Use of genetic and genomic approaches for combating cotton leaf curl disease

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Authors

Rahman, Mehboob-ur-1; Ali, Ahmed1; Qaiser khan, Ali1; Abbas, Ammad1; Rahmat, Zainab1; Sarfraz, Zareen1; Khalid, Anum1; Gul, Maryam1; Munir, Atif1; Atifiqbal, Muhammad1; Scheffler, Jodi2; Scheffler, Brain2;

1National Institute for Biotechnology & Genetic Engineering (NIBGE) Faisalabad, Pakistan. 2Jamie Whitten Delta States Research Center, Stoneville, Mississippi, USA

Abstract

Cotton leaf curl, a disease of viral origin, is transmitted by a whitefly (Bemisiatabaci), was first reported in 1912 in Nigeria, and later spread to Egypt, Sudan, India and Pakistan, and recently in China. The disease has significantly challenged the sustainability of cotton production in Pakistan with annual yield penalty of two million bales. Efforts were made in developing resistant cotton varieties, which upheld the resistance for couple of years but overcame by the evolution of new strain of the virus (now called as cotton leaf curl Burewala virus). For protecting the most important natural fiber producing crop, a mega project aiming at the improvement of genetics of the cotton plant for combating the disease, was initiated in 2011 under Pak-US (managed through ICARDA, Pakistan) joint venture program. Till now, more than 3500 cotton accessions have been screened; and 33 accessions were found asymptomatic while G. hirsutum 2472-3 and G. hirsutum 3661 showed high tolerance to the disease. Among the asymptomatic, G. hirsutum Mac-07 (photoperiod insensitive) is being used extensively by multiple cotton research institutes for developing resistant cotton cultivars. A number of mapping populations by involving tolerant and resistant cotton genotypes with the mostsusceptible cotton species were developed. For example, mapping populations were developed by crossingG. hirsutum 2472-3 (tolerant), G. hirsutum Mac-07 (resistant) and highly sensitive genotypes G. barbadense PGMB-66, G. barbadense PIMA S7, respectively. A total of 1200 SSRs were surveyed on parent genotypes of G. hirsutum 2472-3 and G. barbadense PGMB-66 (Cross-I). Out of these, 113 were found polymorphic. These were surveyed on F2population. In second population (derived from a cross G. hir 2472-3/G. bar PIMA S-7, Cross-II), we surveyed 170 SSRs. Out of these, 24 polymorphic were surveyed on F2population. Similarly, we too surveyed 435 SSRs on the parent genotypes of third mapping population (Mac-7/PIMA S-7, Cross-III). A total of 18 polymorphic primers were surveyed on F2 population. Based on our limited studies, we were able to identify two QTLs i.e. QCLCuD25 and QCLCuD26 from Cross-I population study, six QTLs i.e. QCLCuD3, QCLCuD4, QCLCuD7, QCLCuD8, QCLCuD9, QCLCuD14 from Cross-II population study, and three QTLs from cross-III population. These studies will pave the way for not only initiating marker-assisted breeding for the development of resistant cotton cultivars in Pakistan but will also provide a comprehensive information to the international cotton community for combating the disease.

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Nuclear male sterility in desi cotton (gossypium arboreum l.)

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Author

Dharminder Pathak

Department of Plant Breeding and Genetics

Punjab Agricultural University, Ludhiana – 141004, Punjab, India

Abstract

Heterosis breeding has played rich dividends in crop plants including cotton and is a sure way of increasing crop production and productivity in a shorter time span. In India, all the four cultivated species of cotton and their interspecific (G. hirsutum x G. barbadense; G. arboreum x G. herbaceum) hybrids are grown. In fact, India has been a leader in the production and commercialization of cotton hybrids. Earlier, hand emasculation and pollination was used for the production of hybrid seeds in G. arboreum in India. LDH 11 (1994) was the first commercial intra-arboreum hybrid in the entire North Indian cotton growing states. However, manual emasculation of the floral buds makes hybrid seed production more labour intensive. Availability of genetic male sterile (GMS) lines such as DS-5, GAK 423 has resulted in the development and commercialization of several desi cotton hybrids. Some of the intra-arboreum hybrids released for commercial cultivation in different North Zone states using DS 5 as the female parent include AAH 1, Moti (LMDH 8), Raj DH 9, CICR 2, PAU 626H, and FMDH 9. There are certain limitations nuclear male sterility system. For example, no marker linked to male sterility trait is available at the seedling state in DS 5 and male sterile/fertile plants have to be identified at the flowering stage only. As in a GMS line male fertile and sterile plants are observed in a frequency of about 1:1, and fertile plants have to be removed, about half of the plants in a GMS line are available for hybrid seed production, that increases the cost of the hybrid seed. Though, genetic control of male sterility in DS-5 is simple (monogenic), yet the transfer of this trait/gene in different lines is very time consuming due to its recessive nature. Efforts to map the gene conditioning male sterility in DS 5 with molecular markers are going on in our Department. Mapping of this gene will facilitate its precise  transfer across the genotypes and identification of male sterile plants at the seedling stage.

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

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Authors

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

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

*Email: katageriis@uasd.in

Abstract

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

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Author

Lale Efe

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

Abstract

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.

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

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Author

Suresh handi and I.S.Katageri*

*Professor and Head,

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

Abstract

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.

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A graphical method to determine dominant and recessive gene percents using diallel analysis in cotton

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Authors

Ercan EFE

KahramanmarasSutcuimam University, TURKEY

Abstract

In diallel analysis widely used by plant breeders, WrvsVr graph gives important knowledge about the parents. In this graph, it’s possible to interpret distribution of dominant and recessive genes among the parents by investigating the relations between W*r=[Volo x Vr]1/2 parabola and unit slope regression line.

In this study, finding intercept of unit slope line and the values corresponding the two points where parabola is cut by this regression lineand dividing the distance between those points into four equal parts are given with a numerical sample in cotton.

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

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Authors

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

Abstract

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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Authors

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 : bjanagoudar56@gmail.com, deanacd@uasd.in

Abstract

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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Author

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

Abstract

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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Evaluation of genetic diversity in short duration cotton (Gossypium hirsutum L.)

[Background] Cotton (Gossypium hirsutum L.) is an important fiber crop in Bangladesh. Genetic diversity among the genotypes of a germplasm has a great importance for cotton breeding. An experiment was carried out at the experimental field of Cotton Research, Training and Seed Multiplication Farm, Sreepur, Gazipur during the cropping season of 2015–2016 with 100 genotypes to evaluate genetic diversity of cotton genotypes for short duration using field performance.

[Results] The genotypes under study were grouped into ten clusters through multivariate analysis using GENSTAT-5. Cluster III contained maximum number of genotypes (16) while cluster X contained the least number of genotypes (7). The inter cluster distances were larger than intra cluster distances in all cases suggesting wider genetic diversity among the genotypes of different clusters. The maximum and minimum inter cluster distances were observed between clusters II and V (10.78) and clusters VIII and IX (3.30), respectively. The results indicated diverse and close relationship among the genotypes of those clusters. Earliness index, single boll weight and days to boll opening showed the higher contribution to the genetic divergence among 19 characters.

[Conclusion] Based on the results of genetic diversity and earliness index, the genotypes from cluster II could be used as parent in hybridization program for the development of short duration cotton variety.

Evaluation of genetic diversity in short duration cotton (Gossypium hirsutum L.)

AKTER T., ISLAM A. K. M. A., RASUL M. G., KUNDU S., KHALEQUZZAMAN and AHMED J. U.
Journal of Cotton Research. 2019; 2:1.
https://doi.org/10.1186/s42397-018-0018-6