Identification and characterization of herbicide tolerant mutant lines using SNP marker(s) in chickpea (Cicer arietinum L.)

Teggi, A.M. (2017) Identification and characterization of herbicide tolerant mutant lines using SNP marker(s) in chickpea (Cicer arietinum L.). Masters thesis, Professor Jayashankar Telangana State Agriculture University.

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Supervisors NameSupervisors ID
Dangi, K.S.PJTSA University
Thudi, M.ICRISAT(Patancheru)


Chickpea is a major food legume and an important source of protein in many countries of south Asia and sub-Saharan African. Globally, chickpea is cultivated over an area of 13.9 million hectares, with the production of 13.7 million tons. Besides a number of biotic and abiotic stresses that lead to significant yield losses in chickpea, weeds are also reported to reduce yield up to 84%, and severe yield losses as high as 98% are reported in autumn-sown chickpea. Hand weeding and mechanical weed control methods traditionally followed are becoming expensive owing to increased cost of human labour. Chickpea cultivars with herbicide tolerance can serve as an alternative to this problem. Hence, it is essential to identify sources of herbicide tolerance and utilize them in developing herbicide tolerant cultivars. Development of chickpea cultivars with herbicide resistance is considered to be an economic and effective way for weed control. Earlier studies have reported large genetic variation existing in chickpea germplasm for Imidazolinone (IMI) herbicide tolerance.IMI group of herbicides are considered as powerful means of weed control, and have many agronomic advantages. Imidazolinones are protein synthesis inhibitors and act by inhibiting the enzyme acetohydroxyacid synthase (AHAS, also known as acetolactate synthase, ALS), which is a critical enzyme in the biosynthsis pathway of branched chain amino acids. A point mutation in the chickpea AHAS gene at Cytocine675 to Thymin675 confers resistance to imidazolinones. Thompson and Taran (2014) developed an allele-specific SNP (KASPar) marker using this point mutation to predict the phenotypic response of the genotypes to IMI herbicides. This KASPar marker was used to genotype set of forty EMS mutant lines (developed in the background of JG 11 and KAK 2) and eighty four breeding lines in this study. In total of 124 genotypes along with check varieties (JG 11 and KAK 2) were phenotyped for herbicide resistance under field conditions at ICRISAT, Patancheru during Rabi, 2016. Herbicide tolerance ratings based on plant injury on a 1-5 scale (Gaur et al., 2013) was used for phenotyping. All the genotypes exhibited plant injury symptoms under IMI herbicide treatment. Among 126 genotypes, 8 were highly susceptible, 24 were moderately tolerant and others were susceptible. The highly susceptible lines had 80-100% mortality. The genotypes which survived put forth secondary growth after 20-25 days of herbicide application leading to flowering and pod set. Upon genotyping with the KASPar marker 124 out of 126 genotypes yielded the fluorescent data. Graphical visualization of the SNP genotyping data (KlusterCaller software) showed all the genotypes forming a single cluster near to allele ‘C’, associated with IMI susceptibility. In addition to KASPar genotyping, an attempt was made to find the possibility of other allelic variation associated with herbicide tolerance. The AHAS gene sequence was blasted in the chickpea reference genome, and the best hit was used as query sequence to find SNP candidates from the available resequencing data of chickpea genotypes. Among all the variations obtained, one SNP showing consistent variation was selected and converted to CAPS marker. Forty randomly selected genotypes belonging to different phenotypic classes were analysed using the CAPS marker. All the genotypes exhibited similar banding pattern showing no variation at the locus. The KASPar marker reported by Thompson and Taran does not serve as a diagnostic tool in identification of herbicide tolerance. As none of the genotypes used in the study were highly resistant, further screening of a large set of germplasm lines for herbicide tolerance and amplicon sequencing of the AHAS gene in these lines will help in the identification of alternate alleles and the development of diagnostic marker for herbicide resistance.

Item Type: Thesis (Masters)
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea,genotypes, crops, herbicide, tolerance
Subjects: Mandate crops > Chickpea
Depositing User: Mr T L Gautham
Date Deposited: 07 Nov 2017 09:35
Last Modified: 07 Nov 2017 09:35
Acknowledgement: UNSPECIFIED
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