Identification of genomic regions governing moisture and heat stress tolerance employing association mapping in rice (Oryza sativa L.).

BACKGROUND: Rice crop is damaged extremely by abiotic stress world-wide. The best approach to enhance drought tolerance in rice varieties is to identify and introgress yield QTLs with major effects. The Association mapping approach helps in the identification of genomic regions governing physiological, yield and yield attributes under moisture and heat stress conditions in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. METHODS AND RESULTS: The association mapping panel of 110 rice germplasm lines exhibited significant variation for all the traits in both irrigated and moisture stress conditions. The extent of yield reduction ranged to 83% during rabi, 2018-19, 53% in rabi, 2019-20 and 68% in pooled analysis. The genotypes Badami, Badshabhog, Pankaj, Varalu, Vasundhara, Vivekdhan, Krishna and Minghui63 exhibited drought tolerance with least yield penalty under moisture stress conditions. The genotypes Konark, MTU3626, NLR33671, PR118 and Triguna exhibited minimal reduction in heat stress tolerance traits. Association mapping of germplasm using 37808 SNP markers detected a total of 10 major MTA (Marker-trait association) clusters distributed on chromosomes 1, 3, 4 and 11 through mixed linear model (MLM) governing multiple traits from individual data analysis which are consistent across the years and situations. The pooled data generated a total of five MTA clusters located on chromosome 6. In addition, several novel unique MTAs were also identified. Heat stress analysis generated a total of 23 MTAs distributed on chromosomes 1, 5, 6 and 11. Candidate gene analysis detected a total of 53 and 38 genes under individual and pooled data analysis for various yield and yield attributes under control and moisture stress conditions, respectively and a total of 11 candidate genes in heat stress Conditions. CONCLUSION: The major and novel MTAs identified in the present investigation for various drought and heat tolerant traits can be utilized for breeding climate-resilient rice varieties. The candidate genes predicted for key MTAs are of great value to deploy into the rice breeding after functional characterization.

A novel barcode system for rapid identification of rice (Oryza sativa L.) varieties using agro-morphological descriptors and molecular markers.

Rice varietal identification is a crucial aspect in breeding, seed production and trade in order to protect the interests of the farmers and consumers. As the number of varieties released is rising every year, the need to identify them unambiguously also increases. Here, we developed a novel barcode system to identify 62 rice genotypes using agro-morphological descriptors and molecular markers. In all, 62 rice genotypes, for 22 agro-morphological traits were recorded. In addition, 19 molecular markers were used for developing genotype-specific DNA fingerprints. The descriptor notes of 10 essential agro-morphological traits and allele codes of the polymorphic markers were used to generate two-dimensional (2-D) barcodes for the rice genotypes. Using agro-morphological traits, 31 rice genotypes were unambiguously distinguished while, with the polymorphic markers we were able to distinguish all rice genotypes except BPT2295 and Jaya. However, using both agro-morphological descriptors and molecular markers in combination, it was possible to distinguish all the rice genotypes used in the present study. These agro-morphological notes and allele codes from the molecular marker data together were used to develop QR (Quick Response) codes for rapid identification of rice genotypes as they facilitate storage of more data. In the present investigation, we have demonstrated the potentiality of agro-morphological traits and molecular markers in distinguishing rice genotypes. The novel QR code system proposed in the present study can also be extended to other crops not only for varietal identification but also for germplasm management and trade.