A Chromosome Segment Substitution Library of Weedy Rice for Genetic Dissection of Complex Agronomic and Domestication Traits

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.

Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace ‘Pokkali’

“…Likewise, ILs were developed and used in QTL mapping for fusarium head blight resistance in wheat [3], mineral accumulation in beans [4], yield attributes in soybean [5], and nematode and fusarium wilt disease resistance in cotton [6]. In rice, several introgression line populations were developed to transfer and map QTLs for agronomic and domestication traits [7–8], yield and morphological traits [9–11], Zn and Fe content in grain [12], and photosynthesis parameters [13]. …”

Development and Evaluation of Chromosome Segment Substitution Lines Carrying Overlapping Chromosome Segments of the Whole Wild Rice Genome

“…As a result, CSSLs could barely cover the whole genome of donor parents. However, incomplete coverage of a donor genome in the CSSL population might, in turn miss some QTLs responsible for useful traits (Subudhi et al, 2015). In this paper, with the help of HCSSLs, CSSLs carrying one substituted segment could be obtained.…”

“…Specifically, CSSLs can be used for detecting and fine mapping of QTLs as a single Mendelian factor by blocking background genetic noise. So far, several CSSLs in rice have been developed and many QTLs for traits of biological and economic interest have been detected (Kubo et al, 2002; Ebitani et al, 2005; Mei et al, 2006; Takai et al, 2007; Zhu et al, 2009; Xu et al, 2010; Chen et al, 2014; Nagata et al, 2015; Subudhi et al, 2015). These achievements have undoubtedly enhanced the understanding of complex traits and promoted plant genomic studies.…”

Evolutionary and social consequences of introgression of nontransgenic herbicide resistance from rice to weedy rice in Brazil

“…, ; Subudhi et al. ) as opposed to the presence of a major gene in cultivated rice of the indica (Li et al. ) or japonica type (Konishi et al.…”

“…The regulation of most of these processes is complex mainly in the weedy types of the cospecific crops. For example, the seed shattering regulation in weedy rice is under the control of multiple genes (Nunes et al 2014(Nunes et al , 2015Subudhi et al 2015) as opposed to the presence of a major gene in cultivated rice of the indica (Li et al 2006) or japonica type (Konishi et al 2006). Therefore, the development of the biotechnological-based strategies designed for reducing gene flow between cultivated rice and weedy rice should be taken into account for the multiple regulation of the trait involved in the gene flow containment or mitigation.…”