Publications by authors named "Xiongming Du"

62 Publications

GWAS Mediated Elucidation of Heterosis for Metric Traits in Cotton ( L.) Across Multiple Environments.

Front Plant Sci 2021 20;12:565552. Epub 2021 May 20.

State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China.

For about a century, plant breeding has widely exploited the heterosis phenomenon-often considered as hybrid vigor-to increase agricultural productivity. The ensuing F hybrids can substantially outperform their progenitors due to heterozygous combinations that mitigate deleterious mutations occurring in each genome. However, only fragmented knowledge is available concerning the underlying genes and processes that foster heterosis. Although cotton is among the highly valued crops, its improvement programs that involve the exploitation of heterosis are still limited in terms of significant accomplishments to make it broadly applicable in different agro-ecological zones. Here, F hybrids were derived from mating a diverse Upland Cotton germplasm with commercially valuable cultivars in the Line × Tester fashion and evaluated across multiple environments for 10 measurable traits. These traits were dissected into five different heterosis types and specific combining ability (SCA). Subsequent genome-wide predictions along-with association analyses uncovered a set of 298 highly significant key single nucleotide polymorphisms (SNPs)/Quantitative Trait Nucleotides (QTNs) and 271 heterotic Quantitative Trait Nucleotides (hQTNs) related to agronomic and fiber quality traits. The integration of a genome wide association study with RNA-sequence analysis yielded 275 candidate genes in the vicinity of key SNPs/QTNs. Fiber micronaire (MIC) and lint percentage (LP) had the maximum number of associated genes, i.e., each with 45 related to QTNs/hQTNs. A total of 54 putative candidate genes were identified in association with HETEROSIS of quoted traits. The novel players in the heterosis mechanism highlighted in this study may prove to be scientifically and biologically important for cotton biologists, and for those breeders engaged in cotton fiber and yield improvement programs.
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http://dx.doi.org/10.3389/fpls.2021.565552DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8173050PMC
May 2021

Genome wide identification, classification and functional characterization of heat shock transcription factors in cultivated and ancestral cottons (Gossypium spp.).

Int J Biol Macromol 2021 May 7;182:1507-1527. Epub 2021 May 7.

Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China. Electronic address:

Heat shock transcription factors (HSF) have been demonstrated to play a significant transcriptional regulatory role in plants and considered as an integral part of signal transduction pathways against environmental stresses especially heat stress. Despite of their importance, HSFs have not yet been identified and characterized in all cotton species. In this study, we report the identification of 42, 39, 67, and 79 non-redundant HSF genes from diploid cottons G. arboreum (A2) and G. raimondii (D5), and tetraploid cottons G. barbadense (AD2) and G. hirsutum (AD1) respectively. The chromosome localization of identified HSFs revealed their random distribution on all the 13 chromosomes of A and D genomes of cotton with few regions containing HSFs in clusters. The genes structure and conserved domain analysis revealed the family-specific conservation of intron/exon organization and conserved domains in HSFs. Various abiotic stress-related cis-regulatory elements were identified from the putative promoter regions of cotton HSFs suggesting their possible role in mediating abiotic stress tolerance. The combined phylogenetic analysis of all the cotton HSFs grouped them into three subfamilies; with 145 HSFs belong to class A, 85 to class B, and 17 to class C subfamily. Moreover, a detailed analysis of HSF gene family in four species of cotton elucidated the role of allopolyploid and hybridization during evolutionary cascade of allotetraploid cotton. Comparatively, existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Phylogenetic, collinearity and multiple synteny analyses exhibited dispersed, segmental, proximal, and tandem gene duplication events in HSF gene family. Duplication of gene events suggests that HSF gene family of cotton evolution was under strong purifying selection. Expression analysis revealed that GarHSF04 were found to be actively involved in PEG and salinity tolerance in G. arboreum. GhiHSF14 upregulated in heat and downregulated in salinity whilst almost illustrated similar behavior under cold and PEG treatments and GhiHSF21 exhibited down regulation almost across all the stresses in G. hirsutum. Overwhelmingly, present study paves the way to better understand the evolution of cotton HSF TFs and lays a foundation for future investigation of HSFs in improving abiotic stress tolerance in cotton.
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http://dx.doi.org/10.1016/j.ijbiomac.2021.05.016DOI Listing
May 2021

The genomic basis of geographic differentiation and fiber improvement in cultivated cotton.

Nat Genet 2021 Jun 15;53(6):916-924. Epub 2021 Apr 15.

State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.

Large-scale genomic surveys of crop germplasm are important for understanding the genetic architecture of favorable traits. The genomic basis of geographic differentiation and fiber improvement in cultivated cotton is poorly understood. Here, we analyzed 3,248 tetraploid cotton genomes and confirmed that the extensive chromosome inversions on chromosomes A06 and A08 underlies the geographic differentiation in cultivated Gossypium hirsutum. We further revealed that the haplotypic diversity originated from landraces, which might be essential for understanding adaptative evolution in cultivated cotton. Introgression and association analyses identified new fiber quality-related loci and demonstrated that the introgressed alleles from two diploid cottons had a large effect on fiber quality improvement. These loci provided the potential power to overcome the bottleneck in fiber quality improvement. Our study uncovered several critical genomic signatures generated by historical breeding effects in cotton and a wealth of data that enrich genomic resources for the research community.
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http://dx.doi.org/10.1038/s41588-021-00844-9DOI Listing
June 2021

Genome-wide association and transcriptome analysis of root color-related genes in Gossypium arboreum L.

Planta 2021 Apr 11;253(5):95. Epub 2021 Apr 11.

School of Agriculture Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China.

Main Conclusion: The significant number loci and candidate genes of root color in Gossypium arboreum are identified and provide a theoretical basis of root color for cotton. A stimulating phenomenon was observed on the 4th day of sowing in the root color of some G. arboreum accessions that turned red. To disclose the genetic mechanisms of root color formation via genome and transcript levels, we identified the significant number of SNPs and candidate genes that are related to root color through genome-wide association study (GWAS) and RNAseq analysis in G. arboreum. Initially, 215 no. of G. arboreum accessions was collected, and the colors of root on the 4th, 6th and 9th day of germination were recorded. The GWAS demonstrated that 225 significant SNPs and 47 candidate genes have been identified totally. The strongest signal SNP A04_91824 could greatly distinguish the root color with most "C" allele accessions have displayed white and "T" allele accessions displayed red. RNAseq was performed on accessions having the white and red root, and results revealed that 12 and 138 DEGs were detected on 2nd and 4th day, respectively. ACD6, UFGT, and LYM2 were the most related genes of root color, later, verified by qRT-PCR. The mature zone of red and the white roots was observed by the histological section method, and results shown that cells were more closely arranged in the white root, and both average cell length and cell width were longer in the red root. This study will be helpful to cotton breeders for utilization of several elite genes and related SNPs related to root color, in addition to find linkage with economically important traits of interests.
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http://dx.doi.org/10.1007/s00425-021-03622-3DOI Listing
April 2021

Identification and functional analysis of 9-cis-epoxy carotenoid dioxygenase (NCED) homologs in G. hirsutum.

Int J Biol Macromol 2021 Mar 31;182:298-310. Epub 2021 Mar 31.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China. Electronic address:

9-cis-epoxy carotenoid dioxygenase (NCED) is a fundamental enzyme, which plays an essential role in the process of organ development and stress resistance by regulating abscisic acid (ABA) synthesis in plant. In this study, a total of 7, 7, 14 and 14 NCED genes were identified from the genomes of G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. Phylogenetic tree showed that all forty-two NCED genes could be classified into three groups in cotton genus. Collinear analysis revealed that the NCED genes in G. hirsutum were not amplified by tandem repeats after polyploidy events. The function of NCED genes was evaluated between two accessions with contrasting plant height. The results showed that expression of the NCED genes in dwarf accession was higher than that in taller ones. GhNCED1-silenced cotton plants confirmed that suppression of NCED genes could increase the plant height, but reduce the resistance abilities to drought and salt stress. Our study systematically identified the homologs of NCED genes and their functions in cotton, which could provide new genetic resources for improving plant height and stress in future cotton breeding.
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http://dx.doi.org/10.1016/j.ijbiomac.2021.03.154DOI Listing
March 2021

Differentiation in the genetic basis of stem trichome development between cultivated tetraploid cotton species.

BMC Plant Biol 2021 Feb 25;21(1):115. Epub 2021 Feb 25.

The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China.

Background: Cotton stem trichomes and seed fibers are each single celled structures formed by protrusions of epidermal cells, and were found sharing the overlapping molecular mechanism. Compared with fibers, cotton stem trichomes are more easily observed, but the molecular mechanisms underlying their development are still poorly understood.

Results: In this study, Gossypium hirsutum (Gh) and G. barbadense (Gb) were found to differ greatly in percentages of varieties/accessions with glabrous stems and in trichome density, length, and number per trichopore. Gh varieties normally had long singular and clustered trichomes, while Gb varieties had short clustered trichomes. Genetic mapping using five F populations from crosses between glabrous varieties and those with different types of stem trichomes revealed that much variation among stem trichome phenotypes could be accounted for by different combinations of genes/alleles on Chr. 06 and Chr. 24. The twenty- six F generations from crosses between varieties with different types of trichomes had varied phenotypes, further suggesting that the trichomes of tetraploid cotton were controlled by different genes/alleles. Compared to modern varieties, a greater proportion of Gh wild accessions were glabrous or had shorter and denser trichomes; whereas a smaller proportion of Gb primitive accessions had glabrous stems. A close correlation between fuzz fiber number and stem trichome density was observed in both Gh and Gb primitive accessions and modern varieties.

Conclusion: Based on these findings, we hypothesize that stem trichomes evolved in parallel with seed fibers during the domestication of cultivated tetraploid cotton. In addition, the current results illustrated that stem trichome can be used as a morphological index of fiber quality in cotton conventional breeding.
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http://dx.doi.org/10.1186/s12870-021-02871-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7905624PMC
February 2021

Assessment of heterosis based on parental genetic distance estimated with SSR and SNP markers in upland cotton (Gossypium hirsutum L.).

BMC Genomics 2021 Feb 18;22(1):123. Epub 2021 Feb 18.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.

Background: Heterosis has been extensively utilized in different crops and made a significant contribution to global food security. Genetic distance (GD) is one of the valuable criteria for selecting parents in hybrid breeding. The objectives of this study were to estimate the GD between parents using both simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) markers and to investigate the efficiency of the prediction of hybrid performance based on GD. The experiment comprised of four male parents, 282 female parents and 1128 F, derived from NCII mating scheme. The hybrids, their parents and two check cultivars were evaluated for two years. Performance of F, mid-parent heterosis (MPH), and best parent heterosis (BPH) were evaluated for ten agronomic and fiber quality traits, including plant height, boll weight, boll number, lint percentage, fiber length, fiber strength, fiber uniformity, fiber elongation ratio, micronaire, and spinning consistent index.

Results: Heterosis was observed in all hybrids and, the traits like plant height, boll number, boll weight and lint percentage exhibited higher heterosis than the fiber quality traits. Correlations were significant between parental and F performances. The F performances between three hybrid sets (Elite×Elite, Exotic×Elite, and Historic×Elite) showed significant differences in eight traits, including boll number, lint percentage, fiber length, fiber strength, fiber uniformity, fiber elongation ratio, micronaire, and spinning consistent index. The correlation of the GD assessed by both SSR and SNP markers was significantly positive. The cluster analysis based on GD results estimated using SNP showed that all the female parents divided into five groups and the F performance between these five groups showed significant differences in four traits, including lint percentage, micronaire, fiber strength, and fiber elongation ratio. The correlation between GD and F performance, MPH and BPH were significant for lint percentage and micronaire.

Conclusions: Our results suggested that GD between parents could be helpful in heterosis prediction for certain traits. This study reveals that molecular marker analysis can serve as a basis for assigning germplasm into heterotic groups and to provide guidelines for parental selection in hybrid cotton breeding.
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http://dx.doi.org/10.1186/s12864-021-07431-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7891138PMC
February 2021

Large-fragment insertion activates gene GaFZ (Ga08G0121) and is associated with the fuzz and trichome reduction in cotton (Gossypium arboreum).

Plant Biotechnol J 2021 Jun 7;19(6):1110-1124. Epub 2021 Feb 7.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.

Cotton seeds are typically covered by lint and fuzz fibres. Natural 'fuzzless' mutants are an ideal model system for identifying genes that regulate cell initiation and elongation. Here, using a genome-wide association study (GWAS), we identified a ~ 6.2 kb insertion, larINDEL , located at the end of chromosome 8, composed of a ~ 5.0 kb repetitive sequence and a ~ 1.2 kb fragment translocated from chromosome 12 in fuzzless Gossypium arboreum. The presence of larINDEL was associated with a fuzzless seed and reduced trichome phenotypes in G. arboreum. This distant insertion was predicted to be an enhancer, located ~ 18 kb upstream of the dominant-repressor GaFZ (Ga08G0121). Ectopic overexpression of GaFZ in Arabidopsis thaliana and G. hirsutum suggested that GaFZ negatively modulates fuzz and trichome development. Co-expression and interaction analyses demonstrated that GaFZ might impact fuzz fibre/trichome development by repressing the expression of genes in the very-long-chain fatty acid elongation pathway. Thus, we identified a novel regulator of fibre/trichome development while providing insights into the importance of noncoding sequences in cotton.
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http://dx.doi.org/10.1111/pbi.13532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196653PMC
June 2021

Identification, characterization and expression profiling of circular RNAs in the early cotton fiber developmental stages.

Genomics 2021 Jan 15;113(1 Pt 1):356-365. Epub 2020 Dec 15.

Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, China. Electronic address:

Circular RNA is one of the endogenous non-coding RNAs with a covalently closed loop structure and largely involved in regulating gene expression. However, the abundance of circular RNAs and their regulatory functions during the early stages of fiber development are still not known. In this work, we conducted high-throughput sequencing of the Ligonlintless-1 and its wild-type at 0 DPA, 8 DPA and stem. A total of 2811 circular RNAs were identified and unevenly distributed across cotton chromosomes. We found 34, 142 and 27 circular RNAs were differentially expressed between Ligonlintless-1 and wild-type at 0 DPA, 8 DPA and stem, respectively. Both circular RNA-microRNA-mRNA network and MeJA treatment results in Ligonlintless-1 and wild-type might provide a strong indication of four circular RNAs and ghr_miR169b being important biological molecular associating with fiber development. The results provide new insight into the putative molecular function of circular RNAs in the regulation of fiber development.
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http://dx.doi.org/10.1016/j.ygeno.2020.12.023DOI Listing
January 2021

A copy number variant at the HPDA-D12 locus confers compact plant architecture in cotton.

New Phytol 2021 02 6;229(4):2091-2103. Epub 2020 Dec 6.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.

Improving yield is a primary mission for cotton (Gossypium hirsutum) breeders; development of cultivars with suitable architecture for high planting density (HPDA) can increase yield per unit area. We characterized a natural cotton mutant, AiSheng98 (AS98), which exhibits shorter height, shorter branch length, and more acute branch angle than wild-type. A copy number variant at the HPDA locus on Chromosome D12 (HPDA-D12), encoding a dehydration-responsive element-binding (DREB) transcription factor, GhDREB1B, strongly affects plant architecture in the AS98 mutant. We found an association between a tandem duplication of a c. 13.5 kb segment in HPDA-D12 and elevated GhDREB1B expression resulting in the AS98 mutant phenotype. GhDREB1B overexpression confers a significant decrease in plant height and branch length, and reduced branch angle. Our results suggest that fine-tuning GhDREB1B expression may be a viable engineering strategy for modification of plant architecture favorable to high planting density in cotton.
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http://dx.doi.org/10.1111/nph.17059DOI Listing
February 2021

Genome-wide dissection of hybridization for fiber quality- and yield-related traits in upland cotton.

Plant J 2020 12 11;104(5):1285-1300. Epub 2020 Nov 11.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.

An evaluation of combining ability can facilitate the selection of suitable parents and superior F hybrids for hybrid cotton breeding, although the molecular genetic basis of combining ability has not been fully characterized. In the present study, 282 female parents were crossed with four male parents in accordance with the North Carolina II mating scheme to generate 1128 hybrids. The parental lines were genotyped based on restriction site-associated DNA sequencing and 306 814 filtered single nucleotide polymorphisms were used for genome-wide association analysis involving the phenotypes, general combining ability (GCA) values, and specific combining ability values of eight fiber quality- and yield-related traits. The main results were: (i) all parents could be clustered into five subgroups based on population structure analyses and the GCA performance of the female parents had significant differences between subgroups; (ii) 20 accessions with a top 5% GCA value for more than one trait were identified as elite parents for hybrid cotton breeding; (iii) 120 significant single nucleotide polymorphisms, clustered into 66 quantitative trait loci, such as the previously reported Gh_A07G1769 and GhHOX3 genes, were found to be significantly associated with GCA; and (iv) identified quantitative trait loci for GCA had a cumulative effect on GCA of the accessions. Overall, our results suggest that pyramiding the favorable loci for GCA may improve the efficiency of hybrid cotton breeding.
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http://dx.doi.org/10.1111/tpj.14999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756405PMC
December 2020

Incredible Role of Osmotic Adjustment in Grain Yield Sustainability under Water Scarcity Conditions in Wheat ( L.).

Plants (Basel) 2020 Sep 15;9(9). Epub 2020 Sep 15.

Institute of Biological Sciences, University of Talca, Talca 3460000, Chile.

Interrogations of local germplasm and landraces can offer a foundation and genetic basis for drought tolerance in wheat. Potential of drought tolerance in a panel of 30 wheat genotypes including varieties, local landraces, and wild crosses were explored under drought stress (DS) and well-watered (WW) conditions. Considerable variation for an osmotic adjustment (OA) and yield components, coupled with genotype and environment interaction was observed, which indicates the differential potential of wheat genotypes under both conditions. Reduction in yield per plant (YP), thousand kernel weight (TKW), and induction of OA was detected. Correlation analysis revealed a strong positive association of YP with directly contributing yield components under both environments, indicating the impotence of these traits as a selection-criteria for the screening of drought-tolerant genotypes for drylands worldwide. Subsequently, the association of OA with TKW which contributes directly to YP, indicates that wheat attains OA to extract more water from the soil under low water-potential. Genotypes including WC-4, WC-8 and LLR-29 showed more TKW under both conditions, among them; LLR-29 also has maximum OA and batter yield comparatively. Result provides insight into the role of OA in plant yield sustainability under DS. In this study, we figure out the concept of OA and its incredible role in sustainable plant yield in wheat.
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http://dx.doi.org/10.3390/plants9091208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7569908PMC
September 2020

Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum).

Theor Appl Genet 2020 Dec 25;133(12):3273-3285. Epub 2020 Aug 25.

Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.

Key Message: Three extensive eco-haplotypes associated with population differentiation and environmental adaptability in Upland cotton were identified, with A06_85658585, A08_43734499 and A06_113104285 considered the eco-loci for environmental adaptability. Population divergence is suggested to be the primary force driving the evolution of environmental adaptability in various species. Chromosome inversion increases reproductive isolation between subspecies and accelerates population divergence to adapt to new environments. Although modern cultivated Upland cotton (Gossypium hirsutum L.) has spread worldwide, the noticeable phenotypic differences still existed among cultivars grown in different areas. In recent years, the long-distance migration of cotton cultivation areas throughout China has demanded that breeders better understand the genetic basis of environmental adaptability in Upland cotton. Here, we integrated the genotypes of 419 diverse accessions, long-term environment-associated variables (EAVs) and environment-associated traits (EATs) to evaluate subgroup differentiation and identify adaptive loci in Upland cotton. Two highly divergent genomic regions were found on chromosomes A06 and A08, which likely caused by extensive chromosome inversions. The subgroups could be geographically classified based on distinct haplotypes in the divergent regions. A genome-wide association study (GWAS) also confirmed that loci located in these regions were significantly associated with environmental adaptability in Upland cotton. Our study first revealed the cause of population divergence in Upland cotton, as well as the consequences of variation in its environmental adaptability. These findings provide new insights into the genetic basis of environmental adaptability in Upland cotton, which could accelerate the development of molecular markers for adaptation to climate change in future cotton breeding.
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http://dx.doi.org/10.1007/s00122-020-03668-zDOI Listing
December 2020

Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland Cotton.

Front Plant Sci 2020 6;11:929. Epub 2020 Jul 6.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.

Understanding the genetic diversity and population structure of germplasms is essential when selecting parents for crop breeding. The genomic changes that occurred during the domestication and improvement of Upland cotton () remains poorly understood. Besides, the available genetic resources from cotton cultivars are limited. By applying restriction site-associated DNA marker sequencing (RAD-seq) technology to 582 tetraploid cotton accessions, we confirmed distinct genomic regions on chromosomes A06 and A08 in Upland cotton cultivar subgroups. Based on the pedigree, reported QTLs, introgression analyses, and genome-wide association study (GWAS), we suggest that these divergent regions might have resulted from the introgression of exotic lineages of landraces and their wild relatives. These regions were the typical genomic signatures that might be responsible for maturity and fiber quality on chromosome A06 and chromosome A08, respectively. Moreover, these genomic regions are located in the putative pericentromeric regions, implying that their application will be challenging. In the study, based on high-density SNP markers, we reported two genomic signatures on chromosomes A06 and A08, which might originate from the introgression events in the Upland cotton population. Our study provides new insights for understanding the impact of historic introgressions on population divergence and important agronomic traits of modern Upland cotton cultivars.
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http://dx.doi.org/10.3389/fpls.2020.00929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7381389PMC
July 2020

Genome-wide identification and characterization of HSP70 gene family in four species of cotton.

Genomics 2020 11 31;112(6):4442-4453. Epub 2020 Jul 31.

Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38040, Pakistan. Electronic address:

Heat shock proteins (HSPs) are important elements of the cellular group of molecular chaperones. Specifically, HSP70 proteins protect cells from being damaged when plants are exposed to environmental stresses. These proteins are catalysts that manage the correct folding of other proteins, and they play a key role in the development of tolerance against biotic and abiotic stresses. In the present study, 113 HSP70 genes were retrieved from the available genome assemblies of four cotton species, including Gossypium hirsutum, G. barbadense, G. arboreum, and G. raimondii. The HSP70 genes were clustered into 11 subfamilies based on phylogeny. One hundred and nine (109) gene duplications were found across these four species. Localization of genes revealed that several HSP70 genes reside in the cytoplasm. Synonymous and non-synonymous substitution rates revealed that functional segregation of HSP70 genes in cotton is due to purifying selection. Furthermore, HSP70 genes in cotton are expressed constitutively during developmental stages. These findings are valuable to understand the complex mechanism of HSP70 gene regulation that occurs in signaling pathways in response to plant stress.
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http://dx.doi.org/10.1016/j.ygeno.2020.07.039DOI Listing
November 2020

Genome-Wide Identification and Comparative Analysis of Myosin Gene Family in Four Major Cotton Species.

Genes (Basel) 2020 06 30;11(7). Epub 2020 Jun 30.

State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China.

Myosin protein as a molecular motor, binding with Actin, plays a significant role in various physiological activities such as cell division, movement, migration, and morphology; however, there are only a few studies on plant Myosin gene family, particularly in cotton. A total of 114 Myosin genes were found in , , , and . All Myosins could be grouped into six groups, and for each group of these genes, similar gene structures are found. Study of evolution suggested that the whole genome duplications event occurring about 13-20 MYA (millions of years ago) is the key explanation for Myosins expanse in cotton. Cis-element and qPCR analysis revealed that plant hormones such as abscisic acid, methyl jasmonate, and salicylic acid can control the expression of Myosins. This research provides useful information on the function of Myosin genes in regulating plant growth, production, and fiber elongation for further studies.
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http://dx.doi.org/10.3390/genes11070731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397272PMC
June 2020

Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton.

Plants (Basel) 2020 Jun 3;9(6). Epub 2020 Jun 3.

Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang 455000, China.

Upland cotton is the most economically important fibre crop. The human-mediated selection has resulted in modern upland cultivars with higher yield and better fibre quality. However, changes in genome structure resulted from human-mediated selection are poorly understood. Comparative population genomics offers us tools to dissect the genetic history of domestication and helps to understand the genome-wide effects of human-mediated selection. Hereby, we report a comprehensive assessment of landraces, obsolete cultivars and modern cultivars based on high throughput genome-wide sequencing of the core set of genotypes. As a result of the genome-wide scan, we identified 93 differential regions and 311 selection sweeps associated with domestication and improvement. Furthermore, we performed genome-wide association studies to identify traits associated with the differential regions and selection sweeps. Our study provides a genetic basis to understand the domestication process in Chinese cotton cultivars. It also provides a comprehensive insight into changes in genome structure due to selection and improvement during the last century. We also identified multiple genome-wide associations (GWAS associations) for fibre yield, quality and other morphological characteristics.
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http://dx.doi.org/10.3390/plants9060711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356552PMC
June 2020

Casparian strip membrane domain proteins in Gossypium arboreum: genome-wide identification and negative regulation of lateral root growth.

BMC Genomics 2020 May 4;21(1):340. Epub 2020 May 4.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.

Background: Root systems are critical for plant growth and development. The Casparian strip in root systems is involved in stress resistance and maintaining homeostasis. Casparian strip membrane domain proteins (CASPs) are responsible for the formation of Casparian strips.

Results: To investigate the function of CASPs in cotton, we identified and characterized 48, 54, 91 and 94 CASPs from Gossypium arboreum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively, at the genome-wide level. However, only 29 common homologous CASP genes were detected in the four Gossypium species. A collinearity analysis revealed that whole genome duplication (WGD) was the primary reason for the expansion of the genes of the CASP family in the four cotton species. However, dispersed duplication could also contribute to the expansion of the GaCASPs gene family in the ancestors of G. arboreum. Phylogenetic analysis was used to cluster a total of 85 CASP genes from G. arboreum and Arabidopsis into six distinct groups, while the genetic structure and motifs of CASPs were conserved in the same group. Most GaCASPs were expressed in diverse tissues, with the exception of that five GaCASPs (Ga08G0113, Ga08G0114, Ga08G0116, Ga08G0117 and Ga08G0118) that were highly expressed in root tissues. Analyses of the tissue and subcellular localization suggested that GaCASP27 genes (Ga08G0117) are membrane protein genes located in the root. In the GaCASP27 silenced plants and the Arabidopsis mutants, the lateral root number significantly increased. Furthermore, GaMYB36, which is related to root development was found to regulate lateral root growth by targeting GaCASP27.

Conclusions: This study provides a fundamental understanding of the CASP gene family in cotton and demonstrates the regulatory role of GaCASP27 on lateral root growth and development.
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http://dx.doi.org/10.1186/s12864-020-6723-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7199351PMC
May 2020

High-density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China.

Plant J 2020 07 4;103(2):677-689. Epub 2020 May 4.

Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832000, China.

The two new world tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, are cultivated worldwide and are characterised by a high yield and superior fibre quality, respectively. Historical genetic introgression has been reported between them; however, the existence of introgression and its genetic effects on agronomic traits remain unclear with regard to independent breeding of G. hirsutum (Upland cotton) and G. barbadense (Pima cotton) elite cultivars. We collected 159 G. hirsutum and 70 G. barbadense cultivars developed in Xinjiang, China, along with 30 semi-wild accessions of G. hirsutum, to perform interspecific introgression tests, intraspecific selection analyses and genome-wide association studies (GWAS) with fibre quality and yield component traits in multiple environments. In total, we identified seven interspecific introgression events and 52 selective sweep loci in G. hirsutum, as well as 17 interspecific introgression events and 19 selective sweep loci in G. barbadense. Correlation tests between agronomic traits and introgressions showed that introgression loci were mutually beneficial for the improvement of fibre quality and yield traits in both species. In addition, the phenotypic effects of four interspecific introgression events could be detected by intraspecific GWAS, with Gb_INT13 significantly improving fibre yield in G. barbadense. The present study describes the landscape of genetic introgression and selection between the two species, and highlights the genetic effects of introgression among populations, which can be used for future improvement of fibre yield and quality in G. barbadense and G. hirsutum, respectively.
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http://dx.doi.org/10.1111/tpj.14760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7496985PMC
July 2020

Genotyping by Sequencing Revealed QTL Hotspots for Trichome-Based Plant Defense in .

Genes (Basel) 2020 03 28;11(4). Epub 2020 Mar 28.

Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China.

Cotton possesses certain physical features, including leaf and stem trichomes that help plants deter damage caused by insect pests, and to some extent, from abiotic factors as well. Among those features, trichomes (pubescence) hold a special place as a first line of defense and a managemental tool against sucking insect pests of cotton. Different insect pests of cotton (whiteflies, aphids, jassids, and boll weevil) severely damage the yield and quality of the crop. Likewise, whiteflies, aphids, jassids, and other insect pests are considered as potential carriers for cotton leaf curl viruses and other diseases. Genotyping by sequencing (GBS) study was conducted to understand and explore the genomic regions governing hairy (Pubescence) leaves and stem phenotypes. A total of 224 individuals developed from an intraspecific cross (densely haired cotton (Liaoyang duomao mian) × hairless cotton (Zong 128)) and characterized phenotypically for leaf and stem pubescence in different environments. Here we identify and report significant QTLs (quantitative trait loci) associated with leaf and stem pubescence, and the response of plant under pest (aphid) infestation. Further, we identified putative genes colocalized on chromosome A06 governing mechanism for trichome development and host-pest interaction. Our study provides a comprehensive insight into genetic architecture that can be employed to improve molecular marker-assisted breeding programs aimed at developing biotic (insect pests) resilient cotton cultivars.
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http://dx.doi.org/10.3390/genes11040368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7231212PMC
March 2020

Expression patterns and functional divergence of homologous genes accompanied by polyploidization in cotton (Gossypium hirsutum L.).

Sci China Life Sci 2020 Oct 24;63(10):1565-1579. Epub 2020 Feb 24.

Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, China.

Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization. However, the global gene pattern variation during early fiber development was unknown. In this study, through RNA-seq technology, we comprehensively investigated the expression patterns of homologous genes between allotetraploid cotton (G. hirsutum) and its diploid progenitors (G. arboreum and G. raimondii) at the fiber early development stage. In tetraploid cotton, genes showed expression level dominance (ELD) bias toward the A genome. This phenomenon was explained by the up-/downregulation of the homologs from the nondominant progenitor (D genome). Gene ontology (GO) enrichment results indicated that the ELD-A genes might be a prominent cause responsible for fiber property change through regulating the fatty acid biosynthesis/metabolism and microtubule procession, and the ELD-D genes might be involved in transcription regulation and stress inducement. In addition, the number and proportion of completely A- and D-subfunctionalized gene were similar at different fiber development stages. However, for neofunctionalization, the number and proportion of reactivated D-derived genes were greater than those of A at 3 and 5 DPA. Eventually, we found that some homologous genes belonging to several specific pathways might create novel asymmetric transcripts between two subgenomes during polyploidization and domestication process, further making the fiber property meet the human demands. Our study identified determinate pathways and their involved genes between allotetraploid cotton and their progenitors at early fiber development stages, providing new insights into the mechanism of cotton fiber evolution.
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http://dx.doi.org/10.1007/s11427-019-1618-7DOI Listing
October 2020

Investigation of the Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development.

Plants (Basel) 2020 Jan 20;9(1). Epub 2020 Jan 20.

Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China.

The ethylene-insensitive3-like/ethylene-insensitive3 () protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the protein family in cotton. In turn, this paved the way to identifying and characterizing the protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species.
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http://dx.doi.org/10.3390/plants9010128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7020184PMC
January 2020

Insights into Drought Stress Signaling in Plants and the Molecular Genetic Basis of Cotton Drought Tolerance.

Cells 2019 Dec 31;9(1). Epub 2019 Dec 31.

State Key Laboratory of Cotton Biology, Institute of Cotton Research (ICR), Chinese Academy of Agricultural Sciences (CAAS), 455000 Anyang, China.

Drought stress restricts plant growth and development by altering metabolic activity and biological functions. However, plants have evolved several cellular and molecular mechanisms to overcome drought stress. Drought tolerance is a multiplex trait involving the activation of signaling mechanisms and differentially expressed molecular responses. Broadly, drought tolerance comprises two steps: stress sensing/signaling and activation of various parallel stress responses (including physiological, molecular, and biochemical mechanisms) in plants. At the cellular level, drought induces oxidative stress by overproduction of reactive oxygen species (ROS), ultimately causing the cell membrane to rupture and stimulating various stress signaling pathways (ROS, mitogen-activated-protein-kinase, Ca, and hormone-mediated signaling). Drought-induced transcription factors activation and abscisic acid concentration co-ordinate the stress signaling and responses in cotton. The key responses against drought stress, are root development, stomatal closure, photosynthesis, hormone production, and ROS scavenging. The genetic basis, quantitative trait loci and genes of cotton drought tolerance are presented as examples of genetic resources in plants. Sustainable genetic improvements could be achieved through functional genomic approaches and genome modification techniques such as the CRISPR/Cas9 system aid the characterization of genes, sorted out from stress-related candidate single nucleotide polymorphisms, quantitative trait loci, and genes. Exploration of the genetic basis for superior candidate genes linked to stress physiology can be facilitated by integrated functional genomic approaches. We propose a third-generation sequencing approach coupled with genome-wide studies and functional genomic tools, including a comparative sequenced data (transcriptomics, proteomics, and epigenomic) analysis, which offer a platform to identify and characterize novel genes. This will provide information for better understanding the complex stress cellular biology of plants.
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http://dx.doi.org/10.3390/cells9010105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016789PMC
December 2019

Identification and characterization analysis of sulfotransferases (SOTs) gene family in cotton (Gossypium) and its involvement in fiber development.

BMC Plant Biol 2019 Dec 30;19(1):595. Epub 2019 Dec 30.

State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, 271018, China.

Background: Sulfotransferases (SOTs) (EC 2.8.2.-) play a crucial role in the sulphate conjugation reaction involved in plant growth, vigor, stress resistance and pathogen infection. SOTs in Arabidopsis have been carried out and divided into 8 groups. However, the systematic analysis and functional information of SOT family genes in cotton have rarely been reported.

Results: According to the results of BLASTP and HMMER, we isolated 46, 46, 76 and 77 SOT genes in the genome G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. A total of 170 in 245 SOTs were further classified into four groups based on the orthologous relationships comparing with Arabidopsis, and tandem replication primarily contributed to the expansion of SOT gene family in G. hirsutum. Expression profiles of the GhSOT showed that most genes exhibited a high level of expression in the stem, leaf, and the initial stage of fiber development. The localization analysis indicated that GhSOT67 expressed in cytoplasm and located in stem and leaf tissue. Additionally, the expression of GhSOT67 were induced and the length of stem and leaf hairs were shortened after gene silencing mediated by Agrobacterium, compared with the blank and negative control plants.

Conclusions: Our findings indicated that SOT genes might be associated with fiber development in cotton and provided valuable information for further studies of SOT genes in Gossypium.
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http://dx.doi.org/10.1186/s12870-019-2190-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6938023PMC
December 2019

A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton.

Genes (Basel) 2019 10 21;10(10). Epub 2019 Oct 21.

Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China.

Millions of hectares of land are too saline to produce economically valuable crop yields. Salt tolerance in cotton is an imperative approach for improvement in response to ever-increasing soil salinization. Little is known about the genetic basis of salt tolerance in cotton at the seedling stage. To address this issue, a genome-wide association study (GWAS) was conducted on a core collection of a genetically diverse population of upland cotton ( L.) comprising of 419 accessions, representing various geographic origins, including China, USA, Pakistan, the former Soviet Union, Chad, Australia, Brazil, Mexico, Sudan, and Uganda. Phenotypic evaluation of 7 traits under control (0 mM) and treatment (150 mM) NaCl conditions depicted the presence of broad natural variation in the studied population. The association study was carried out with the efficient mixed-model association eXpedited software package. A total of 17,264 single-nucleotide polymorphisms (SNPs) associated with different salinity stress tolerance related traits were found. Twenty-three candidate SNPs related to salinity stress-related traits were selected. Final key SNPs were selected based on the r value with nearby SNPs in a linkage disequilibrium (LD) block. Twenty putative candidate genes surrounding SNPs, A10_95330133 and D10_61258588, associated with leaf relative water content, RWC_150, and leaf fresh weight, FW_150, were identified, respectively. We further validated the expression patterns of twelve candidate genes with qRT-PCR, which revealed different expression levels in salt-tolerant and salt-sensitive genotypes. The results of our GWAS provide useful knowledge about the genetic control of salt tolerance at the seedling stage, which could assist in elucidating the genetic and molecular mechanisms of salinity stress tolerance in cotton plants.
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http://dx.doi.org/10.3390/genes10100829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6826536PMC
October 2019

Genome-wide analysis of cotton C2H2-zinc finger transcription factor family and their expression analysis during fiber development.

BMC Plant Biol 2019 Sep 11;19(1):400. Epub 2019 Sep 11.

State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.

Background: C2H2-zinc finger protein family is commonly found in the plant, and it is known as the key actors in the regulation of transcription and vital component of chromatin structure. A large number of the C2H2-zinc finger gene members have not been well characterized based on their functions and structure in cotton. However, in other plants, only a few C2H2-zinc finger genes have been studied.

Results: In this work, we performed a comprehensive analysis and identified 386, 196 and 195 C2H2-zinc finger genes in Gossypium hirsutum (upland cotton), Gossypium arboreum and Gossypium raimondii, respectively. Phylogenetic tree analysis of the C2H2-zinc finger proteins encoding the C2H2-zinc finger genes were classified into seven (7) subgroups. Moreover, the C2H2-zinc finger gene members were distributed in all cotton chromosomes though with asymmetrical distribution patterns. All the orthologous genes were detected between tetraploid and the diploid cotton, with 154 orthologous genes pair detected between upland cotton and Gossypium arboreum while 165 orthologous genes were found between upland cotton and Gossypium raimondii. Synonymous (Ks) and non-synonymous (Ka) nucleotide substitution rates (Ka/Ks) analysis indicated that the cotton C2H2-zinc finger genes were highly influenced mainly by negative selection, which maintained their protein levels after the duplication events. RNA-seq data and RT-qPCR validation of the RNA seq result revealed differential expression pattern of some the C2H2-zinc finger genes at different stages of cotton fiber development, an indication that the C2H2-zinc finger genes play an important role in initiating and regulating fiber development in cotton.

Conclusions: This study provides a strong foundation for future practical genome research on C2H2-zinc finger genes in upland cotton. The expression levels of C2H2-zinc finger genes family is a pointer of their involvement in various biochemical and physiological functions which are directly related to cotton fiber development during initiation and elongation stages. This work not only provides a basis for determining the nominal role of the C2H2-zinc finger genes in fiber development but also provide valuable information for characterization of potential candidate genes involved in regulation of cotton fiber development.
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http://dx.doi.org/10.1186/s12870-019-2003-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739942PMC
September 2019

Long non-coding RNAs and their potential functions in Ligon-lintless-1 mutant cotton during fiber development.

BMC Genomics 2019 Aug 19;20(1):661. Epub 2019 Aug 19.

Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.

Background: Long non-coding RNAs (LncRNAs) are part of genes, which are not translated into proteins and play a vital role in plant growth and development. Nevertheless, the presence of LncRNAs and how they functions in Ligon-lintless-1 mutant during the early cessation of cotton fiber development are still not well understood. In order to investigate the function of LncRNAs in cotton fiber development, it is necessary and important to identify LncRNAs and their potential roles in fiber cell development.

Results: In this work, we identified 18,333 LncRNAs, with the proportion of long intergenic noncoding RNAs (LincRNAs) (91.5%) and anti-sense LncRNAs (8.5%), all transcribed from Ligon-lintless-1 (Li1) and wild-type (WT). Expression differences were detected between Ligon-lintless-1 and wild-type at 0 and 8 DPA (day post anthesis). Pathway analysis and Gene Ontology based on differentially expressed LncRNAs on target genes, indicated fatty acid biosynthesis and fatty acid elongation being integral to lack of fiber in mutant cotton. The result of RNA-seq and RT-qPCR clearly singles out two potential LncRNAs, LNC_001237 and LNC_017085, to be highly down-regulated in the mutant cotton. The two LncRNAs were found to be destabilized or repressed by ghr-miR2950. Both RNA-seq analysis and RT-qPCR results in Ligon-lintless-1 mutant and wild-type may provide strong evidence of LNC_001237, LNC_017085 and ghr-miR2950 being integral molecular elements participating in various pathways of cotton fiber development.

Conclusion: The results of this study provide fundamental evidence for the better understanding of LncRNAs regulatory role in the molecular pathways governing cotton fiber development. Further research on designing and transforming LncRNAs will help not only in the understanding of their functions but will also in the improvement of fiber quality.
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http://dx.doi.org/10.1186/s12864-019-5978-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700839PMC
August 2019

Functional analysis of the gene associated with branching development in cotton.

PeerJ 2019 14;7:e6901. Epub 2019 May 14.

State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Bioinformatics Center, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, China.

Plant architecture, including branching pattern, is an important agronomic trait of cotton crops. In recent years, strigolactones (SLs) have been considered important plant hormones that regulate branch development. In some species such as Arabidopsis, DWARF14 is an unconventional receptor that plays an important role in the SL signaling pathway. However, studies on SL receptors in cotton are still lacking. Here, we cloned and analysed the structure of the GbD14 gene in and found that it contains the domains necessary for a SL receptor. The GbD14 gene was expressed primarily in the roots, leaves and vascular bundles, and the GbD14 protein was determined via GFP to localize to the cytoplasm and nucleus. Gene expression analysis revealed that the GbD14 gene not only responded to SL signals but also was differentially expressed between cotton plants whose types of branching differed. In particular, GbD14 was expressed mainly in the axillary buds of normal-branching cotton, while it was expressed the most in the leaves of nulliplex-branch cotton. In cotton, the GbD14 gene can be induced by SL and other plant hormones, such as indoleacetic acid, abscisic acid, and jasmonic acid. Compared with wild-type Arabidopsis, GbD14-overexpressing Arabidopsis responded more rapidly to SL signals. Moreover, we also found that GbD14 can rescue the multi-branched phenotype of Arabidopsis Atd14 mutants. Our results indicate that the function of GbD14 is similar to that of AtD14, and GbD14 may be a receptor for SL in cotton and involved in regulating branch development. This research provides a theoretical basis for a profound understanding of the molecular mechanism of branch development and ideal plant architecture for cotton breeding improvements.
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http://dx.doi.org/10.7717/peerj.6901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524629PMC
May 2019

Association Analysis of Salt Tolerance in Asiatic cotton () with SNP Markers.

Int J Mol Sci 2019 May 1;20(9). Epub 2019 May 1.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.

Salinity is not only a major environmental factor which limits plant growth and productivity, but it has also become a worldwide problem. However, little is known about the genetic basis underlying salt tolerance in cotton. This study was carried out to identify marker-trait association signals of seven salt-tolerance-related traits and one salt tolerance index using association analysis for 215 accessions of Asiatic cotton. According to a comprehensive index of salt tolerance (CIST), 215 accessions were mainly categorized into four groups, and 11 accessions with high salinity tolerance were selected for breeding. Genome-wide association studies (GWAS) revealed nine SNP rich regions significantly associated with relative fresh weight (RFW), relative stem length (RSL), relative water content (RRWC) and CIST. The nine SNP rich regions analysis revealed 143 polymorphisms that distributed 40 candidate genes and significantly associated with salt tolerance. Notably, two SNP rich regions on chromosome 7 were found to be significantly associated with two salinity related traits, RFW and RSL, by the threshold of -log ≥ 6.0, and two candidate genes (Cotton_A_37775 and Cotton_A_35901) related to two key SNPs (Ca7_33607751 and Ca7_77004962) were possibly associated with salt tolerance in . These can provide fundamental information which will be useful for future molecular breeding of cotton, in order to release novel salt tolerant cultivars.
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http://dx.doi.org/10.3390/ijms20092168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6540053PMC
May 2019

Identifying favorable alleles for improving key agronomic traits in upland cotton.

BMC Plant Biol 2019 Apr 11;19(1):138. Epub 2019 Apr 11.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.

Background: Gossypium hirsutum L. is grown worldwide and is the largest source of natural fiber crop. We focus on exploring the favorable alleles (FAs) for upland cotton varieties improvement, and further understanding the history of accessions selection and acumination of favorable allele during breeding.

Results: The genetic basis of phenotypic variation has been studied. But the accumulation of favorable alleles in cotton breeding history in unknown, and potential favorable alleles to enhance key agronomic traits in the future cotton varieties have not yet been identified. Therefore, 419 upland cotton accessions were screened, representing a diversity of phenotypic variations of 7362 G. hirsutum, and 15 major traits were investigated in 6 environments. These accessions were categorized into 3 periods (early, medium, and modern) according to breeding history. All accessions were divided into two major groups using 299 polymorphic microsatellite markers: G1 (high fiber yield and quality, late maturity) and G2 (low fiber yield and quality, early maturity). The proportion of G1 genotype gradually increased from early to modern breeding periods. Furthermore, 21 markers (71 alleles) were significantly associated (-log P > 4) with 15 agronomic traits in multiple environments. Seventeen alleles were identified as FAs; these alleles accumulated more in the modern period than in other periods, consistent with their phenotypic variation trends in breeding history. Our results demonstrate that the favorable alleles accumulated through breeding effects, especially for common favorable alleles. However, the potential elite accessions could be rapidly screened by rare favorable alleles.

Conclusion: In our study, genetic variation and genome-wide associations for 419 upland cotton accessions were analyzed. Two favorable allele types were identified during three breeding periods, providing important information for yield/quality improvement of upland cotton germplasm.
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http://dx.doi.org/10.1186/s12870-019-1725-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458685PMC
April 2019