Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China

[Background] Cotton fiber yield is a complex trait, which can be influenced by multiple agronomic traits. Unravelling the genetic basis of cotton fiber yield-related traits contributes to genetic improvement of cotton.

[Results] In this study, 503 upland cotton varieties covering the four breeding stages (BS1–BS4, 1911–2011) in China were used for association mapping and domestication analysis. One hundred and forty SSR markers significantly associated with ten fiber yield-related traits were identified, among which, 29 markers showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4, and 26 markers showed decreased trend effect. Four favorable alleles of 9 major loci (R2 ≥ 3) were strongly selected during the breeding stages, and the candidate genes of the four strongly selected alleles were predicated according to the gene function annotation and tissue expression data.

[Conclusion] The study not only uncovers the genetic basis of 10 cotton yield-related traits but also provides genetic evidence for cotton improvement during the cotton breeding process in China.

[Title] Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China

[Authors] GUO Chunping, PAN Zhenyuan, YOU Chunyuan, ZHOU Xiaofeng, HUANG Cong, SHEN Chao, ZHAO Ruihai, YANG Qingyong, ZHU Longfu, SHAHZAD Raheel, MENG Fande, LIN Zhongxu & NIE Xinhui

Journal of Cotton Research 2021, 410

Towards complete deconstruction of cotton transcriptional landscape

Journal of Cotton Research

Abstract: Recently, Wang et al. systematically explored the transcription landscape in diploid cotton Gossypium arboreum. In the study, they integrated four high-throughput sequencing techniques, including Pacbio sequencing, strand-specific RNA sequencing (ssRNA-seq), Cap analysis gene expression sequencing (CAGE-seq), and PolyA sequencing (PolyA-seq) to profile the RNA transcriptome of G. arboreum. They developed a pipeline, IGIA to construct accurate gene structure annotation based on the updated genome of G. arboreum and the multi-strategic RNA-seq data. Their study revealed some intriguing phenomena and potential novel mechanisms in the regulation of RNA transcription in plants, and also provided valuable resources for further functional genomic research in cotton.

[Title] Towards complete deconstruction of cotton transcriptional landscape

[Author] LI Fuguang

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

Use of Male Sterility in Cotton and Molecular markers for Fertility Restoration in CGMS of G.hirstum Cotton

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I.S. Katageri, *Rashmi Ranjan Toppo, and B.M. Khadi

 *Department of Biotechnology, College of Agriculture University of Agricultural Sciences, Dharwad – 580 005, India



Cotton is one among the few often cross-pollinated crops, where the achievement of commercial exploitation of heterosis is comparable to even that of cross-pollinated crops like  maize.  The main bottleneck in exploitation of hybrid vigour in cotton is the complicated technique of seed production, which involves hand emasculation and pollination that makes hybrid cotton seed more costly. To improve the remunerative value of hybrid seed production and commercial cultivation of hybrid it is necessary to develop productive male sterile based hybrids. Although Cytoplasmic Genetic Male Sterility is available, the identification of restorer for 100 percent fertility restoration was problematic. Molecular markers are coming handy in identifying such plants. The present study, therefore, comprised 413 individual plants comprising of 164 A-line and B-line, 124 IPS of R-line, 13 hybrids, 3 cultivars, 4 wild species, 24 G. hirsutum germplasm lines, 80 RILs and 1 GMS line were studied during 2012-13 and 2013-14 at ARS, Dharwad farm. Twenty four molecular markers known to be associated with fertility restoration (10 RAPD, 7 SSR, 6 STS, and 1 TRAP) were studied. Out of these, 3 STS markers (Y1107, UBC 147 and UBC 607) were able to amplify only in 44 plants out of 124 belong to DR-7 (known for fertility restoration). No amplification was observed in diverse genetic background of A-lines and their respective B-lines, wild species, G. barbadense var. SBYF 425, G. arboreum var. DLSa 17, G. herbaceum var. Jayadhar, G. hirsutum germplasm lines and Abadhita GMS line (sterile and its maintainer line). However amplification by these three markers was recorded in 6 out of 80 RILs of DCH-32 hybrids. Co-segregation for 98-100 percent fertility restoration and molecular markers associated was observed in F2 of cross between A line and fertility restorer carrying three molecular markers.

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Comparative chloroplast genome sequence analyses of gossypium thurberi with two cultivated allotetraploid gossypium species

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Farshid Talat

West Azerbaijan Agricultural and Natural Resources Research Center, AREEO, Urmia, Iran


The chloroplast is the sole site for photosynthetic activities in green plants and contains the whole enzymatic machinery needed for this purpose. Gossypium thurberi is a wild diploid species and also one of the most important taxa in the genus which widely has been used to improve cultivated allotetraploid cotton with its great potential of genetic resources. Present study was conducted in order to analyse sequence of its chloroplast. The thurberi chloroplast  (cp) genome  is 160264 bp  in length which has conserved quadripartite structure. Single copy region of cp genome is separated by the two inverted regions. The large single copy region is 88,737 bp, and the small single copy region is 20,271 bp whereas the inverted repeat 25,628 bp each. The genome has 113 single genes and 20 duplicated genes. These single genes comprised of 79 protein coded genes, 4 ribosomal RNA genes and 30 transfer RNA genes. Out of all the genes, 18 genes have 1 or 2 introns. As Compared to cpDNA from the two cultivated allotetraploid Gossypium species, rps18 was duplicated only in thurberi.

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Effects of interspecific hybridization on cotton (Gossypium hirsutum L.*Gossypium Barbadense L.)

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Mehmet ÇOBAN1, Aydın ÜNAY2, Hakan ÇİFCİ3,Birnur İLHAN4

1Cotton Research Institute, 09800 Nazilli, Turkey

2Department of Crop Science, Adnan Menderes University, 09100 Aydin, Turkey

3Sheep Breeding Research Institute, 10200 Bandırma, Turkey

4General Directorate of Agricultural Research and Policies, 06171 Ankara, Turkey


The experimental material Claudia, Candia, Şahin 2000, BA 308, Naz 07 and Fantom (Gossypium hirsutum L.) were used as a female parents and Giza 45 and Avesto (Gossypium barbadense L.) used as a male parents. The selected cotton genotypes were crossed by line tester method. An experiment was carried out in randomized complete block design with four replications to assess hereditary and heterotic effects on yield components and fiber quality traits. The research was carried outat Cotton Research Station Nazilli during the year 2011. Positive heterosis percentage was obtained from all hybrids for fiber length and fiber strength. Standard heterosis values were positive and significant for fiber length, fiber strength and micronaire.The performance of all combinations for yield and fiber quality traits at F1 generations showed that Claudia x Giza 45, Candia x Giza 45, Şahin 2000 x Giza 45, BA 308 x Avesto, Naz 07 x Giza 45 and Fantom x Avesto hybrid populations would be used for improve cotton lines having enhanced for fiber length with acceptable yield potentials.

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Leaf reddening index as an indicator of leaf reddening malady in bt cotton hybrids: causes and remedies

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Y. Rakshitha1, B. S. Janagoudar* and A. Amaregouda2

1 Postgraduate scholar, 2 Professor of Crop Physiology

*        Correspondence : Dr. B. S. Janagoudar, Dean (Agri), College of Agriculture,

University of Agricultural Sciences, Dharwad – 580 005, Karnataka, India e-mail :,


In the recent past, leaf reddening has been a major problem in Bt-cotton and this is an outcome of interaction of location, variety, environmental condition and nutrients. In general, inter and intra specific tetraploid Bt hybrids are more sensitive and vulnerable to this malady may be because of Bt gene interaction. Leaf reddening may occur at any growth stage of the crop. At grand growth  phase (flowering and boll development) any hindrance in the assimilate production, translocation and distribution intensifies the leaf reddening effect and symptoms are prolific in nature under extreme stress situations (Poongothai et  al., 2010).

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

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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.

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Seventh ‘Asian Cotton Research and Development Network’ Meeting, 15-17 Sept 2017, Nagpur India.

The Seventh Meeting of the Asian Cotton Research and Development Network was held at Nagpur during 15-17 September 2017. The Indian Society for Cotton Improvement (ISCI), Mumbai hosted the meeting together with the ICAR-CICR (Central Institute for Cotton Research), Nagpur and ICAR-CIRCOT (Central Institute for Research on Cotton Technologies). The main theme of the meeting was PRODUCING QUALITY FIBRE & DOUBLING COTTON FARMERS INCOME. Cotton researchers from public and the private sector participated. Dr. C. D. Mayee, President, Indian Society for Cotton Improvement, was the chairman, of the organizing Committee. The meeting elected Dr. Prashant G. Patil as Chairman of the Network until the next meeting. Eminent cotton experts i.e., Dr. Timorthy Dennehy, Dr Judith Brown, Dr Albert Santos from US; Dr Derek Russell from Australia, Dr Negm from Egypt and several senior research leaders from India and Bangladesh attended the meeting. The proceedings, recommendations, presentations and abstracts of the meeting can be accessed here.