Identification and characterization of genes for drought tolerance in upland rice cultivar 'Banglami' of North East India

Identification of significant SNPs and candidate loci for blast disease resistance via GWAS and population structure analysis in ARC panel of Oryza sativa

Pyricularia (syn. Magnaporthe) oryzae is responsible for the blast disease in rice resulting in a greater extent of yield loss. However, some of the cultivars of rice have the ability to survive this devastating infection due to the presence of R (resistance) genes. Therefore, genome wide association study (GWAS) was undertaken using a panel of 400 rice landraces (ARC panel) and a set of filtered 38,723 single nucleotide polymorphisms (SNPs). The highest SNPs were mapped to chromosome 1 with a number of 4332 SNPs and lowest (2252) in chromosome 12. The ARC panel was evaluated phenotypically which revealed that 6% of the selected cultivars has resistance to rice blast disease with SES score of 1. The majority of the resistant cultivars belong to the group Asra of the panel. The population structure analysis was executed wherein three genetic subpopulations were identified namely RC1, RC2, RC3 and an admixture population constituting 48 accessions. Further, GWAS detected 15 significant association signal with P value in the range of 1.03E-05 to 1.03E-04, effect ranged from - 1.18 to 1.06, phenotypic variance explained was from 0 to 7.14%, R2 of 0.047 to 0.058, and minor allele frequency of 0.107 to 0.444. Eleven (Os01g39980, Os01g56130, Os01g67100, Os01g67110, Os03g41030, Os04g33310, Os07g42104, Os09g06464, Os09g08920, Os09g38800, Os12g37680) out of these 15 significant associations were identified as the candidate loci for the blast resistance in rice that will serve as an important genetic resistance source to be introgressed into an elite rice line in future breeding programs for deciphering blast resistance in rice. The GWAS study presented in this article helped to uncover significant gene regions which encode proteins to resist blast infection in rice plant. This is the first report on the GWAS analysis for blast resistance in unique landraces of rice from Northeast India employing single nucleotide polymorphism.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01518-6.

Plant biomarkers as early detection tools in stress management in food crops: a review

MAIN CONCLUSION

Plant Biomarkers are objective indicators of a plant's cellular state in response to abiotic and biotic stress factors. They can be explored in crop breeding and engineering to produce stress-tolerant crop species. Global food production safely and sustainably remains a top priority to feed the ever-growing human population, expected to reach 10 billion by 2050. However, abiotic and biotic stress factors negatively impact food production systems, causing between 70 and 100% reduction in crop yield. Understanding the plant stress responses is critical for developing novel crops that can adapt better to various adverse environmental conditions. Using plant biomarkers as measurable indicators of a plant's cellular response to external stimuli could serve as early warning signals to detect stresses before severe damage occurs. Plant biomarkers have received considerable attention in the last decade as pre-stress indicators for various economically important food crops. This review discusses some biomarkers associated with abiotic and biotic stress conditions and highlights their importance in developing stress-resilient crops. In addition, we highlighted some factors influencing the expression of biomarkers in crop plants under stress. The information presented in this review would educate plant researchers, breeders, and agronomists on the significance of plant biomarkers in stress biology research, which is essential for improving plant growth and yield toward sustainable food production.

Molecular mapping of drought-responsive QTLs during the reproductive stage of rice using a GBS (genotyping-by-sequencing) based SNP linkage map

BACKGROUND

In rice, drought stress at reproductive stage drastically reduces yield, which in turn hampers farmer's efforts towards crop production. The majority of the rice varieties have resistance genes against several abiotic and biotic stresses. Therefore, the traditional landraces were studied to identify QTLs/candidate genes associated with drought tolerance.

METHODS AND RESULTS

A high-density SNP-based genetic map was constructed using a Genotyping-by-sequencing (GBS) approach. The recombinant inbred lines (RILs) derived from crossing 'Banglami × Ranjit' were used for QTL analysis. A total map length of 1306.424 cM was constructed, which had an average inter-marker distance of 0.281 cM. The phenotypic evaluation of F₆ and F₇ RILs were performed under drought stress and control conditions. A total of 42 QTLs were identified under drought stress and control conditions for yield component traits explaining 1.95-13.36% of the total phenotypic variance (PVE). Among these, 19 QTLs were identified under drought stress conditions, whereas 23 QTLs were located under control conditions. A total of 4 QTLs explained a PVE ≥ 10% which are considered as the major QTLs. Moreover, bioinformatics analysis revealed the presence of 6 candidate genes, which showed differential expression under drought and control conditions.

CONCLUSION

These QTLs/genes may be deployed for marker-assisted pyramiding to improve drought tolerance in the existing rice varieties.