Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L.

Lichtenzveig, Judith; Scheuring, Chantel F.; Dodge, J A; Abbo, Shahal; Zhang, Han

doi:10.1007/s00122-004-1857-8

Cited by 127 publications

(118 citation statements)

References 42 publications

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“…Problems of redundancy in enriched libraries have been reported in other crops (Rallo et al, 2000;Mba et al, 2001) as well as sesame (Dixit et al, 2005). The AG/TC class of dinucleotide repeats was the most abundant in the enriched library as well as in the ESTderived SSRs, as has been the case in other crops (Ferguson et al, 2004;Lichtenzveig et al, 2005). In a study analyzing wheat (Triticum aestivum L.), rice (Oryza sativa L.), maize (Zea mays), and soybean (Glycine max) ESTs, TC repeats have been found to be the most frequent, suggesting that dinucleotide repeats could be the most abundant in coding regions of most plant genomes (Gao et al, 2003).…”

Section: Discussionmentioning

confidence: 89%

Development of microsatellite markers in sesame (Sesamum indicum L.)

Badri¹,

Yepuri²,

Anuradha³

et al. 2014

Turk J Agric For

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Sesame (Sesamum indicum L.) is an important oilseed crop with high-quality seed oil and many antioxidant properties. Owing to its commercial and medicinal values, there is a renewed interest among agricultural scientists in this ancient crop. Efforts to strengthen the sesame-specific marker base have been initiated in the recent past; however, the available number of microsatellite markers is still not sufficient for the development of high-resolution genetic linkage maps for important agronomic traits and there is a need to increase the number of informative DNA markers in sesame. In the present study, we developed 25 microsatellite markers by employing the selective hybridization strategy and 95 mining expressed sequence tags of the NCBI database. This new set of microsatellite markers was characterized and screened for genetic diversity in an array of 16 sesame germplasms. Of the 120 SSRs, 92 were polymorphic, consisting of 18 SSRs from selective hybridization and 74 from the EST data set. The number of alleles per microsatellite locus ranged from 2 to 5, with an average of 3.11 alleles. The allele size ranged widely (100-510 bp) among the primer pairs. Polymorphic information content estimates ranged from 0.2982 to 0.912. Jaccard's similarity coefficient ranged from 0.21 to 0.82. The potential of the markers was assessed by diversity analysis using the sequential hierarchical agglomerative nonoverlapping clustering technique of the unweighted pair group method of arithmetic means on a set of 16 genotypes of sesame, including 2 wild species. Results supported the hypothesis that S. malabaricum could be the immediate progenitor of the cultivar species and that S. mulayanum is distinct from S. malabaricum and S. indicum, while suggesting hardly any diversity among the cultivars.

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Section: Discussionmentioning

confidence: 89%

Development of microsatellite markers in sesame (Sesamum indicum L.)

Badri¹,

Yepuri²,

Anuradha³

et al. 2014

Turk J Agric For

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“…Simple Sequence Repeat (SSR) markers are widely used due to their high reproducibility, multi-allelic nature and co-dominant inheritance (Tautz 1989). Several SSR markers were developed and used in chickpea (Hüttel et al 1999;Udupa and Baum 2001;Lichtenzveig et al 2005;Sethy et al 2006;Choudhary et al 2006;Saxena et al 2014;Parida et al 2015;Khajuria et al 2015). Most of them have a known genomic localization, following linkage analysis (Winter et al 2000;Nayak et al 2010;Jamalabadi et al 2013;Khajuria et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Genetic variation of a global germplasm collection of chickpea (Cicer arietinum L.) including Italian accessions at risk of genetic erosion

Giovanni

Pavan

Taranto

et al. 2016

Physiol Mol Biol Plants

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Chickpea (Cicer arietinum L.) is one of the most important legumes worldwide. We addressed this study to the genetic characterization of a germplasm collection from main chickpea growing countries. Several Italian traditional landraces at risk of genetic erosion were included in the analysis. Twenty-two simple sequence repeat (SSR) markers, widely used to explore genetic variation in plants, were selected and yielded 218 different alleles. Structure analysis and hierarchical clustering indicated that a model with three distinct subpopulations best fits the data. The composition of two subpopulations, named K1 and K2, broadly reflects the commercial classification of chickpea in the two types desi and kabuli, respectively. The third subpopulation (K3) is composed by both desi and kabuli genotypes. Italian accessions group both in K2 and K3. Interestingly, this study highlights genetic distance between desi genotypes cultivated in Asia and Ethiopia, which respectively represent the chickpea primary and the secondary centres of diversity. Moreover, European desi are closer to the Ethiopian gene pool. Overall, this study will be of importance for chickpea conservation genetics and breeding, which is limited by the poor characterization of germplasm collection.

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“…More than 3000 simple sequence repeat (SSR) markers have been developed over the last 8 years (Lichtenzveig et al 2005;Sethy et al 2006;Nayak et al 2010;Gujaria et al 2011;Thudi et al 2011;Agarwal et al 2012). In addition, a huge number of SSRs have become available from genome analysis , which have further enriched the available marker repertoire for chickpea.…”

Section: Genetic and Genomic Resourcesmentioning

confidence: 99%

Genomics-assisted breeding for drought tolerance in chickpea

Thudi

Gaur

Krishnamurthy

et al. 2014

Functional Plant Biol.

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Abstract.Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomicsassisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73 Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density diversity array technology (15 360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10-24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea.

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Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L.

Cited by 127 publications

References 42 publications

Development of microsatellite markers in sesame (Sesamum indicum L.)

Development of microsatellite markers in sesame (Sesamum indicum L.)

Genetic variation of a global germplasm collection of chickpea (Cicer arietinum L.) including Italian accessions at risk of genetic erosion

Genomics-assisted breeding for drought tolerance in chickpea

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