scholarly journals Inheritance Pattern and Molecular Markers for Resistance to Blackleg Disease in Cabbage

Plants ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 583
Author(s):  
Mostari Jahan Ferdous ◽  
Mohammad Rashed Hossain ◽  
Jong-In Park ◽  
Arif Hasan Khan Robin ◽  
Denison Michael Immanuel Jesse ◽  
...  
Keyword(s):  
Molecular Markers ◽  
High Resolution Melting ◽  
Leptosphaeria Maculans ◽  
Inbred Lines ◽  
Indel Marker ◽  
Detection Accuracy ◽  
Nucleotide Polymorphisms ◽  
Blackleg Disease ◽  
Marker Assisted Breeding ◽  
Single Nucleotide

The inheritance and causal loci for resistance to blackleg, a devastating disease of Brassicaceous crops, are yet to be known in cabbage (Brassica oleracea L.). Here, we report the pattern of inheritance and linked molecular marker for this trait. A segregating BC1 population consisting of 253 plants was raised from resistant and susceptible parents, L29 (♀) and L16 (♂), respectively. Cotyledon resistance bioassay of BC1 population, measured based on a scale of 0–9 at 12 days after inoculation with Leptosphaeria maculans isolate 03–02 s, revealed the segregation of resistance and ratio, indicative of dominant monogenic control of the trait. Investigation of potential polymorphism in the previously identified differentially expressed genes within the collinear region of ‘B. napus blackleg resistant loci Rlm1′ in B. oleracea identified two insertion/deletion (InDel) mutations in the intron and numerous single nucleotide polymorphisms (SNPs) throughout the LRR-RLK gene Bol040029, of which six SNPs in the first exon caused the loss of two LRR domains in the susceptible line. An InDel marker, BLR-C-InDel based on the InDel mutations, and a high resolution melting (HRM) marker, BLR-C-2808 based on the SNP C2808T in the second exon were developed, which predicated the resistance status of the BC1 population with 80.24%, and of 24 commercial inbred lines with 100% detection accuracy. This is the first report of inheritance and molecular markers linked with blackleg resistance in cabbage. This study will enhance our understanding of the trait, and will be helpful in marker assisted breeding aiming at developing resistant cabbage varieties.

scholarly journals Genetic Analysis of a Horizontal Resistance Locus BLMR2 in Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Qiang Zhang ◽  
Hanna Dandena ◽  
Madison McCausland ◽  
Huizhi Liu ◽  
Zheng Liu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Brassica Napus ◽  
Chromosome Region ◽  
Leptosphaeria Maculans ◽  
Snp Markers ◽  
Resistance Locus ◽  
Horizontal Resistance ◽  
Blackleg Disease ◽  
Single Nucleotide ◽  
Sequence Characterized Amplified Regions

Leptosphaeria maculans causes blackleg disease in Brassica napus. The blackleg disease is mainly controlled by resistance genes in B. napus. Previous studies have shown that the blackleg resistant BLMR2 locus that conferred horizontal resistance under field conditions, is located on chromosome A10 of B. napus. The purpose of this study is to fine map this locus and hence identify a candidate gene underlying horizontal resistance. The spectrum of resistance to L. maculans isolates of the resistance locus BLMR2 was analyzed using near isogenic lines, resistant, and susceptible cultivars. The results showed that this locus was horizontally resistant to all isolates tested. Sequence characterized amplified regions (SCAR), simple sequence repeats (SSR), and single nucleotide polymorphism (SNP) markers were developed in the chromosome region of BLMR2 and a fine genetic map was constructed. Two molecular markers narrowed BLMR2 in a 53.37 kb region where six genes were annotated. Among the six annotated genes, BnaA10g11280D/BnaA10g11290D encoding a cytochrome P450 protein were predicted as the candidate of BLMR2. Based on the profiling of pathogen induced transcriptome, three expressed genes in the six annotated genes were identified while only cytochrome P450 showed upregulation. The candidate corresponds to the gene involved in the indole glucosinolate biosynthesis pathway and plant basal defense in Arabidopsis thaliana. The molecular markers identified in this study will allow the quick incorporation of the BLMR2 allele in rapeseed cultivars to enhance blackleg resistance.

scholarly journals Development of Molecular Markers for Predicting Radish (Raphanus sativus) Flesh Color Based on Polymorphisms in the RsTT8 Gene

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1386
Author(s):  
Soyun Kim ◽  
Keunho Yun ◽  
Han Yong Park ◽  
Ju Young Ahn ◽  
Ju Yeon Yang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Raphanus Sativus ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cosmetic Industry ◽  
Natural Colorants ◽  
Health Promoting ◽  
Primer Sets ◽  
Red Radish ◽  
Simple Sequence

Red radish (Raphanus sativus L.) cultivars are a rich source of health-promoting anthocyanins and are considered a potential source of natural colorants used in the cosmetic industry. However, the development of red radish cultivars via conventional breeding is very difficult, given the unusual inheritance of the anthocyanin accumulation trait in radishes. Therefore, molecular markers linked with radish color are needed to facilitate radish breeding. Here, we characterized the RsTT8 gene isolated from four radish genotypes with different skin and flesh colors. Sequence analysis of RsTT8 revealed a large number of polymorphisms, including insertion/deletions (InDels), single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs), between the red-fleshed and white-fleshed radish cultivars. To develop molecular markers on the basis of these polymorphisms for discriminating between radish genotypes with different colored flesh tissues, we designed four primer sets specific to the RsTT8 promoter, InDel, SSR, and WD40/acidic domain (WD/AD), and tested these primers on a diverse collection of radish lines. Except for the SSR-specific primer set, all primer sets successfully discriminated between red-fleshed and white-fleshed radish lines. Thus, we developed three molecular markers that can be efficiently used for breeding red-fleshed radish cultivars.

scholarly journals Single Nucleotide Polymorphisms and Indel Markers from the Transcriptome of Garlic

2016 ◽  
Vol 141 (1) ◽  
pp. 62-65 ◽  
Author(s):  
Michael J. Havey ◽  
Yul-Kyun Ahn
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Characteristics ◽  
Single Nucleotide ◽  
Germplasm Collections ◽  
Indel Markers ◽  
Production Environments ◽  
Culinary Uses

Garlic (Allium sativum) is cultivated worldwide and appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great morphological variation and adaptability to diverse production environments. Molecular markers and phenotypic characteristics have been used to assess the genetic diversity among garlics. In this study, we undertook transcriptome sequencing from a single garlic plant to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid (DH) of onion (Allium cepa). Single nucleotide polymorphisms (SNPs) and insertion–deletion (indel) events were identified in 4355 independent garlic assemblies. A sample of the indels was verified using the original complementary DNA (cDNA) library and genomics DNAs from diverse garlics, and segregations confirmed by sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for estimates of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.

scholarly journals Association of Twelve Candidate Gene Polymorphisms with the Intramuscular Fat Content and Average Backfat Thickness of Chinese Suhuai Pigs

Animals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 858 ◽  
Author(s):  
Wang ◽  
Li ◽  
Zhou ◽  
Gao ◽  
Liu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Gene Polymorphisms ◽  
Genetic Correlations ◽  
Intramuscular Fat ◽  
Fat Content ◽  
Backfat Thickness ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Coefficients Of Variation ◽  
Intramuscular Fat Content

The present study aimed to identify the molecular markers for genes that influence intramuscular fat content (IFC), but not average backfat thickness (ABT). A total of 330 Suhuai pigs were slaughtered, and measurements of IFC and ABT were obtained. Phenotypic and genetic correlations between IFC and ABT were calculated. Thirteen single nucleotide polymorphisms (SNPs) among 12 candidate genes for IFC were analyzed, including FABP3, LIPE, IGF1, IGF2, LEP, LEPR, MC4R, PHKG1, RETN, RYR1, SCD, and UBE3C. Associations of the evaluated SNPs with IFCIFC and ABT were performed. Our results showed that the means of IFC and ABT were 1.99 ± 0.03 % and 26.68 ± 0.28 mm, respectively. The coefficients of variation (CVs) of IFC and ABT were 31.21% and 19.36%, respectively. The phenotypic and genetic correlations between IFC and ABT were moderate. Only the FABP3 (rs1110770079) was associated with IFC (p < 0.05) but not with ABT. Besides, there was a tendency for associations of RYR1 (rs344435545) and SCD (rs80912566) with IFC (p < 0.1). Our results indicated that the FABP3 (rs1110770079) SNP could be used as a marker to improve IFC without changing ABT in the Suhuai pig breeding system.

scholarly journals Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qiu-jie Li ◽  
Na Su ◽  
Ling Zhang ◽  
Ru-chang Tong ◽  
Xiao-hui Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Medicinal Value ◽  
Cp Genome

AbstractPulsatilla (Ranunculaceae) consists of about 40 species, and many of them have horticultural and/or medicinal value. However, it is difficult to recognize and identify wild Pulsatilla species. Universal molecular markers have been used to identify these species, but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes of seven Pulsatilla species. The chloroplast genomes of Pulsatilla were very similar and their length ranges from 161,501 to 162,669 bp. Eight highly variable regions and potential sources of molecular markers such as simple sequence repeats, large repeat sequences, and single nucleotide polymorphisms were identified, which are valuable for studies of infra- and inter-specific genetic diversity. The SNP number differentiating any two Pulsatilla chloroplast genomes ranged from 112 to 1214, and provided sufficient data for species delimitation. Phylogenetic trees based on different data sets were consistent with one another, with the IR, SSC regions and the barcode combination rbcL + matK + trnH-psbA produced slightly different results. Phylogenetic relationships within Pulsatilla were certainly resolved using the complete cp genome sequences. Overall, this study provides plentiful chloroplast genomic resources, which will be helpful to identify members of this taxonomically challenging group in further investigation.

DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No.9’ Using 101 New Developed HRM-Based SNP Markers

2019 ◽  
Author(s):  
X. J. Fu ◽  
J. X. Pei ◽  
Y. T. Zheng ◽  
D. D. Guo ◽  
Q. H. Yang ◽  
...  
Keyword(s):  
High Resolution Melting ◽  
Snp Markers ◽  
Soybean Cultivar ◽  
Polymorphic Markers ◽  
Nucleotide Polymorphisms ◽  
Analysis Method ◽  
Vegetable Soybean ◽  
Genomic Information ◽  
Single Nucleotide ◽  
Plant Genomes

Single nucleotide polymorphisms (SNPs) have been proved to be powerful markers in genetic analysis due to their high abundance and polymorphism in plant genomes. The recently developed high-resolution melting (HRM) analysis method provides a novel, quick, and close-tube PCR approach to analyze SNP variations. In present study, 101 HRM-based SNP markers from 20 soybean chromosomes were developed for genotyping vegetable soybean cultivar ‘Zhexian No.9’ with ‘Williams 82’ as reference. 33.7% of these markers were polymorphic between ‘Zhexian No.9’ and ‘Williams 82’. Polymorphic markers were found on 85% (17 of 20) of the soybean chromosomes when comparing ‘Zhexian No.9’ and ‘Williams 82’. Finally, an array of 101 in-sequence nucleotide letters was generated as the first precise SNP fingerprint of ‘Zhexian No.9’. The described marker-developing methodology could be used in other crops with known genomic information.

scholarly journals The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm

2021 ◽  
Vol 22 (6) ◽  
Author(s):  
TENGKU IMAM SAPUTRA ◽  
ROBERDI ROBERDI ◽  
YOGO ADHI NUGROHO ◽  
WULAN ARTUTININGSIH ◽  
OLIVIA S. PURBA ◽  
...  
Keyword(s):  
High Resolution ◽  
Oil Palm ◽  
High Resolution Melting ◽  
Elaeis Guineensis ◽  
Acyl Carrier Protein ◽  
Nucleotide Polymorphisms ◽  
Snp Discovery ◽  
Single Nucleotide ◽  
Elaeis Oleifera ◽  
Genotype Model

Abstract. Saputra TI, Roberdi, Nugroho YA, Artutiningsih W, Purba OS, Maryanto SD, Yono D, Utomo C, Liwang T. 2021. The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm. Biodiversitas 22: 3356-3362. The unlabeled probes-high resolution melting (UP-HRM) marker is a useful tool for detecting of single nucleotide polymorphisms (SNPs). The objectives of this study were to develop UP-HRM markers to differentiate specific SNPs patterns on oil palm. The marker was developed and tested with Elaeis guineensis (Eg), Elaeis oleifera (Eo), Eo x Eg (hybrid), and was validated with 53 individuals of BC1F1 populations ((Eo x Eg) x Eg). Four UP-HRM markers were developed based on 2 SNPs in the stearoyl-acyl-carrier-protein 9-desaturase (EgSAD), 1 SNP in the auxin-responsive protein IAA27-like (EgIAA27), and 1 SNP in the 1-amino cyclopropane-1-carboxylate oxidase (EgACC) genes. The SNP discovery result showed that Eg was represented a reference homozygote genotype, while Eo was represented as an alternative homozygote genotype and the Eo x Eg hybrid was represented as a heterozygote genotype in all genes. The typical UP-HRM melt curve graph was successfully generated. This result was consistent with each genotype model for all four markers. The UP-HRM markers can distinguish each genotype according to the single-pass sequencing results. Furthermore, dendrogram analysis on validation divided 53 BC1F1 samples into three cluster groups.

scholarly journals Characterization of Checo/F95-927 pea (Pisum sativum L.) population for winter frost tolerance using molecular markers

2021 ◽  
Vol 26 (1) ◽  
pp. 2262-2268
Author(s):  
ANCUȚA CRÎNGAȘU (BĂRBIERU) ◽  
MATILDA CIUCĂ ◽  
CRISTINA DANIEL ◽  
CĂLINA-PETRUȚA CORNEA ◽  
GHEORGHE ITTU ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Essential Role ◽  
Field Experiments ◽  
Recombinant Inbred Lines ◽  
Frost Tolerance ◽  
Inbred Lines ◽  
Marker Assisted Breeding ◽  
Pisum Sativum L

Winter pea has several advantages on spring pea: higher yield, more rapid spring growth that helps this crop to compete weeds, wider growing area, etc. The aim of this paper was to evaluate the association of some molecular markers with frost tolerance of pea. Forty-one pea recombinant inbred lines (RILs), from F5 generation, obtained by crossing the winter cultivar Checo with the spring line F95-927 were examined during this work both by in vitro (molecular markers analysis) and in field experiments. The results obtained showed a significant correlation betweeen frost tolerance and molecular markers EST1109 and AD59. Also, it has been found that the molecular marker AD159 is associated with earliness character. These associated markers could play an essential role in marker-assisted breeding for winter-hardy pea cultivars.

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