Association studies of dormancy and cooking quality traits in direct-seeded indica rice

Abstract

Association analysis was applied to a panel of accessions of Assam rice (indica) using 98 SSR markers for dormancy-related traits and cooking quality. Analysis of population structure revealed 10 subgroups in the population. The mean r(2) and D' value for all intrachromosomal loci pairs was 0.24 and 0.51, respectively. Linkage disequilibrium between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). Genome-wide scanning, detected a total of seven significant marker-trait associations (P < 0.01), with the R(2) values ranging from 12.0 to 18.0%. The significant marker associations were for grain dormancy (RM27 on chromosome 2), α-amylase activity (RM27 and RM234 on chromosomes 2 and 7, respectively), germination (RM27 and RM106 on chromosome 2), amylose (RM282 on chromosome 3) and grain length elongation ratio (RM142 on chromosome 4). The present study revealed the association of marker RM27 with traits like dormancy, α-amylase activity and germination. Simple correlation analysis of these traits revealed that these traits were positively correlated with each other and this marker may be useful for simultaneous improvement of these traits. The study indicates the presence of novel QTLs for a few traits under consideration. The study reveals association of traits like dormancy, α-amylase activity, germination, amylose content, grain length elongation ratio with SSR markers indicating the feasibility of undertaking association analysis in conjunction with germplasm characterization.

Identification of genomic regions linked to seed dormancy related traits using bulk segregant analysis in rice (Oryza sativa L.)

“…The results revealed that marker i.e., RM22565 on chromosome 8 exhibited significant (P<0.0001) association with germination (%) at five days after harvesting. Similar results for significant association of seed dormancy and germination at five days after harvesting with RM106 on chromosome 2 were reported by Rathi et al (2014). Several groups have attempted to identify the genomic regions/QTLs linked to dormancy and found some QTLs on different chromosomes of rice.…”

Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers

“…Rathi et al . 86 have reported ten subgroups in a population of 100 indica rice using 98 SSR markers. Anandan et al .…”

Analysis of Genotype-Environment Interaction and Yield Stability of Introduced Upland Rice in the Groundnut Basin Agroclimatic Zone of Senegal

“…e principal components 1 and 2 accounted for 48.11 and 20.85% of the total variation, respectively. Based on the average-environment coordination (AEC), the genotypes NERICA 14 (8), ART3-7-L9P8-1-B-B-1 (9), and NERICA 8 (7) appeared as the highest yielding genotypes among which NERICA 8 and ART3-7-L9P8-1-B-B-1 were the most stable across environment. CNAX 3031-78-2-1-7, NERICA 6, and ART16-12-22-1-3-1-1-B-1-B were the lowest yielding genotypes.…”

“…e upland rice appears as a promising sustainable crop that can contribute to cope with food security issue [6]. Development of new upland rice varieties has become a serious research interest for some Asian countries such as Vietnam [7], India [8], and China [9]. With regard to Africa, recent efforts were done by Africa Rice and their collaborators in order to develop upland rice varieties adapted to growing conditions in tropical regions.…”