locations. Phenotypic analysis showed that the MAGIC lines have a wider variation amplitude and coefficient than the founders. A total of 284 polymorphic SSR markers among eight parents screened from a high-density genetic map were used to genotype the MAGIC population. The MAGIC population showed abundant genetic variation and fast linkage disequilibrium (LD) decay (0.76 cM, r2 > 0.1), which revealed the advantages of high efficiency and power in QTL exploration. Association mapping via a mixed linear model identified 52 significant loci associated with six fiber quality traits.

Transcriptomic profiling of developing fiber in levant cotton (Gossypium herbaceum L.)
Parekh MJ et al.
Funct Integr Genomics. 2018 Mar;18(2):211-223. doi: 10.1007/s10142-017-0586-4. Epub 2018 Jan 13
Corresponding author:

Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but produce coarse lint. This undesirable characteristic strongly needs the knowledge of fiber development at molecular basis. The present study reported the transcriptome sequence of the developing fiber of G. herbaceum on pyrosequencing and its analysis.

Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation.
He Pet al.
New Phytol. 2018 Apr;2018(1):167-182. doi: 10.1111/nph.14999. Epub 2018 Feb 8.
Corresponding author:

RNA editing is a post-transcriptional maturation process affecting organelle transcripts in land plants. However, the molecular functions and physiological roles of RNA editing are still poorly understood. Using high-throughput sequencing, we identified 692 RNA editing sites in the Gossypium hirsutum mitochondrial genome. A total of 422 editing sites were found in the coding regions and all the edits are cytidine (C) to uridine (U) conversions. Comparative analysis showed that two editing sites in Ghatp1, C1292 and C1415, had a prominent difference in editing efficiency between fiber and ovule. Biochemical and genetic analyses revealed that the two vital editing sites were important for the interaction between the α and β subunits of ATP synthase, which resulted in ATP accumulation and promoted cell growth in yeast. Ectopic expression of C1292, C1415, or doubly edited Ghatp1 in Arabidopsis caused a significant increase in the number of trichomes in leaves and root length

Advanced Backcross QTL Analysis of Fiber Strength and Fineness in a Cross between Gossypium hirsutum and G. mustelinum.
Wang B et al.
Front Plant Sci. 2017 Oct 25;8:1848. doi: 10.3389/fpls.2017.01848.
Corresponding author: and

The molecular genetic basis of cotton fiber strength and fineness in crosses between Gossypium mustelinum and Gossypium hirsutum(Upland cotton) was dissected using 21 BC3F2 and 12 corresponding BC3F2:3 and BC3F2:4 families. The BC3F2 families were genotyped with simple sequence repeat markers from a G. hirsutum by G. mustelinum linkage map, and the three generations of BC3-derived families were phenotyped for fiber strength (STR) and fineness (Micronaire, MIC). A total of 42 quantitative trait loci (QTLs) were identified through one-way analysis of variance, including 15 QTLs for STR and 27 for MIC, with the percentage of variance explained by individual loci averaging 13.86 and 14.06%, respectively. Eighteen of the 42 QTLs were detected at least twice near the same markers in different generations/families or near linked markers in the same family, and 28 of the 42 QTLs were identified in both mixed model-based composite interval mapping and one-way variance analyses.

Physiological and molecular mechanism of defense in cotton against Verticillium dahlia
Shaban M et al.
Plant Physiol Biochem. 2018 Feb 13; 125:193-204. doi: 10.1016/j.plaphy.2018.02.011
Corresponding author:

Cotton, a natural fiber producing crop of huge importance for textile industry, has been reckoned as the backbone in the economy of many developing countries. Verticillium wilt caused by Verticillium dahliae reflected as the most devastating disease of cotton crop in several parts of the world. Average losses due to attack of this disease are tremendous every year. There is urgent need to develop strategies for effective control of this disease. In the last decade, progress has been made to understand the interaction between cotton-V. dahliae and several growth and pathogenicity related genes were identified. Still, most of the molecular components and mechanisms of cotton defense against Verticillium wilt are poorly understood. However, from existing knowledge, it is perceived that cotton defense mechanism primarily depends on the pre-formed defense structures including thick cuticle, synthesis of phenolic compounds and delaying or hindering the expansion of the invader through advanced measures such as reinforcement of cell wall structure, accumulation of reactive oxygen species (ROS), release of phytoalexins, the hypersensitive response and the development of broad spectrum resistance named as, systemic acquired resistance (SAR)

Multivariate Analysis of the Cotton Seed Ionome Reveals a Shared Genetic Architecture
Pauli D et al.
G3 (Bethesda). 2018 Feb 1. pii: g3.300479.2017. doi: 10.1534/g3.117.300479.
Corresponding author:

To mitigate the effects of heat and drought stress, a better understanding of the genetic control of physiological responses to these environmental conditions is needed. To this end, we evaluated an upland cotton (Gossypium hirsutum L.) mapping population under water-limited and well-watered conditions in a hot, arid environment. The elemental concentrations (ionome) of seed samples from the population were profiled in addition to those of soil samples taken from throughout the field site to better model environmental variation. The elements profiled in seeds exhibited moderate to high heritabilities, as well as strong phenotypic and genotypic correlations between elements that were not altered by the imposed irrigation regimes. Quantitative trait loci (QTL) mapping results from a Bayesian classification method identified multiple genomic regions where QTL for individual elements colocalized, suggesting that genetic control of the ionome is highly interrelated.

Evolutionary dynamics of 3D genome architecture following polyploidization in cotton
Wang M et al.
Nat Plants. 2018 Feb; 4(2):90-97. doi: 10.1038/s41477-017-0096-3. Epub 2018 Jan 29
Corresponding author:

The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor. Here, we characterize 3D genome architectures for diploid and tetraploid cotton, and find the existence of A/B compartments and topologically associated domains (TADs). By comparing each subgenome in tetraploids with its extant diploid progenitor, we find that genome allopolyploidization has contributed to the switching of A/B compartments and the reorganization of TADs in both subgenomes.

Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress.
Deng Fet al.
BMC Plant Biol. 2018 Jan 25;18(1):23. doi: 10.1186/s12870-018-1238-0
Corresponding author:

Long non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed into shorter microRNAs (miRNAs) and small interfering RNAs. Long noncoding RNAs (lncRNAs) are arbitrarily defined as RNA genes larger than 200 nt in length that have no apparent coding potential. lncRNAs have emerged as playing important roles in various biological regulatory processes and are expressed in a more tissue-specific manner than mRNA. Emerging evidence shows that lncRNAs participate in stress-responsive regulation.

Genome-wide identification and analysis of the evolution and expression patterns of the cellulose synthase gene superfamily in Gossypium species.
Zou X et al.
Gene. 2018 Mar 10; 646:28-38. doi: 10.1016/j.gene.2017.12.043.
Corresponding author:

The cellulose synthase gene superfamily, which includes the cellulose synthase (Ces) and cellulose synthase-like (Csl) families, is involved in the synthesis of cellulose and hemicellulose. This superfamily is critical for cotton fiber development in Gossypium species. Applying a series of bioinformatic methods, we identified 228 Ces/Csl genes from four Gossypium species (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii). These genes were then grouped into 11 subfamilies based on phylogenetic relationships. A subsequent analysis of gene evolution revealed sites in CSLG and CSLJ genes that were under long-term positive selection pressure, with a posterior probability >0.95. Moreover, the dN:dS value for the CSLJ clade was 1.305, suggesting this subfamily was under positive selection pressure.

High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum) using CRISPR/Cas9 system.
Wang Pet al.
Plant Biotechnol J. 2018 Jan; 16(1):137-150. doi: 10.1111/pbi.12755
Corresponding author: and

Gossypium hirsutum is an allotetraploid with a complex genome. Most genes have multiple copies that belong to At and Dt subgenomes. Sequence similarity is also very high between gene homologues. To efficiently achieve site/gene-specific mutation is quite needed. Due to its high efficiency and robustness, the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system has exerted broad site-specific genome editing from prokaryotes to eukaryotes. In this study, we utilized a CRISPR/Cas9 system to generate two sgRNAs in a single vector to conduct multiple sites genome editing in allotetraploid cotton. An exogenously transformed gene Discosoma red fluorescent protein2 (DsRed2) and an endogenous gene GhCLA1 were chosen as targets. The DsRed2-edited plants in T0 generation reverted its traits to wild type, with vanished red fluorescence the whole plants.

Genome wide identification of cotton (Gossypium hirsutum)-encoded microRNA targets against Cotton leaf curl Burewala virus
Shweta, Akhter Y and Khan JA.
Gene. 2018 Jan 5; 638: 60-65. doi: 10.1016/j.gene.2017.09.061.
Corresponding author:

Cotton leaf curl Burewala virus (CLCuBV, genus Begomovirus) causes devastating cotton leaf curl disease. Among various known virus controlling strategies, RNAi-mediated one has shown potential to protect host crop plants. Micro(mi) RNAs, are the endogenous small RNAs and play a key role in plant development and stress resistance. In the present study we have identified cotton (Gossypium hirsutum)-encoded miRNAs targeting the CLCuBV. Based on threshold free energy and maximum complementarity scores of host miRNA-viral mRNA target pairs, a number of potential miRNAs were annotated. Among them, ghr-miR168 was selected as the most potent candidate, capable of targeting several vital genes namely C1, C3, C4, V1 and V2 of CLCuBV genome. In addition, ghr-miR395a and ghr-miR395d were observed to target the overlapping transcripts of C1 and C4 genes. We have verified the efficacy of these miRNA targets against CLCuBV following suppression of RNAi-mediated virus control through translational inhibition or cleavage of viral mRNA.

A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation.
Wang M et al.
New Phytol. 2018 Jan; 217(1):163-178. doi: 10.1111/nph.14762.
Corresponding author:

Alternative splicing (AS) is a crucial regulatory mechanism in eukaryotes, which acts by greatly increasing transcriptome diversity. The extent and complexity of AS has been revealed in model plants using high-throughput next-generation sequencing. However, this technique is less effective in accurately identifying transcript isoforms in polyploid species because of the high sequence similarity between coexisting subgenomes. Here we characterize AS in the polyploid species cotton. Using Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq), we developed an integrated pipeline for Iso-Seq transcriptome data analysis (

GPhenoVision: A Ground Mobile System with Multi-modal Imaging for Field-Based High Throughput Phenotyping of Cotton
Yu Jiang et al.
Scientific Reports volume 8, Article number: 1213 (2018)

Imaging sensors can extend phenotyping capability, but they require a system to handle high-volume data. The overall goal of this study was to develop and evaluate a field-based high throughput phenotyping system accommodating high-resolution imagers. The system consisted of a high-clearance tractor and sensing and electrical systems. The sensing system was based on a distributed structure, integrating environmental sensors, real-time kinematic GPS, and multiple imaging sensors including RGB-D, thermal, and hyperspectral cameras. Custom software was developed with a multilayered architecture for system control and data collection. The system was evaluated by scanning a cotton field with 23 genotypes for quantification of canopy growth and development. A data processing pipeline was developed to extract phenotypes at the canopy level, including height, width, projected leaf area, and volume from RGB-D data and temperature from thermal images.

Upregulation of GhTT2-3A in Cotton Fibers during Secondary Wall Thickening Results in Brown Fibers with Improved Quality.
Yan Q et al.
Plant Biotechnol J. 2018 Mar 6. doi: 10.1111/pbi.12910

Brown cotton fibers are the most widely used naturally colored raw materials for the eco-friendly textile industry. Previous studies have indicated that brown fiber pigments belong to proanthocyanidins (PAs) or their derivatives, and fiber coloration is negatively associated with cotton productivity and fiber quality. To date, the molecular basis controlling the biosynthesis and accumulation of brown pigments in cotton fibers is largely unknown. In the present study, based on expressional and transgenic analyses of cotton homologs of Arabidopsis PA regulator TRANSPARENT TESTA 2 (TT2) and fine mapping of the cotton dark brown fiber gene (Lc1), we show that a TT2 homolog, GhTT2-3A, controls PA biosynthesis and brown pigmentation in cotton fibers.

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