Effects of irrigation and planting geometry on cotton (Gossypium hirsutum L.) fiber quality and seed composition

[Background] Cotton fiber quality and seed composition play vital roles in the economics of cotton production systems and the cottonseed meal industry. This research aimed to examine the effects of different irrigation levels and planting geometries on fiber quality and seed composition of cotton (Gossypium hirsutum L.). We conducted a 2-year study in 2018 and 2019 in a warm, humid area in the Southeast United States on Dundee silt loam soil. There were three irrigation treatments in the study. The treatments included irrigating every furrow, or full irrigation (FI), every alternate furrow, or half irrigation (HI), and no irrigation, or rain-fed (RF). Planting geometries were on ridges spaced 102 cm apart and either a single-row (SR) or twin-rows (TR).

[Results] The results of high-volume instrument (HVI), advanced fiber information systems (AFIS) and near-infrared reflectance spectroscopy (NIRS) showed that irrigation and planting treatments played a significant role in fiber quality and seed composition. Across irrigation treatments, significant differences were seen in fiber properties, including fineness, maturity ratio, micronaire, neps, short fiber, strength, uniformity, upper half mean length (UHML), upper quartile length by weight (UQLw), and yellowness (+b). Irrigation and planting geometry (PG) had a significant effect on micronaire, strength, and UHML while their interaction was significant only for micronaire. The micronaire was negatively affected by irrigation as FI-SR, FI-TR, HI-SR, and HI-TR recorded 11% ~ 12% lower over the RF-SR and TR treatments. The PG played a minor role in determining fiber quality traits like micronaire and nep count. Irrigation treatments produced significantly lower (3% ~ 4%) protein content than rain-fed, while oil content increased significantly (6% ~ 10%).

[Conclusion] The study results indicate a potential for improving cotton fiber and seed qualities by managing irrigation and planting geometries in cotton production systems in the Mississippi (MS) Delta region. The HI-TR system appears promising for lint and seed quality.

[Title] Effects of irrigation and planting geometry on cotton (Gossypium hirsutum L.) fiber quality and seed composition

[Authors]  PINNAMANENI Srinivasa R., ANAPALLI Saseendran S., SUI Ruixiu, BELLALOUI Nacer & REDDY Krishna N. 

Journal of Cotton Research 2021, 42


Calibration of HVI cotton elongation measurements

[Background] The strength of cotton fiber has been extensively studied and significant improvements in fiber strength have been made, but fiber elongation has largely been ignored, despite it contributing to the energy needed to break fibers, which affects fiber handling and processing. High Volume Instruments (HVI) measure fiber elongation but have not been calibrated for this property, making the measurement unavailable for comparative work among instruments. In prior work, a set of elongation calibration materials had been developed based on Stelometer results. A round trial of ten Australian and U.S. instruments was conducted on six cotton samples representing a range of 4.9% to 8.1% elongation.

[Results] By scaling the HVI elongation values of each instrument to the values of the two calibration samples, the coefficient of variation in instrument measurements was reduced from an average of 34% for the uncalibrated measurements to 5% for the calibrated measurements. The reduction in variance allows for the direct comparison of results among instruments. A single-point elongation calibration was also assessed but found to be less effective than the proposed two-point calibration.

[Conclusion] The use of an effective calibration routine on HVI measurement of cotton significantly reduces the coefficient of variation of the elongation measurement within and between instruments. The implementation of the elongation calibration will allow testing and breeding programs to implement high-speed elongation testing which makes the use of elongation values possible in breeding programs.

[Title] Calibration of HVI cotton elongation measurements

[Authors] DELHOM Christopher D., HEQUET Eric F., KELLY Brendan, ABIDI Noureddine and MARTIN Vikki B.

Journal of Cotton Research 2020, 331


Stability, variation, and application of AFIS fiber length distributions

Journal of Cotton Research

[Background] Fiber length is one of the primary quality parameters for the cotton industry when considering the textile performance and end-use quality of cotton. Currently, many decisions regarding cotton fiber length utilize the industry standard measurement device, i.e., the High Volume Instrument (HVI). However, it is documented that complete fiber length distributions hold more information than the currently reported HVI length parameters, i.e., upper half mean length (UHML) and uniformity index (UI). An alternative measurement device, the Advanced Fiber Information System (AFIS), is able to capture additional information about fiber length distribution. What is currently not known is how much additional information the AFIS length distribution holds.

[Results] The stability of differences in within-sample variation in fiber length captured by the AFIS length distribution by number characterizing differences between samples was deemed stable across the extended testing period. A diverse breeding population was evaluated and four significant sources of within sample variation in length were identified. A comparison of the ability between HVI length parameters and AFIS fiber length distribution to correctly categorize breeding lines to their family was performed. In all cases, the AFIS fiber length distribution more accurately identified germplasm families.

[Conclusions] The long-term stability test of the AFIS fiber length distribution by number shows that the measurement is stable and can be used to assess differences across samples. However, more information about within-sample variation in fiber length than that can be captured by length parameters is needed to assess differences across samples in many applications. Four length parameters outperform two length parameters when trying to identify the familial background of the samples in this set. These parameters characterize distributional shape differences that are not captured by the standard AFIS length parameters, UQL and short fiber content by number (SFCn). These findings suggest that additional types of variation in cotton fiber length are not captured and are therefore not currently used in most cotton breeding programs.
[Title] Stability, variation, and application of AFIS fiber length distributions

[Authors]  HINDS Zachary, KELLY Brendan Robert & HEQUET Eric Francois

Evaluation of the genetic diversity of fibre quality traits in upland cotton (Gossypium hirsutum L.) inferred from phenotypic variations

[Background] Evaluating phenotypic traits is very important for the selection of elite lines in Gossypium hirsutum L. Cotton breeders are interested in using diverse genotypes in hybridization that can segregate for traits of interested with the possibility of selection and genetic gain. Information on phenotypic and molecular diversity helps the breeders for parental selection.

[Methods] In this study, 719 global collections of G. hirsutum L. were evaluated for five fibre-related traits during two consecutive years in eight different environments. A series of phenotypic data for fibre quality traits were obtained and the elite accessions were further screened using principal component analysis and phylogenetic tree construction based on single nucleotide polymorphism markers.

[Results] We found that fibre quality traits showed a wide range of variation among the G. hirsutum accessions over 2 years. In general, accessions from outside China tended to have higher fibre length (FL) and fibre strength (FS) than did Chinese accessions. Among different regional accessions in China, North/Northwest accessions tended to have the highest FL, FS and best fibre macronaire. By assessing five fibre quality traits over 2 years with genotypic data, 31 elite germplasms reaching double-thirty quality values (FL ≥ 30 mm and FS ≥ 30 cN·tex− 1) were selected.

[Conclusions] This study provided a detailed phenotypic diversity description of a population representing a wide range of upland cotton germplasm. Our findings provide useful information about possible elite fibre quality parents for cotton breeding programs.
[Title] Evaluation of the genetic diversity of fibre quality traits in upland cotton (Gossypium hirsutum L.) inferred from phenotypic variations

[Authors] SUN Zhengwen, WANG Xingfen, LIU Zhengwen, GU Qishen, ZHANG Yan, LI Zhikun, KE Huifeng, YANG Jun, WU Jinhua, WU Liqiang, ZHANG Guiyin and MA Zhiying
Journal of Cotton Research2019; 2:22



Genetic analysis of yield and fiber quality traits in upland cotton (Gossypium hirsutum L.) cultivated in different ecological regions of China

Journal of Cotton Research

[Background] Cotton is an important fiber crop worldwide. The yield potential of current genotypes of cotton can be exploited through hybridization. However, to develop superior hybrids with high yield and fiber quality traits, information of genetic control of traits is prerequisite. Therefore, genetic analysis plays pivotal role in plant breeding.

[Results] In present study, North Carolina II mating design was used to cross 5 female parents with 6 male parents to produce 30 intraspecific F1 cotton hybrids. All plant materials were tested in three different ecological regions of China during the year of 2016–2017. Additive-dominance-environment (ADE) genetic model was used to estimate the genetic effects and genotypic and phenotypic correlation of yield and fiber quality traits. Results showed that yield traits except lint percentage were mainly controlled by genetic and environment interaction effects, whereas lint percentage and fiber quality traits were determined by main genetic effects. Moreover, dominant and additive-environment interaction effects had more influence on yield traits, whereas additive and dominance-environment interaction effects were found to be predominant for fiber traits. Broad-sense and its interaction heritability were significant for all yield and most of fiber quality traits. Narrow-sense and its interaction heritability were non-significant for boll number and seed cotton yield. Correlation analysis indicated that seed cotton yield had significant positive correlation with other yield attributes and non-significant with fiber quality traits. All fiber quality traits had significant positive correlation with each other except micronaire.

[Conclusions] Results of current study provide important information about genetic control of yield and fiber quality traits. Further, this study identified that parental lines, e.g., SJ48–1, ZB-1, 851–2, and DT-8 can be utilized to improve yield and fiber quality traits in cotton.

[Title] Genetic analysis of yield and fiber quality traits in upland cotton (Gossypium hirsutum L.) cultivated in different ecological regions of China

[Authors] SHAHZAD Kashif+, LI Xue+, QI Tingxiang, GUO Liping, TANG Huini, ZHANG Xuexian, WANG Hailin, ZHANG Meng, ZHANG Bingbing, QIAO Xiuqin, XING Chaozhu* & WU Jianyong*

Journal of Cotton Research. 2019, 2: 14



JCR-QTL mapping for fiber quality and yield-related traits across multiple generations in segregating population of CCRI 70

Journal of Cotton Reseach

[Background] Cotton is a significant economic crop that plays an indispensable role in many domains. Gossypium hirsutum L. is the most important fiber crop worldwide and contributes to more than 95% of global cotton production. Identifying stable quantitative trait locus (QTLs) controlling fiber quality and yield related traits are necessary prerequisites for marker-assisted selection (MAS).

[Results] A genetic linkage map was constructed with 312 simple sequence repeat (SSR) loci and 35 linkage groups using JoinMap 4.0; the map spanned 1 929.9 cM, with an average interval between two markers of 6.19 cM, and covered approximately 43.37% of the cotton genome. A total of 74 QTLs controlling fiber quality and 41 QTLs controlling yield-related traits were identified in 4 segregating generations. These QTLs were distributed across 20 chromosomes and collectively explained 1.01%~27.80% of the observed phenotypic variations. In particular, 35 stable QTLs could be identified in multiple generations, 25 common QTLs were consistent with those in previous studies, and 15 QTL clusters were found in 11 chromosome segments.

[Conclusion] These studies provide a theoretical basis for improving cotton yield and fiber quality for molecular marker-assisted selection.

[Title] QTL mapping for fiber quality and yield-related traits across multiple generations in segregating population of CCRI 70

[Authors] DENG Xiaoying, GONG Juwu, LIU Aiying, SHI Yuzhen, GONG Wankui, GE Qun, LI Junwen, SHANG Haihong, WU Yuxiang & YUAN Youlu

Journal of Cotton Research. 2019, 2:13



Feasibility assessment of phenotyping cotton fiber maturity using infrared spectroscopy and algorithms for genotyping analyses

[Background] Cotton fiber maturity is an important property that partially determines the processing and performance of cotton. Due to difficulties of obtaining fiber maturity values accurately from every plant of a genetic population, cotton geneticists often use micronaire (MIC) and/or lint percentage for classifying immature phenotypes from mature fiber phenotypes although they are complex fiber traits. The recent development of an algorithm for determining cotton fiber maturity (MIR) from Fourier transform infrared (FT-IR) spectra explores a novel way to measure fiber maturity efficiently and accurately. However, the algorithm has not been tested with a genetic population consisting of a large number of progeny plants.

[Results] The merits and limits of the MIC- or lint percentage-based phenotyping method were demonstrated by comparing the observed phenotypes with the predicted phenotypes based on their DNA marker genotypes in a genetic population consisting of 708 F2 plants with various fiber maturity. The observed MIC-based fiber phenotypes matched to the predicted phenotypes better than the observed lint percentage-based fiber phenotypes. The lint percentage was obtained from each of F2 plants, whereas the MIC values were unable to be obtained from the entire population since certain F2 plants produced insufficient fiber mass for their measurements. To test the feasibility of cotton fiber infrared maturity (MIR) as a viable phenotyping tool for genetic analyses, we measured FT-IR spectra from the second population composed of 80 F2 plants with various fiber maturities, determined MIR values using the algorithms, and compared them with their genotypes in addition to other fiber phenotypes. The results showed that MIR values were successfully obtained from each of the F2 plants, and the observed MIR-based phenotypes fit well to the predicted phenotypes based on their DNA marker genotypes as well as the observed phenotypes based on a combination of MIC and lint percentage.

[Conclusions] The MIR value obtained from FT-IR spectra of cotton fibers is able to accurately assess fiber maturity of all plants of a population in a quantitative way. The technique provides an option for cotton geneticists to determine fiber maturity rapidly and efficiently.

[Authors] KIM Hee Jin, LIU Yongliang, FANG David D. and DELHOM Christopher D.

Journal of Cotton Research2019; 2:8


Development of better naturally colored cotton lines (gossypium hirsutum l.) regarding seed cotton yield, ginning outturn and fiber technological properties under kahramanmaras conditions

Back to Content


Lale Efe

Kahramanmaras Sutcu Imam University, Faculty of Agriculture, Field Crops Department


The aim of this project carried out in 2011-2013 under Kahramanmaras conditions was to develop superior lines for seed cotton yield, ginning outturn and fiber technological properties from four naturally coloured cotton populations (Gossypium hirsutum L.) crossing naturally and having genetic variation using method  of  pedigree selection. Naturally coloured cotton populations used as materials had fibers coloured light brown, dark brown, green and creamy.

In 2011 year, 100 individual plants were selected from each coloured population according to field observations such as fiber colour, plant form, boll and leaf form, plant height, number of monopodia, number of sympodia, boll number per plant (for four colour 4×100=400 plants). Each  plant was harvested separately. In  100 plants (for each colour) seed cotton yield, ginning outturn, 100 seed weight, boll weight, seed cotton weight per boll, fiber length, fiber fineness, fiber strength, fiber elongation, fiber uniformity, short fiber index, trash area, trash count, trash degree were recorded. According to seed cotton yield, ginning outturn, 100 seed weight, boll and fiber traits 50 individual plants were selected to be sown in next year. In 2012 year, self pollinated seeds of 50 plants selected from four populations having different fiber colours were sown in the separate rows 5 m in length. Thus, 200 progeny rows were formed in total (50 dark brown, 50 light brown, 50 green, 50 creamy). The all plants in rows were self pollinated during flowering period. Individual plant selection were repeated in progeny rows according to field observations. 2 or 3 plants selected according to field observations in each row were harvested  separately (For each colour 50×2=100 plants, in total 100×4=400 plants). For each colour in 100 plants seed cotton yield, ginning outturn, 100 seed weight, boll and fiber traits were recorded. According to these traits 50 individual plants were selected. Self pollinated seeds of these plants were sown in the next year. In 2013 year these steps were replicated.

As a result, in each colour individual plants higher yielding and having higher lint properties were obtained. Second part of this project continuous to obtain homozygous and pure lines using self pollination from 2014 to 2016.

Back to Content

Association mapping for seed cotton yield, its contributing and fiber quality traits in Upland Cotton (G. hirsutum L.) germplasm lines.

Back to Content


Suresh handi and I.S.Katageri*

*Professor and Head,

Institute of Agribiotechnology, University of Agricultural Sciences, Dharwad, Karnataka, INDIA, katageriis@uasd.in


Determination of the genetic  basis of complex quantitative traits has been one of the major scientific challenges in the process of crop improvement. To assist in this effort, an increasing number of genomic and genetic resources are today exploitable,  including genome sequences, germplasm collections and public databases of genomic information. The availability of these resources, the recent advances in high-throughput genomic platforms and the increasing interest in exploring natural genetic diversity, make association mapping an appealing and affordable approach to identify genes responsible for quantitative variation of complex traits. Association mapping requires high-density oligonucleotide arrays to efficiently identify SNPs distributed across the genome at a density that accurately reflects genome wide LD structure and haplotype diversity. For Cotton, a high-density infinium array (63K SNP array) was recently built (Hulse-Kemp et al., 2015), with 63058 SNPs developed from different species which resulted in suitability for genome wide association analysis.

Association or linkage disequilibrium (LD) mapping revolutionized genetic mapping in humans, and is increasingly used to examine in plant genetics; it is an efficient way of determining the genetic basis of complex traits. In the present study, association mapping was examined with the use 201 germplasm of G. hirsutum lines evaluated for yield, yield components and fiber quality traits. Results from fastSTRCUTURE identified 12 subgroups in the population.  The critical value of R2 was set to 0.243 was taken as a threshold to claim LD between two loci. About 3.13 % marker pairs showed significant high LD (R2=1) and about 82.72 percent pairs of loci were in linkage equilibrium with R2 values less than 0.3. Mixed linear model accounting for population structure and kinship has identified 349 significant marker trait associations for yield, yield components and fiber quality traits effectively controlling false positives reported in GLM (642 markers). More number of markers showing significant association were situated on D genome indicates than ‘A’ genome indicates detection of diverse SNP markers than ‘D’ genome or this may also because of the dense marker coverage in the D genome. The phenotypic variation explained by makers in this study was smaller suggesting minor QTLs or polygenic nature of these traits.

Back to Content

Molecular breeding: cotton transcriptome analysis, characterisation and validation of fibre strength genes assistive in marker assisted selection

Back to Content


B.R.Patil,I.S. Katageri,B.M Khadi, G. Balasubramani, K.P.Raghvendra, J.Amudha, S.K.Deshpande


The relative gene expression of GhcesA1, GhcesA2, and GhcesA7 orthologus of AtcesA8, AtcesA4, and AtcesA7 respectively, Ghcobl4, Ghfla3 and GhMT1genes using Recombinant Inbred Lines mapping population was studied through q PCR. The results showed that GhcesA1, GhcesA2, Ghfla3 and Ghcobl4 were strongly associated with secondary wall synthesis and hence the plan is to prepare the gene construct with an appropriate fibre specific promoter to transform a suitable genotype. To validate the q PCR analysis, Scanning Electron Microscope study was conducted to confirm that cellulose is a key entity for conferring high fibre strength. The high fiber strength line HBS144 (28.0 g/tex) and low fiber strength line, HBS 187 (20.0 g/tex ) fiber’s micrograph showed that HBS 144 had strong series of fibrillar structure which was found less in HBS 187.A fibre diameter of 17µm was observed in HBS144 while ,a 10 µm fiber diameter was recorded in HBS 187.The fibrils which relate to deposition of cellulose had a diameter of 0.2 µm for HBS 144 and 0.1 µm for HBS 187 respectively. The RNA sequence analysis of HBS 144 and 187 revealed 74.6 million and 53.4 million raw reads respectively through Illumina. The number of unigenes expressed for genotype HBS-144 were 11328 while , 6866 unigenes were observed for HBS-187. A total of 14828 unigenes were up regulated while, a total of 13468 unigenes were down regulated in both genotypes employed for the study.The total number of identified SSR’s for HBS 144 were 29868 while, 21680 SSR’s were identified for HBS 187.The total number of variants (SNP) were 90857 for HBS 144 while, 74161 variants were observed for HBS 187.The plan is to utilize these SSR’ s and SNP ‘s for Marker assisted selection after validation by Gold standard linkage map.

Back to Content