Identification of QTLS and Genes for Drought Tolerance Using Linkage Mapping and Association Mapping Approaches in Chickpea (Cicer arietinum)

Nayak, S N (2010) Identification of QTLS and Genes for Drought Tolerance Using Linkage Mapping and Association Mapping Approaches in Chickpea (Cicer arietinum). PHD thesis, Osmania University, Hyderabad, India.

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Supervisors NameSupervisors ID
Varshney, R KICRISAT
Kavi Kishor, P BOsmania Univeristy


Low levels of polymorphism and lack of sufficient numbers of molecular markers such as microsatellite or simple sequence repeats (SSRs) are the main constraints in chickpea improvement. Hence to increase the number of SSR markers, 1,655 novel SSRs were developed from SSR-enriched genomic library (311) and mining the BAC-end sequences (1,344). These markers, along with already available markers were tested for polymorphism on parental genotypes of the inter-specific (ICC 4958 × PI 489777) and intra-specific mapping population (ICC 4958 × ICC 1882). As a result, a comprehensive inter-specific genetic map of 621 marker loci, spanning a genetic distance of 984.11cM was prepared. For identification of QTLs for drought tolerance traits, an intra-specific map (segregating for drought tolerance related traits) consisting of 230 SSR loci, spanning 466.95cM genetic distance was constructed after screening 2,409 SSR markers. The QTL analysis detected 47 significant QTLs for the ten root traits, of which seven were major QTLs (>20% phenotypic variation). The QTL analysis revealed the presence of a “QTL hot-spot” region explaining 49.9% phenotypic variation was detected. For undertaking association mapping for drought tolerance, two approaches namely candidate gene sequencing and genome-wide scanning approaches were used on the reference set comprising of 318 chickpea genotypes. In case of the candidate gene sequencing approach, five candidate genes associated with drought tolerance were selected namely, chickpea Apetala2 (CAP2-which is the homolog of DREB2A), abscisic acid stress and ripening hormone (ASR), sucrose synthase (SuSy), sucrose phosphate synthase (SPS) and ERECTA genes. Highest nucleotide diversity was observed in case of ERECTA followed by ASR gene and the lowest for CAP2 gene. Association analysis based on candidate gene sequencing showed the association of two genes (ASR and CAP2 promoter) with drought tolerance related traits. Apart from this, the genome-wide association studies using 1,157 DArT markers showed the significant association of 26 DArT markers with eight drought tolerance related traits.

Item Type: Thesis (PHD)
Agro Tags: <b>Agrotags</b> - genes | chickpeas | genetics | social groups | drought | planting | dna | tolerance | genomes | genotypes <br><b>Fishtags</b> - drying | pearls | roes <br><b>Geopoliticaltags</b> - asia | india | near east | africa | usa | turkey | europe | afghanistan | east africa | ethiopia
Subjects: Mandate crops > Chickpea
Depositing User: Siva Shankar
Date Deposited: 26 Jul 2011 04:27
Last Modified: 11 Nov 2011 05:12
Acknowledgement: UNSPECIFIED
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