Identification of molecular markers and association mapping of selected loci associated with agronomic traits in rice

Discriminate Analysis as a procedure was evaluated to select molecular markers associated with complex traits in US rice germplasm. Markers for percent head rice, percent total rice, and grain yield were identified with high levels of correct classification that mapped within or near traditional Quantitative Trait Loci (QTL). Mixed model-regression procedure to identify molecular markers that predict phenotypic variance associated with four agronomic traits was created and validated in two distinct rice inbred populations. Main and epistatic effects were identified by standard hypothesis testing and Bayesian information criteria in a multivariate format. The new procedure increased power and enhanced prediction ability of markers in validation samples from both populations. A new SNP discovery and genotyping protocol referred to as Alternative Ecotilling has identified four previously reported and 14 new SNPs in the alk and waxy genes among 57 accessions based on comparisons with sequencing results. The new procedure has been published in 2006 in the journal Plant Molecular Biology Reporter. Application of haplotype-specific markers in exon 7 of the BAD2 gene for marker-assisted identification and introgression of the aroma gene in U.S. rice was evaluated. Aromatic/non-aromatic phenotypes were consistent with corresponding marker haplotypes for all progeny tested which shows the potential of this procedure for marker assisted breeding of new aromatic varieties. Similarly, an allele-specific PCR assays were developed to distinguish between homozygous and heterozygous imazethapyr-resistant S₆₅₃D and G₆₅₄E SNP alleles of the rice ALS gene. Field collections were successfully screened for the presence of S₆₅₃D SNP, and F₂ progeny lines of natural CL 121 x red rice outcrosses were screened for the presence of the G₆₅₄E SNP. These assays were proven successful and are currently used for detection of outcrossing and seed purity for the LSU AgCenter Rice Breeding Project.

Name thesis:degree_name

Doctor of Philosophy (PhD)

Level thesis:degree_level

Dissertation

Grantor

Plant, Environmental Management and Soil Sciences

Year dc:date.available

2007

Author dc:creator

• Kadaru, Suresh Babu

• alternative ecotilling
• mixed model-regression analysis
• mixed model
• discriminant analysis
• aroma
• imazethapyr resistance

Statement dc:rights

• unrestricted
• Release the entire work immediately for access worldwide.

Identifier

etd-05092007-143026
https://repository.lsu.edu/gradschool_dissertations/231

OAI identifier oai:identifier

oai:repository.lsu.edu:gradschool_dissertations-1230