Molecular profiling of an interspecific rice population derived from a cross between WAB 56-104 (Oryza sativa) and CG 14 (Oryza glaberrima)

Abstract

NERICA rices are interspecific inbred progeny derived from crosses between 4% (1,508 cM), while the observed average proportion of O. glaberrima donor genome was 6.3% (108 cM). Non-parental alleles were detected in 83% of the lines and contributed an average of 38 cM per line (~2.2% of genomic DNA). Lines that had undergone eight generations of inbreeding in the field contained significantly more non-parental alleles (av. 2.7%) compared to the DH lines (av. 1.3%) that were developed from BC 2 anthers. Using both cluster and principal component analyses, two major groups were detected in these materials. The NERICA varieties (NERICA 1 to 7) clustered in one group while the remaining 63 lines clustered in another group, suggesting that the second group may offer significant opportunities for further selection and variety development.

Genetic analysis and identification of QTLs associated with yield-enhancing traits in Oryza sativa IR64 × Oryza glaberrima interspecific backcross populations

“…The microsatellite (SSR) markers were successfully used in the molecular profiling of O. glaberrima interspecific progenies because they are co-dominant and highly polymorphic even among very closely related individuals. In the present study, 99 SSR markers evenly distributed on 12 rice chromosomes were employed, compared with 36 (Agnoun et al 2012), 60 (Ndjiondjop et al 2008), 114 (Moukoumbi et al 2015) and 130 (Semagn et al 2007) SSR markers in the literature. Similarly, genome coverage using molecular markers in the O. sativa × O. glaberrima interspecific population varied among the studies.…”

“…In total, 146 BC 1 F 2 interspecific progenies were genotyped with SSR markers and subjected to GGT 2.0 software to decipher genome composition of the mapping population. Molecular profiling of mapping populations enhances the ability of breeders to determine the inheritance and parentage of specific genomic regions and to monitor the introgression of specific chromosome segments that are linked to desirable traits in breeding lines (Semagn et al 2007). The microsatellite (SSR) markers were successfully used in the molecular profiling of O. glaberrima interspecific progenies because they are co-dominant and highly polymorphic even among very closely related individuals.…”

“…The first interspecific (O. sativa × O. glaberrima) microsatellite based linkage map covered a map length of 1923 cM with mean interval length of 17 cM (Lorieux et al 2000). Semagn et al (2007) reported genome coverage of 1725 cM, and later, Bimpong et al (2011) reported genome coverage of 371.1 Mb with a marker density of 8.3 per chromosome in the IR64 × O. glaberrima population.…”

“…As Moukoumbi et al (2015) suggested, these disparities may arise from the number of markers and their distribution, effects of environment on plant growth and development, interspecific sterility and unconscious selection during population development. Semagn et al (2007) reported that the proportion of recurrent parent (O. sativa) genome in 70 interspecific rice populations (WAB 56-104 × CG14, BC 2 F 8 ) varied from 64.3% on chromosome 6 to 94.7% on chromosome 11. Similarly, the proportion of O. glaberrima alleles ranged from 25.5% on chromosome 3 to 87.5% on chromosome 12, with an average of 7.5%.…”

“…Further, there are reports of quantitative trait loci (QTLs) derived from O. glaberrima associated with grain quality (Li et al 2004;Wambugu et al 2018), rice stripe necrosis (Gutiérrez et al 2010), iron toxicity (Dufey et al 2015) and competitiveness against weeds (Bharamappanavara et al 2020). Molecular profiling of interspecific progeny of O. glaberrima has been performed (Semagn et al 2007;Ndjiondjop et al 2008;Bimpong et al 2011;Agnoun et al 2012;Moukoumbi et al 2015) to provide insight into the extent of the O. glaberrima genome inherited in the progenies.…”