Development Of Functional Markers And Transcript Map Of Chickpea (Cicer arietinum L)

Gujaria, Neha (2012) Development Of Functional Markers And Transcript Map Of Chickpea (Cicer arietinum L). PHD thesis, Dr. Hari Singh Gour University Sagar(Madhya Pradesh).

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Supervisors NameSupervisors ID
Bhide, ManaglaDr. Hari Singh Gour University Sagar(Madhya Pradesh)
Varshney, Rajeev KICRISAT(Patancheru)


To develop repertoire of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP) and intron spanning region (ISR) based markers, in chickpea, the third food legume crop of the world and the first food legume crop of India. In first approach, Solexa 1 Gb was carried out on pooled RNA from all drought challenged root tissues of genotypes ICC 4958 and ICC 1882. 15.6 and 22.1 million reads were generated and aligned against chickpea transcriptome assembly. A total of 26,082 SNPs were identified between these two genotypes. In second approach for SNP discovery through allele re-sequencing, primer pairs were designed for 970 genes/ expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of heterologous (closely related to chickpea) species and 2,046 SNPs were identified in 84,073 bp sequence data. In the third approach, ISR markers were designed by aligning chickpea unigenes to Medicago truncatula. In the forth approach, KASPar assay was designed for 96-plex SNPs and 56 polymorphic markers were identified on the parental genotypes and genotyping was done by designing Veracode assay for BeadXpress reader. From all the approaches: 87-EST-SNPs, 1627 allele-specific sequencing from chickpea and heterologous species, 121- intron spanning region (CISR) and 56 CKAM from KASPar assay were designed. SNP2CAPS analysis of 87 and 264 sequence alignments from in silico mining of ESTs and allele specific primers, as mentioned above, provided a total of 311 CAPS candidates. 311 CAPS candidates provided scorable amplification in 205 (65.92%) cases of which predicted assays were validated in 152 (74.15%) cases (CGMM). Screening of easily assayable 295 markers including 152 CGMMs, 87 CISRs and 56 CKAM on 5 parental genotypes of three mapping populations identified 75 polymorphic markers on the intra-specific mapping population. 73 of these GMMs together with 241 earlier developed markers could be integrated into the intra-specific genetic map. The transcript map developed here, therefore, has a total of 285 maker loci including 50 GMMs loci and spans 595.73 cM with an average inter marker distance of 2.09 cM. Identification of QTL for drought related root traits resulted in 12 significant QTLs. The QTL analysis revealed the presence of a ―QTL hot-spot‖ region on LG04 that contained QTLs for several drought tolerance traits explaining upto 38.03% phenotypic variation. These resources will be useful not only for genome analysis and genetics and breeding applications of chickpea but also for comparative legume genomics. Moreover, markers and genes associated with QTLs for drought tolerance related traits will be useful for molecular breeding for drought tolerance in chickpea improvement.

Item Type: Thesis (PHD)
Uncontrolled Keywords: Cicer arietinum L, Chickpea, genic molecular markers,
Subjects: Mandate crops > Chickpea
Depositing User: Mr Siva Shankar
Date Deposited: 14 Feb 2012 07:46
Last Modified: 20 Nov 2015 05:02
Acknowledgement: UNSPECIFIED
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