Sequence-tagged microsatellite site markers for chickpea (&lt;i&gt;Cicer arietinum&lt;/i&gt; L.)

Hüttel, Bruno; Winter, Peter; Weising, Kurt; Choumane, Wafaa; Weigand, F.; Kahl, Günter

doi:10.1139/gen-42-2-210

Cited by 59 publications

(38 citation statements)

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“…Sixty five primer pairs of STMS markers were chosen to represent all LGs in previously reported STMS maps of chickpea . The PCR procedures and the primer names and sequences for STMS markers have been described in Huttel et al (1999) and Winter et al (1999). Ten RGA primer pairs were used in the initial parental screening to detect polymorphism between parents.…”

Section: Methodsmentioning

confidence: 99%

Integration of sequence tagged microsatellite sites to the chickpea genetic map

2002

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Fifty sequence-tagged microsatellite site (STMS) markers and a resistant gene-analog (RGA) locus were integrated into a chickpea ( Cicer arietinum L., 2n = 2 x = 16 chromosomes) genetic map that was previously constructed using 142 F(6)-derived recombinant inbred lines (RILs) from a cross of C. arietinum x Cicer reticulatum Lad. The map covers 1,174.5 cM with an average distance of 7.0 cM between markers in nine linkage groups (LGs). Nine markers including the RGA showed distorted segregation ( P < 0.05). The majority of the newly integrated markers were mapped to marker-dense regions of the LGs. Six co-dominant STMS markers were integrated into two previously reported major quantitative trait loci (QTLs) conferring resistance to Ascochyta blight caused by Ascochyta rabiei (Pass.) Labr. Using common STMS markers as anchors, three maps developed from different mapping populations were joined, and genes for resistance to Ascochyta blight, Fusarium wilt (caused by Fusarium oxysporum Schlechtend.: Fr. f. sp. ciceris), and for agronomically important traits were located on the combined linkage map. The integration of co-dominant STMS markers improves the map of chickpea and makes it possible to consider additional fine mapping of the genome and also map-based cloning of important disease resistance genes.

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Section: Methodsmentioning

confidence: 99%

Integration of sequence tagged microsatellite sites to the chickpea genetic map

2002

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“…2). The map spanned 1,497.7 cM with an average marker Sethy et al 2003Sethy et al , 2006Lichtenzveig et al 2005) 310 130 (41.9) 126 STMS markers Hüttel et al 1999 LGs were designated in Arabic numerals corresponding to the map of Winter et al (2000) and are mentioned at the top of each…”

Section: Construction Of the Linkage Mapmentioning

confidence: 99%

“…Distances of the loci (cM) are shown to the left and the name of loci are shown to the right side of the linkage groups. STMS markers which were used as the anchor markers (Winter et al 2000;Hüttel et al 1999) ESTPs, 57 SNPs, and 2 MtEST) and 126 were gSSRs. Segregation distortion was observed for 176 (41.3%) loci as determined by v 2 test (P \ 0.05) and out of these 167 were mapped (Fig.…”

Section: Construction Of the Linkage Mapmentioning

confidence: 99%

“…For various applications in plant genetics and breeding, PCR-compatible markers based on microsatellites, also known as simple sequence repeats (SSRs) are often considered the most efficient and reliable source for detecting genetic variation in several crop species (Varshney et al 2007) including chickpea (Sharma et al 1995;Hüttel et al 1999;Sethy et al 2003Sethy et al , 2006. Published linkage maps have been generated in both intra-specific (Radhika et al 2007; Gaur et al 2011) as well as inter-specific crosses (Winter et al 2000;Nayak et al 2010;Gujaria et al 2011) using amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and sequence tagged microsatellite site (STMS) markers.…”

Section: Introductionmentioning

confidence: 99%

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EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea

et al. 2012

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Well-saturated linkage maps especially those based on expressed sequence tag (EST)-derived genic molecular markers (GMMs) are a pre-requisite for molecular breeding. This is especially true in important legumes such as chickpea where few simple sequence repeats (SSR) and even fewer GMM-based maps have been developed. Therefore, in this study, 2,496 ESTs were generated from chickpea seeds and utilized for the development of 487 novel EST-derived functional markers which included 125 EST-SSRs, 151 intron targeted primers (ITPs), 109 expressed sequence tag polymorphisms (ESTPs), and 102 single nucleotide polymorphisms (SNPs). Whereas ESTSSRs, ITPs, and ESTPs were developed by in silico analysis of the developed EST sequences, SNPs were identified by allele resequencing and their genotyping was performedusing the Illumina GoldenGate Assay. Parental polymorphism was analyzed between C. arietinum ICC4958 and C. reticulatum PI489777, parents of the reference chickpea mapping population, using a total of 872 markers: 487 new gene-based markers developed in this study along with 385 previously published markers, of which 318 (36.5%) were found to be polymorphic and were used for genotyping. The genotypic data were integrated with the previously published data of 108 markers and an advanced linkage map was generated that contained 406 loci distributed on eight linkage groups that spanned 1,497.7 cM. The average marker density was 3.68 cM and the average number of markers per LG was 50.8. Among the mapped markers, 303 new genomic locations were defined that included 177 gene-based and 126 gSSRs (genomic SSRs) thereby producing the most advanced gene-rich map of chickpea solely based on co-dominant markers.

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“…Of the six ISSR primers that did produce markers for mapping, five were di-nucleotide repeats [(AG) 8 YC, (AC) 8 T, (AG) 8 T, (GA) 8 T, (GA) 8 A] and one was a pentanucleotide repeat (GGAGA) 3 . The repeat (GA) n was previously found to be abundant in the related chickpea genome (Hüttel et al 1999). In the lentil map, 4 out of 11 mapped ISSR markers were obtained from (AC) repeat motif.…”

Section: Mapping Of Issr and Rga Markersmentioning

confidence: 99%

Construction of an intraspecific linkage map of lentil (Lens culinaris ssp. culinaris)

2003

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The first intraspecific linkage map of the lentil genome was constructed with 114 molecular markers (100 RAPD, 11 ISSR and three RGA) using an F(2) population developed from a cross between lentil cultivars ILL5588 and ILL7537 which differed in resistance for ascochyta blight. Linkage analysis at a LOD score of 4.0 and a maximum recombination fraction of 0.25 revealed nine linkage groups comprising between 6 and 18 markers each. The intraspecific map spanned a total length of 784.1 cM. The markers were distributed throughout the genome, however markers were clustered in the middle or near the middle of the linkage groups, suggesting the location of centromeres. Of 114 mapped markers, 16 (14.0%) were distorted, usually at the end or middle of the linkage groups. The utility of ISSR and RGA markers for mapping in lentil was explored, and the primer with an (AC) repeat motif was found to be useful.

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Sequence-tagged microsatellite site markers for chickpea (<i>Cicer arietinum</i> L.)

Cited by 59 publications

References 0 publications

Integration of sequence tagged microsatellite sites to the chickpea genetic map

Integration of sequence tagged microsatellite sites to the chickpea genetic map

EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea

Construction of an intraspecific linkage map of lentil (Lens culinaris ssp. culinaris)

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