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Development of high-throughput and trait-linked markers are of great interest in genomics-assisted breeding. The aim of present study was to develop and validate novel KASP (Kompetitive Allele-Specific PCR) markers associated with traits improving germination and seedling vigor of deep sown direct seeded rice (DSR).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Out of 58 designed KASP assays, four KASP assays did not show any polymorphism in any of the eleven genetic backgrounds considered in the present study. The 54 polymorphic KASP assays were then validated for their robustness and reliability on the F<jats:sub>1<\/jats:sub>s plants developed from eight different crosses considered in the present study. The third next validation was carried out on 256 F<jats:sub>3<\/jats:sub>:F<jats:sub>4<\/jats:sub> and 713 BC<jats:sub>3<\/jats:sub>F<jats:sub>2:3<\/jats:sub> progenies. Finally, the reliability of the KASP assays was accessed on a set of random 50 samples from F<jats:sub>3<\/jats:sub>:F<jats:sub>4<\/jats:sub> and 80\u2013100 samples from BC<jats:sub>3<\/jats:sub>F<jats:sub>2:3<\/jats:sub> progenies using the 10 random markers. From the 54 polymorphic KASP, based on the false positive rate, false negative rate, KASP utility in different genetic backgrounds and significant differences in the phenotypic values of the positive (desirable) and negative (undesirable) traits, a total of 12 KASP assays have been selected. These 12 KASP include 5 KASP on chromosome 3, 1 on chromosome 4, 3 on chromosome 7 and 3 on chromosome 8. The two SNPs lying in the exon regions of <jats:italic>LOC_Os04g34290<\/jats:italic> and <jats:italic>LOC_Os08g32100<\/jats:italic> led to non-synonymous mutations indicating a possible deleterious effect of the SNP variants on the protein structure.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The present research work will provide trait-linked KASP assays, improved breeding material possessing favourable alleles and breeding material in form of expected pre-direct-seeded adapted rice varieties. The marker can be utilized in introgression program during pyramiding of valuable QTLs\/genes providing adaptation to rice under DSR. The functional studies of the genes <jats:italic>LOC_Os04g34290<\/jats:italic> and <jats:italic>LOC_Os08g32100<\/jats:italic> possessing two validated SNPs may provide valuable information about these genes.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12284-024-00711-1","type":"journal-article","created":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T08:01:38Z","timestamp":1715328098000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Development of Novel KASP Markers for Improved Germination in Deep-Sown Direct Seeded Rice"],"prefix":"10.1186","volume":"17","author":[{"given":"Nitika","family":"Sandhu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jasneet","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ade Pooja","family":"Ankush","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaurav","family":"Augustine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Om Prakash","family":"Raigar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vikas Kumar","family":"Verma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gomsie","family":"Pruthi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arvind","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,10]]},"reference":[{"issue":"3","key":"711_CR1","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1111\/pbi.12635","volume":"15","author":"AM Allen","year":"2017","unstructured":"Allen AM, Winfield MO, Burridge AJ, Downie RC, Benbow HR, Barker GL et al (2017) Characterization of a Wheat Breeders\u2019 Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). 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