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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The capacity for ion compartmentalization among different tissues and cells is the key mechanism regulating salt tolerance in plants. In this study, we investigated the ion compartmentalization ...capacity of two upland cotton genotypes with different salt tolerances under salt shock at the tissue, cell and molecular levels. We found that the leaf glandular trichome could secrete more salt ions in the salt-tolerant genotype than in the sensitive genotype, demonstrating the excretion of ions from tissue may be a new mechanism to respond to short-term salt shock. Furthermore, an investigation of the ion distribution demonstrated that the ion content was significantly lower in critical tissues and cells of the salt-tolerant genotype, indicating the salt-tolerant genotype had a greater capacity for ion compartmentalization in the shoot. By comparing the membrane H
-ATPase activity and the expression of ion transportation-related genes, we found that the H
-ATPase activity and Na
/H
antiporter are the key factors determining the capacity for ion compartmentalization in leaves, which might further determine the salt tolerance of cotton. The novel function of the glandular trichome and the comparison of Na
compartmentalization between two cotton genotypes with contrasting salt tolerances provide a new understanding of the salt tolerance mechanism in cotton.
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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.
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.
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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Abstract
Upland cotton (
Gossypium hirsutum
L.) is an important economic crop for renewable textile fibers. However, the simultaneous improvement of yield and fiber quality in cotton is difficult as ...the linkage drag. Compared with breaking the linkage drag, identification of the favorable pleiotropic loci on the genome level by genome-wide association study (GWAS) provides a new way to improve the yield and fiber quality simultaneously. In our study restriction-site-associated DNA sequencing (RAD-seq) was used to genotype 316 cotton accessions. Eight major traits in three categories including yield, fiber quality and maturation were investigated in nine environments (3 sites × 3 years). 231 SNPs associated with these eight traits (− log
10
(
P
) > 5.27) were identified, located in 27 genomic regions respectively by linkage disequilibrium analysis. Further analysis showed that four genomic regions (the region 1, 6, 8 and 23) held favorable pleiotropic loci and 6 candidate genes were identified. Through genotyping, 14 elite accessions carrying the favorable loci on four pleiotropic regions were identified. These favorable pleiotropic loci and elite genotypes identified in this study will be utilized to improve the yield and fiber quality simultaneously in future cotton breeding.
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Abstract
Oxidative stress occurs when crop plants are exposed to extreme abiotic conditions that lead to the excessive production and accumulation of reactive oxygen species (ROS). Those extreme ...abiotic conditions or stresses include drought, high temperature, heavy metals, salinity, and ultraviolet radiation, and they cause yield and quality losses in crops. ROS are highly reactive species found in nature that can attack plant organelles, metabolites, and molecules by interrupting various metabolic pathways until cell death occurs. Plants have evolved defense mechanisms for the production of antioxidants to detoxify the ROS and to protect the plant against oxidative damage. Modern researches in crop plants revealed that low levels of ROS act as a signal which induces tolerance to environmental extremes by altering the expression of defensive genes. In this review, we summarized the processes involved in ROS production in response to several types of abiotic stress in cotton plants. Furthermore, we discussed the achievements in the understanding and improving oxidative stress tolerance in cotton in recent years. Researches related to plant oxidative stresses have shown excellent potential for the development of stress-tolerant crops.
Main conclusion
The elevation of transcript levels of
GhDREB1B
causes the accumulation of osmoregulants and mitigation of reactive oxygen species, which contributes to the enhanced resistance to ...chilling stress in
AiSheng98
cotton.
Low temperature is one of the key environmental stresses that impairs cotton growth and restricts fiber productivity. Dehydration responsive element binding (DREB) transcription factors play an important role in cold response in plants by modulating the transcription level of cold-responsive genes to protect the plants from low-temperature stress. Here, we showed that
GhDREB1B
, a copy number variant in the
AiSheng98
(
AS98
) cotton mutant, significantly improved chilling tolerance in cotton seedlings, while silencing of
GhDREB1B
made transgenic cotton sensitive to chilling stress in
AS98
cotton compared with control plants. Elevated
GhDREB1B
transcript level activated the expression of major cold-responsive genes. Genome-wide expression profiling by RNA sequencing revealed the upregulation of genes related to fatty acids, lipid proteins, osmoprotection, and anti-oxidative enzymes in
AiSheng98
. Excessive accumulation of malondialdehyde (MDA) and higher ion leakage rates occurred in wild-type LFH10 plants when compared to those of
Aisheng98
during chilling stress, signifying lower chilling tolerance in the wild-type than in
Aisheng98
. Furthermore, the
Aisheng98
mutant under chilling stress accumulated higher levels of free proline and soluble sugar than LFH10 accumulated. These results suggest that
GhDREB1B
is a positive regulator and its variant can alter the expression patterns of major low-temperature stress-related genes and enhance chilling tolerance in cotton.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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.
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.
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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Abstract
Background
Cotton is known for fiber extraction and it is grown in tropical and sub-tropical areas of the world due to having hot weather. Cotton crop has a significant role in GDP of ...Pakistan. Therefore, the two-years research was conducted to estimate heritability and association among various yield contributing parameters of cotton,
i.e
.
,
plant height, number of bolls per plant, number of sympodial branches per plant, seed cotton yield, boll weight, seed index, ginning outturn (GOT), fiber length, fiber strength, and fiber fineness.
Results
Association analysis revealed that seed cotton yield had a significant positive correlation with plant height, number of bolls per plant, number of sympodial branches per plant, GOT, staple length and fiber strength. Staple length and fiber strength were negatively linked with each other. Estimates of heritability were high for all of the traits except the number of sympodial branches per plant and boll weight.
Conclusion
The parent IUB-222 was found to be the best for plant height, the number of bolls per plant, boll weight, GOT, seed cotton yield, and seed index. The genotypes namely, NIAB-414 and VH-367 were identified as the best parents for fiber length, strength, and fineness. Among the crosses NIAB-414 × IUB-222 was the best for the number of bolls per plant, seed index, seed cotton yield and fiber fineness, whereas, the cross of NIAB-414 × CIM-632 was good for plant height. The combination of A555 × CIM-632 was the best for the number of sympodial branches per plant, boll weight, fiber length, and strength, and VH-367 × CIM-632 proved the best for GOT.
Enhancing both fiber yield and quality is crucial in cotton breeding programs. Typically, a negative correlation exists between fiber yield and quality, and the strategy to decouple this relationship ...remains obscure. In this study, we generated three multi-parent intercross populations, encompassing 2,852 F2:3 lines, which represent fiber yield potential (FY), fiber quality potential (FQ), and a combination of both potentials (FYQ), derived from sixteen diverse Upland cotton cultivars. We utilized twenty-four kompetitive allele specific PCR (KASP) molecular markers, based on previously identified loci associated with fiber quality (FL5/FS1, FL3/FS2, and FL2) and fiber yield (BW1, BW2, and LP1), for genotyping purposes. The pyramiding of favorable haplotypes from three fiber quality-associated loci resulted in an increase exceeding 10% in fiber length (FL5+FL3+FL2+LP1) and in an increase exceeding 17% in fiber strength (FL5+FL3+FL2). Notably, our findings suggest that the combination of FL3+FL2+BW1+LP1 alleles has the potential to disrupt the negative correlation between fiber yield and quality. Lines harboring these alleles simultaneously exhibited an elevated lint percentage (LP), as well as enhanced fiber length and quality. This study offers robust molecular markers for the efficient selection of superior progeny with desired phenotypes in the early stages of cotton breeding. Furthermore, the allelic combination that concurrently improves fiber quality and yield sheds light on for further exploration the molecular basis of breaking unfavorable linkages in crop breeding.
Display omitted
•The successful development of twenty-four KASP molecular markers, based on loci known to influence fiber yield and quality.•Pyramiding of favorable haplotypes from three loci related to fiber quality can significantly improve fiber quality.•The specific allelic combination appears promising in breaking the negative correlation between fiber yield and quality.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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.
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.
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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