Development of a routine procedure for single nucleotide polymorphism marker design based on the Tm-shift genotyping method

Fukuoka, Hiroyuki; Miyatake, Koji; Negoro, Satomi; Nunome, Toshiro; Ohyama, Akio; Yamaguchi, Haruhisa

doi:10.1270/jsbbs.58.461

Cited by 12 publications

(7 citation statements)

References 12 publications

(9 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, the growth of P. vulgaris was decreased with the increase in sewage sludge concentration from 60% to 100%. The findings were also supported by Fukuoka et al (2010) who reported that the growth of eggplant was decreased due to the application of more concentration of sewage effluent. (Khan et al, 2007;Kumar & Chopra, 2012).…”

Section: Effect Of Sewage Sludge On Vegetative Growth Of S Melongenasupporting

confidence: 70%

“…Eggplant (Solanum melongena L.) is identified as one of the most valuable vegetable packed with essential nutrients (Fukuoka et al, 2010;Dar et al, 2014). The eggplant is a delicate, tropical perennial often cultivated as a tender or half-hardy annual in temperate climates (Nunome et al, 2001;Hirakawa et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…Nutritionally, eggplant is low in fat, protein, and carbohydrates. It is rich in dietary fiber, sugar, sodium and potassium (Fukuoka et al, 2010). It also contains important vitamins like A, B 6 , C, D and calcium, iron and magnesium.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Agronomical Performance of High Yielding Cultivar of Eggplant (Solanum melongena L.) Grown in Sewage Sludge Amended Soil

Kumar

Chopra

2016

View full text Add to dashboard Cite

show abstract

Section: Effect Of Sewage Sludge On Vegetative Growth Of S Melongenasupporting

confidence: 70%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Agronomical Performance of High Yielding Cultivar of Eggplant (Solanum melongena L.) Grown in Sewage Sludge Amended Soil

Kumar

Chopra

2016

View full text Add to dashboard Cite

show abstract

“…Sequence data were processed using the phred/ phrap/cross_match package (Ewing et al 1998). SNPs found between parental lines of mapping populations were mainly genotyped using the melting temperature (T m )-shift PCR method , with some modifications (Fukuoka et al 2008). When reliable allele specificity could not be achieved using T m -shift PCR, such SNPs were genotyped by direct sequencing using the same primer sets used for SNP discovery.…”

Section: Snp and Indel Discovery Marker Development And Genotypingmentioning

confidence: 99%

Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets

et al. 2012

Self Cite

View full text Add to dashboard Cite

We constructed an integrated DNA marker linkage map of eggplant (Solanum melongena L.) using DNA marker segregation data sets obtained from two independent intraspecific F(2) populations. The linkage map consisted of 12 linkage groups and encompassed 1,285.5 cM in total. We mapped 952 DNA markers, including 313 genomic SSR markers developed by random sequencing of simple sequence repeat (SSR)-enriched genomic libraries, and 623 single-nucleotide polymorphisms (SNP) and insertion/deletion polymorphisms (InDels) found in eggplant-expressed sequence tags (ESTs) and related genomic sequences [introns and untranslated regions (UTRs)]. Because of their co-dominant inheritance and their highly polymorphic and multi-allelic nature, the SSR markers may be more versatile than the SNP and InDel markers for map-based genetic analysis of any traits of interest using segregating populations derived from any intraspecific crosses of practical breeding materials. However, we found that the distribution of microsatellites in the genome was biased to some extent, and therefore a considerable part of the eggplant genome was first detected when gene-derived SNP and InDel markers were mapped. Of the 623 SNP and InDel markers mapped onto the eggplant integrated map, 469 were derived from eggplant unigenes contained within Solanum orthologous (SOL) gene sets (i.e., sets of orthologous unigenes from eggplant, tomato, and potato). Out of the 469 markers, 326 could also be mapped onto the tomato map. These common markers will be informative landmarks for the transfer of tomato's more saturated genomic information to eggplant and will also provide comparative information on the genome organization of the two solanaceous species. The data are available from the DNA marker database of vegetables, VegMarks (http://vegmarks.nivot.affrc.go.jp).

show abstract

“…All SNPs markers developed by Fukuoka et al (submitted), total of 630 markers, were screened for detecting polymorphisms among parents of ALF2/NAF2 populations (ESM_1). To genotype these SNPs, we used the Tm-shift genotyping method originally reported by Wang et al (2005) and partially modified by Fukuoka et al (2008) to improve detection efficiency. We genotyped 135 ALF2 and 93 NAF2 F 2 plants with the markers.…”

Section: Snp Analysismentioning

confidence: 99%

Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.)

et al. 2012

Self Cite

View full text Add to dashboard Cite

Parthenocarpy, the ability to set fruits without pollination, is a useful trait for setting fruit under unfavorable conditions. To identify the loci controlling parthenocarpy in eggplant (Solanum melongena L.), we constructed linkage maps by using co-dominant simple sequence repeat and single nucleotide polymorphism markers in F(2) populations derived from intraspecific crosses between two non-parthenocarpic lines (LS1934 and Nakate-Shinkuro) and a parthenocarpic line (AE-P03). Total map distances were 1,414.6 cM (ALF2: LS1934 x AE-P03) and 1,153.8 cM (NAF2: Nakate-Shinkuro x AE-P03), respectively. Quantitative trait locus (QTL) analyses revealed two QTLs on chromosomes 3 and 8, which we denoted as Controlling parthenocarpy3.1 (Cop3.1) and Cop8.1, respectively. The percentage of phenotypic variance explained (PVE) of Cop3.1 was 6.3% in ALF2 (LOD = 4.2) and 10.6% in NAF2 (LOD = 3.0). The PVE of Cop8.1 was 45.7% in ALF2 (LOD = 23.8) and 29.7% in NAF2 (LOD = 7.9). Using a population of backcross inbred lines, we confirmed the effect of Cop8.1, but there was no evidence to support the contribution of Cop3.1. We need to verify the effect of Cop3.1 under various temperature conditions. In addition, we clarified the effectiveness of selective SSR markers, emf21H22 and emh11J10, mapped on each side of Cop8.1 in other F(2) populations derived from various parental combinations. This is the first report concerning QTL analysis of parthenocarpy in eggplant using molecular markers. It will be useful in marker-assisted selection and in revealing the genomic mechanism underlying parthenocarpy in eggplant.

show abstract

Development of a routine procedure for single nucleotide polymorphism marker design based on the Tm-shift genotyping method

Cited by 12 publications

References 12 publications

Agronomical Performance of High Yielding Cultivar of Eggplant (Solanum melongena L.) Grown in Sewage Sludge Amended Soil

Agronomical Performance of High Yielding Cultivar of Eggplant (Solanum melongena L.) Grown in Sewage Sludge Amended Soil

Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets

Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.)

Contact Info

Product

Resources

About