Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review

Reyes, Vincent P.; Kitony, Justine; Nishiuchi, Shunsaku; Makihara, Daigo; Doi, Kouki

doi:10.3390/life12111752

Cited by 15 publications

(8 citation statements)

References 76 publications

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“…Microsatellite or SSR markers incur high development costs and generally exhibit low throughput, surveying only a limited number of loci ( Putman and Carbone, 2014 ). GBS, while advantageous in generating many SNP markers, encounters challenges, especially in bioinformatic analyses, particularly for polyploid organisms like alfalfa or those lacking reference genomes (e.g., annual medics), leading to resource-intensive analysis processes ( Bhatia et al., 2013 ; He et al., 2014 ; Rajendran et al., 2022 ; Reyes et al., 2022 ). The alfalfa DArT panel, however, offers a promising solution, addressing many of the limitations associated with these methodologies.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine

Zhao,

Sapkota,

Lin

et al. 2024

Front. Plant Sci.

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Annual medic (Medicago spp.) germplasm was collected from the Crimean Peninsula of Ukraine in 2008 to fill gaps in geographic coverage in the United States department of Agriculture, Agricultural Research Service, National Plant Germplasm System (NPGS) temperate-adapted forage legume collection. A total of 102 accessions across 10 Medicago species were collected. To assess genetic diversity, population structure, and to confirm taxonomic identities, the collections were phenotypically and genetically characterized. Phenotyping included the use of 24 descriptor traits while genetic characterization was accomplished using a 3K Diversity Array Technologies (DArTag) panel developed for alfalfa (Medicago sativa L.). For both field and molecular characterizations, a reference set of 92 geographically diverse and species-representative accessions were obtained from the NPGS collection. Phenotypic descriptors showed consistency among replicated plants within accessions, some variation across accessions within species, and evident distinctions between species. Because the DArTag panel was developed for cultivated alfalfa, the transferability of markers to the species being evaluated was limited, resulting in an average of ~1,500 marker loci detected per species. From these loci, 448 markers were present in 95% of the samples. Principal component and phylogenetic analysis based on a larger set of 2,396 selected markers clustered accessions by species and predicted evolutionary relationships among species. Additionally, the markers aided in the taxonomic identity of a few accessions that were likely mislabeled. The genotyping results also showed that sampling individual plants for these mostly self-pollinating species is sufficient due to high reproducibility between single (n=3) and pooled (n=7) biological replicate leaf samples. The phenotyping and the 2,396 Single Nucleotide Polymorphism (SNP) marker set were useful in estimating population structure in the Crimean and reference accessions, highlighting novel and unique genetic diversity captured in the Crimean accessions. This research not only demonstrated the utility of the DArTag marker panel in evaluating the Crimean germplasm but also highlighted its broader application in assessing genetic resources within the Medicago genus. Furthermore, we anticipate that our findings will underscore the importance of leveraging genetic resources and advanced genotyping tools for sustainable crop improvement and biodiversity conservation in annual medic species.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine

Zhao,

Sapkota,

Lin

et al. 2024

Front. Plant Sci.

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“…Thus, it is evident that Kaliboro has contributed many positive alleles for yield and yield related traits and for improved grain Zn concentration. These favorable alleles can be pooled through genomics assisted breeding to develop rice varieties ( Blanc et al., 2006 ; Grenier et al., 2015 ; Varshney et al., 2021 ; Xu et al., 2021 ; Reyes et al., 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits

Palanog

Nha²,

Descalsota-Empleo³

et al. 2023

Front. Plant Sci.

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Breeding staple crops with increased micronutrient concentration is a sustainable approach to address micronutrient malnutrition. We carried out Multi-Cross QTL analysis and Inclusive Composite Interval Mapping for 11 agronomic, yield and biofortification traits using four connected RILs populations of rice. Overall, MC-156 QTLs were detected for agronomic (115) and biofortification (41) traits, which were higher in number but smaller in effects compared to single population analysis. The MC-QTL analysis was able to detect important QTLs viz: qZn5.2, qFe7.1, qGY10.1, qDF7.1, qPH1.1, qNT4.1, qPT4.1, qPL1.2, qTGW5.1, qGL3.1, and qGW6.1, which can be used in rice genomics assisted breeding. A major QTL (qZn5.2) for grain Zn concentration has been detected on chromosome 5 that accounted for 13% of R2. In all, 26 QTL clusters were identified on different chromosomes. qPH6.1 epistatically interacted with qZn5.1 and qGY6.2. Most of QTLs were co-located with functionally related candidate genes indicating the accuracy of QTL mapping. The genomic region of qZn5.2 was co-located with putative genes such as OsZIP5, OsZIP9, and LOC_OS05G40490 that are involved in Zn uptake. These genes included polymorphic functional SNPs, and their promoter regions were enriched with cis-regulatory elements involved in plant growth and development, and biotic and abiotic stress tolerance. Major effect QTL identified for biofortification and agronomic traits can be utilized in breeding for Zn biofortified rice varieties.

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“…Researchers design microarrays with probes that hybridize to specific target sequences. This technique has been used for genotyping crops like rice and maize [99,100].…”

Section: Microarray-based Platformsmentioning

confidence: 99%

Advances in Molecular Marker Technology and their Significance in Plant Improvement Strategies

Kamal Meena,

Vardhan Singh Shekhawat,

Chand

et al. 2023

Recent Trends in Plant Breeding and Genetic Improvement

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Molecular markers are powerful tools that have revolutionized plant improvement strategies by allowing breeders to select plants with desirable traits at an early stage. These markers are specific DNA sequences that can be used to identify genes responsible for important plant traits such as disease resistance, drought tolerance, and yield potential. Advances in molecular marker technology have greatly improved their efficiency and accuracy, making them an essential tool in plant breeding programs. One such advance is the development of high-throughput sequencing technologies, which allow for the rapid and cost-effective identification of large numbers of molecular markers. Additionally, new marker systems such as SNPs have been developed, which offer a high level of accuracy and reproducibility. The use of molecular markers in plant breeding has several advantages over traditional breeding methods. For instance, markers can be used to identify desirable traits that are not easily observable, or to select plants with multiple desirable traits at once. This has led to the development of new and improved crop varieties that are more resistant to diseases, better adapted to changing environmental conditions, and have higher yields. In conclusion, the continued development of molecular marker technology is crucial for the advancement of plant improvement strategies.

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Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review

Cited by 15 publications

References 76 publications

Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine

Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine

Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits

Advances in Molecular Marker Technology and their Significance in Plant Improvement Strategies

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