Browsing by Author "Rai, Mayank"
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ThesisItem Open Access Bulk segregant analysis for blast resistance in F2 population derived from two contrasting rice genotypes of north eastern hill region(College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University, Imphal, 2018) Sumpi, Hage; Rai, MayankRice blast caused by fungus Magnaporthe grisea is one of the most devastating diseases worldwide. Use of resistant cultivar is the most effective way to control this disease. The identification of markers linked to blast resistance is very important as they can be used in marker assisted selection to develop new resistant cultivars. Bulk Segregant Analysis (BSA) is a method that works with selected individuals which hastens the process by reducing the number of required assays, providing rapid and simple alternative for identification of markers linked to a trait and gene mapping. The present study used this technique to select extreme phenotypes in a bi-parental population (F2) derived from two contrasting rice genotype LR5, also known as Lal Jangali (a local landrace of rice resistant to blast) and LR26 (Manipuri black rice traditionally known as Chakhao, susceptible to blast). Disease assessment for blast on progenies and parental genotype was carried out under natural disease occurrence. F2 progenies showing extreme phenotype were selected and subjected to genotyping with the polymorphic markers (including SSRs and SNPs and some previously reported blast markers) obtained from polymorphism survey on the parental genotype in order to identify markers linked to blast resistance. Association of the markers with phenotypic trait in the selected progenies was identified by statistical analysis. Chi square test for goodness of fit revealed that RM1337 (p-value=0.003, 0.002), RM7102 (p-value=0.002, 0.001), snpOS0310 (p-value=0.02, 0.007), snpOS0316 (p-value=0.001, 0) and snpOS0318 (p-value=0.002, 0.001) showed association with tolerance and susceptibility against leaf blast, whereas RM247 (p-value=0.025, 0.016) and snpOS0316 (p-value=0.0.05, 0.004) showed association with these two groups for neck blast. Except for snpOS0310 which is on chromosome 6, all other markers are present on chromosome 12. RM1337 and RM7102 co-localize with already reported Pi20t gene, suggesting its role in resistance to local pathotypes. Regression for blast resistance was also evaluated to estimate the relationship between the marker genotype and blast severity. Population structure analysis was also performed on the selected group of progenies to determine the ancestry, which revealed that the progenies showing resistance to both leaf and neck blast carried maximum percentage of ancestry from the resistant parent LR5 and those susceptible to blast carried more of LR26 ancestry. Larger population and more polymorphic markers can be used to further fine map the segment of chromosome 12 identified in this study.ThesisItem Open Access Characterization and evaluation of advanced breeding lines of lowland rice with respect to agro-morphological traits(College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University, Imphal, 2018) Rai, Ashish; Rai, MayankRice (Oryza sativa L.) is the primary food source for more than a third of the world’s population. There is an urgent need of developing HYVs to increase rice productivity in India as well as North Eastern Hill Region. The present investigation was carried out to evaluate twenty four breeding line of rice with respect to performance, variability, heritability, character association and genetic divergence of sixteen qualitative characters and sixteen quantitative characters. The experiment was laid out at CPGS Campus, Umiam, Meghalaya in a randomized block design with three replications during kharif season, 2017. Visual observations were recorded on five plant basis as per standard descriptors on sixteen qualitative characters viz., basal leaf sheath color, leaf auricle, leaf ligule, ligule shape, leaf collar, flag leaf: attitude of blade, leaf sheath anthocyanin colouration, leaf blade: anthocyanin, panicle secondary branch, leaf senescence, spikelet: color of tip of lemma, panicle: exsertion, panicle: awns and lemma: anthocyanin coloration of area below apex. Data were recorded on days to 50% flowering, plant height, tillers per plant, panicle per plant, panicle length, leaf length, leaf width, leaf area index, canopy temperature, biological yield, spikelet per plant, no. of grains per plant, spikelet fertility (SF), harvest index, 1000 grain weight and grain yield per plant. Analysis of variance indicated the existence of significant differences among genotypes for all the characters studied except leaf width and harvest index. The characters viz., days to 50% flowering, leaf length, leaf width exhibited high heritability and panicle per plant, canopy temperature, spikelet per plant, no. of grains per plant, spikelet fertility, harvest index, and yield per hectare exhibited medium heritability. Character association studies revealed significant and positive association of grain yield per plant with tillers per plant, panicle per plant, no. of grains per plant, spikelet fertility. Therefore, these characters could be used as criteria for selection of genotypes with high seed yield. Path coefficient analysis revealed highest direct effect on grain yield for number of grains per panicles and 1000 grains weight.1000 grains weight exhibited strong positive direct effect on seed yield, however, it contributed negatively seed yield through number of grains per panicle. Based on 16 quantitative character and 16 qualitative character Euclidean distance was calculated between each set of progeny and the two checks. The maximum distance was observed between CAUS122 and CAUS110 and minimum distance was observed between CAUS120 AND CAUS106. Clustering analysis led to the grouping of lines into 2 major groups. Both the checks were grouped in second cluster which was further dividing in 3 sub-clusters. Based on per se performance with respect to yield components, blast resistance and divergence, CAUS105, CAUS104, CAUS107, CAUS121 were identified as the best progenies that could be nominated for multilocation trials, or used as parents for further population improvement.ThesisItem Open Access Development and characterization of transgenic elite indica rice lines accumulating B-carotene in the endosperm(G.B.Pant University of Agriculture and Technology, Pantnagar (Uttarakhand), 2004) Rai, Mayank; Chawla, H.S.ThesisItem Embargo Divergence analysis of advanced breeding lines of rice in terms of SSR markers, yield and grain quality characteristics(College of Post Graduate Studies in Agricultural Sciences, CAU-Imphal, Umiam, 2022-03) Lokeshkumar K; Rai, MayankThe present study was carried out to estimate the genetic variability and diversity among advanced breeding lines of rice along with two checks (CAUR1 and Shasharang) for yield and yield attributing traits, grain quality traits and SSR markers. Agronomic data obtained from 52 advanced breeding lines and two checks were analysed using ANOVA for various yield and yield attributing traits revealed significant variance among the lines. PCA analysis for yield and yield attributing traits showed that the first five principal components contributed for about 94.06 % of the total variation. Grain quality for 78 advanced breeding lines along with two checks varied significantly for all the traits studied. Seed length (6.040 to 12.172 mm), seed breadth (1.796 to 4.243 mm), seed length breadth ratio (1.81 to 5.38), kernel length (5.005 to 10.084 mm), kernel breadth (1.632 to 3.403 mm), kernel length breadth ratio (1.70 to5.19), grain length after cooking (6.116 to 11.241 mm), linear elongation ratio (1.00 to 1.99), amylose content (14.59 to 29.03 %), protein content (5.09 to 11.02 %) differed significantly. 40 lines showed no grain chalkiness, while 17 lines with less chalkiness and 23 lines with high chalkiness were identified. Alkali spreading value is negatively correlated with Gelatinization Temperature (GT). Based on gelatinization temperature, the advanced breeding lines were classified into three groups: 55 with high GT, 10 were intermediate, and 15 lines had low GT. PCA analysis for grain quality traits showed that the first seven principal components contributed for about 87.40 % of the total variation. 36 selected advanced breeding lines along with two checks were characterized using 27 SSR markers. Out of 27 SSR markers, 14 markers were found to be polymorphic and 13 markers were monomorphic. RM154 exhibited maximum number of amplicons with 5 alleles, followed by RM152, RM271, RM125 with 4 alleles each, followed by RM237, RM413, RM431, RM447 with 3 alleles each, followed by RM44, RM124, RM161, RM215, RM495, RM514 with 2 alleles each. The 38 rice cultivars were grouped into 12 major clusters, where cluster 1 and 2 comprised of highest number of lines with some minor groups. Cluster 3 with 4 lines, cluster 4, 5, 6 and 7 with 2 lines each, remaining five lines clustered independently. STRUCTURE analysis (K=5) revealed that majority of the lines were characterised as admixtures. This indicates that the group of advanced breeding lines carry new combination of alleles and are genetically diverse. With the availability of more genetic diversity within improved lines for morphological, yield components and quality traits, increased genetic gain can be achieved through hybridization based rice improvement programme.ThesisItem Embargo Early generation MAS for selecting transgressive segregants carrying Pi9, PSTOL1 and yield related genes in elite X elite crosses of rice(2022-09) Magudeeswari P.; Rai, MayankIn order to enhance rice productivity under acidic soils of North Eastern Hill Region of India, breeding and selection for blast resistance and low P tolerance is most important along with yield component traits. Phenotypic selection in early segregating generations is not considered to be effective due to low to moderate heritability for most of the agronomic traits. However, use of allele specific DNA markers may enhance selection efficiency and heritability, thereby leading to higher genetic gain in a breeding programme. To test this hypothesis, 21 biparental populations developed from 13 parents were subjected to a combination of phenotypic selection along with MAS for PSTOL1 (phosphorus starvation tolerance), Pi9 (a major blast resistance genes), SPIKE (increased spikelet number) and Gn1a (increased grain number). Parental polymorphism survey for allele specific markers while SCM2 was fixed in all parents, DEP1 and OsSPL14 were completely absent. The segregating populations were subjected to early generation (F2) marker-assisted selection for Pi9 (ULRC66, ULRC67) and PSTOL1 (ULRC69) during the offseason and the remaining crosses were subjected to MAS for the abovementioned genes on phenotypically selected lines (kharif 2020). The MAS for PSTOL1 gene on phenotypically selected lines of eight segregating populations (ULRC52, ULRC56, ULRC57, ULRC69, ULRC70, ULRC72, ULRC73, ULRC77) was carried out and the results showed the presence of PSTOL1 significantly increased the tiller number at 60 days in all crosses and grain yield in ULRC56. Further, the segregating lines were evaluated for low phosphorous (P) tolerance under soil micro plot with normal (P+) and stress (P-) conditions. Analysis of variance (ANOVA) revealed the lines were significantly different for all traits and the interaction was found significant for tiller number at 45 days (TN45), spikelets per plant (SPP), filled grains per plant (FGPP), and plant height (PH). Shoot Phosphorus Use Efficiency (PUE) and P Efficiency Ratio (PER) were significantly correlated with biomass and grain yield under stress (minus P) conditions, suggesting that selection for PUE and PER may increase grain yield under low soil P conditions. Simultaneously, to find tolerant genotypes under stress conditions, eight stress tolerance indices (STI, GMP, TOL, SSI, YR, YI, PYR, YSI) were calculated and the data were subjected to PCA and unrooted cluster analysis. The results of PCA showed STI and GMP had positively contributed to PC1, and it revealed STI and GMP can be better indices to discriminate the tolerant and susceptible genotypes. Biplot and unrooted cluster tree clearly showed two groups, in which ULRC52-5, ULRC62-1, ULRC62-5 and ULRC62-SSD-5 were found more stable under both low P and normal conditions. MAS for Pi9 was carried out on four F2 populations (ULRC64, ULRC65, ULRC66, ULRC67) and evaluated for leaf blast disease under natural field conditions (kharif 2020 and kharif 2021) and artificial inoculated conditions. The results clearly showed that Pi9 (+ve) plants had recorded a low blast score compared to Pi9 (-ve) plants. From the Pi9 segregating populations, eleven lines carrying Pi9 at a homozygous state with high grain yield per plant were phenotypically selected and they can be used as a donor for Pi9 in future breeding programme. MAS for yield genes i.e., SPIKE and Gn1a was carried out on phenotypically selected lines of five and six segregating populations, respectively. The results showed the genes were significantly associated with high SPP, FGPP and GYPP in some, but not across all populations, suggesting interaction of these genes with genotypic “background” in determining the phenotype. ANOVA of segregating populations revealed the lines were significantly different for all the eleven traits in Kharif 2020 and the lines showed a significant difference for all traits except NP, SF, GYPP and BY in Kharif 2021. Response to selection was highest for ULRC52 (81.9%) followed by ULRC77 (54.2%), ULRC76 (25.2%) and ULRC68 (21%). The genetic gain for grain yield per plant was observed to be highest for ULRC76 (96%), followed by ULRC70 (25%), ULRC52 (13.61%) and ULRC62 (12.35%). Based on the evaluation of F4/F5 progenies the breeding value of parents was calculated and the results showed Maudamani reported a high breeding value for grain yield per plant (17.68) followed by CAUS103 (16.92), HPR2921(15.37) and CAUS107 (14.22). The parents with high breeding value can be used in a breeding programme to increase the genetic gain. The effectiveness of MAS and phenotypic selection were compared among the populations and it was found that mean of phenotypically selected lines was higher than the MAS selected lines. Genotypic selection alone for one or a few loci in early segregating generations may not lead to increased genetic gain compared to a combination of phenotypic and genotypic selection. Based on the presence of desirable alleles and superior performance under acidic soil ULRC52-SSD-2- 3-1, ULRC52-SSD-1-4 1, ULRC57-SSD-2-3-1, ULRC62-SSD-4-4-1 and ULRC62-SSD-5-6-1 lines were selected for further multilocational evaluation.ThesisItem Open Access Evaluation of Linseed (Linum usitatissimum) genotypes and their F1 hybrids under acidic upland conditions of Meghalaya(College of Post Graduate Studies in Agricultural Sciences, CAU-Imphal, Umiam, 2020-08) Bezil M.; Rai, MayankLinseed is the rabi crop cultivated for oilseed rich in omega -3 fatty acid and lustrous fibre. There is a potential for linseed cultivation in North Eastern Hill Region (NEHR) of India due to favourable climatic conditions. However, predominantly acidic soils in the region lead to phosphorus (P) deficiency and aluminium (Al) toxicity in upland conditions, which cause low crop productivity. Therefore, the study evaluated linseed genotypes under acidic upland field conditions for yield contributing traits. Evaluation of 35 genotypes across two seasons revealed significant variations among genotypes for all the traits except root length. Seasonal interactions were significant for all the traits. Phenotypic coefficient of variation was high for plant weight and yield per plant. Heritability was found to be high for test weight, followed by plant height. Yield was positively correlated with secondary branches, inflorescence length, number of capsules per plant, plant weight, days to 50% flowering and maturity. Path analysis showed that plant biomass and harvest index contribute the highest direct effect on yield. Based on GEI biplot, LMS-2015-14 was the most stable genotype. Clustering analysis elucidated that NL356 was the most divergent genotype forming the separate cluster. Comparative evaluation of these lines in soil microplot under P deficient and P deficient conditions identified LMS-2015-11 and BAU-15-03 as best lines with respect to P deficiency tolerance and yield. From the first season field experiment, five contrasting genotypes were identified to study their response to P deficiency and Al toxicity under hydroponics and sand culture. LMS-2015-11 was the tolerant genotype under both the stress condition. T397 was the susceptible genotype under Al3+ toxicity and SLS115 was the susceptible genotype under low P condition. In silico analysis was performed to find putative linseed orthologs, which showed 40% identity with maize and 45% identity with B. oleraceae. Selected five parents were crossed in diallele fashion to generate F1 hybrids, which were evaluated in second season along with 35 genotypes. Diallele cross analysis showed that variance due to GCA was significant for all traits except number of secondary branches, root length, number capsules per plant, plant weight, yield per plant and variance due to specific combining ability was significant for all the traits except number of primary branches and secondary branches. Low GCA/SCA ratio indicated predominant non- additive gene action for all traits. GCA effects were significant for test weight and days to 50% maturity. RLC 163 X SLS 115 (C1) and its reciprocal cross (C5) had high SCA effects for yield, indicating that RLC 163 (P1) and SLS 115 (P2) were the better combination to increase the yield. The genotypes and crosses identified will lead to better understanding of acidic condition response in linseed and development of breeding material suitable for acidic soils of NEHR.ThesisItem Open Access Genetic analysis of elite rice breeding lines for allelic status of agronomically important genes and combining ability(College of Post Graduate Studies in Agricultural Sciences, CAU-Imphal, Umiam, 2019) Shanmugam A.; Rai, MayankRice productivity in the North Eastern (NE) India is significantly lower than the national average. With its unique eco-geographical features, North Eastern (NE) India not only serves as the hotspot for indigenous rice landraces but is also considered to be the centre of diversity for blast pathogen (Magnaporthe grisea). Apart from this biotic factor, soil acidity and phosphorous deficiency are considered as the major constraints for rice production in NE India. Rapid development in genomics in terms of mapping and cloning of several agronomically important genes, marker validation and available plant molecular database has facilitated rice breeding with an aim to develop haplotype having all the favourable combination of resistance/tolerance genes along with high yielding genes. Hence, the present investigation was conducted to study the allelic status of blast resistance (Pi1, Pi12, Pib, Piz, Piz-5, Pi9, Pb1, Pita, Pi20(t), Pikm, Pi38, Pi54, Pi64, qPbm11), phosphorous (P) deficiency tolerance (PsTOL1) and yield related (Gn1a, OsSPL14, SCM2, DEP1, SPIKE, GS5, TGW6) genes in selected elite breeding lines intended to be used as parents in rice improvement programme. The eight parents were also crossed in Line X Tester (3 X 5) design to estimate their combining ability. Parental genotyping was performed using candidate gene-based/ linked SSR, SNP and InDel markers for the above-mentioned genes. Favourable haplotype for Pi1, Pi12, Piz, Pb1, qPbm11, SCM2 and TGW6 alleles were found fixed in the elite lines. None of the parents carried favourable alleles for OsSPL14 and DEP1. Four parents carried favourable allele for PsTOL1. Fifteen F1 hybrids, eight parents and two standard checks were evaluated for yield contributing traits under lowland field condition in randomized block design. Correlation analysis revealed that biological yield, P Use Efficiency (PUE), panicle number and tiller number were significantly correlated with grain yield. Highest GCV (30.60 %) was recorded for spikelet fertility, followed by grain yield. Moderate to high heritability was found for yield attributes indicating that selection for these traits would be effective. Dominant gene action was preponderant for all the traits studied except plant height and spikelet fertility. CAUS 105 (L2) and VL 40387 (T3) were best general combiners. Among the crosses, CAUS 105 x VL 40387 (L2 x T3) was the most prominent specific cross having significant SCA effect with the highest heterotic value (191.39 %) for grain yield followed by CAUS 103 x UPRI-3908-18-2-1-1 (L1 x T1). CAUS 105 and HPR 2921 had the highest P uptake (PUP) and L2 xT3 performed well for PUE. Finally, promising parents, crosses and the marker loci that would be segregating in the progenies of these crosses were identified to facilitate Marker Assisted Selection (MAS) for development of pure lines carrying genes that may enhance rice productivity in the region.ThesisItem Embargo Genetic analysis of grain characteristics and blast resistance in biparental crosses involving coloured rice of North-Eastern Region (NER)(College of Post Graduate Studies in Agricultural Sciences, CAU-Imphal, Umiam, 2021-12) Lap, Bharati; Rai, MayankThe North-Eastern Region (NER) of India is home to various unique landraces with coloured, nutritionally rich aromatic grains that have high economic value in national and international markets. However, many of such landraces are low yielding and suffer from susceptibility to diseases like blast. The present study was undertaken involving three important landraces of Chakhao Poireiton (purple pericarp), Mang Meikri (light brown pericarp) and Kala Joha to understand the inheritance of pericarp colour and aroma using different biparental populations (F2, F2:F3, RILs) derived from crosses between these landraces and elite high yielding varieties. The presence of the fragrance gene badh2 was found in all the three aromatic cultivars of Chakhao Poireiton, Kala Joha and Pusa Basmati 1121. Selective crosses were made between the eight parental genotypes, and three populations (ULRC34, ULRC43 and ULRC45) were targeted for further detailed analysis. The reported gene for light brown pericarp Rc was observed in two cultivars Shahsarang and Mang Meikri. In contrast, the Kala4 allele for purple colour was present in Chakhao Poirieton, Kala Joha and Mang Meikri irrespective of their pericarp colour. The Kala4 gene was highly associated with the purple pericarp in all three populations. However, in the segregating population ULRC43, white pericarp was observed in the presence of the Kala4 allele suggesting that the presence of Kala4 does not always lead to purple pigmentation in the pericarp, as indicated by the colour white and light brown in Kala Joha and Mang Meikri that carry the Kala4 allele. This indicates the presence of novel loci that may be responsible for purple pericarp independent of Kala4. Segregation distortion was observed in the cross ULRC43, where Rc locus was also segregating along with Kala4 and Kala3 genes. The Rc allele was only present in seven individuals out of 183 F2:F3. Data on blast were recorded for three consecutive years in RILs of ULRC34 having contrasting parents. Nineteen candidate genes and sixty-four random markers, including SNPs, were scored in the RIL population. Markers PB3810, PR5-2, snpOS0024, snpOS0296, snpOS0305, snpOS0317 on chromosomes 11, 5, 1, 4 and 12 respectively were found to be associated with leaf blast resistance, and HvSSR02- 33, HvSSR07-44 on chromosome numbers 2 and 7, respectively, were associated with neck blast resistance at 1% level of significance. In the three populations studied, seed anthocyanin pigmentation was negatively correlated with grain yield. However, certain high yielding progenies with desired grain characteristics were selected that yielded higher than the parent landraces in early segregating generations of different crosses. Per cent superiority of selected lines over their parent landrace ranged from -57.92 to +203.49%. Anthocyanin estimation was also done for selected progenies with coloured pericarp. It ranged from 0.0001 to 3.324 μg/100mg, suggesting nine lines, i.e., ULRC46-326(4), ULRC43-67(2), ULRC43-546(1), ULRC48-379(2), ULRC43-316(1), ULRC34-202(2)-1, ULRC34-242(4)-2, ULRC34-87(3)-5, ULRC34-195(4)-2 having aroma, high anthocyanin content, blast resistance and better yield than the parents.ThesisItem Open Access Genetic analysis of leaf and neck blast resistance in rice.(College of Post Graduate Studies in Agricultural Sciences, CAU-Imphal, Umiam, 2018-11) Debnath, Ashim; Rai, MayankRice blast is one of the most devastating biotic stresses that limits rice productivity in NE region and causes yield loss from 40 to 46 %. The NEH region is considered to be the centre of diversity for both rice and Magnaporthe grisea. Here, host resistance is short-lived in the disease-prone environments because of high level of variability in the pathogen population. Therefore, the present study was carried out to elucidate the genetic basis of leaf and neck blast resistance under Meghalaya conditions in terms of genes and loci associated with resistance to the local patho types, and intra and inter allelic interactions, if any, that play a role in the expression of the resistance pathotype and other related yield contributing traits. The field experiments involved a set of 80 genotypes and six generations of a cross between LR-5 (Lal Jangali) and Sambha mahsuri SUB 1. The study involved association analysis of reported major gene linked markers with leaf and neck blast resistance in natural and F2 populations to identify effective genes under local conditions; and generation mean analysis to understand the genetic components of mean and variance for resistance and other yield related traits. A set of 80 genotypes were screened across two seasons, under two different rice ecosystems (upland and lowland) and a panel of 43 tolerant and susceptible genotypes was identified for marker trait association study. Marker trait association studies revealed seven different loci to be associated with blast resistance. These genes/loci were Pi54, Pi2, Pib, Pi2/9 locus, Pi5, Pb1/qPbm locus and Pi20(t). Genes Pi5 and Pi54 were found to be associated with leaf blast resistance in both, natural population and biparental F2 population. Pib and qPbm showed some degree of association with neck blast resistance in natural population. Generation mean analysis revealed that dominance genetic variance was higher than additive variance for majority of the traits under study. It also suggested that the epistatic interaction model was found adequate to explain the gene action in the blast resistant related traits like Leaf Blast Score, Percent Infected Leaf, Neck Blast Percentage and Spikelet Fertility Percentage. Narrow sense heritability was found to be moderate for Leaf Blast Score and Neck Blast Percentage indicating that marker assisted selection would be an effective way to augment phenotypic selection for blast resistance. The study indicates that leaf and neck blast resistance is primarily governed by dominant alleles of multiple genes that interact with each other to impart resistance. The markers and genes identified in this study can be used for marker assisted selection of breeding material to increase the frequency of favourable alleles at these loci in the elite rice breeding populations so that varieties with durable resistance can be developed.ThesisItem Open Access Genetic Analysis of Yield Contributing Traits in Lowland Rice Genotypes and NILs Under Acidic Soil(College of Post Graduate Studies, CAU, Imphal, 2014-06) Debnath, Ashim; Rai, MayankRice (Oryza sativa) farming is the largest single use of land for producing food. India is the largest rice growing country and 2nd in terms of production. Rice belongs to the genus Oryza of the family Gramineae and forms the staple food of 2.7 billion people. Various abiotic stresses limit rice production in acidic soil environments. Among these various abiotic stresses Iron (Fe) and Aluminium (Al) toxicity affect the rice production under low and upland conditions respectively. The present study was conducted on a set of promising genotypes, their F1s, and a set of NILs (Near isogenic Lines) to determine the combining ability of parents adapted to acidic soil conditions through L X T analysis and also for evaluation of parents and NILs under acidic soil, aluminium and iron toxic hydroponics conditions. A relationship between seedling stage aluminium and iron toxicity tolerance under hydroponics condition and field performance under acidic soil was also made in this study. In the genetic analysis, among the lines, L1 and L5 (Priya and Sahbhagi Dhan), while among the testers T1 and T3 (IR 24 and Kasalath) showed the best general combining ability while the crosses Sahbhagi Dhan X Kasalath (L5 X T3), Shahsarang X Sambamasuri (L4 X T2), Priya X IR 24 (L1 X T1) showed the best specific combining ability. Also, Sahbhagi Dhan X Kasalath (L5XT3) showed maximum heterosis for seven of the ten traits studied when compared to the best commercial cultivar of the region, Shahsarang. Field level screening of NILs in acidic soil was done in augmented design along with three checks Swarna, Shahsarang, Sahbhagi Dhan. Based on nine different traits superior, average and inferior performing lines were selected. By means of hydroponic experiment conducted using Magnavaca’s nutrient solution (for Al toxicity screening) and Yoshida‘s solution (for iron toxicity screening), different superior and inferior lines were identified based on parameters like root growth, root/shoot biomass. It may however be mentioned that there were no significant correlation between superior and inferior lines in field and hydroponics but some lines were identified which perform well in both condition and perform poor in field as well as hydroponics condition. The information generated would help identify suitable parents for breeding programme under acidic soils and the phenotypic data on the NILs may serve as a base for future mapping of loci responsible for yield under acidic soils, aluminium and iron toxic conditions.ThesisItem Open Access Marker assisted pyramiding of drought tolerant QTLs qDTY 1.1 and qDTY 3.1 in rice variety Samba Mahsuri Sub-1(College of Post Graduate Studies in Agricultural Sciences, CAU-Imphal, Umiam, 2020-10) Dake, Deepika; Rai, MayankWater deficit is one of the most important abiotic factors causing huge loss in rice productivity. Therefore, the present study was aimed to develop a multiple stress tolerant genotype by pyramiding drought tolerant yield QTLs qDTY1.1 and qDTY3.1 into high yielding rice variety Samba Mahsuri Sub-1(SMS) through Marker Assisted Pyramiding (MAS). This was achieved by crossing six introgression lines of SMS carrying qDTY1.1 (SAB lines) with DRR-50, a released variety carrying qDTY3.1. The SAB lines are taller than SMS due to tight linkage between qDTY1.1 and wild type SD-1 that could not be broken during backcrossing. Therefore, the study also focused on screening the F2 generation of crosses for recombinants between SD-1 gene and qDTY1.1 on chromosome 1. From the 35 F1 hybrids obtained, three F2 populations from crosses DRR-50 X SAB-4-2-20 and DRR-50 X SAB 7-13-5 were grown in the field in Kharif, 2019 and about 1530 F2 plants were screened. Desired recombinants were not obtained from DRR-50 X SAB 7-13-5 population. 305 dwarf F2 plants were phenotypically selected and screened for the presence of qDTY1.1. Three dwarf F2 plants having qDTY1.1 were obtained. These three lines along with three others carrying qDTY1.1 and qDTY3.1 were forwarded to F3 generation. From the six SABD F3 lines fourteen pyramided lines were selected and forward to F4 generation. The six SABD F3 lines SABD-7, SABD-8, SABD-9, SABD-76, SABD-79 and SABD-80 along with parents were evaluated under moisture stress for various physiological parameters. The soil moisture content decreased drastically during the reproductive stage compared to vegetative stage when irrigation was withheld for 15 days during both the stages. Chlorophyll content and Relative Water Content (RWC) was more; canopy temperature and malonaldehyde (MDA) content were lesser in SABD lines when compared to parents indicating tolerance under water stress. Variance due to genotypes was found to be highly significant for all the yield related traits except for test weight. Variance among irrigated and moisture stress conditions for all the parameters was found to be non-significant except for panicle number, panicle length and test weight. The GXE interaction was found to be significant for tiller number, grains/panicles and harvest index. SABD-9, SABD-76, SABD-79 and SABD-80 were performing better for most of the morphological and physiological parameters, exhibiting greater tolerance for drought when compared to other pyramided lines and parents under moisture stressed conditions. The present study was done to identify recombinants between qDTY1.1 and sd-1; and progeny fixed for qDTY1.1 and qDTY3.1. However, fixed lines for all the 3 loci could not be confirmed. Further progeny screening/hybridization is required in order to fix all the 3 loci i.e., qDTY1.1, sd-1 and qDTY3.1 in the same genotype.ThesisItem Open Access Marker assisted selection of transgressive segregants in rice carrying favourable alleles for P-deficiency and submergence tolerance under acidic low land soils(College of Post Graduate Studies in Agricultural Sciences, CAU-Imphal, Umiam, 2017-04) Kumar, Shiva; Rai, MayankRice (Oryza sativa L., 2n= 2x= 24) is affected by several biotic and abiotic stresses (constraints) in North-Eastern region of India. More than 95% area in the North Eastern Hill Region is affected by soil acidity and frequently prone to flash floods. P deficiency and submergence are therefore, two of the most prevalent stresses in the region. As markers and donors for tolerance to these stresses have been identified, they were used in the present study to generate and select transgressive segregants carrying desired alleles for traits of interest. Four biparental crosses (Shasarang x Kasaltah, Shasarang x Samba mashuri-sub1, Lal jangli x Sahbhagi Dhan, Lal jangli x Priya) were established. Generated F2 populations were evaluated under lowland acidic soils during 2014 and total of 52 transgressive segregants from four F2 populations were selected, harvested individually and carried forwarded to F3 generation, along with Single Seed Descent (SSD) from each F2 population. The 52 F3 families along with SSD progenies were evaluated in Kharif, 2015 for different agronomic traits to obtain response to selection and heritability estimates. Simultaneously, in each generation, phenotypically selected lines were subjected to marker assisted selection for Sub1 and Pup1 loci in respective progenies. The F3 progeny showed significant positive regression on their selected F2 parents for grain yield, plant height, Panicles length and harvest index indicating the effectiveness of selection for these traits in early segregating generation. But, with respect to days to 50% flowering, Tiller no. at 30 days, tiller no. at 60 days, panicle number, spikelet fertility, biological yield and test weight, non-significant regression in F3 generation was observed. This Indicated the direct selection for these characters during early generation (F2) may not be effective. Significant response to selection for grain yield was observed for all the crosses, ranging from 22 to 35 per cent over F2 mean. Four selected F3 families of the cross Shasarang x Samba mashuri-sub1 viz. ULRC 29-1 and ULRC 29-15, ULRC29-115 and ULRC-170 were found to be homozygous for submergence tolerance. In case of the cross Shasarang x Kasaltah, F3 families ULRC24-30 and ULRC 24-48 were identified as carrying both, K46-1 and K46-2, while ULRC24-4 family was positive for K46-2 and PR1-2 for tolerant Pup1 alleles. Seedlings of selected F4 families were subjected to submergence and hydroponic screening (under P deficient condition) for trait validation. Under hydroponics ULRC 24-99-1 was found to be performing consistently for shoot length, root length, fresh shoot weight and fresh root weight under both control and treatment conditions. Lines ULRC 24-99-1, ULRC 33-57-1 showed higher amount of P uptake in association with phosphorous use efficiency (PUE) under P deficient conditions. On the other hand, majority of the lines selected from cross Shasarang x Samba mashuri-sub1 showed equal level of tolerance to the donor for submergence tolerance. The study highlights the feasibility, importance and effectiveness of MAS in early segregating generations, which led to identification of transgressive progenies with desired genotypic and phenotypic constitution. These lines, once stable may be tested at multiple locations can be released directly as variety to enhance the productivity in the NEH region and can also serve as potential donors in future breeding programs aimed at developing improved cultivars with desirable agronomic traits in acidic lowland rice ecosystems.ThesisItem Open Access Molecular characterization of advanced breeding lines of lowland rice and their evaluation for grain quality traits(College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University, Imphal, 2018) I. Gopinath; Rai, MayankEvery third person on earth consumes rice every day in one form or another, hence it is called as the staple food. India shares the largest area under rice cultivation but stands as the second largest producer of rice, next to china. The demand for rice will increase with population growth, whereby the decline in milled rice production is challenging. This necessitates the need for diverse and highly productive breeding lines combined with good quality traits for future breeding programs or for multiplication and better returns for farmers. Hence the present investigation was undertaken to characterize twenty two advanced breeding lines of lowland rice derived from nine pedigrees to ascertain genetic relationship and diversity among the genotypes using a set of thirty SSR markers and twenty four random SNPs with ten gene specific SNPs followed by evaluation for fifteen grain quality traits. Population structure analysis using STRUCTURE software revealed the ancestry shared among the breeding lines. Sixteen breeding lines were catergorized as admixtures as they showed less than 85% of the estimated ancestry. These admixtures or breeding lines having differences in ancestry share could be preferred for further breeding programs or multiplication. Divergence analysis showed that maximum Euclidean distance was observed between CAUS116 and CAUS117 followed by CAUS116 and CAUS120, whereas, the minimum Euclidean distance was observed between CAUS110 and CAUS111. Ward’s hierarchical clustering approach grouped genotypes into two major clusters that were further subdivided into sub groups. Maximum variation among the genotypes was observed for amylose content, seed breadth and gelatinization temperature which classified the breeding lines into three classes while the traits such as grain length:breadth ratio, linear elongation and protein content categorized the breeding lines into two classes, respective to the values recorded under each trait. Highly significant variation was observed for all the traits evaluated. Amylose content ranged from 18% to 27% among the breeding lines while the protein content ranged from 11% to 5.5%. CAUS122 and CAUS107 were found to contain highest amount of iron and zinc. Highest GCV was recorded for amylose content suggesting selection based on the trait would be effective. Similarly, among physical traits highest GCV was recorded for grain length breadth ratio. The heritability recorded for the quality traits was high indicating that selection for quality traits is effective. Therefore, based on these results the diverse breeding lines having higher yield with better grain quality could be considered for future breeding methods as parents or can be released as varieties after multi-locational evaluation.ThesisItem Open Access Molecular mapping for low light intensity tolerance using the contrasting rice genotypes of Eastern India(College of Post Graduate Studies in Agricultural Sciences, CAU-Imphal, Umiam, 2017-05) Dutta, Suvendhu Sekhar; Rai, MayankRice (Oryza sativa L.) is the most important cereal crop of the Eastern and North-Eastern India. Low light induced problems include high tiller mortality at vegetative stage, reduction in spikelet number, spikelet sterility and reduced dry matter production. A set of contrasting genotypes in the NEHR mini core set during kharif-2014 and a set of 110 rice genotypes from different parts of eastern India were screened for low light intensity tolerance during kharif-2015. Total grain yield, spikelet fertility, biological yield, number of effective panicles, specific leaf weight and chlorophyll content were found to be the key traits response to low light intensity (30 % less than normal). A panel of forty six genotypes made up of top twenty three tolerant and susceptible genotypes each, based on field screening in kharif-2015 along with previously reported checks (Swarnaprabha- tolerant and IR 8-suceptible) was used for mapping study. By using the online rice databases, a set of ninety eight genes previously reported for light response were identified, which was then narrowed down to twenty. Molecular markers (forty five HvSSRs and newly designed twenty eight gene based primers) were used for molecular mapping for low light intensity tolerance. Standardization of these seventy three primers in a set of eight contrasting genotypes led to identification of fifteen HvSSR and two gene based polymorphic (CAU-CG-ILA1-3 and CAU-CG-RK3) primers. These polymorphic primers were run on the mapping panel. Marker-trait association studies based on t test and regression analysis revealed seven HvSSR and one gene based markers associated with the key traits viz., HvSSR01-66, HvSSR02-54 and CAU-CG-ILA1-3 with grain yield, HvSSR02-52, HvSSR06-56, HvSSR06-69 and HvSSR09-45 with spikelet fertility and with biological yield HvSSR02-44, HvSSR02-52, HvSSR06-69, HvSSR09-45. Expression analysis for the genes used for mapping (LGD1, PNH1, ILA1, CAB2R and LP2) was performed on a panel of eight contrasting rice genotypes grown under normal light and low light intensity (75 % of ambient) at two time points (one hour and two days). Relative expression of the five selected genes in the leaf next to flag leaf showed that there was significant down regulation of transcripts after one hour of low light treatment insusceptible genotypes for genes LGD1 and PNH1, whereas the transcript levels were maintained in tolerant genotypes. Transcription was significantly down regulated and up regulated, respectively for ILA1 and LP2 genes specifically in tolerant genotypes under one hour low light treatment. However, no significant differences in gene expression levels for the five genes were observed after two days of stress treatment for tolerant and susceptible genotypes. The genotypes and markers associated with traits identified in this study, after further evaluation, can be used to develop more productive rice varieties for low light affected regions.