Peanut variety identification is essential for protecting the intellectual property rights of researchers, ensuring quality management for producers, and safeguarding the interests of seed production stakeholders. In this research, we developed a molecular marker set for peanut variety identification using single nucleotide polymorphism (SNP) markers. We used genotyping data and selection procedures, including decision tree and optimal combination selection, to identify a minimal set of informative SNP sites. These SNPs were then converted into Kompetitive allele-specific PCR (KASP) markers. We selected a subset of 14 informative SNPs from a pool of 22 candidate markers, representing the minimum number of combinations required to distinguish cultivars. SNPs obtained from the microarrays were converted to KASP markers and then evaluated across 51 peanut varieties. The developed marker set, which consists of a minimal number of markers, is expected to be a rapid and cost-effective tool for peanut variety identification.
SNP-based markers have been widely used to identify tolerant varieties harboring major genes related to abiotic stress tolerance. Here, we developed Fluidigm markers for the core set of SNPs underlying tolerance to abiotic stresses such as salinity, drought, anaerobic germination and submergence. The core set of SNPs was selected from the major genes and/or QTLs for the abiotic stresses previously reported in rice;
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Watermelon [
Powdery mildew (PM), caused by the biotrophic fungus
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Squash (
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The plants of the Papaveraceae family are used for ornamental purposes because of their varicolored flowers, and are known as medicinal crops. Some species of poppy are used in foods such as salads or sorbets, utilizing the seeds, leaves, pedicels, and petals. There are several morphological similarities among the species of this family, which make it difficult to distinguish the seeds of different species or identify opium poppies. The family is known to contain about 100 species. The leaves of Iceland poppy (
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Cowpea is an annual legume crop; although it is an essential food in developing countries, cowpea is now grown worldwide. For the genetic improvement of plants, flowering time is one of the major selection criteria. In general, flowering is regulated by photoperiod and temperature, along with the interaction between environmental factors. In this study, we aimed to investigate the candidate genes associated with flowering time using genome-wide association study (GWAS). To investigate the flowering time-related genes, 384 cowpea germplasms were genotyped with 51,128 single nucleotide polymorphisms (SNPs). The main genetic component of days to flowering (DTF) was analyzed using genome association and prediction integrated tool (GAPIT) and elastic-net analyses. From the GAPIT and elastic-net analyses, a total of 23 SNPs were significantly associated with DTF among five (chr. 2, 3, 7, 9, and 11) and seven (chr. 1, 2, 3, 4, 5, 8, and 9) different chromosomes, respectively. Based on our analysis,
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Salinity is a common and increasing problem in many coastal rice producing areas around the world. Salinity tolerance at the reproductive stage in rice is crucial as it determines grain yield. An F2 mapping population was developed from two modern rice cultivars contrasting in tolerance: NSIC Rc222 (a high-yielding salt-sensitive variety released in the Philippines) and BRRI dhan 47 (a salt-tolerant variety released in Bangaldesh). The performance of the F2 population showed transgressive segregation in the yield components under salinity stress of EC 10 dS/m under salinized field conditions. Ninety-six single nucleotide polymorphism (SNP) markers using 96-plex FluidigmTM genotyping were used to construct a linkage map of 1306.2 cM (Kosambi), with an average interval size of 13.6 cM. Seven putative quantitative trait loci (QTLs) for reproductive stage salinity tolerance traits having LOD values ranging from 2.9 to 4.1 were identified on chromosomes 1, 2, 5 and 11, explaining 13.4 to 18.4% of the phenotypic variation. Results of this mapping study identified a genomic region on chromosome 2 that confers salinity tolerance at the reproductive stage as measured by the number of filled spikelets, percent filled spikelets and yield. This study reports the molecular mapping of QTLs controlling reproductive-stage salinity tolerance-related traits, which will be useful in marker-assisted selection and breeding population development in rice.
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The
objective
of this study was to develop high-throughput SNP or SNP-based markers by re-sequencing of two peanut cultivars, ‘K-Ol’ and ‘Pungan’. The whole genome re-sequencing for the two cultivars was performed to produce sequences of 35.3 × 109 bp with 350 × 106 reads and 32.0 × 109 bp with 318 × 106 reads, respectively. As compared with the peanut reference genome, the distribution of homozygous and heterozygous SNPs on each chromosome showed very similar patterns between ‘K-Ol’ and ‘Pungan’, and most of them were in intergenic-region regardless of the peanut cultivars and reference genome type. The SNPs identified between the two peanut cultivars were evenly distributed across chromosomes of peanut diploid A and B reference genomes. It indicated that these SNPs could be available to construct a genetic map using the segregating population derived from a cross between ‘K-Ol’ and ‘Pungan’. Total 61 CAPS marker were developed and tested for their availability. Of the CAPS markers, 60 CAPS markers produced normal PCR products and 18 out of them presented polymorphism among 6 peanut varieties. Results of the present study could provide useful genetic resources to facilitate marker-assisted selection for breeding programs as well as germplasm screening for peanut.
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Single nucleotide polymorphisms (SNPs) are abundantly and evenly distributed throughout the genomes of most plant species. These markers have become popular for use in genetic research in many crops. SNP markers can be used to screen maize cultivars rapidly during the early growth stages. In this study, to develop additional SNP markers for maize, we chose 20 SNP sites per chromosome from the maizeGDB website (
We identified a
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Tomato (
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Low temperature germinability (LTG) is an important trait for stand establishment in the direct-seeding method of rice cultivation. In temperate growing regions, water temperature during sowing season is frequently below 15°C resulting in poor crop establishment. The
objective
of this study was to select enhanced rice germplasm for low temperature germinability. Association of the phenotype for LTG with the genotype for
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Closely-related cultivars generally used for crossing in breeding lack sufficient known DNA polymorphisms with already developed DNA markers even though they exhibit remarkable phenotype difference. However, next-generation sequencing (NGS) enables the identification of massive DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. This study conducted a whole-genome re-sequencing of two Korean
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Simple sequence repeats (SSRs) have been the marker of choice for rice molecular breeding due to the high level of polymorphism, technical simplicity and low cost. Recent advances in rice genomics have led to the discovery of abundant single nucleotide polymorphism (SNPs) which have enormous potential for rice molecular breeding. To assess both marker systems for molecular breeding in rice, SSR and SNP markers were evaluated on a set of 23 genotypes representing
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Recent advances in next-generation sequencing (NGS) and single nucleotide polymorphism (SNP) genotyping promise to greatly accelerate crop improvement if properly deployed. High-throughput SNP genotyping offers a number of advantages over previous marker systems, including an abundance of markers, rapid processing of large populations, a variety of genotyping systems to meet different needs, and straightforward allele calling and database storage due to the bi-allelic nature of SNP markers. NGS technologies have enabled rapid whole genome sequencing, providing extensive SNP discovery pools to select informative markers for different sets of germplasm. Highly multiplexed fixed array platforms have enabled powerful approaches such as genome-wide association studies. On the other hand, routine deployment of trait-specific SNP markers requires flexible, low-cost systems for genotyping smaller numbers of SNPs across large breeding populations, using platforms such as Fluidigm’s Dynamic Arrays™, Douglas Scientific’s Array Tape™, and LGC’s automated systems for running KASP™ markers. At the same time, genotyping by sequencing (GBS) is rapidly becoming popular for low-cost high-density genome-wide scans through multiplexed sequencing. This review will discuss the range of options available to modern breeders for integrating SNP markers into their programs, whether by outsourcing to service providers or setting up in-house genotyping facilities, and will provide an example of SNP deployment for rice research and breeding as demonstrated by the Genotyping Services Lab at the International Rice Research Institute.
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A novel allele of the putative soybean raffinose synthase gene,
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