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Sugarcane is an economically important commercial crop which provides raw material for the production of sugar, jaggery, bioethanol, biomass and other by-products. Sugarcane breeding till today heavily relies on conventional breeding approaches which is time consuming, laborious and costly. Integration of marker-assisted selection (MAS) in sugarcane genetic improvement programs for difficult to select traits like sucrose content, resistance to pests and diseases and tolerance to abiotic stresses will accelerate varietal development. In the present study, association mapping approach was used to identify QTLs and genes associated with sucrose and other important yield-contributing traits. A mapping panel of 110 diverse sugarcane genotypes and 148 microsatellite primers were used for structured association mapping study. An optimal subpopulation number (ΔK) of 5 was identified by structure analysis. GWAS analysis using TASSEL identified a total of 110 MTAs which were localized into 27 QTLs by GLM and MLM (Q + K, PC + K) approaches. Among the 24 QTLs sequenced, 12 were able to identify potential candidate genes, viz., starch branching enzyme, starch synthase 4, sugar transporters and G3P-DH related to carbohydrate metabolism and hormone pathway-related genes ethylene insensitive 3-like 1, reversion to ethylene sensitive1-like, and auxin response factor associated to juice quality- and yield-related traits. Six markers, NKS 5_185, SCB 270_144, SCB 370_256, NKS 46_176 and UGSM 648_245, associated with juice quality traits and marker SMC31CUQ_304 associated with NMC were validated and identified as significantly associated to the traits by one-way ANOVA analysis. In conclusion, 24 potential QTLs identified in the present study could be used in sugarcane breeding programs after further validation in larger population. The candidate genes from carbohydrate and hormone response pathway presented in this study could be manipulated with genome editing approaches to further improve sugarcane crop. [ABSTRACT FROM AUTHOR]

Phosphorus (P) is an essential macronutrient required for respiration, photosynthesis/carbohydrate metabolism, redox homeostasis, signaling, and synthesis/function of nucleic acids, cellular membranes, enzymes, etc. To cope with P-deficiency, plants reprogram gene expression for necessary alterations in metabolic/signaling pathways. To attain P homeostasis, plants readjust metabolism through transcriptional, post-transcriptional, and/or post-translational machinery involving biochemical, physiological, genomic, epigenomic, proteomic, and metabolomic functions. However, the underlying molecular mechanisms/pathways/genes for P-deficiency tolerance in crop plants remain elusive. To decipher the mechanisms/pathways adopted by rice under P-starvation/deficiency stress, a pair of contrasting rice [Pusa-44 (high-yielding, P-deficiency sensitive) and its near-isogenic line (NIL)-23, P-deficiency tolerant) for Pup1 QTL] genotype was used for comparative analyses. Omics analyses of shoot and root tissues from 45-day-old plants grown hydroponically in P-sufficient (16 ppm Pi), P-deficient (4 ppm Pi) or P-starved (0 ppm Pi) medium revealed important roles of P transporters, transcription factors (TFs), Transposable elements (TEs), auxin-responsive proteins, cell wall modulation, fatty acid metabolism, and chromatin architecture/epigenetic modifications in making NIL-23 tolerant to stress. The proteins involved in photosynthesis, sucrose-/starch-/energy-metabolism, transcription factors, and phytohormone signaling were observed to be differentially expressed in NIL-23. Since only a few coding genes are located on the QTL, modulations in morpho-physio-biochemical and molecular parameters under P-starvation/deficiency stress were attributed to the regulatory functions of Pup1 through TFs, TEs, epigenetic/chromatin architectural changes, etc. introgressed in Pusa-44 genetic background. Thus, the study provides new insights into molecular/regulatory functions of Pup1 under P-starvation/deficiency stress in rice, which might be useful to improve P-use efficiency in rice for better productivity in P-deficient soils. [ABSTRACT FROM AUTHOR]

Grain yield is a product of biomass (BM) and harvest index (HI). HI, not BM, is the major constraint of chickpea productivity in the long season environments of northern Indian plains. This is the first genome wide association study (GWAS) of shelling percentage (Sh.%), HI and related traits in chickpea using genotyping by sequencing approach. Genotyping of 178 germplasm lines involving varieties, trait specific genotypes and advance breeding lines found 35,795 high-throughput single nucleotide polymorphisms (SNPs). The objectives of the study were to unravelling the genomic regions responsible for variation in flowering time, shelling percentage, HI and related traits in chickpea. The phenotypic analysis across three environments showed high variability and connections among HI and related traits. Population structure analysis revealed two sub-populations (k = 2). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 172 marker-trait associations (MTAs) were identified for HI and related traits using FarmCPU model, of which days to 50% flowering (DAF), HI and shelling percentage showed significant associations. The current study has identified consistent pleiotropic MTAs, SNC_021165.1_57891716 and SNC_021165.1_57917493, SNC_021164.1_6073633 and SNC_021165.1_33405826 for biomass, pod and seed yield/plant, pod and seed number/plant HI and Sh.%, respectively. All the MTAs observed for SYPL, PYPL and maximum number of MTAs for HI and BM were located on the same chromosome number 6. Further maximum number of MTAs for PPL and SN were distributed on chromosome 5. One of the important findings is that most of the MTAs for SYPL, PYPL, BM, and 100SW are distributed within 25 kb genomic region of chromosome 6. A total of 16 MTAs were retained for Insilco analysis (− log10(p) > 4.0) and searched for their candidate genes in a 100-kb flanking region against the reference genome. The maximum number of genes noticed for DAF (50), followed by Sh.% (48), HI (16), SYPL (13), BM (10), and PYPL (8). The transcripts for DAF, Arabinogalactan proteins and pentatricopeptide repeat were involved in flowering of Arabidopsis. For both PYPL and SYPL, MTA found linked to the genes coding for pentatricopeptide repeat, serine/threonine-protein kinase and E3 ubiquitin-protein ligase. These transcripts played role mainly in pollen maturation, fertilization and flowering time. Chaperone protein DnaJ linked to HI, and receptor-like protein kinase (RLK) for Sh.% were involved in improving yield in Arabidopsis and rice, respectively. The present study also validated one of the MTA linked to DAF which showed r2 value of 12.62%. [ABSTRACT FROM AUTHOR]

Cooking quality in rice grains is a complex trait which requires improvement. Earlier reports show varying genetic influence on these traits, except for a common agreement on waxy ( Wx) and alkali degeneration ( Alk) loci on chromosome 6. The present study involved 86 doubled haploid lines derived from an indica × japonica cross involving IR64 and Azucena. Grain parameters viz., raw grain length (RGL), raw grain breadth (RGB), cooked grain length (CGL), cooked grain breadth (CGB), gelatinization temperature (GT), grain shape (RGS), length elongation ratio (LER) and breadth expansion ratio (BER) were subjected to mixed model mapping of quantitative trait loci (QTL). Segregation data of 175 markers covering a distance of 2395.5 cM spanning the entire genome were used. Fifteen main effect QTLs were detected spread over the genome, except on chromosomes 4, 8 and 11. Thirty epistatic interactions significantly influencing the traits were detected. Twelve of the main effect QTLs were involved in epistatic interactions. One main effect QTL associated with LER was detected near Alk locus. QTLs located for grain length on chromosomes 9 and 10 are reported for the first time. Detection of many epistatic loci and involvement of main effect QTLs in interactions demand for judicious selection of QTLs in marker-assisted selection programmes. [ABSTRACT FROM AUTHOR]

Rice landraces from the fragile riverine ecosystems surrounding Majuli islands in Assam are pivotal for local livelihoods, as well as for their potential in developing flood tolerant varieties. We characterized 87 landraces from Majuli, Dhemaji, and North Lakhimpur districts in Assam by assessing 36 agro‐morphological traits, submergence tolerance, and microsatellite diversity. Multivariate analyses revealed that grain and leaf characteristics, plant height, and tillering are important traits differentiating the cultivar types. Sixty‐six SSR markers generated 271 alleles with an average of 4.1 alleles per marker with population structuring in two clusters having an allele frequency divergence of 0.124. The Bao or deep‐water landraces displayed the highest phenotypic and genetic diversity, with potential genetic links to the aus and wild species. Sali (winter rice) and bora (sticky rice) landraces were predominantly indica type. Nearly 47% of the germplasm exhibited tolerance to two‐week submergence at seedling stage. Surveying SUB1A and SNORKEL genes revealed the presence of SUB1A‐1 and SNORKEL genes in 64% and 57% of the tolerant accessions, respectively. This study highlights the untapped potential of rice landraces in a fragile ecological region, providing insights into their agronomical traits, submergence tolerance, and genetic diversity. The findings lay the foundation for improved germplasm management and developing flood‐resilient rice varieties, crucial for sustainable agriculture in riverine ecosystems. [ABSTRACT FROM AUTHOR]

Food insecurity is a looming threat for the burgeoning world population. Phosphorus (P), which is absorbed from soil as inorganic phosphate (Pi), is an essential macronutrient for the growth of all agricultural crops. This study reports phenotype analysis for P responses in natural field and greenhouse conditions, using 54 genotypes of foxtail millet (Setaria italica) representing wide geographic origins. The genotype responses were assessed in natural field conditions in two different seasons (monsoon and summer) under Pi-fertilized (P+) and unfertilized (P-) soil for eight above-ground traits. Enormous variations were seen among the genotypes in phenotypic responses for all the measured parameters under low P stress conditions. Variations were significant for plant height, leaf number and length, tillering ability and seed yield traits. Genotypes ISe 1234 and ISe 1541 were P+ responders, and the genotypes ISe 1181, ISe 1655, ISe 783 and ISe 1892 showed tolerance to low P for total seed yield. Genotypes that performed well under P- conditions were almost as productive as genotypes that performed well under P+ conditions suggesting some genotypes are well adapted to nutrient-poor soils. In the greenhouse, most of the genotypes produced changes in root architecture that are characteristic of P- stress, but to differing degrees. Significant variation was seen in root hair density and root hair number and in fresh and dry weight of shoot and root under P- stress. However, there was not much difference in the shoot and root total P and Pi levels of five selected high and low responding genotypes. We noticed contrasting responses in the greenhouse and natural field experiments for most of these genotypes. The leads from the study form the basis for breeding and improvement of foxtail millet for better Pi-use efficiency. [ABSTRACT FROM AUTHOR]

Pusa Basmati 1509 (PB1509) is one of the major foreign-exchange-earning varieties of Basmati rice; it is semi-dwarf and early maturing with exceptional cooking quality and strong aroma. However, it is highly susceptible to various biotic stresses including bacterial blight and blast. Therefore, bacterial blight resistance genes, namely, xa13 + Xa21 and Xa38, and fungal blast resistance genes Pi9 + Pib and Pita were incorporated into the genetic background of recurrent parent (RP) PB1509 using donor parents, namely, Pusa Basmati 1718 (PB1718), Pusa 1927 (P1927), Pusa 1929 (P1929) and Tetep, respectively. Foreground selection was carried out with respective gene-linked markers, stringent phenotypic selection for recurrent parent phenotype, early generation background selection with Simple sequence repeat (SSR) markers, and background analysis at advanced generations with Rice Pan Genome Array comprising 80K SNPs. This has led to the development of Near isogenic lines (NILs), namely, Pusa 3037, Pusa 3054, Pusa 3060 and Pusa 3066 carrying genes xa13 + Xa21, Xa38, Pi9 + Pib and Pita with genomic similarity of 98.25%, 98.92%, 97.38% and 97.69%, respectively, as compared to the RP. Based on GGE-biplot analysis, Pusa 3037-1-44-3-164-20-249-2 carrying xa13 + Xa21, Pusa 3054-2-47-7-166-24-261-3 carrying Xa38, Pusa 3060-3-55-17-157-4-124-1 carrying Pi9 + Pib, and Pusa 3066-4-56-20-159-8-174-1 carrying Pita were identified to be relatively stable and better-performing individuals in the tested environments. Intercrossing between the best BC3F1s has led to the generation of Pusa 3122 (xa13 + Xa21 + Xa38), Pusa 3124 (Xa38 + Pi9 + Pib) and Pusa 3123 (Pi9 + Pib + Pita) with agronomy, grain and cooking quality parameters at par with PB1509. Cultivation of such improved varieties will help farmers reduce the cost of cultivation with decreased pesticide use and improve productivity with ensured safety to consumers. [ABSTRACT FROM AUTHOR]

A germplasm assembly of 128 finger millet genotypes from 18 countries was evaluated for seedling-stage phosphorus (P) responses by growing them in P sufficient (Psuf) and P deficient (Pdef) treatments. Majority of the genotypes showed adaptive responses to low P condition. Based on phenotype behaviour using the best linear unbiased predictors for each trait, genotypes were classified into, P responsive, low P tolerant and P non-responsive types. Based on the overall phenotype performance under Pdef, 10 genotypes were identified as low P tolerants. The low P tolerant genotypes were characterised by increased shoot and root length and increased root hair induction with longer root hairs under Pdef, than under Psuf. Association mapping of P response traits using mixed linear models revealed four quantitative trait loci (QTLs). Two QTLs (qLRDW.1 and qLRDW.2) for low P response affecting root dry weight explained over 10% phenotypic variation. In silico synteny analysis across grass genomes for these QTLs identified putative candidate genes such as Ser-Thr kinase and transcription factors such as WRKY and basic helix-loop-helix (bHLH). The QTLs for response under Psuf were mapped for traits such as shoot dry weight (qHSDW.1) and root length (qHRL.1). Putative associations of these QTLs over the syntenous regions on the grass genomes revealed proximity to cytochrome P450, phosphate transporter and pectin methylesterase inhibitor (PMEI) genes. This is the first report of the extent of phenotypic variability for P response in finger millet genotypes during seedling-stage, along with the QTLs and putative candidate genes associated with P starvation tolerance. [ABSTRACT FROM AUTHOR]

Rice is the principal food crop for majority of the global population and its production is frequently affected by drought. The objective of this study was to have improved understanding on drought resistance as a trait, study its molecular genetics and also to identify the potential drought resistant segregants. The genetic material used in this study comprised of near-isogenic lines of IR64 (BC2F7 generation) with random introgression from drought resistant land race Norungan. There was a significant reduction of 25 per cent and 75 per cent in mean plot yield under moderate and severe stress conditions respectively from that under irrigated control which reflected the varied stress intensities between the treatments. The genetic material exhibited significant phenotypic variation for 16 traits studied under three experimental conditions. Marker - trait association was assessed by single marker analysis. Totally 121 markers were used out of that eighteen markers showed putative association with at least one of the investigated trait. A candidate gene based marker for DREB 1 positioned in chromosome 8 was associated with yield under severe stress whereas SSR markers viz, RM 256 in chromosome 8; RM 245 in chromosome 9 were linked with yield under moderate stress. These markers were also linked with other associated traits viz, harvest index, leaf senescence and leaf rolling. These might be useful for marker assisted selection for rainfed rice improvement. [ABSTRACT FROM AUTHOR]

Drought resistance is becoming an indispensable character for rice improvement due to the dwindling global water resources. Genetic improvement for drought resistance is achieved through physiological dissection and genetic analysis of independent component traits associated with crop productivity under stress. A subset mapping population of 93 near flowering recombinant inbred lines with uniform phenology was constituted for genetic analysis of reproductive stage drought resistance. The population was phenotyped for 22 physio-morphological traits under two contrasting water regimes imposed at reproductive stage. Broad sense heritabilities of morphological traits were lower under stress than irrigated. Predominant association of plant height, panicle exsertion and harvest index with grain yield were observed under stress. The sustenance of panicle exsertion through maintaining growth during moisture stress was found as a significant trait associated with the grain yield through minimizing spikelet sterility. Selective genotyping was carried out with 23 polymorphic microsatellite markers of the established target genomic regions for drought resistance. The study validated the association of a QTL region on the long arm of chromosome 1 with plant height, panicle length, panicle exsertion, biological yield and stomatal conductance under stress. This region, flanked by markers RM246 and RM315, was known to possess the semi-dwarf gene, sd-1. Role of another major interval lying between RM256 and RM149 on chromosome 8 in defining the drought resistance could be established through identification of QTLs associated with leaf rolling, panicle exsertion, plant height, panicle length, senescence and biological yield under moisture stress condition. Few other QTLs were also identified. [ABSTRACT FROM AUTHOR]

Background: Phosphorus (P), being one of the essential components of nucleic acids, cell membranes and enzymes, indispensable for diverse cellular processes like photosynthesis/carbohydrate metabolism, energy production, redox homeostasis and signaling. Crop yield is severely affected due to Phosphate (Pi) deficiency; and to cope with Pi-deficiency, plants have evolved several strategies. Some rice genotypes are compatible with low Pi availability, whereas others are sensitive to Pi deficiency. However, the underlying molecular mechanism for low Pi tolerance remains largely unexplored. Result: Several studies were carried out to understand Pi-deficiency responses in rice at seedling stage, but few of them targeted molecular aspects/responses of Pi-starvation at the advanced stage of growth. To delineate the molecular mechanisms for low Pi tolerance, a pair of contrasting rice (Oryza sativa L.) genotypes [viz. Pusa-44 (Pi-deficiency sensitive) and its near isogenic line (NIL-23, Pi-deficiency tolerant) harboring Phosphorus uptake 1 (Pup1) QTL from an aus landrace Kasalath] were used. Comparative morphological, physiological, and biochemical analyses confirmed some of the well-known findings. Transcriptome analysis of shoot and root tissues from 45-day-old rice plants grown hydroponically under P-sufficient (16 ppm Pi) or P-starved (0 ppm Pi) medium revealed that Pi-starvation stress causes global transcriptional reprogramming affecting several transcription factors, signaling pathways and other regulatory genes. We could identify several significantly up-regulated genes in roots of NIL-23 under Pi-starvation which might be responsible for the Pi starvation tolerance. Pathway enrichment analysis indicated significant role of certain phosphatases, transporters, transcription factors, carbohydrate metabolism, hormone-signaling, and epigenetic processes in improving P-starvation stress tolerance in NIL-23. Conclusion: We report the important candidate mechanisms for Pi acquisition/solubilization, recycling, remobilization/transport, sensing/signalling, genetic/epigenetic regulation, and cell wall structural changes to be responsible for P-starvation tolerance in NIL-23. The study provides some of the novel information useful for improving phosphorus-use efficiency in rice cultivars. [ABSTRACT FROM AUTHOR]

Background: Direct-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties. Results: We used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) "Robin" into the genetic background of an elite popular Basmati rice variety, Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BC4F4 near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin. Conclusion: Overall, the present study reports successful development of HT NILs in the genetic background of popular Basmati rice variety, PB 1121 by introgression of mutated AHAS allele. This is the first report on the development of HT Basmati rice. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation. [ABSTRACT FROM AUTHOR]

In the present study, we introgressed two genes each governing resistance to major diseases of rice namely, bacterial blight (BB) (xa13 and Xa21) and blast (Pi2 and Pi54) into a popular Basmati cultivar, Pusa Basmati 1509 (PB 1509) through marker assisted backcross breeding (MABB). Through foreground selection, seven plants homozygous for all the four genes were selected from a large population of 1832 BC2F2 plants and subjected to background selection coupled with phenotypic selection for agronomic and grain quality traits of the recurrent parent. BC2F2 selections were further advanced to BC2F4 generation to develop near-isogenic lines (NILs). Six NILs from the BC2F4 families with an RPG recovery ranging from 82.5% to 90.5% were evaluated in multi-location trials for agronomic performance, grain quality traits and disease resistance. The level of resistance to BB and blast diseases in all the selected NILs was similar to that of the donor parent. Three BB races, race 2, 4 and 6, respectively produced on average 1.8, 2.3 and 2.5 cm of lesion length in the NILs as against 15.6, 18.1 and 20.8 cm in PB1509. Further, the NILs recorded a disease score of 1.0 and 1.7 for two blast isolates Mo-nwi-38 and Mo-nwi-kas, respectively, as against the score of 4.0 in PB 1509 for both the isolates. The NILs were similar to PB 1509 for major agronomic and grain quality traits with the advantage of resistance to BB and blast diseases. [ABSTRACT FROM AUTHOR]

Finger millet is one of the small millets with high nutritive value. This crop is vulnerable to blast disease caused by Pyricularia grisea, which occurs annually during rainy and winter seasons. Leaf blast occurs at early crop stage and is highly damaging. Mapping of resistance genes and other quantitative trait loci (QTLs) for agronomic performance can be of great use for improving finger millet genotypes. Evaluation of one hundred and twenty-eight finger millet genotypes in natural field conditions revealed that leaf blast caused severe setback on agronomic performance for susceptible genotypes, most significant traits being plant height and root length. Plant height was reduced under disease severity while root length was increased. Among the genotypes, IE4795 showed superior response in terms of both disease resistance and better agronomic performance. A total of seven unambiguous QTLs were found to be associated with various agronomic traits including leaf blast resistance by association mapping analysis. The markers, UGEP101 and UGEP95, were strongly associated with blast resistance. UGEP98 was associated with tiller number and UGEP9 was associated with root length and seed yield. Cross species validation of markers revealed that 12 candidate genes were associated with 8 QTLs in the genomes of grass species such as rice, foxtail millet, maize, Brachypodium stacei, B. distachyon, Panicum hallii and switchgrass. Several candidate genes were found proximal to orthologous sequences of the identified QTLs such as 1,4-β-glucanase for leaf blast resistance, cytokinin dehydrogenase (CKX) for tiller production, calmodulin (CaM) binding protein for seed yield and pectin methylesterase inhibitor (PMEI) for root growth and development. Most of these QTLs and their putatively associated candidate genes are reported for first time in finger millet. On validation, these novel QTLs may be utilized in future for marker assisted breeding for the development of fungal resistant and high yielding varieties of finger millet. [ABSTRACT FROM AUTHOR]

Marker-assisted simultaneous but stepwise backcross breeding ( MASS- BB) was utilized in the present study for pyramiding blast resistance genes, Piz5 and Pi54, from non-Basmati donors, C101A51 and Tetep, respectively, into PRR78, an elite Basmati restorer line of rice hybrid, Pusa RH10. Marker-assisted foreground selection coupled with stringent phenotypic selection and background analysis was carried out for hastening the recovery of recurrent parent phenome ( RPP) and genome ( RPG) in two separate backcross series to produce BC2F1 plants with individual blast resistance gene. The best BC2F1 plant from each backcross series was intercrossed, and the resultant F1 was selfed to pyramid both blast-resistance genes into PRR78. The plants homozygous for both the genes in the F2 were advanced through pedigree selection to produce superior blast-resistant F5 lines. Background analysis revealed that the RPG recovery was up to 91.6%. Improved versions of Pusa RH10 developed using the improved PRR78 lines ( PRR78+ Piz5+ Pi54) performed on par with the original Pusa RH10 and showed resistance to blast disease both under artificial screening and at hot spot locations. [ABSTRACT FROM AUTHOR]

The wild species of Sesamum have long been recognized as an important source of many valuable pest and disease resistance genes and other novel traits such as male sterility and plant type for the cultivated taxon. Utilization of these species in crop improvement is marginal because of their inherent low crossability with the cultigen. An understanding of the biological nature of incompatibility systems that impede hybridization offers tools for successful introgressions into cultivated sesame. The objective of this investigation was to observe pollen germination and pollen tube growth in cross pollinated S. indicum pistils as an indicator of pre-zygotic barriers operating in wide crosses involving S. indicum. Three wild species: S. alatum, S. radiatum and S. laciniatum were used as pollen donors in hybridization with S. indicum. In the cross S. indicum × S. alatum 85.23% of pollen grains germinated and pollen tubes reached ovaries within 8 h after pollination. In other two crosses, S. indicum × S. laciniatum and S. indicum × S. radiatum the level of incompatibility was high as evidenced by a reduced pollen germination and slow rate of pollen tube growth. Measures to circumvent incompatibility in these crosses to produce interspecific hybrids are discussed. [ABSTRACT FROM AUTHOR]

Marker assisted backcross breeding was used to transfer Saltol, a major QTL for seedling stage salinity tolerance from the donor FL478 to Pusa Basmati 1509 (PB 1509), a high yielding and early maturing Basmati rice variety. Foreground selection was carried out using three markers namely, AP3206f, RM3412b and RM10793, linked to Saltol. In addition, 105 genome-wide SSR markers polymorphic between FL478 and PB 1509 were used in background selection. Among the BC3F4 near isogenic lines (NILs) developed, recurrent parent genome recovery ranged from 96.67 to 98.57%. Multi-season evaluation identified some of the NILs showing significantly higher yield with grain and cooking quality comparable to PB 1509. All the NILs exhibited tolerance to salinity with significantly higher relative water content, membrane stability index and proline content as compared to PB 1509. The root and shoot concentration of Na+, K+ and Na+/K+ in NILs was at par with FL478 under stress conditions. The gene OsHKT1;5 located in the Saltol region showed higher expression levels under stress indicating its role in conferring salinity tolerance. Salt tolerant NILs of PB 1509 will be useful in stabilizing production in salt affected areas. [ABSTRACT FROM AUTHOR]

One hundred diverse iso-cytoplasmic restorer (ICR) lines carrying WA cytoplasm indicated significant but moderate variability for agro-morphological traits as well as for the microsatellite-based allele patterns. There were two major groups of ICRs based on agro-morphological clustering. Simple sequence repeat (SSR) markers identified allelic variants with an average of 2.48 alleles per locus and the gene diversity (GD) ranged from 0.02 to 0.62 at different loci. ICR lines showed a genetic structure involving two sub-populations, POP1 and POP2. Both the subpopulations had the presence of admixture lines. Nearest ancestry-based grouping of ICRs by neighbour-joining (NJ) method showed near similar grouping as that of sub-population division. The POP2 was the largest group but with fewer admixed lines. POP1 was more distinct than POP2. Since the hybrid parents of the ICRs had limited diversity on maternal lineage, paternal lineage was concluded as the major contributor to the observed divergence and population differentiation. ICRs developed from certain hybrids were more genetically distinct than other hybrids. Even with the moderate variability, ICRs could be considered as a potential source of fertility restoration in hybrid development because of their distinct population structure and the full complement of restorer genes they contained. ICR lines with high per se performance can be utilized in hybrid rice development by estimating their combining ability. [ABSTRACT FROM AUTHOR]