Date of Graduation

5-2013

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Cell & Molecular Biology (PhD)

Degree Level

Graduate

Department

Biological Sciences

Advisor/Mentor

Nilda R. Burgos

Committee Member

Pengyin Chen

Second Committee Member

James C. Correll

Third Committee Member

Amy Lawton-Rauh

Fourth Committee Member

Richard, D. Cartwright

Keywords

Biological sciences, Blackhull strawhull, Genetic diversity, Molecular evolution, Phenological diversity, Seed dormancy, Weedy red rice

Abstract

Rice is the grain with the third-highest global production. In the US, Arkansas is the largest rice producing state; however, an estimated 62% of the rice fields in the state are infested with red rice, and can cause up to 80% yield reduction in rice. Among its weedy traits, seed dormancy plays an important role in its persistence, and helps red rice escape weed management techniques thereby increasing the red rice soil seedbank. Red rice also has the potential to hybridize among themselves and with cultivated rice, thus resulting in diverse phenotypes and genotypes. In this study we measured variation in seed dormancy at different after-ripening times, and incubation temperatures; determined the genetic diversity of dormant and non-dormant red rice populations; measured diversity in phenological and morphological traits among and within red rice populations collected across Arkansas; and, determined the genotype-phenotype relationship and population structure of old and recent red rice collections using sequence tagged site (STS) markers. The germination response of red rice to three temperatures (1°C, 15°C, and 35°C) and four after-ripening periods (0, 30, 60, and 90 d), was evaluated. Germination varied among and within red rice populations in response to different temperatures and after-ripening period. Highest variation in germination was observed at 15°C incubation (44-97%). Among the after-ripening periods, the optimum time to release primary dormancy was 90 d. Blackhull red rice ecotypes was more dormant and also showed higher intrapopulation variation in dormancy compared to strawhull ecotypes. To determine the genetic diversity of dormant and non-dormant red rice populations, 25 simple sequence repeat (SSR) markers associated with seed dormancy loci were used. A considerable amount of genetic variation among red rice accessions was found (Nei's gene diversity (h) = 0.355), and blackhull populations (h = 0.398) were more diverse than strawhull populations (h = 0.245). Higher genetic diversity was observed within and among dormant populations than non-dormant red rice populations. Phenological and morphological characteristics were found to significantly vary among 113 strawhull, 71 blackhull, and 24 brownhull red rice accessions. Greater variation was observed among blackhull red rice, the tallest, late flowering, and highly tillering among the ecotypes. Strawhull red rice generally tillered less, but produced higher grain yield. Sequence analysis of 27 old (2002-2003 collection) and 52 recent (2008-2009 collection) red rice accessions, using 48 STS markers revealed a total of 447 SNPs. Recent blackhull red rice accessions had higher nucleotide diversity (Pi = 2.43 per Kb) than the old blackhull accessions (Pi = 1.21 per Kb). Old strawhull had lower sequence polymorphisms than old blackhull red rice. Genetic and phenotypic diversity among and within red rice ecotypes suggests the adoption of diverse weed management techniques in order to successfully control this troublesome weed.

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