Development and validation of a novel core set of KASP markers for the traits improving grain yield and adaptability of rice under direct-seeded cultivation conditions

Sandhu, Nitika; Singh, Jasneet; Singh, Gaganpreet; Sethi, Mehak; Singh, Mohini; Pruthi, Gomsie; Raigar, Om Prakash; Kaur, Rupinder; Sarao, Preetinder Singh; Lore, Jagjeet Singh; Singh, Uma Maheshwar; Dixit, Sreenath; Sagare, Deepti B.; Singh, Suresh Prasad; Sreedhar, V. M.; Singh, Vikas K.; Kumar, Arvind

doi:10.1016/j.ygeno.2022.110269

Cited by 13 publications

(6 citation statements)

References 71 publications

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“…The polymorphic markers were used to fine map the identified genomic region using BC 2 F 2:3 population. The KASP genotyping assays were carried out following protocol as mentioned in Sandhu et al ( 2022 ).…”

Section: Methodsmentioning

confidence: 99%

Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice

Sandhu,

Ankush,

Singh

et al. 2023

Rice

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Background Ongoing large-scale shift towards direct seeded rice (DSR) necessitates a convergence of breeding and genetic approaches for its sustenance and harnessing natural resources and environmental benefits. Improving seedling vigour remains key objective for breeders working with DSR. The present study aims to understand the genetic control of seedling vigour in deep sown DSR. Combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes were performed in the present study. Results Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations. The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 881 kb region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results identified and validated seven potential candidate genes. The four promising introgression lines free from linkage drag and with longer mesocotyl length, longer root length, semi-dwarf plant height have been identified. Conclusion The study will provide rice breeders (1) the pre breeding material in the form of anticipated DSR adapted introgression lines possessing useful traits and alleles improving germination under deep sown DSR field conditions (2) the base for the studies involving functional characterization of candidate genes. The development and utilization of improved introgression lines and molecular markers may play an important role in genomics-assisted breeding (GAB) during the pyramiding of valuable genes providing adaptation to rice under DSR. Our results offer a robust and reliable package that can contribute towards enhancing genetic gains in direct seeded rice breeding programs.

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Section: Methodsmentioning

confidence: 99%

Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice

Sandhu,

Ankush,

Singh

et al. 2023

Rice

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Section: Methodsmentioning

confidence: 99%

“…A total 15 KASP (Kompetitive Allele-Specific PCR) markers in the identified genomic region on chromosome 7 associated with the traits improving germination of rice under deep sowing depth were designed following protocol as mentioned in Sandhu et al 2022. The designed 15 KASP markers were used for the polymorphic survey of the donor (IRGC 128442) and the recipient backgrounds (PR126) used in the present study.…”

Section: Designing Of Kasp Markers and Kasp Assaymentioning

confidence: 99%

Harnessing genetic variations improving seedling vigor for successful crop establishment in deep sown direct-seeded rice

Sandhu

Ankush

Singh

et al. 2023

Preprint

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Improving seedling vigour remains key objective for breeders working with direct-seeded rice (DSR). To understand the genetic control of seedling vigour in deep sown DSR, combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes was performed. Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations. The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 3.79 Mb region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results identified and validated seven potential candidate genes. The potential candidate gene, LOC_Os07g25150 codes for Myb-30-related transcription factor. The LOC_Os07g25150 codes for Myb 30-related transcription factor, LOC_Os07g17689 annotated as protein translation factor, LOC_Os07g17770 as tryptophanyl-tRNA synthetase, LOC_Os07g15440 as alanyl-tRNA synthetase family protein, LOC_Os07g24100 as retrotransposon protein and the remaining others as expressed proteins. The antagonistic relationship between Myb-30 and ethylene-mediated signalling (EIN-3) in regulating mesocotyl elongation have been observed. The functional characterization and knocking of LOC_Os07g25150 codes for Myb 30-related transcription factor may provide better understanding of the mechanism behind mesocotyl elongation. The four promising introgression lines with longer mesocotyl length, longer root length and semi-dwarf plant height have been identified.

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“…42,43 For instance, studies have recently been conducted to develop multiple stress-adaptable rice species that are disease and climate resilient using genomics-assisted breeding techniques such as quantitative trait locus (QTL), gene/markers-phenotype association and phenotype selection. [44][45][46] Pea breeding projects used genetic marker-trait associations to boost valued yield and market-preferred agronomic traits. 47,48 Miedaner et al 43 used highdensity genotype arrays and comprehensive phenotyping of the same species population across diverse conditions, locations, and seasons in genomic selection and population mapping to speed the breeding of disease resistance traits in maize, small-grain cereals, and wheat.…”

Section: Plant Genome Sequences and Bioinformatics Resourcesmentioning

confidence: 99%

Machine learning algorithms: their applications in plant omics and agronomic traits’ improvement

et al. 2022

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Agronomic traits of plants especially those of economic or aesthetic importance are threatened by climatic and environmental factors such as climate change, biotic, and abiotic stresses. These threats are now being mitigated through the analyses of omics data like genomics, transcriptomics, proteomics, metabolomics, and phenomics. The emergence of high-throughput omics technology has led to an avalanche of plant omics data. Plant research demands novel analytical paradigms to extract and harness large plant omics data for plant improvement effectively and efficiently. Machine learning algorithms are well-suited analytical and computational approaches for the integrative analysis of large unstructured, heterogeneous datasets. This study presents an overview of omics approaches to improve plant agronomic traits and crucial curated plant genomic data sources. Furthermore, we summarize machine learning algorithms and software tools/programming packages used in plant omics research. Lastly, we discuss advancements in machine learning algorithms' applications in improving agronomic traits of economically important plants. Extensive application of machine learning would advance plant omics studies. These advancements would consequently help agricultural scientists improve economically important plants’ quality, yield, and tolerance against abiotic and biotic stresses and other plant health-threatening issues.

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Development and validation of a novel core set of KASP markers for the traits improving grain yield and adaptability of rice under direct-seeded cultivation conditions

Cited by 13 publications

References 71 publications

Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice

Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice

Harnessing genetic variations improving seedling vigor for successful crop establishment in deep sown direct-seeded rice

Machine learning algorithms: their applications in plant omics and agronomic traits’ improvement

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