Dataset Information

Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection.

ABSTRACT: The semi-dwarfing allele, sd1-d, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), sd1-d, derived from a spontaneous mutation, has a 383-bp deletion in the SD1 gene. To date, as many as seven alleles of the SD1 gene have been identified and used in rice improvement, either with a functional single-nucleotide polymorphism (SNP), with insertion-deletions (InDels), or both. Here, we report discovery of a novel SNP in the SD1 gene from the rice genotype, Pusa 1652. Genetic analysis revealed that the inheritance of the semi-dwarfism in Pusa 1652 is monogenic and recessive, but it did not carry the sd1-d allele. However, response to exogenous gibberellic acid (GA3) application and the subsequent bulked segregant and linkage analyses confirmed that the SD1 gene is involved in the plant height reduction in Pusa 1652. Sequencing of the SD1 gene from Pusa 1652 revealed a novel transition in exon 3 (T/A) causing a nonsense mutation at the 300th codon. The stop codon leads to premature termination, resulting in a truncated protein of OsGA20ox2 obstructing the GA3 biosynthesis pathway. This novel recessive allele, named sd1-bm, is derived from Bindli Mutant 34 (BM34), a ?-ray induced mutant of a short-grain aromatic landrace, Bindli. BM34 is the parent of an aromatic semi-dwarf cultivar, Pusa 1176, from which Pusa 1652 is derived. The semi-dwarfing allele, sd1-bm, was further validated by developing a derived cleaved amplified polymorphic sequence (dCAPS) marker, AKS-sd1. This allele provides an alternative to the most widely used sd1-d in rice improvement programs and the functional dCAPS marker will facilitate marker-assisted introgression of the semi-dwarf trait into tall genotypes.

SUBMITTER: Bhuvaneswari S

PROVIDER: S-EPMC7570060 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection.

Bhuvaneswari Shivashankar S Gopala Krishnan Subbaiyan S Ellur Ranjith Kumar RK Vinod Kunnummal Kurungara KK Bollinedi Haritha H Bhowmick Prolay Kumar PK Bansal Vijay Prakash VP Nagarajan Mariappan M Singh Ashok Kumar AK Singh Ashok Kumar AK

Plants (Basel, Switzerland) 20200914 9

The semi-dwarfing allele, sd1-d, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), sd1-d, derived from a spontaneous mutation, has a 383-bp deletion in the SD1 gene. To date, as many as seven alleles of the SD1 gene have been identified and used in rice improvement, either with a functional single-nucleotide polymorphism (SNP), with insertion-deletions (InDels), or ...[more]

PMID: 32937792

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Project description:Background:Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers' nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection results. Results:Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7-8 ng/?L) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~?99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost-benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. Conclusion:This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development.

Dataset Information

Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection.

Publications

Discovery of a Novel Induced Polymorphism in <i>SD</i>1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection.

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