Abstract
Chromosome segment substitution lines (CSSLs) are a powerful alternative for locating quantitative trait loci (QTL), analyzing gene interactions, and providing starting materials for map-based cloning projects. We report the development and characterization of a CSSL library of a U.S. weedy rice accession ‘PSRR-1’ with genome-wide coverage in an adapted rice cultivar ‘Bengal’ background. The majority of the CSSLs carried a single defined weedy rice segment with an average introgression segment of 2.8 % of the donor genome. QTL mapping results for several agronomic and domestication traits from the CSSL population were compared with those obtained from two recombinant inbred line (RIL) populations involving the same weedy rice accession. There was congruence of major effect QTLs between both types of populations, but new and additional QTLs were detected in the CSSL population. Although, three major effect QTLs for plant height were detected on chromosomes 1, 4, and 8 in the CSSL population, the latter two escaped detection in both RIL populations. Since this was observed for many traits, epistasis may play a major role for the phenotypic variation observed in weedy rice. High levels of shattering and seed dormancy in weedy rice might result from an accumulation of many small effect QTLs. Several CSSLs with desirable agronomic traits (e.g. longer panicles, longer grains, and higher seed weight) identified in this study could be useful for rice breeding. Since weedy rice is a reservoir of genes for many weedy and agronomic attributes, the CSSL library will serve as a valuable resource to discover latent genetic diversity for improving crop productivity and understanding the plant domestication process through cloning and characterization of the underlying genes.
Highlights
Weedy rice (Oryza sativa), commonly known as red rice, is an annual weed of the same genus and species as cultivated rice, characterized by high genetic flexibility and phenotypic plasticity [1]
Hybrids derived from the cross between Bengal and PSRR-1 were backcrossed consecutively for three generations with Bengal as the female parent to develop the Chromosome segment substitution lines (CSSLs) of the weedy rice accession PSRR-1
One hundred BC1F1 plants were genotyped with simple sequence repeat (SSR) markers, and 65 plants were selected for further backcrossing
Summary
Weedy rice (Oryza sativa), commonly known as red rice, is an annual weed of the same genus and species as cultivated rice, characterized by high genetic flexibility and phenotypic plasticity [1]. It is prevalent in most rice growing states in the southern United States, Europe, Central and South America where no wild or weedy relatives are present in natural habitat. Molecular marker studies indicated a possible origin of U.S weedy rice from hybridization between Asian cultivated rice and the wild ancestor of rice, Oryza rufipogon [4, 5]. The ability of weedy rice to hybridize with closely related cultivated rice facilitates synthesis of unique genetic materials to study the genetic mechanisms associated with weedy rice evolution and the domestication process
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