Microarray-based markers such as Diversity Arrays Technology (DArT) have become the genetic markers of choice for construction of high-density maps, quantitative trait loci (QTL) mapping and genetic diversity analysis based on their efficiency and low cost. More recently, the DArT technology was further developed in combination with high-throughput next-generation sequencing (NGS) technologies to generate the DArTseq platform representing a new sequencing tool of complexity-reduced representations. In this study, we used DArTseq markers to investigate genetic diversity and genome-wide association studies (GWAS) of grain quality traits in rice (Oryza sativa L.). The study was performed using 59 rice genotypes with 525 SNPs derived from DArTseq platform. Population structure analysis revealed only two distinct genetic clusters where genotypes were grouped based on environmental adaptation and pedigree information. Analysis of molecular variance indicated a low degree of differentiation among populations suggesting the need for broadening the genetic base of the current germplasm collection. GWAS revealed 22 significant associations between DArTseq-derived SNP markers and rice grain quality traits in the test genotypes. In general, 2 of the 22 significant associations were in chromosomal regions where the QTLs associated with the given traits had previously been reported, the other 20 significant SNP marker loci were indicative of the likelihood discovery of novel alleles associated with rice grain quality traits. DArTseq-derived SNP markers that include SNP12_100006178, SNP13_3052560 and SNP14_3057360 individually co-localised with two functional gene groups that were associated with QTLs for grain width and grain length to width ratio on chromosome 3, indicating trait dependency or pleiotropic-effect loci. This study demonstrated that DArTseq markers were useful genomic resources for genome-wide association studies of rice grain quality traits to accelerate varietal development and release.
SUMMARYRice (Oryza sativa L.) is an important staple crop in South Sudan. Current rice consumption in the country is approximately 23,000 mg year−1 of which more than 75% is imported. We investigated farmers’ perceived rice production and productivity constraints and choice of rice ideotypes across rainfed and irrigated rice agro-ecologies in South Sudan to guide breeding and policy interventions. Data were gathered through participatory rural approaches and a formal structured survey involving 136 rice farmers from major rice growing areas of South Sudan. Farmers generally cultivated old rice varieties with low yields varying from 0.4 to 1.6 mg ha−1. Pair-wise ranking based on respondents score indicated yield, early maturity, cooking and eating quality, nutritional importance and drought tolerance as the most desirable traits of rice ideotypes. Further, imported rice varieties were best ranked for their sweet and appealing taste, rich aroma, grain shape and size, swelling capacity and non-stickiness during cooking. Major perceived constraints to rice production were unreliable rainfall, poor access to credit facilities, poor soil and water management practices, poor rice storage facilities, inadequate and poor processing machines as well as limited technical skills in rice production. The results show a need for integration of farmers’ and stakeholders’ preferences in variety development process and the desirability of releasing site-specific rice cultivars given the differences in bio-physical, socio-cultural and farmers preferences across major rice growing areas of South Sudan.
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