Cotton Accessions Research Articles

Evaluation of the <i>GhMAPK</i> gene expression level under salt stress in cotton cultivars

Background: Abiotic environmental stress factors such as salt stress, drought, oxidative stress adversely affect the development and productivity of plants. To combat adverse environmental conditions, plants have developed a number of protective mechanisms. MAP kinases are protein kinases that regulate cellular activity in response to extracellular stimuli. Given the significant role of MAP kinase mechanisms in universal biological processes, elucidation of its role and mechanisms can be used to create stress-resistant genotypes. The use of stimulators and blockers of MAP kinase mechanisms is promising as a new direction in the management of plant stress resistance. The main goal of the conducted research is the comparative analysis of expression patterns of cotton accessions under salt stress conditions, the study of the relation between an increase in salt concentration and the change in the level of transcripts. Thirteen cultivars from Azerbaijan, nine from Turkey, four from Uzbekistan, four from Greece and one from Kyrgyzstan were used in the research, and changes in the expression level of the GhMAPK gene in cotton accessions was studied with the application of the real-time PCR analysis. In the present study, the evaluation of thirty-one cotton cultivars under different salt stress (NaCl) concentrations revealed significant differences in gene expression levels between cultivars of the same species. The ‘Navai-9’ cultivar from Uzbekistan had the highest expression level at both 100 mM and 200 mM salt concentrations compared to all other cultivars. Among local cultivars, cv. ‘Ganja-110’ (at 100 mM salt concentration), and cv. ‘Zafar’ (at 200 mM) differed from others in the level of changes in transcripts. In addition, there was a wide variation in the expression levels of stress-related genes between groups of accessions identified as resistant and sensitive, and within groups. Thus, both the increase and decrease in the expression level were found within these groups. This diversity in gene expression in sensitive and resistant cultivars in response to the salt stress shows that the mechanisms providing salt tolerance in the studied cultivars are different.

Identification and characterization of candidate genes for primary root length in Asiatic cotton (Gossypium arboreum L.).

One major gene controlling primary root length (PRL) in Gossypium arboreum is identified and this research provides a theoretical basis for root development for cotton. Primary root elongation is an essential process in plant root system structure. Here, we investigated the primary root length (PRL) of 215 diploid cotton (G. arboreum) accessions at 5, 8, 10, 15days after sowing. A Genome-wide association study was performed for the PRL, resulting in 49 significant SNPs associated with 32 putative candidate genes. The SNP with the strongest signal (Chr07_8047530) could clearly distinguish the PRLs between accessions with two haplotypes. GamurG is the only gene that showed higher relative expression in the long PRL genotypes than the short PRL genotypes, which indicated it was the most likely candidate gene for regulating PRL. Moreover, the GamurG-silenced cotton seedlings showed a shorter PRL, while the GamurG-overexpressed Arabidopsis exhibited a significantly longer PRL. Our findings provide insight into the regulation mechanism of cotton root growth and will facilitate future breeding programs to optimize the root system structure in cotton.

Dissecting the major genetic components underlying cotton lint development.

Numerous genetic loci and several functionally characterized genes have been linked to determination of lint percentage (lint%), one of the most important cotton yield components, but we still know little about the major genetic components underlying lint%. Here, we first linked the genetic loci containing MYB25-like_At and HD1_At to the fiberless seed trait of 'SL1-7-1' and found that MYB25-like_At and HD1_At were very lowly expressed in 'SL1-7-1' ovules during fiber initiation. We then dissected the genetic components involved in determination of lint% using segregating populations derived from crosses of fuzzless mutants and intermediate segregants with different lint%, which not only confirmed the HD1_At locus but identified the HD1_Dt locus as being the major genetic components contributing to fiber initiation and lint%. The segregating populations also allowed us to evaluate the relative contributions of MYB25-like_At, MYB25-like_Dt, HD1_At, and HD1_Dt to lint%. Haplotype analysis of an Upland cotton (Gossypium hirsutum) population with 723 accessions (including 81 fuzzless seed accessions) showed that lint% of the accessions with the LP allele (higher lint%) at MYB25-like_At, MYB25-like_Dt, or HD1_At was significantly higher than that with the lp allele (lower lint%). The lint% of the Upland cotton accessions with 3 or 4 LP alleles at MYB25-like and HD1 was significantly higher than that with 2 LP alleles. The results prompted us to propose a strategy for breeding high-yielding cotton varieties, i.e. pyramiding the LP alleles of MYB25-like and HD1 with new lint% LP alleles without negative impact on seed size and fiber quality.

Breeding of high seed oil oleate levels into Upland cotton from wild Gossypium barbadense L. germplasm

AbstractA high seed oil oleate trait identified in wild Gossypium barbadense L. cotton accession GB713 (PI 608139) was bred into Upland cotton (Gossypium hirsutum L.) cultivar Sure‐Grow 747 (SG747, PVP 9800118). Starting from the F2 generation of an initial cross between GB713 and SG747, plants were selected by measuring the seed oil fatty acid distributions by gas chromatography. Selected F3 plants were crossed to M Rk‐Rn 6, a line previously created from GB713 and SG747 for improved nematode resistance. High‐oleate plants were selected in the F2 population. Selected plants were then crossed to HOa1 (a ∼35% oleate line derived from M Rk‐Rn 1, a sibling line to M Rk‐Rn 6), and high‐oleate plants were again selected in the F2 population. F3 plants were re‐selected for the high‐oleate trait, and four selected F4 lines were evaluated in 2022 field plots. The four lines had oleate levels between 52% and 57%, approximately triple that found in normal cottonseed oil (15%–19%) and higher than in either the high‐oleate wild GB713 parent (∼40%) or in the previously released HOa cotton plant lines (33%–35%). The increased oleate levels occurred with an approximately equal reduction in linoleic acid. Other seed and fiber properties were largely like those of SG747, although some residual GB713 character existed within the lines. The resulting oil composition should be ideal for use in deep fat frying, with the high level of oleic acid improving the oil's oxidative stability but with sufficient linoleic acid to maintain frying flavor.

Exploitation of various physio-morphological and biochemical traits for the identification of drought tolerant genotypes in cotton

BackgroundDrought is one of the limiting factors for quality and quantity of cotton lint in tropical and sub-tropical regions. Therefore, development of drought tolerant cotton genotypes have become indispensable. The identification of drought tolerant genotypes is pre-requisite to develop high yielding cultivars suitable for drought affected areas.MethodsForty upland cotton accessions were selected on the basis of their adaptability and yield. The collected germplasm accessions were evaluated at seedling stage on the basis of morphological, physiological and biochemical parameters. The experiment was conducted under controlled conditions in greenhouse where these genotypes were sown under different levels of drought stress by following factorial under completely randomized design. The data were collected at seedling stages for root and shoot lengths, relative leaf water content, excised leaf water losses, peroxidase content and hydrogen peroxide concentrations in leaf tissues.ResultsThe biometrical analysis revealed that germplasm is significantly varied for recorded parameters, likewise interaction of genotypes and water stress was also significantly varied. The cotton germplasm was categorized in eight clusters based on response to water stress. The genotype Cyto-124 exhibited lowest H2O2 content under drought conditions, minimum excised leaf water loss under stress environment was exhibited by genotypes Ali Akber-802 and CEMB-33. Overall, on the basis of morphological and biochemical traits, SL-516 and Cyto-305 were found to be drought tolerant. Genotypes 1852 − 511, Stoneville 15–17 and Delta Pine-55 showed low values for root length, peroxidase activity and higher value for H2O2 contents. On the basis of these finding, these genotypes were declared as drought susceptible. ConclusionThe categorization of cotton germplasm indicating the differential response of various parameters under the control and drought stress conditions. The recorded parameters particularly relative leaf water contents and biochemical assays could be utilized to screen large number of germplasm of cotton for water deficit conditions. Besides, the drought tolerant genotypes identified in this research can be utilized in cotton breeding programs for the development of improved cultivars.

Long noncoding RNA TRABA suppresses β-glucosidase-encoding BGLU24 to promote salt tolerance in cotton.

Salt stress severely damages the growth and yield of crops. Recently, long noncoding RNAs (lncRNAs) were demonstrated to regulate various biological processes and responses to environmental stresses. However, the regulatory mechanisms of lncRNAs in cotton (Gossypium hirsutum) response to salt stress are still poorly understood. Here, we observed that a lncRNA, trans acting of BGLU24 by lncRNA (TRABA), was highly expressed while GhBGLU24-A was weakly expressed in a salt-tolerant cotton accession (DM37) compared to a salt-sensitive accession (TM-1). Using TRABA as an effector and proGhBGLU24-A-driven GUS as a reporter, we showed that TRABA suppressed GhBGLU24-A promoter activity in double transgenic Arabidopsis (Arabidopsis thaliana), which explained why GhBGLU24-A was weakly expressed in the salt-tolerant accession compared to the salt-sensitive accession. GhBGLU24-A encodes an endoplasmic reticulum (ER)-localized β-glucosidase that responds to salt stress. Further investigation revealed that GhBGLU24-A interacted with RING-type E3 ubiquitin ligase (GhRUBL). Virus-induced gene silencing (VIGS) and transgenic Arabidopsis studies revealed that both GhBGLU24-A and GhRUBL diminish plant tolerance to salt stress and ER stress. Based on its substantial effect on ER-related degradation (ERAD)-associated gene expression, GhBGLU24-A mediates ER stress likely through the ERAD pathway. These findings provide insights into the regulatory role of the lncRNA TRABA in modulating salt and ER stresses in cotton and have potential implications for developing more resilient crops.

The root system dominates the growth balance between the aboveground and belowground parts of cotton

Growth balance is very important for plants, which is the coordination of resource acquisition between the aboveground and belowground parts. Extensive research has focused on the aboveground portion, and less attention has been given to the root system. Furthermore, the specific regulatory mechanisms responsible for maintaining the growth balance between aboveground and belowground in crops are still unclear. We examined the root/shoot ratio and leaf area/root length ratio in 19 pima cotton (Gossypium barbadense) and 19 upland cotton (Gossypium hirsutum) accessions, and the effects of root traits on the growth balance were explored. The results indicated that growth balance could affect the biomass accumulation of cotton, and the root system was the core part of controlling growth balance. The difference was that the specific root length played a major role in pima cotton, while the root mass fraction was more important in upland cotton. Despite these differences, both types of cotton achieved similar resource acquisition capability through the synergistic effect of mass fraction and morphological characteristics of leaves and roots. Our study is the first to demonstrate that the root system dominates the growth balance in pima and upland cotton. Selecting accessions with similar phenotypes may represent a promising new direction for increasing the success probability of interspecific hybridization and introgression breeding. These findings expand our understanding of the resource acquisition and utilization of crops and provide a valuable perspective for ecological research and crop breeding.

Genetic dissection of lint percentage in short-season cotton using combined QTL mapping and RNA-seq.

In total, 17 QTLs for lint percentage in short-season cotton, including three stable QTLs, were detected. Twenty-eight differentially expressed genes located within the stable QTLs were identified, and two genes were validated by qRT-PCR. The breeding and use of short-season cotton have significant values in addressing the question of occupying farmlands with either cotton or cereals. However, the fiber yields of short-season cotton varieties are significantly lower than those of middle- and late-maturing varieties. How to effectively improve the fiber yield of short-season cotton has become a focus of cotton research. Here, a high-density genetic map was constructed using genome resequencing and an RIL population generated from the hybridization of two short-season cotton accessions, Dong3 and Dong4. The map contained 4960 bin markers across the 26 cotton chromosomes and spanned 3971.08cM, with an average distance of 0.80cM between adjacent markers. Based on the genetic map, quantitative trait locus (QTL) mapping for lint percentage (LP, %), an important yield component trait, was performed. In total, 17 QTLs for LP, including three stable QTLs, qLP-A02, qLP-D04, and qLP-D12, were detected. Three out of 11 non-redundant QTLs overlapped with previously reported QTLs, whereas the other eight were novel QTLs. A total of 28 differentially expressed genes associated with the three stable QTLs were identified using RNA-seq of ovules and fibers at different seed developmental stages from the parental materials. The two genes, Ghir_A02G017640 and Ghir_A02G018500, may be related to LP as determined by further qRT-PCR validation. This study provides useful information for the genetic dissection of LP and promotes the molecular breeding of short-season cotton.

Uncovering genomic and transcriptional variations facilitates utilization of wild resources in cotton disease resistance improvement.

Upland cotton wild/landraces represent a valuable resource for disease resistance alleles. Genetic differentiation between genotypes, as well as variation in Verticillium wilt (VW) resistance, has been poorly characterized for upland cotton accessions on the domestication spectrum (from wild/landraces to elite lines). To illustrate the effects of modern breeding on VW resistance in upland cotton, 37 wild/landraces were resequenced and phenotyped for VW resistance. Genomic patterns of differentiation were identified between wild/landraces and improved upland cotton, and a significant decline in VW resistance was observed in association with improvement. Four genotypes representing different degrees of improvement were used in a full-length transcriptome analysis to study the genetic basis of VW resistance. ROS signaling was highly conserved at the transcriptional level, likely providing the basis for VW resistance in upland cotton. ASN biosynthesis and HSP90-mediated resistance moderated the response to VW in wild/landraces, and loss of induction activity of these genes resulted in VW susceptibility. The observed genomic differentiation contributed to the loss of induction of some important VW resistance genes such as HSP90.4 and PR16. Besides providing new insights into the evolution of upland cotton VW resistance, this study also identifies important resistance pathways and genes for both fundamental research and cotton breeding.

Comparative transcriptional and co-expression network analysis of two upland cotton accessions with extreme phenotypic differences reveals molecular mechanisms of fiber development.

Upland cotton (Gossypium hirsutum) is the main source of natural fiber in the global textile industry, and thus its fiber quality and yield are important parameters. In this study, comparative transcriptomics was used to analyze differentially expressed genes (DEGs) due to its ability to effectively screen candidate genes during the developmental stages of cotton fiber. However, research using this method is limited, particularly on fiber development. The aim of this study was to uncover the molecular mechanisms underlying the whole period of fiber development and the differences in transcriptional levels. Comparative transcriptomes are used to analyze transcriptome data and to screen for differentially expressed genes. STEM and WGCNA were used to screen for key genes involved in fiber development. qRT-PCR was performed to verify gene expression of selected DEGs and hub genes. Two accessions of upland cotton with extreme phenotypic differences, namely EZ60 and ZR014121, were used to carry out RNA sequencing (RNA-seq) on fiber samples from different fiber development stages. The results identified 704, 376, 141, 269, 761, and 586 genes that were upregulated, and 1,052, 476, 355, 259, 702, and 847 genes that were downregulated at 0, 5, 10, 15, 20, and 25 days post anthesis, respectively. Similar expression patterns of DEGs were monitored using short time-series expression miner (STEM) analysis, and associated pathways of DEGs within profiles were investigated. In addition, weighted gene co-expression network analysis (WGCNA) identified five key modules in fiber development and screened 20 hub genes involved in the development of fibers. Through the annotation of the genes, it was found that the excessive expression of resistance-related genes in the early fiber development stages affects the fiber yield, whereas the sustained expression of cell elongation-related genes is critical for long fibers. This study provides new information that can be used to improve fibers in newly developed upland cotton genotypes.

Genetic dissection and origin of pleiotropic loci underlying multi-level fiber quality traits in upland cotton (Gossypium hirsutum L.)

Cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile products. However, the limitations of measurement instruments have hindered the accurate evaluation of some important fiber characteristics such as fiber maturity, fineness, and neps, which in turn has impeded the genetic improvement and industrial utilization of cotton fiber. Here, 12 single fiber quality traits were measured using Advanced Fiber Information System (AFIS) equipment among 383 accessions of upland cotton (Gossypium hirsutum L.). In addition, eight conventional fiber quality traits were assessed by the High Volume Instrument (HVI) System. Genome-wide association study (GWAS), linkage disequilibrium (LD) block genotyping and functional identification were conducted sequentially to uncover the associated elite loci and candidate genes of fiber quality traits. As a result, the previously reported pleiotropic locus FL_D11 regulating fiber length-related traits was identified in this study. More importantly, three novel pleiotropic loci (FM_A03, FF_A05, and FN_A07) regulating fiber maturity, fineness and neps, respectively, were detected based on AFIS traits. Numerous highly promising candidate genes were screened out by integrating RNA-seq and qRT-PCR analyses, including the reported GhKRP6 for fiber length, the newly identified GhMAP8 for maturity and GhDFR for fineness. The origin and evolutionary analysis of pleiotropic loci indicated that the selection pressure on FL_D11, FM_A03 and FF_A05 increased as the breeding period approached the present and the origins of FM_A03 and FF_A05 were traced back to cotton landraces. These findings reveal the genetic basis underlying fiber quality and provide insight into the genetic improvement and textile utilization of fiber in G. hirsutum.

The plasmodesmata-associated β-1,3-glucanase gene GhPdBG regulates fiber development in cotton

Trichomes are specialized structures that originate from epidermal cells of organs in higher plants. The cotton fiber is a unique single-celled trichome that elongates from the seed coat epidermis. Cotton (Gossypium hirsutum) fibers and trichomes are models for cell differentiation. In an attempt to elucidate the intercellular factors that regulate fiber and trichome cell development, we identifieda plasmodesmal β-1,3-glucanase gene (designated GhPdBG) controlling the opening and closing of plasmodesmata in cotton fibers. Structural and evolutionary analysis showed haplotypic variation in the promoter region of the GhPdBG gene among 352 cotton accessions, but high conservation in the coding region. GhPdBG was expressed predominantly in cotton fibers and localized to plasmodesmata (PD). Expression patterns of PdBG that corresponded to PD permeability were apparent during fiber development in G. hirsutum and G. barbadense. The PdBG-mediated opening-closure of PD appears to be involved in fiber development and may account for the contrasting fiber traits of these two species. Ectopic expression of GhPdBG revealed that it functions in regulating fiber and trichome length and/or density by modulating plasmodesmatal permeability. This finding suggests that plasmodesmal targeting of GhPdBG, as a switch of intercellular channels, regulates single-celled fiber and trichome development in cotton.

Population Genomics Unravels the Characteristic Relationship between Introgression and Geographical Distribution in Upland Cotton

Introgression is an important driver of new genetic variation that increases species and genetic diversity. However, the relationship between introgression and geographic distribution of upland cotton is still unclear. Herein, we explored geographically comprehensive genomic data based on 890 upland cotton accessions to decipher the degree of introgression between different geographic distributions and its effect on selection and fiber quality. We found introgression intervals to exist across different geographic distributions. Introgression is affected by the similarity of the environment in which they live, and those with similar ecological environments tend to share the same introgression area. Introgression is affected by artificial selection. A genome-wide association study (GWAS) meta-analysis was performed with 6 fiber traits and identified 261 quantitative trait loci (QTLs). We found that 67 QTLs had introgression signals, and the genome interval size was 118.81 Mb, while 123 QTLs had selection signals, and the genomic interval was 28.38 Mb. These results provide insights into the population-scaled introgression landscape, suggesting that introgression contributed to the cotton genetic improvement, which provides a useful reference for studying intraspecific introgressions from different geographical distributions in other species.

Validating field regeneration capacity for selected accessions of Gossypium hirsutum using callus induction and regeneration capacity

BackgroundGossypium hirsutum undergoes rapid clonal propagation to regenerate a mature plant through tissue culture. However, the correlation between cotton leaf regeneration, callus induction, and regeneration ability was still obscure. In this research, cotton leaf regeneration level for 21 accessions in the field (new leaves) was observed after the first harvest, and a comparison between field regeneration level and callus induction with its regeneration capacity (new shoots and roots) for the same 21 accessions was carried out. Agronomic traits, including plant height, leaf area, fresh leaf weight, dry leaf weight, the number of flowers and bolls, and biochemical (proline content) and physiological (chlorophyll and carotenoid content) traits during the flowering stage of 21 upland cotton accessions, were investigated.ResultA significant correlation between physiological parameters and callus induction was discovered. Callus induction and regeneration capacity of roots and shoots for hypocotyl, cotyledons, and shoot tip tissues were used to validate field leaf regeneration level after the first harvest. CCRI 24 showed significant leaf regeneration in the field and callus induction capacity through callus induction and regeneration.ConclusionWe found a substantial relationship between field regeneration capability and callus induction with its regeneration capacity for the hypocotyl, cotyledons, and shoot tip. The results showed that ZS061, Lumian 378, Jimian 863, and ZS065 have the highest moisture retention capacity, while CCRI 24, Liaoyang Duomaomian, and Beizhe Gongshemian have the lowest moisture retention capacity. CCRI 24 has the highest leaf regeneration capacity in the field, while Beizhe Gongshemian has the lowest leaf regeneration capacity. All our result provides a clue for checking the regeneration capacity through leaf regeneration level in the field.

UAV-based time-series phenotyping reveals the genetic basis of plant height in upland cotton.

Plant height (PH) is an important agronomic trait affecting crop architecture, biomass, resistance to lodging and mechanical harvesting. Elucidating the genetic governance of plant height is crucial because of the global demand for high crop yields. However, during the rapid growth period of plants the PH changes a lot on a daily basis, which makes it difficult to accurately phenotype the trait by hand on a large scale. In this study, an unmanned aerial vehicle (UAV)-based remote-sensing phenotyping platform was applied to obtain time-series PHs of 320 upland cotton accessions in three different field trials. The results showed that the PHs obtained from UAV images were significantly correlated with ground-based manual measurements, for three trials (R2 = 0.96, 0.95 and 0.96). Two genetic loci on chromosomes A01 and A11 associated with PH were identified by genome-wide association studies (GWAS). GhUBP15 and GhCUL1 were identified to influence PH in further analysis. We obtained a time series of PH values for three field conditions based on remote sensing with UAV. The key genes identified in this study are of great value for the breeding of ideal plant architecture in cotton.

Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton

BackgroundVerticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known to be vulnerable to its fungal pathogen, Verticillium dahliae, yet the related genetic mechanism remains unknown.ResultsBy genome-wide association studies of 419 accessions of the upland cotton, Gossypium hirsutum, we identify ten loci that are associated with resistance against Verticillium wilt. Among these loci, SHZDI1/SHZDP2/AYDP1 from chromosome A10 is located on a fragment introgressed from Gossypium arboreum. We characterize a large cluster of Toll/interleukin 1 (TIR) nucleotide-binding leucine-rich repeat receptors in this fragment. We then identify a dual-TIR domain gene from this cluster, GhRVD1, which triggers an effector-independent cell death and is induced by Verticillium dahliae. We confirm that GhRVD1 is one of the causal gene for SHZDI1. Allelic variation in the TIR domain attenuates GhRVD1-mediated resistance against Verticillium dahliae. Homodimerization between TIR1-TIR2 mediates rapid immune response, while disruption of its αD- and αE-helices interface eliminates the autoactivity and self-association of TIR1-TIR2. We further demonstrate that GhTIRP1 inhibits the autoactivity and self-association of TIR1-TIR2 by competing for binding to them, thereby preventing the resistance to Verticillium dahliae.ConclusionsWe propose the first working model for TIRP1 involved self-association and autoactivity of dual-TIR domain proteins that confer compromised pathogen resistance of dual-TIR domain proteins in plants. The findings reveal a novel mechanism on Verticillium dahliae resistance and provide genetic basis for breeding in future.

Targeted development of diagnostic SNP markers for resistance to Fusarium wilt race 4 in Upland cotton (Gossypium hirsutum)

Fusarium wilt caused by the soil-borne fungus Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) has become one of the most important emerging diseases in US cotton production. Numerous QTLs have been reported for resistance to FOV; however, no major FOV4-resistance QTL or gene has been identified and used in breeding Upland cotton (Gossypium hirsutum) for FOV4 resistance. In this study, a panel of 223 Chinese Upland cotton accessions was evaluated for FOV4 resistance based on seedling mortality rate (MR) and stem and root vascular discoloration (SVD and RVD). SNP markers were developed based on targeted genome sequencing using AgriPlex Genomics. The chromosome region at 2.130-2.292Mb on D03 was significantly correlated with both SVD and RVD but not with MR. Based on the two most significant SNP markers, accessions homozygous for AA or TT SNP genotype averaged significantly lower SVD (0.88 vs. 2.54) and RVD (1.46 vs. 3.02) than those homozygous for CC or GG SNP genotype. The results suggested that a gene or genes within the region conferred resistance to vascular discoloration caused by FOV4. The Chinese Upland accessions had 37.22% homozygous AA or TT SNP genotype and 11.66% heterozygous AC or TG SNP genotype, while 32 US elite public breeding lines all had the CC or GG SNP genotype. Among 463 obsolete US Upland accessions, only 0.86% possessed the AA or TT SNP genotype. This study, for the first time, has developed diagnostic SNPs for marker-assisted selection and identified FOV4-resistant Upland germplasms with the SNPs.

Estimation of Drought Tolerance Indices in Upland Cotton under Water Deficit Conditions

Cotton is a precious commodity that offers raw material to the textile industry. This crop is grown in tropical and sub-tropical regions of the world. Abiotic stresses exerts negative impact on cotton production, but water scarcity has the worst impact. It is rising due to current situation, in which global warming is producing a decrease in precipitation while an increase in evapo-transpiration is causing an agricultural drought. Thus, it is a difficult task for cotton breeders to identify cotton lines that can respond to areas with limited water supplies without lowering yields and might be utilized as suitable parents in a breeding program to produce drought-tolerant indices. The primary objective of this research was the estimation of drought tolerance indices in upland cotton under water deficit conditions. For this purpose, fifty accessions of upland cotton were assessed for their ability to tolerate the water stress under three conditions, namely control, 50% FC, and 75% FC. These genotypes showed significant variations based on morpho-physiological and biochemical characteristics. At control conditions, these genotypes exhibited enhanced growth and better performance. Whereas, the behavior of some indices under 75% FC showed less growth as compared to control, while under the 50% FC highly significant reductions were observed among genotypes. The genotypes that are resistant to drought and those that are susceptible were found using the K-means cluster and biplot analysis. In terms of performance, the genotypes namely Cyto-515, CIM-595, FH-142, and IR-3701 exhibited relatively better in all the treatments and low excised leaf water loss, high relative water contents, chlorophyll contents, free proline contents, and peroxidase activity were observed to be useful selection criteria for drought resistance. These identified genotypes namely, Cyto-515, CIM-595, FH-142, and IR-3701 may be grown in water deficit areas of the country to assess their potential, could be used in breeding programs for development of germplasm suitable for water stress conditions.

A mutant cotton fatty acid desaturase 2-1d allele causes protein mistargeting and altered seed oil composition

BackgroundCotton (Gossypium sp.) has been cultivated for centuries for its spinnable fibers, but its seed oil also possesses untapped economic potential if, improvements could be made to its oleic acid content.ResultsPrevious studies, including those from our laboratory, identified pima accessions containing approximately doubled levels of seed oil oleic acid, compared to standard upland cottonseed oil. Here, the molecular properties of a fatty acid desaturase encoded by a mutant allele identified by genome sequencing in an earlier analysis were analyzed. The mutant sequence is predicted to encode a C-terminally truncated protein lacking nine residues, including a predicted endoplasmic reticulum membrane retrieval motif. We determined that the mutation was caused by a relatively recent movement of a Ty1/copia type retrotransposon that is not found associated with this desaturase gene in other sequenced cotton genomes. The mutant desaturase, along with its repaired isozyme and the wild-type A-subgenome homoeologous protein were expressed in transgenic yeast and stably transformed Arabidopsis plants. All full-length enzymes efficiently converted oleic acid to linoleic acid. The mutant desaturase protein produced only trace amounts of linoleic acid, and only when strongly overexpressed in yeast cells, indicating that the missing C-terminal amino acid residues are not strictly required for enzyme activity, yet are necessary for proper subcellular targeting to the endoplasmic reticulum membrane.ConclusionThese results provide the biochemical underpinning that links a genetic lesion present in a limited group of South American pima cotton accessions and their rare seed oil oleic acid traits. Markers developed to the mutant desaturase allele are currently being used in breeding programs designed to introduce this trait into agronomic upland cotton varieties.

Genome and haplotype provide insights into the population differentiation and breeding improvement of Gossypium barbadense

IntroductionSea-island cotton (Gossypium barbadense, Gb) is one of the major sources of high-grade natural fiber. Besides the common annual Gb cotton, perennial Gb cotton is also cultivated, but studies on perennial Gb cotton are rare. ObjectivesWe aimed to make a systematic analysis of perennial sea-island cotton and lay a foundation for its utilization in breeding, and try to identify the representative structural variations (SVs) in sea-island cotton, and to reveal the population differentiation and adaptive improvement of sea-island cotton. MethodsThrough genome assembly of one perennial Gb cotton accession (named Gb_M210936) and comparative genome analysis, variations during Gb cotton domestication were identified by comparing Gb_M210936 with annual Gb accession 3–79 and with wild allotetraploid cotton G. darwinii. Six perennial Gb accessions combining with the resequenced 1,129 cotton accessions were used to conduct population and genetic analysis. Large haplotype blocks (haploblocks), generated from interspecific introgressions and intraspecific inversions, were identified and were used to analyze their effects on population differentiation and agronomic traits of sea-island cotton. ResultsOne reference genome of perennial sea-island cotton was assembled. Representative SVs in sea-island cotton were identified, and 31 SVs were found to be associated with agronomic traits. Perennial Gb cotton had a closer kinship with the wild-to-landrace continuum Gb cotton from south America where Gb cotton is originally domesticated. Haploblocks were associated with agronomic traits improvement of sea-island cotton, promoted sea-island cotton differentiation into three subgroups, were suffered from breeding selection, and may drive Gb cotton to be adapted to central Asian. ConclusionOur study made up the lack of perennial Gb cotton genome, and clarified that exotic introgressions improved the traits of sea-island cotton, promoted the population differentiation, and drove sea-island cotton adaptive to central Asia, which will provide new insights for the genetic breeding improvement of sea-island cottons.