Identification of AFLP fragments linked to seed coat colour in Brassica juncea and conversion to a SCAR marker for rapid selection

Negi, Madan Singh; Devic, Martine; Delseny, Michel; Lakshmikumaran, Malathi

doi:10.1007/s001220051463

Cited by 153 publications

(105 citation statements)

References 23 publications

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“…SCAR markers are an ideal choice for MAS, because they are detected by single genetically defined loci, are identified as distinct bands in agarose gels, are easier to score, are less sensitive to reaction conditions, and are more reproducible. Many successful cases of such conversions have been reported (Shan et al 1999, Negi et al 2000, Miftahudin et al 2002. Not all AFLP markers can be successfully converted, however, perhaps because undesired AFLP fragments contaminate the isolation of true fragments from gels.…”

Section: Discussionmentioning

confidence: 99%

Identification of AFLP markers linked to Ms, a genic multiple allele inherited male-sterile gene in Chinese cabbage

et al. 2009

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As a first step toward cloning the genic multiple allele inherited male-sterile gene Ms in Chinese cabbage (Brassica rapa L. ssp pekinensis (Lour.) Olsson), we attempted the molecular tagging of this male-sterility locus using the amplified fragment length polymorphism (AFLP) technique. A BC 1 mapping population (130 plants) segregating for male sterility/fertility was constructed for the tagging using the bulked segregant analysis (BSA) method. Screening 144 primer combinations, four AFLP markers were identified to be tightly linked to the Ms gene, the nearest one of which, AFLP01, was converted to a SCAR marker for the markerassisted selection (MAS). Finally, a genetic map of the Ms gene was constructed with four AFLP markers and one SCAR marker, covering a total interval of 13.9 cM. Two markers AFLP01(SCAR01) and AFLP04 flanked the Ms locus at distances of 2.3 and 7.8 cM, respectively.

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Section: Discussionmentioning

confidence: 99%

Identification of AFLP markers linked to Ms, a genic multiple allele inherited male-sterile gene in Chinese cabbage

et al. 2009

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“…Earlier studies suggested that AFLP fragments with lengths between 150-300 bp needed information about the flanking regions for conversion to SCAR markers (De Jong et al 1997;Negi et al 2000). In the present study, the inverse PCR approach was carried out to obtain DNA sequences adjacent to the AFLP marker.…”

Section: Inverse Pcrmentioning

confidence: 96%

“…In the present study, the inverse PCR approach was carried out to obtain DNA sequences adjacent to the AFLP marker. Inverse PCR was chosen because of its simplicity and the simultaneous use of the two specific internal primers (Ochman et al 1988;Brigneti et al 1997;De Jong et al 1997;Bradeen and Simon 1998;Qu et al 1998) instead of genome walking (Negi et al 2000;Brugmans et al 2003).…”

Section: Inverse Pcrmentioning

confidence: 99%

Development of a diagnostic DNA marker for the geographic origin of Shorea leprosula

2016

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Abstract:The development of sequence characterized amplified region (SCAR) markers derived from amplified fragment length polymorphisms (AFLPs) is described for Shorea leprosula. An AFLP fragment that showed nearly complete differentiation between Borneo and Sumatra was gel-extracted, sequenced, and converted into a SCAR marker using the inverse polymerase chain reaction (PCR) technique. The single nucleotide polymorphism (SNP) that originally caused the AFLP was found in the MseI restriction site. Differentiation between islands was detected either as size variation of the codominant SCAR marker or after digestion of the PCR products with the restriction enzyme MseI (PCR-RFLP). Size variation was due to insertions/deletions found within the sequenced region that flanked the original AFLP fragment. After genotyping 151 samples of S. leprosula from 14 populations in Sumatra and Borneo, all but one sample from Sumatra were homozygous for one size variant (427 bp), while S. leprosula populations from Borneo showed different genotypes than Sumatra populations and variation not only among populations but also within populations. Complete differentiation and fixation on alternative variants was found for the geographic regions of Sumatra and Borneo by the PCR-RFLP method. The SCAR marker did not amplify in Shorea parvifolia and thus can also be used to distinguish between S. leprosula and S. parvifolia. The marker was successfully amplified from wood DNA extracts suggesting its applicability to track the geographic origin of timber.

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“…그러나 RAPD 방법은 10개 정도의 nucleotide의 짧은 random primer를 이용하여 낮은 annealing 온도에서 증폭이 일어나기 때문에 반응조건 에 따라 결과가 달라질 수 있다 (Cutler et al, 2006 (Negi et al, 2000;Paran and Michelmore, 1993).…”

Section: 방법과 비교하여 간편하게 이용할 수 있고 빠른 시간에 적 용할 수 있는 장점을 가지고 있어서 계통분류학이나 식물unclassified

Development of RAPD-SCAR Molecular Marker Related to Seed-hair Characteristic in Carrot

Shim¹,

Park²,

Oh³

et al. 2013

Korean Journal of Horticultural Science and Technology

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Abstract. Mechanical hair removal of carrot seed causes seed injuries and suppresses the germination in carrot cultivation. This study was performed to develop molecular markers for breeding high quality cultivars with short-hair seed. To meet this objective, random amplified polymorphic DNA (RAPD)-sequence characterized amplified region (SCAR) markers specifically linked to seed-hair characteristic were identified using CT-SMR 616 OP 389-1 line with short-haired seed and CT-SMR 616 OP 616-33 line with long-haired seed, bred by self-pollination for 6 years from 2008 to 2013, as parents. After seed hair lengths of these lines were analyzed using microscope, next generations were advanced and compared with the molecular markers polymorphism. From RAPD analysis using fixed lines in 2011, twelve RAPD primers showing polymorphic bands specific between the two lines were identified from 80 random primers. To develop RAPD-SACR marker, SCAR primers were designed based on sequence analysis of these specific RAPD bands and more than three combinations of primers were tested. As a result, it was found that the SCA21.2 amplified single polymorphic band from short-haired seed line. To confirm this result, SCA21.2 marker was retested by applying to the 2012 and 2013 progenies. Finally, it was concluded that the developed SCA21.2 marker distinguished short-haired line from long-haired seed line. Therefore, SCAR marker, SCA21.2 is expected to be utilized for breeding of the short-haired seed cultivars.Additional key words: breeding program, long-hair seed, polymorphism, short-hair seed *Corresponding author: ydpark@khu.ac.kr † These authors contributed equally to this work. ※

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Identification of AFLP fragments linked to seed coat colour in Brassica juncea and conversion to a SCAR marker for rapid selection

Cited by 153 publications

References 23 publications

Identification of AFLP markers linked to Ms, a genic multiple allele inherited male-sterile gene in Chinese cabbage

Identification of AFLP markers linked to Ms, a genic multiple allele inherited male-sterile gene in Chinese cabbage

Development of a diagnostic DNA marker for the geographic origin of Shorea leprosula

Development of RAPD-SCAR Molecular Marker Related to Seed-hair Characteristic in Carrot

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