participate in VLCFA synthesis
[86–88]
. Modulating biosynthesis
of VLCFA biosynthesis can affect fiber elongation
[86–89]
.
These findings may provide new insights in dissecting candi-
date gene functions in modulating SCW cellulose biosynthesis dur-
ing fiber development. Further studies and verification of their
specific functions will have great interests and significance in
understanding their orchestrating mechanism of fiber quality
formation.
Ethical statement
This article does not contain any studies with human or animal
materials.
CRediT authorship contribution statement
Ruìxián Liú: Investigation, Software. Xiànghu
ı Xia¯o: Investiga-
tion, Methodology, Visualization. Jw Go¯ng: Investigation, Formal
analysis, Visualization. Jùnwén Lıˇ: Investigation. Hàoliàng Yán:
Investigation, Formal analysis. Qún Geˇ: . Quánwe
ˇi Lú: . Péngta¯o
Lıˇ: . Jìngta¯o Pa¯n: . Ha
ˇihóng Sha¯ng: . Yùzhe¯n Shí: Methodology.
Qúanjia¯ Chén: Supervision, Investigation, Methodology. Yo
ˇulù
Yuán: Supervision, Funding acquisition, Resources. Wànkuí Go
ˇng:
Supervision.
Data availability
The datasets generated during and/or analyzed during the cur-
rent study are available from the corresponding author on reason-
able request.
Declaration of competing interest
The authors declare that they have no known competing finan-
cial interests or personal relationships that could have appeared
to influence the work reported in this paper.
Acknowledgements
The authors thank supports by the grants from the National
Natural Science Foundation of China (32070560), China Agriculture
Research System—Cotton (CARS-15-02), the National Agricultural
Science and Technology Innovation Project for Chinese Academy
of Agricultural Sciences (CAAS-ASTIP-2016-ICR), Central Public-
interest
Scientific
Institution
Basal
Research
Fund
(CN)
(1610162023013), Project of Kashgar Regional Science and Tech-
nology Plan (KS2023003), and the Natural Science Foundation of
Xinjiang Uygur Autonomous Region (2021D01B114), Talent Devel-
opment Program for Innovation and Expansion in Xinjiang for
Youlu Yuan Group. The authors acknowledge Sci Lang for its lin-
guistic assistance during the preparation of this manuscript.
Appendix A. Supplementary material
Supplementary data to this article can be found online at
https://doi.org/10.1016/j.jare.2023.12.005
.
References
[1]
Ma Z, Zhang Y, Wu L, Zhang G, Sun Z, Li Z, et al. High-quality genome assembly
and resequencing of modern cotton cultivars provide resources for crop
improvement. Nat Genet 2021;53(9):1385–91
.
[2]
Huang G, Wu Z, Percy RG, Bai M, Li Y, Frelichowski JE, et al. Genome sequence
of Gossypium herbaceum and genome updates of Gossypium arboreum and
Gossypium hirsutum provide insights into cotton A-genome evolution. Nat
Genet 2020;52(5):516–24
.
[3]
Hu Y, Chen J, Fang L, Zhang Z, Ma W, Niu Y, et al. Gossypium barbadense and
Gossypium hirsutum genomes provide insights into the origin and evolution of
allotetraploid cotton. Nat Genet 2019;51(4):739–48
.
[4]
Paterson AH, Saranga Y, Menz M, Jiang CX, Wright RJ. QTL analysis of genotype
x environment interactions affecting cotton fiber quality. Theor Appl Genet
2003;106(3):384–96
.
[5]
Gu Q, Ke H, Liu Z, Lv X, Sun Z, Zhang M, et al. A high-density genetic map and
multiple environmental tests reveal novel quantitative trait loci and candidate
genes for fibre quality and yield in cotton. Theor Appl Genet 2020;133
(12):3395–408
.
[6]
Zhang Z, Li J, Jamshed M, Shi Y, Liu A, Gong J, et al. Genome-wide quantitative
trait loci reveal the genetic basis of cotton fibre quality and yield-related traits
in a Gossypium hirsutum recombinant inbred line population. Plant Biotechnol J
2020;18(1):239–53
.
[7]
Huang C, Nie X, Shen C, You C, Li W, Zhao W, et al. Population structure and
genetic basis of the agronomic traits of upland cotton in China revealed by a
genome-wide association study using high-density SNPs. Plant Biotechnol J
2017;15(11):1374–86
.
[8]
Chen ZJ, Scheffler BE, Dennis E, Triplett BA, Zhang T, Guo W, et al. Toward
sequencing cotton (Gossypium) genomes. Plant Physiol 2007;145(4):1303–10
.
[9]
Wang K, Wang Z, Li F, Ye W, Wang J, Song G, et al. The draft genome of a diploid
cotton Gossypium raimondii. Nat Genet 2012;44(10):1098–103
.
[10]
Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, et al. Repeated
polyploidization of Gossypium genomes and the evolution of spinnable cotton
fibres. Nature 2012;492(7429):423–7
.
[11]
Li F, Fan G, Wang K, Sun F, Yuan Y, Song G, et al. Genome sequence of the
cultivated cotton Gossypium arboreum. Nat Genet 2014;46(6):567–72
.
[12]
Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, et al. Genome sequence of cultivated
Upland cotton (Gossypium hirsutum TM-1) provides insights into genome
evolution. Nat Biotechnol 2015;33(5):524–30
.
[13]
Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, et al. Sequencing of
allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for
fiber improvement. Nat Biotechnol 2015;33(5):531–7
.
[14]
Wang M, Tu L, Yuan D, Zhu De, Shen C, Li J, et al. Reference genome sequences
of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium
barbadense. Nat Genet 2019;51(2):224–9
.
[15] Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, et al.
Development of a 63K SNP array for cotton and high-density mapping of
intraspecific and interspecific populations of Gossypium spp. G3 (Bethesda)
2015;5(6):1187–209.
[16]
Cai C, Zhu G, Zhang T, Guo W. High-density 80 K SNP array is a powerful tool
for genotyping G. hirsutum accessions and genome analysis. BMC Genomics
2017;18:654
.
[17]
Liu R, Gong J, Xiao X, Zhang Z, Li J, Liu A, et al. GWAS analysis and QTL
identification of fiber quality traits and yield components in upland cotton
using enriched high-density SNP markers. Front Plant Sci 2018;9:1067
.
[18]
Tan Z, Zhang Z, Sun X, Li Q, Sun Y, Yang P, et al. Genetic map construction and
fiber quality QTL mapping using the CottonSNP80K array in upland cotton.
Front Plant Sci 2018;9:225
.
[19]
Zhang K, Kuraparthy V, Fang H, Zhu L, Sood S, Jones DC. High-density linkage
map construction and QTL analyses for fiber quality, yield and morphological
traits using CottonSNP63K array in upland cotton (Gossypium hirsutum L.).
BMC Genomics 2019;20:889
.
[20]
Zhang Z, Ge Q, Liu A, Li J, Gong J, Shang H, et al. Construction of a high-density
genetic map and its application to QTL identification for fiber strength in
upland cotton. Crop Sci 2017;57(2):774–88
.
[21]
Haigler CH, Betancur L, Stiff MR, Tuttle JR. Cotton fiber: a powerful single-cell
model for cell wall and cellulose research. Front Plant Sci 2012;3:104
.
[22]
Mei H, Qi B, Han Z, Zhao T, Guo M, Han J, et al. Subgenome bias and temporal
postponement of gene expression contributes to the distinctions of fiber
quality in Gossypium species. Front Plant Sci 2021;12:819679
.
[23]
Jan M, Liu Z, Guo C, Sun X. Molecular regulation of cotton fiber development: a
review. Int J Mol Sci 2022;23(9):5004
.
[24]
Xiao G, Zhao P, Zhang Y. A pivotal role of hormones in regulating cotton fiber
development. Front Plant Sci 2019;10:87
.
[25]
Sun W, Gao Z, Wang J, Huang Y, Chen Y, Li J, et al. Cotton fiber elongation
requires the transcription factor GhMYB212 to regulate sucrose transportation
into expanding fibers. New Phytol 2019;222(2):864–81
.
R. Liú, X. Lıˇ, Hàoliàng Yán et al.
Journal of Advanced Research xxx (xxxx) xxx
12
[26]
Shi Z, Chen X, Xue H, Jia T, Meng F, Liu Y, et al. GhBZR3 suppresses cotton fiber
elongation by inhibiting very-long-chain fatty acid biosynthesis. Plant J
2022;111(3):785–99
.
[27]
Zhang D, Hrmova M, Wan C-H, Wu C, Balzen J, Cai W, et al. Members of a new
group of chitinase-like genes are expressed preferentially in cotton cells with
secondary walls. Plant Mol Biol 2004;54(3):353–72
.
[28]
Li Y, Tu L, Pettolino FA, Ji S, Hao J, Yuan D, et al. GbEXPATR, a species-specific
expansin, enhances cotton fibre elongation through cell wall restructuring.
Plant Biotechnol J 2016;14(3):951–63
.
[29]
Naoumkina M, Thyssen GN, Fang DD. RNA-seq analysis of short fiber mutants
Ligon-lintless-1 (Li 1) and -2 (Li 2) revealed important role of aquaporins in
cotton (Gossypium hirsutum L.) fiber elongation. BMC Plant Biol 2015;15:65
.
[30]
Tang W, Tu L, Yang X, Tan J, Deng F, Hao J, et al. The calcium sensor GhCaM7
promotes cotton fiber elongation by modulating reactive oxygen species (ROS)
production. New Phytol 2014;202(2):509–20
.
[31] Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, et al. SLAF-seq: an efficient method
of large-scale de novo SNP discovery and genotyping using high-throughput
sequencing. PLoS ONE 2013;8(3):e58700.
[32]
Shen C, Jin X, Zhu D, Lin Z. Uncovering SNP and indel variations of tetraploid
cottons by SLAF-seq. BMC Genomics 2017;18(1):247
.
[33]
Ali I, Teng Z, Bai Y, Yang Q, Hao Y, Hou J, et al. A high density SLAF-SNP genetic
map and QTL detection for fibre quality traits in Gossypium hirsutum. BMC
Genomics 2018;19(1):879
.
[34] Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler
transform. Bioinformatics 2009;25(14):1754–60.
[35]
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al.
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-
generation DNA sequencing data. Genome Res 2010;20(9):1297–303
.
[36] Rastas P. Lep-MAP3: robust linkage mapping even for low-coverage whole
genome sequencing data. Bioinformatics 2017;33(23):3726–32.
[37]
Kosambi DD. The estimation of map distance from recombination values. Ann
Eugen 1944;12:172–5
.
[38] Wang S, Basten C, Zeng Z. Windows QTL Cartographer v2.5. 2012.
[39]
Voorrips RE. MapChart: software for the graphical presentation of linkage
maps and QTLs. J Hered 2002;1:77–8
.
[40] Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL NCBI
BLAST a better web interface. Nucleic Acids Res 2008;36:W5-9.
[41]
Jiang X, Gong J, Zhang J, Zhang Z, Shi Y, Li J, et al. Quantitative trait loci and
transcriptome analysis reveal genetic basis of fiber quality traits in CCRI70 RIL
population of Gossypium hirsutum. Front Plant Sci 2021;12:753755
.
[42]
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation
network analysis. BMC Bioinf 2008;9:559
.
[43]
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-
time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001;25
(4):402–8
.
[44]
Gu Z, Huang C, Li F, Zhou X. A versatile system for functional analysis of genes
and microRNAs in cotton. Plant Biotechnol J 2014;12(5):638–49
.
[45]
Manghwar H, Lindsey K, Zhang X, Jin S. CRISPR/Cas system: recent advances
and future prospects for genome editing. Trends Plant Sci 2019;24
(12):1102–25
.
[46]
Zhou L, Zhu T, Han S, Li S, Liu Y, Lin T, et al. Changes in the Histology of walnut
(Juglans regia L.) infected with Phomopsis capsici and transcriptome and
metabolome analysis. Int J Mol Sci 2023;24(5):4879
.
[47]
Li Z, Wang P, You C, Yu J, Zhang X, Yan F, et al. Combined GWAS and eQTL
analysis uncovers a genetic regulatory network orchestrating the initiation of
secondary cell wall development in cotton. New Phytol 2020;226(6):1738–52
.
[48]
Keerio AA, Shen C, Nie Y, Ahmed MM, Zhang X, Lin Z. QTL mapping for fiber
quality and yield traits based on introgression lines derived from Gossypium
hirsutum
G. tomentosum. Int J Mol Sci 2018;19(1):243
.
[49]
Yang P, Sun X, Liu X, Wang W, Hao Y, Chen L, et al. Identification of candidate
genes for lint percentage and fiber quality through QTL mapping and
transcriptome analysis in an allotetraploid interspecific cotton CSSLs
population. Front Plant Sci 2022;13:882051
.
[50]
Wang F, Zhang J, Chen Y, Zhang C, Gong J, Song Z, et al. Identification of
candidate genes for key fibre-related QTLs and derivation of favourable alleles
in Gossypium hirsutum recombinant inbred lines with G. barbadense
introgressions. Plant Biotechnol J 2020;18(3):707–20
.
[51]
Wang M, Qi Z, Thyssen GN, Naoumkina M, Jenkins JN, McCarty JC, et al.
Genomic interrogation of a MAGIC population highlights genetic factors
controlling fiber quality traits in cotton. Commun Biol 2022;5(1):60
.
[52]
Liu W, Song C, Ren Z, Zhang Z, Pei X, Liu Y, et al. Genome-wide association
study reveals the genetic basis of fiber quality traits in upland cotton
(Gossypium hirsutum L.). BMC Plant Biol 2020;20:395
.
[53]
Liu X, Hou J, Chen Li, Li Q, Fang X, Wang J, et al. Natural variation of GhSI7
increases seed index in cotton. Theor Appl Genet 2022;135(10):3661–72
.
[54]
Fang X, Liu X, Wang X, Wang W, Liu D, Zhang J, et al. Fine-mapping qFS07.1
controlling fiber strength in upland cotton (Gossypium hirsutum L.). Theor Appl
Genet 2017;130(4):795–806
.
[55]
Song X, Meng X, Guo H, Cheng Q, Jing Y, Chen M, et al. Targeting a gene
regulatory element enhances rice grain yield by decoupling panicle number
and size. Nat Biotechnol 2022;40(9):1403–11
.
[56]
Takatsuji H. Regulating tradeoffs to improve rice production. Front Plant Sci
2017;8:171
.
[57]
Wang L, Wang D, Yang Z, Jiang S, Qu J, He W, et al. Roles of FERONIA-like
receptor genes in regulating grain size and quality in rice. Sci China Life Sci
2021;64(2):294–310
.
[58]
Liu L, Gallagher J, Arevalo ED, Chen R, Skopelitis T, Wu Q, et al. Enhancing
grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes.
Nat Plants 2021;7(3):287–94
.
[59]
Hendelman A, Zebell S, Rodriguez-Leal D, Dukler N, Robitaille G, Wu X, et al.
Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-
regulatory dissection. Cell 2021;184(7):1724–1739.e16
.
[60]
Li X, Xie Y, Zhu Q, Liu YG. Targeted genome editing in genes and cis-regulatory
regions improves qualitative and quantitative traits in crops. Mol Plant
2017;10(11):1368–70
.
[61]
Zhang S, Yu H, Wang K, Zheng Z, Liu L, Xu M, et al. Detection of major loci
associated with the variation of 18 important agronomic traits between
Solanum pimpinellifolium and cultivated tomatoes. Plant J 2018;95(2):312–23
.
[62]
Du J, Vandavasi VG, Molloy KR, Yang H, Massenburg LN, Singh A, et al. Evidence
for plant-conserved region mediated trimeric CESAs in plant cellulose
synthase complexes. Biomacromolecules 2022;23(9):3663–77
.
[63]
Polko JK, Kieber JJ. The regulation of cellulose biosynthesis in plants. Plant Cell
2019;31(2):282–96
.
[64]
Wen X, Zhai Y, Zhang Li, Chen Y, Zhu Z, Chen G, et al. Molecular studies of
cellulose synthase supercomplex from cotton fiber reveal its unique
biochemical properties. Sci China Life Sci 2022;65(9):1776–93
.
[65]
Li F, Xie G, Huang J, Zhang R, Li Y, Zhang M, et al. OsCESA9 conserved-site
mutation leads to largely enhanced plant lodging resistance and biomass
enzymatic saccharification by reducing cellulose DP and crystallinity in rice.
Plant Biotechnol J 2017;15(9):1093–104
.
[66]
Wang Y, Fan C, Hu H, Li Y, Sun D, Wang Y, et al. Genetic modification of plant
cell walls to enhance biomass yield and biofuel production in bioenergy crops.
Biotechnol Adv 2016;34(5):997–1017
.
[67] Zhang J, Liu Z, Sakamoto S, Mitsuda N, Ren A, Persson S, et al. ETHYLENE
RESPONSE FACTOR 34 promotes secondary cell wall thickening and strength of
rice peduncles. Plant Physiol 2022;190(3):1806–20.
[68]
Tanaka K, Murata K, Yamazaki M, Onosato K, Miyao A, Hirochika H. Three
distinct rice cellulose synthase catalytic subunit genes required for cellulose
synthesis in the secondary wall. Plant Physiol 2003;133:73–83
.
[69]
Olins JR, Lin L, Lee SJ, Trabucco GM, MacKinnon KJM, Hazen SP. Secondary wall
regulating NACs differentially bind at the promoter at a CELLULOSE SYNTHASE
A4 Cis-eQTL. Front Plant Sci 2018;9:1985
.
[70] Guo B, Huang X, Qi J, Sun H, Lv C, Wang F, et al. Brittle culm 3, encoding a
cellulose synthase subunit 5, is required for cell wall biosynthesis in barley
(Hordeum vulgare L.). Front Plant Sci 2022;13:989406.
[71]
Wang Y, Li Y, Gong S-Y, Qin L-X, Nie X-Y, Liu D, et al. GhKNL1 controls fiber
elongation and secondary cell wall synthesis by repressing its downstream
genes in cotton (Gossypium hirsutum). J Integr Plant Biol 2022;64(1):39–55
.
[72]
Li F, Liu S, Xu H, Xu Q. A novel FC17/CESA4 mutation causes increased biomass
saccharification and lodging resistance by remodeling cell wall in rice.
Biotechnol Biofuels 2018;11:298
.
[73]
Ma X, Li C, Huang R, Zhang K, Wang Q, Fu C, et al. Rice Brittle Culm19 encoding
cellulose synthase subunit CESA4 causes dominant brittle phenotype but has
no distinct influence on growth and grain yield. Rice (N Y) 2021;14:95
.
[74]
Fan C, Feng S, Huang J, Wang Y, Wu L, Li X, et al. AtCesA8-driven OsSUS3
expression leads to largely enhanced biomass saccharification and lodging
resistance by distinctively altering lignocellulose features in rice. Biotechnol
Biofuels 2017;10:221
.
[75]
Fujimoto M, Suda Y, Vernhettes S, Nakano A, Ueda T. Phosphatidylinositol 3-
kinase and 4-kinase have distinct roles in intracellular trafficking of cellulose
synthase complexes in Arabidopsis thaliana. Plant Cell Physiol 2015;56
(2):287–98
.
[76]
Ellis C, Karafyllidis I, Wasternack C, Turner JG. The Arabidopsis mutant cev1
links cell wall signaling to jasmonate and ethylene responses. Plant Cell
2002;14(7):1557–66
.
[77]
Qiao Z, Lampugnani ER, Yan X-F, Khan GA, Saw WG, Hannah P, et al. Structure
of Arabidopsis CESA3 catalytic domain with its substrate UDP-glucose provides
insight into the mechanism of cellulose synthesis. Proc Natl Acad Sci U S A
2021;118(11):e2024015118
.
[78] Huang GQ, Gong SY, Xu WL, Li W, Li P, Zhang CJ, et al. A fasciclin-like
arabinogalactan protein, GhFLA1, is involved in fiber initiation and elongation
of cotton. Plant Physiol 2013;161(3):1278–90.
[79]
Showalter AM, Keppler B, Lichtenberg J, Gu D, Welch LR. A bioinformatics
approach to the identification, classification, and analysis of hydroxyproline-
rich glycoproteins. Plant Physiol 2010;153(2):485–513
.
[80]
Costa M, Pereira AM, Pinto SC, Silva J, Pereira LG, Coimbra S. In silico and
expression analyses of fasciclin-like arabinogalactan proteins reveal functional
conservation during embryo and seed development. Plant Reprod 2019;32
(4):353–70
.
[81]
Ma Y, MacMillan CP, de Vries L, Mansfield SD, Hao P, Ratcliffe J, et al. FLA11 and
FLA12 glycoproteins fine-tune stem secondary wall properties in response to
mechanical stresses. New Phytol 2022;233(4):1750–67
.
[82]
Sato K, Suzuki R, Nishikubo N, Takenouchi S, Ito S, Nakano Y, et al. Isolation of a
novel cell wall architecture mutant of rice with defective Arabidopsis COBL4
ortholog BC
1
required for regulated deposition of secondary cell wall
components. Planta 2010;232(1):257–70
.
R. Liú, X. Lıˇ, Hàoliàng Yán et al.
Journal of Advanced Research xxx (xxxx) xxx
13
[83]
Gritsch C, Wan Y, Mitchell RA, Shewry PR, Hanley SJ, Karp A. G-fibre cell wall
development in willow stems during tension wood induction. J Exp Bot
2015;66(20):6447–59
.
[84]
Sun X, Xiong H, Jiang C, Zhang D, Yang Z, Huang Y, et al. Natural variation of
DROT1 confers drought adaptation in upland rice. Nat Commun 2022;13:4265
.
[85]
Zhao H, Kosma DK, Lü S. Functional role of long-chain acyl-CoA synthetases in
plant development and stress responses. Front Plant Sci 2021;12:640996
.
[86]
Qin YM, Zhu YX. How cotton fibers elongate: a tale of linear cell-growth mode.
Curr Opin Plant Biol 2011;14(1):106–11
.
[87]
Qin YM, Hu CY, Pang Y, Kastaniotis AJ, Hiltunen JK, Zhu YX. Saturated very-
long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by
activating ethylene biosynthesis. Plant Cell 2007;19(11):3692–704
.
[88] Shi YH, Zhu SW, Mao XZ, Feng JX, Qin YM, Zhang L, et al. Transcriptome
profiling, molecular biological, and physiological studies reveal a major role
for ethylene in cotton fiber cell elongation. Plant Cell 2006;18(3):651–64.
[89]
Yang Z, Liu Z, Ge X, Lu L, Qin W, Qanmber G, et al. Brassinosteroids regulate
cotton fiber elongation by modulating very-long-chain fatty acid biosynthesis.
Plant Cell 2023;35:2114–31
.
R. Liú, X. Lıˇ, Hàoliàng Yán et al.
Journal of Advanced Research xxx (xxxx) xxx
14
|
