Allele mining and selective patterns of Pi9 gene in a set of rice landraces from India

Allelic variants of the broad-spectrum blast resistance gene, Pi9 (NBS-LRR region) have been analyzed in Indian rice landraces. They were selected from the list of 338 rice landraces phenotyped in the rice blast nursery at central Rainfed Upland Rice Research Station, Hazaribag. Six of them were further selected on the basis of their resistance and susceptible pattern for virulence analysis and selective pattern study of Pi9 gene. The sequence analysis and phylogenetic study illustrated that such sequences are vastly homologous and clustered into two groups. All the blast resistance Pi9 alleles were grouped into one cluster, whereas Pi9 alleles of susceptible landraces formed another cluster even though these landraces have a low level of DNA polymorphisms. A total number of 136 polymorphic sites comprising of transitions, transversions and InDels were identified in the 2.9kb sequence of Pi9 alleles. Lower variation in the form of mutations (77) (Transition + Transversion), and InDels (59) were observed in the Pi9 alleles isolated from rice landraces studied. The results showed that the Pi9 alleles of the selected rice landraces were less variable, suggesting that the rice landraces would have been exposed to less number of pathotypes across the country. The positive Tajima’s D (0.33580), P > 0.10 (not significant) was observed among the seven rice landraces, which suggests the balancing selection of Pi9 alleles. The value of synonymous substitution (-0.43337) was less than the non-synonymous substitution (0.78808). The greater non-synonymous substitution than the synonymous means that the coding region, mainly the LRR domain was under diversified selection. In this study, the Pi9 gene has been subjected to balancing selection with low nucleotide diversity which is different from the earlier reports, this may be because of the closeness of the rice landraces, cultivated in the same region and under low pathotype pressure

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Genetic Diversity Analysis of Rice Germplasm in Tripura State of Northeast India Using Drought and Blast Linked Markers

We genotyped 74 rice germplasms including Tripura's local landraces, improved varieties, cultivars and breeding lines and other rice varieties using molecular markers for genetic diversity, drought QTLs, and blast resistance genes. The number of alleles per locus ranged from 2 to 5 with an average of 2.9. The polymorphic information content value per locus ranged from 0.059 (RM537) to 0.755 (RM252) with an average of 0.475. Cluster analysis based on 30 simple sequence repeat markers revealed 5 clusters and also indicated the presence of variability within the rice accessions. The drought QTL qDTY2.1 was found in 56.0% of germplasms and qDTY1.1 was detected in only 6.8% of the germplasms. Out of seven rice blast resistance genes screened, only two rice varieties, RCPL-1-82 and Buh Vubuk (Lubuk), were positive for four blast resistance genes while only Releng possessed two blast resistance genes. Among 74 rice germplasms, only three accessions, Releng, RCPL1-82 and Buh Vubuk (Lubuk), possessed both drought-related QTLs and blast resistance genes. Overall, the 74 indigenous rice genotypes showed low level of genetic diversity, which is in contrast to high level of genetic diversity among rice varieties in northeast India, where highlights the good farming practice, conservation of germplasms and the limitation of molecular markers employed in this study. The presence of both drought related QTLs and blast resistance genes in some of the germplasms can be useful in future breeding programmes

Trait Combinations That Improve Rice Yield under Drought: Sahbhagi Dhan and New Drought-Tolerant Varieties in South Asia

Drought is one of the most severe constraints reducing rice (Oryza sativa L.) yield in rainfed environments. ‘Sahbhagi Dhan’ (IR74371-70- 1-1) is a drought-tolerant rice variety that was released in India in 2010—and subsequently in Nepal as ‘Sukha Dhan 3’ and in Bangladesh as ‘BRRI Dhan 56’—and has performed well in rainfed farmers’ fields. This study was conducted to understand the physiological drought response characteristics of Sahbhagi Dhan that contribute to its increased yield under drought. Physiological characterization of Sahbhagi Dhan and other newer breeding lines was conducted across multiple seasons at one site in the Philippines and at four sites in India. Several distinct traits of Sahbhagi Dhan were observed: high emergence rates under direct-seeded germination- stage stress, a high proportion of total root length as lateral roots in some seasons, high harvest index under drought, and high yield stability across wet seasons. However, some unfavorable responses of Sahbhagi Dhan were observed: impaired growth when sown during seasons with early-stage cold temperatures or low solar radiation, resulting in relatively low yield stability across dry seasons. These results point to the importance of combining multiple traits for yield stability across drought-prone environments. Some of the newly developed breeding lines showed even greater yield stability than Sahbhagi Dhan, reflecting the effectiveness of ongoing improvement through direct selection for grain yield under drought that has resulted in advantageous combinations of physiological traits to increase yield in farmers’ fields

Genetic, Physiological, and Gene Expression Analyses Reveal That Multiple QTL Enhance Yield of Rice Mega-Variety IR64 under Drought

<div><p>Background</p><p>Rice (<i>Oryza sativa</i> L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge.</p><p>Methodology/Principal Findings</p><p>Two pairs of backcross inbred lines (BILs) from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC₄F₃ mapping populations produced by crossing the +QTL BILs with the −QTL BILs and IR64, four major-effect QTL - one each on chromosomes 2, 4, 9, and 10 - were identified. Meta-analysis of transcriptome data from the +QTL/−QTL BILs identified differentially expressed genes (DEGs) significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC₄F₃-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha⁻¹ over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia.</p><p>Conclusions/Significance</p><p>Given the importance of rice in daily food consumption and the popularity of IR64, the BC₄F₃ lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include optimizing QTL combinations in different genetic backgrounds to maximize yield advantage under drought.</p></div

Yield of QTL-introgressed IR64 lines in the target ecosystem in Bangladesh, Nepal, and India.

<p>Yield of QTL-introgressed IR64 lines in the target ecosystem in Bangladesh, Nepal, and India.</p

Yield and quality traits of IR64 QTL-introgressed lines at IRRI.

<p>DTF, Days to 50% flowering; PH, Plant height; GY, Grain yield; Bio, Straw biomass at harvest; S, Stress; NS, Non-stress; AC, Amylose content; GT, Gelatinization temperature (I, intermediate; L, low); MP, Milling potential; CS, Chalkiness score; GS, Genetic similarity.</p

Canopy temperature dynamics over the A. 2010DS and B. 2010DS-ROS, as measured mid-day on sunny days with an infrared camera, and C. stomatal conductance during the 2010DS-ROS.

<p>Significant differences among lines are indicated by *(p<0.05) and **(p<0.01). D. Infrared thermal image showing contrasting canopy temperatures of +QTL and –QTL lines, taken 98 days after sowing (DAS) in 2010DS-ROS.</p