Reducing the environmental impact of rice production in subtropical India by minimising reactive nitrogen loss.

The future of reactive nitrogen (N) for subtropical lowland rice to be characterised under diverse N-management to develop adequate sustainable practices. It is a challenge to increase the efficiency of N use in lowland rice, as N can be lost in various ways, e.g., through nitrous oxide (N2O) or dinitrogen (N2) emissions, ammonia (NH3) volatilization and nitrate (NO3-) leaching. A field study was carried out in the subsequent wet (2021) and dry (2022) seasons to assess the impacts of different N management strategies on yield, N use efficiency and different N losses in a double-cropped rice system. Seven different N-management practices including application of chemical fertilisers, liquid organic fertiliser, nitrification inhibitors, organic nutrient management and integrated nutrient management (INM) were studied. The application of soil test-based neem-coated urea (NCU) during the wet season resulted in the highest economic yield, while integrated nutrient management showed the highest economic yield during the dry season. Total N losses by volatilization of NH3, N2O loss and leaching were 0.06-4.73, 0.32-2.14 and 0.25-1.93 kg ha-1, corresponding to 0.06-5.84%, 0.11-2.20% and 0.09-1.81% of total applied N, respectively. The total N-uptake in grain and straw was highest in INM (87-89% over control) followed by the soil test-based NCU (77-82% over control). In comparison, recovery efficiency of N was maximum from application of NCU + dicyandiamide during both the seasons. The N footprint of paddy rice ranged 0.46-2.01 kg N-eq. t-1 during both seasons under various N management. Ammonia volatilization was the process responsible for the largest N loss, followed by N2O emissions, and NO3- leaching in these subtropical lowland rice fields. After ranking the different N management practices on a scale of 1-7, soil test-based NCU was considered the best N management approach in the wet year 2021, while INM scored the best in the dry year 2022.

Transfer of Stress Resilient QTLs and Panicle Traits into the Rice Variety, Reeta through Classical and Marker-Assisted Breeding Approaches.

Reeta is a popular late-maturing high-yielding rice variety recommended for cultivation in the eastern Indian states. The cultivar is highly sensitive to submergence stress. Phosphorus deficiency is an additional constraint for realizing high yield. The quantitative trait loci (QTLs), Sub1, for submergence and Pup1 for low phosphorus stress tolerance along with narrow-grained trait, GW5 were introgressed into the variety from the donor parent, Swarna-Sub1 through marker-assisted breeding. In addition, phenotypic selections for higher panicle weight, grain number, and spikelet fertility were performed in each segregating generation. Foreground selection detected the 3 target QTLs in 9, 8 and 7 progenies in the BC1F1, BC2F1, and BC3F1 generation, respectively. Recurrent parent's genome recovery was analyzed using 168 SSR polymorphic markers. The foreground analysis in 452 BC3F2 progenies showed five pyramided lines in homozygous condition for the target QTLs. No donor fragment drag was noticed in the Sub1 and GW5 QTLs carrier while a segmentwas observed in the Pup1 carrier chromosome. The developed lines were higher yielding, had submergence, and had low phosphorus stress-tolerance alongwith similar to the recipient parent in the studied morpho-quality traits. A promising pyramided line is released in the name of Reeta-Panidhan (CR Dhan 413) for the flood-prone areas of Odisha state.

Unravelling genetic architecture and development of core set from elite rice lines using yield-related candidate gene markers.

Assessing genetic diversity and development of a core set of elite breeding lines is a prerequisite for selective hybridization programes intended to improve the yield potential in rice. In the present study, the genetic diversity of newly developed elite lines derived from indicax tropical japonica and indicax indica crosses were estimated by 38 reported molecular markers. The markers used in the study consist of 24 gene-based and 14 random markers related to grain yield-related QTLs distributed across the rice genome. Genotypic characterization was carried out to determine the genetic similarities between the elite lines. In total, 75 alleles were found using 38 polymorphic markers, with polymorphism information content ranging from 0.10 to 0.51 with an average of 0.35. The genotypes were divided into three groups based on cluster analysis, structure analysis and also dispersed throughout the quadrangle of PCA, but nitrogen responsive lines clustered in one quadrangle. Seven markers (GS3_RGS1, GS3_RGS2, GS5_Indel1, Ghd 7_05SNP, RM 12289, RM 23065 and RM 25457) exhibited PIC values ≥ 0.50 indicating that they were effective in detecting genetic relationships among elite rice. Additionally, a core set of 11 elite lines was made from 96 lines in order to downsize the diversity of the original population into a small set for parental selection. In general, the genetic information collected in this work will aid in the study of grain yield traits at molecular level for other sets of rice genotypes and for selecting diverse elite lines to develop a strong crossing programme in rice. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01190-8.

Genetic relationship, population structure analysis and pheno-molecular characterization of rice (Oryza sativa L.) cultivars for bacterial leaf blight resistance and submergence tolerance using trait specific STS markers.

Rice is an important source of calorie for the growing world population. Its productivity, however is affected by climatic adversities, pest attacks, diseases of bacterial, viral and fungal origin and many other threats. Developing cultivars that are high yielding and stress resilient seems a better solution to tackle global food security issues. This study investigates the potential resistance of 24 rice cultivars against Xanthomonas oryzae pv. Oryzae (Xoo) infection that causes bacterial leaf blight disease and submergence stress. Bacterial leaf blight (BLB) resistance genes (Xa4, xa5, xa13, Xa21, Xa38) and submergence tolerance (Sub1) gene specific markers were used to determine the allelic status of genotypes. The results displayed presence of Xa4 resistance allele (78.95%), xa5 (15.79%) but xa13 and Sub1 tolerance allele were not found in any genotype. However, a new allele for Xa21 (84.21%) and Xa38 (10.52%) were identified in several genotypes. Phenotypic screening for both stress conditions was done to record the cultivars response. None of the genotypes showed resistance against Xoo, although varieties viz., Tapaswini and Konark showed moderate susceptibility. Likewise, survival percentage of genotypes under submergence stress varied from 0 to 100%. Tolerant checks FR13A (100%) and Swarna Sub1 (97.78%) exhibited high survival rate, whereas among genotypes, Gayatri (57.78%) recorded high survivability even though it lacked Sub1 tolerant its genetic background. A total of six trait specific STS and two SSR markers generated an average of 2.38 allele per locus. Polymorphism information content (PIC) value ranged from 0.08 to 0.42 with an average of 0.20. Structure analysis categorized 24 genotypes into two sub-populations, which was in correspondence with Nei's genetic distance-based NJ tree and principal co-ordinate analysis (PCoA). Swarna Sub1 could be differentiated clearly from BLB resistant check, IRBB60 and other 22 genotypes without having Sub1 gene. Analysis of molecular variance (AMOVA) revealed more genetic variation within population than among population. Principal component analysis (PCA) showed that 9 morphological traits collectively explained 76.126% of total variation among all the genotypes studied. The information from this study would be useful in future breeding programs for pyramiding trait specific genes into high yielding cultivars that fall behind with respect to stress resilience. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-00951-1.

Molecular Breeding for Incorporation of Submergence Tolerance and Durable Bacterial Blight Resistance into the Popular Rice Variety 'Ranidhan'.

Ranidhan is a popular late-maturing rice variety of Odisha state, India. The farmers of the state suffer heavy loss in years with flash floods as the variety is sensitive to submergence. Bacterial blight (BB) disease is a major yield-limiting factor, and the variety is susceptible to the disease. BB resistance genes Xa21, xa13, and xa5, along with the Sub1 QTL, for submergence stress tolerance were transferred into the variety using marker-assisted backcross breeding approach. Foreground selection using direct and closely linked markers detected the progenies carrying all four target genes in the BC1F1, BC2F1, and BC3F1 generations, and the positive progenies carrying these genes with maximum similarity to the recipient parent, Ranidhan, were backcrossed into each segregating generation. Foreground selection in the BC1F1 generation progenies detected all target genes in 11 progenies. The progeny carrying all target genes and similar to the recipient parent in terms of phenotype was backcrossed, and a total of 321 BC2F1 seeds were produced. Ten progenies carried all target genes/QTL in the BC2F1 generation. Screening of the BC3F1 progenies using markers detected 12 plants carrying the target genes. A total of 1270 BC3F2 seeds were obtained from the best BC3F1 progeny. Foreground selection in the BC3F2 progenies detected four plants carrying the target genes in the homozygous condition. The bioassay of the pyramided lines conferred very high levels of resistance to the predominant isolates of bacterial blight pathogen. These BB pyramided lines were submergence-tolerant and similar to Ranidhan in 13 agro-morphologic and grain quality traits; hence, they are likely to be adopted by farmers.

Multi-trait association study identifies loci associated with tolerance of low phosphorus in Oryza sativa and its wild relatives.

We studied variation in adaptive traits and genetic association to understand the low P responses, including the symbiotic association of arbuscular mycorrhizal (AM) fungal colonization in Oryza species (O. sativa, O. nivara, and O. rufipogon). In the present experiment, we performed the phenotypic variability of the morphometric and geometric traits for P deficiency tolerance and conducted the association studies in GLM and MLM methods. A positive association between the geometric trait of the top-view area and root traits suggested the possibility of exploring a non-destructive approach in screening genotypes under low P. The AMOVA revealed a higher proportion of variation among the individuals as they belonged to different species of Oryza and the NM value was 2.0, indicating possible gene flow between populations. A sub-cluster with superior-performing accessions had a higher proportion of landraces (42.85%), and O. rufipogon (33.3%) was differentiated by four Pup1-specific markers. Association mapping identified seven notable markers (RM259, RM297, RM30, RM6966, RM242, RM184, and PAP1) and six potential genotypes (IC459373, Chakhao Aumbi, AC100219, AC100062, Sekri, and Kumbhi Phou), which will be helpful in the marker-assisted breeding to improve rice for P-deprived condition. In addition, total root surface area becomes a single major trait that helps in P uptake under deficit P up to 33% than mycorrhizal colonization. Further, the phenotypic analysis of the morphometric and geometric trait variations and their interactions provides excellent potential for selecting donors for improving P-use efficiency. The identified potential candidate genes and markers offered new insights into our understanding of the molecular and physiological mechanisms driving PUE and improving grain yield under low-P conditions.

Development of Submergence-Tolerant, Bacterial Blight-Resistant, and High-Yielding Near Isogenic Lines of Popular Variety, 'Swarna' Through Marker-Assisted Breeding Approach.

The rice variety 'Swarna' is highly popular in the eastern region of India. The farmers of eastern India cultivate mainly rainfed rice and face the adverse effects of climate change very frequently. Rice production in this region is not stable. Swarna variety is highly susceptible to bacterial blight (BB) disease and flash floods, which cause a heavy reduction in the yield. Transfer of five target genes/QTLs was targeted into the variety, Swarna by adopting marker-assisted backcross breeding approach. Direct markers for Sub1A, OsSPL14, and SCM2 QTLs and closely linked markers for xa5 and Xa21 BB resistance genes were screened in the backcross progenies. Swarna-Sub1, CR Dhan 800, and Swarna-Habataki near-isogenic lines (NILs) were used as donor parents in the breeding program. True multiple F1 plants were identified for backcrossing, and 796 BC1F1 seeds were generated. Foreground selection detected all the five target genes in six progenies in BC1F1 generation. The progeny containing all the target genes and more similar with the recipient parent was backcrossed, and a total of 446 BC2F1 seeds were produced. Foreground screening detected four BC2F1 plants carrying the five target genes. A total of 2,145 BC2F2 seeds were obtained from the best BC2F1 progeny. Screening of the progenies resulted in one plant with all five desirable genes, three plants with four, and another three progenies carrying three genes in homozygous conditions. The pyramided lines showed higher BB resistance and submergence tolerance than the recipient parent, Swarna. Culm strength of the pyramided lines showed higher breaking force than the recipient parent, Swarna. The pyramided line, SSBY-16-68-69 yielded the highest grain yield of 7.52 t/ha followed by the lines SSBY-16-68-511 (7.34 t/ha) and SSBY-16-68-1633 (7.02 t/ha). The best-pyramided line showed a yield advantage of 18% over the recipient parent and 6.8% over the yield component donor parent. Seven pyramided lines showed higher yield than the recipient parent, while five lines were better yielders than the yield component donor parent. The pyramided line SSBY-16-68-69 produced 365 grains/panicle, while the recipient had 152. The main morphologic and grain quality features of the recipient parent were retained in the pyramided lines.