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Molecular mapping and application of quantitative trait loci (QTL) associated with a higher level of grain Zinc is a viable option to enhance zinc content in rice through breeding. An F2 population derived from a cross between a high yielding variety, BRRI dhan28, and a locally adapted Zn enriched cultivar,
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High-throughput genotyping has substantially advanced the quality and accuracy of single nucleotide polymorphism (SNP) discovery and provided an effective way to interpret phenotypic variations in a mapping population. High-resolution quantitative trait locus (QTL) mapping is important for understanding agricultural traits. However, constructing a high-resolution map without sufficient markers to detect QTLs/genes of agronomically important traits is laborious and time consuming. In this study, 160 recom-binant inbred lines (RILs) derived from a cross between Milyang23 and Gihobyeo were re-sequenced, and their SNPs were used for high-resolution QTL mapping of yield-related traits. A total of 1,850,671 high-quality SNPs from RILs were detected, and 3,563 bins were used as genetic markers to construct a high-resolution genetic map using the sliding window approach. The total genetic distance was 1,278.62 cM. Using the QTL analysis, we identified 35 QTLs controlling six yield traits, namely, culm length, panicle length, panicle number per plant, primary branch number per panicle, grain number per plant, and 100-grain weight. In addition, we detected major QTLs associated with culm length and grain number, and compared their physical distances using a conventional genetic map. These results showed that rapid, high-resolution QTL mapping using high-quality SNPs as bin markers is a powerful tool for fine-mapping and cloning important QTLs/genes.
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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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Conventional PCR requires purified DNA molecules as templates. Purification of DNA molecules from a large number of samples is laborious, costly and time-consuming. Therefore, various direct-PCR methods using tissues directly employed as templates have been developed. Using direct-PCR, one can deal with large number of plant samples far more rapidly and efficiently. However, conditions and methods of direct-PCR vary for different plant samples. This is why applications of direct-PCR technology to plant science have been limited. In this study, we have established the appropriate condition for effectively lysing various plant cells and developed the plant cell lysis buffer named ‘Alkaline PEG lysis buffer’ for the direct-PCR. The direct-PCR technology using a newly developed Alkaline PEG lysis buffer successfully amplified different targeted endogenous genes in seven different plant species. This technology is expected to be very useful and effective tool in plant breeding dealing with large number of plants for the selection of targeted traits, markers and pedigrees.
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