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ThesisItem Embargo Genetic analysis for morphological and quality traits in field pea (Pisum sativum L.)(Punjab Agricultural University, 2024) Manavpreet Singh; Dr. Usha NaraField pea (Pisum sativum L.) is a self-pollinated crop. The research work was carried out on genetic diversity and inter-relationship in a collection of 132 field pea germplasm accessions along with five checks viz., HFP529, IPFD12-2, P243, P14, HFP8909. The study was done on 14 morphological and 2 biochemical parameters. The diversification in the germplasm was analysed with the help of 119 SSR primers. The research was done at Experimental Field Area, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana during rabi, 2022-23. ANOVA and correlation analysis revealed considerable extent of diversity, and the association among different parameters. Most of the morphological and biochemical parameters showed significant differences in mean values viz., days to 50% flowering ranged from 57 days to 103 days, plant height 15.38 cm to 169.08 cm, seeds per pod 2.53 to 6.93, pods per plant 2.37 to 29.97, days to maturity 80 days to 138 days, 100-seed weight 3.33 g to 31.91 g, biological yield per plant 21.91g to 59.06 g, seed yield per plant 1.25 g and 25.95 g, crude protein 13.53 % to 36.51 % and starch 27.97 % to 50.87 %. The phenotypic coefficient of variation (PCV) for all the traits was higher than genotypic coefficient of variation (GCV) which signified the presence of environmental variation to some extent in the phenotypic expression. Plant height had the highest values of PCV (53.72) and GCV (52.84). Highest broad sense heritability H2 (99.31%) and (96.71%) was estimated for biological yield per plant and seed yield per plant, respectively. Highest Genetic Advance (69.32) was recorded for plant height. Correlation analysis showed high significant positive correlation among different important morphological and biochemical parameters i.e., seed yield per plant showed significant and positive correlation with biological yield per plant, pods per plant, seeds per pod, pod width, days to maturity, pod length, number of primary branches per plant, seed diameter, pod weight, starch % and 100-seed weight. In present study, total of 29 SSR primers out of 119 SSR primers showed 24.36 % of polymorphism and amplified a total of 87 alleles with an average of 3.39 alleles per primer in a size range of 150–450 bp. Mean polymorphism information content (PIC) was 0.63. The dissimilarity matrix values for allelic data ranged from 0.29 to 0.95 with mean value of 0.62 thus exhibiting enormous diversity. Genetic relationship inferred from a neighbour-joining tree separated accessions into 3 groups i.e., A, B and C. Cluster ‘A’ comprised of 5 germplasm accessions. Cluster B formed the major cluster comprising of 87 germplasm accessions and was divided into two main sub-clusters B1 and B2. Sub-cluster B1 comprised of 47 germplasm accessions and sub-cluster B2 comprised of 40 germplasm accessions. Maximum of these were indigenous collection (IC) and was further divided into sub-clusters. Cluster C had 45 germplasm accessions and majority of them were exotic collection (EC). Our investigation successfully grouped germplasm accessions with similar backgrounds into distinct clusters. Thus, the amount of diversity observed during the experiment can be beneficially exploited in breeding programmes by direct selection or by using them donor parents in hybridization programmes.ThesisItem Embargo Studying effect of genotype × environment interaction on bread making quality in wheat(Punjab Agricultural University, 2024) Himanshu Aggarwal; Dr. Puja SrivastavaPunjab has surplus production of wheat, thus having huge potential for the bakery industry. The bakery industry in India is projected to grow, with bread being considered a cheap and basic instant food due to increasing urbanization. The presence of gluten protein in wheat plays a crucial role in producing various processed foods, especially baked goods. The challenge in bread making is loaf volume, often addressed by using artificial additives. With the aim to address this issue, Twenty four bread wheat genotypes were analysed for biochemical, quality, molecular parameters and bread quality characteristics during Rabi season 2021-22 and 2022-23 focussing on factors like protein content and grain hardness. Yield of the genotypes varied from 18.33 to 68.52 quintals per hectare with a mean yield of 41.44 q/ha. The research reveals significant differences in quality traits among genotypes and emphasizes the impact of particle size, protein content, grain hardness, and growing environment on bread loaf volume. Bread quality emerged as a very complex trait with no single component making a direct effect on its quality. Specific wheat genotypes, such as DBW 296, PBW 823, HD 3086, DBW332 and BWL 1663, show better loaf volume. A significant effect of locations was observed on bread quality score. The average loaf volume values ranged between 360-585 ml with 450 μ flour. High loaf volume of upto 810 ml were observed with very fine flour (150 μ). The selected bread wheat genotype BWL 1663 was the best having high protein content (>15%) and good glu-1 score (10) along with high bread quality score. BWL 1663 performed consistently well over the years and locations thus is a perfect candidate for being released as a good bread quality variety in breeding and quality programmes. The study also explores the role of glutenin subunits, highlighting their influence on bread quality and suggesting potential improvements through further research.ThesisItem Embargo Morphological and molecular characterization of advanced backcross Basmati breeding lines for yield and multiple biotic stresses(Punjab Agricultural University, 2024) Anmol Singh; Dr. Navjot SidhuBasmati rice, a gourmet delicacy and pride of the Indian sub-continent, is well known world-wide for its long slender grains with delicate curvature, pleasant aroma, and remarkable linear elongation, low breadthwise swelling combined with impressive flaky texture on cooking. It occupies a premier position in the forex economy of India. Besides being a premium quality rice, its yield potential is affected by lower grain number panicle besides being affected by multiple biotic stresses. In this study, a total of 165 advanced backcross Basmati breeding lines along with cultivated Basmati rice varieties as checks, were evaluated for yield and yield component traits, resistance to bacterial blight, neck blast and brown planthopper. Data was recorded for days to 50% flowering, plant height, number of tillers per plant, panicle length, number of grains per panicle, yield per plot, resistance to bacterial blight, neck blast and brown planthopper. The days to 50% flowering ranged from 80.92 to 103.28 days; plant height varied from 78.88 and 145.08 cm; number of tillers per plant from 7.06 to 19.18; panicle length varied from 23.14 to 31.22 cm; number of grains per panicle from 23.08 to 164.50 and yield per plot ranged from 0.33 to 1.26 kg, indicating wide variability in the advanced backcross breeding lines. Based on phenotypic evaluation, the selected lines were also evaluated with gene based molecular markers for presence of genes for resistance to bacterial blight (Xa4, xa13, Xa21), neck blast (Pi2, Pi54), brown plant hopper (BPH34), aroma and intermediate amylose. Of 165, 41 lines showed significant improvement in yield component traits and resistance to different stresses besides presence of basmati specific traits such as aroma and intermediate amylose content. Seven lines showed significantly higher yield as compared to checks and resistance to bacterial blight. These lines showed presence of three bacterial blight resistance genes namely Xa4+xa13+Xa21. Of these seven, three lines also possessed Pi2 and Pi54 genes for resistance to neck blast. Three lines out 41 selected lines showed presence of BPH34 gene for resistance to brown plant hopper. All the 41 selected lines were genotyped with 145 SSR markers spanning on all the 12 chromosomes of rice. Basmati genome recovery in all these lines ranged from 37.7 to 91% based on all the SSR markers. The advanced backcross breeding lines are the valuable resource for improving the yield potential of basmati rice and developing basmati rice cultivars with higher yields and resistance to multiple biotic stresses.ThesisItem Embargo Morpho-agronomic and molecular characterization of napier grass (Pennisetum purpureum Schumach) germplasm(Punjab Agricultural University, 2024) Gurmeet Kaur; Dr Tarvinder Pal SinghThe study, titled "Morpho-agronomic and Molecular Characterization of Napier Grass (Pennisetum purpureum Schumach) Germplasm," included the evaluation of 34 Napier grass genotypes at two locations. Three experiments were carried out with a focus on morphoagronomic and molecular diversity and to identify donors for better nutritional and high fodder yield. According to mean performance the genotypes, LN-1, LN-6, LN-9, LN-13, LN-16, LN-17, LN-18, Super napier grass, LN-27, LN-28 LN-29, LN-30, LN-31 and Red napier grass showed good performance for better nutritional quality and high fodder yield. The identification of stable genotypes of napier grass is very useful for fodder purpose. Genotype × Environment interaction has been analyzed using GGE biplot. The LN-27, LN-13 and LN-31 were highly stable in Ludhiana, while the LN-30 and LN-23 performed better in Gurdaspur. The genotypes LN-17, LN27, LN-31, LN-29, Red napier grass and LN-6 were found to be stable in both environments. Plant height, dry matter yield, leaf length, crude protein, number of tillers and oxalate content showed highly positive correlation between green fodder yield. The complete linkage technique of hierarchical clustering based on Squared Euclidean Distance grouped 34 genotypes into threedifferent clusters for fodder purposes. These clusters are important for breeding programme, indicating the possibility of heterosis. The analysis of variance demonstrated that genetic variability was confirmed by a significant mean sum of squares. The interaction between genotype and environment was found to be non-significant for oxalate (%) and acid detergent lignin (%), while other traits showed significant interactions. The molecular diversity analysis using 33 SSR markers clustered all the 34 germplasm lines into five clusters and showed a high polymorphism. PIC values ranged from 0.06 to 0.79 with an average of 0.43. The morpho-agronomic and molecular analysis indicated significant genotype variation. In addition, PCA (principal component analysis) indicated the diversity among genotypes. The comprehensive characterization of the study identified promising genotypes with exceptional agro-morphological performance. LN-1, LN-5, LN-6, LN-9, LN-13, LN-16, LN-17, LN-18, Super napier grass, LN25, LN-27, LN-28, LN-29, LN-30, LN-31 and Red napier grass genotypes were identified as having superior performance. In the future, breeding programmes could use the diverse genotypes of napier grass to create interspecific hybrids of Pearl millet napier with high biomass yield.ThesisItem Embargo Characterization of maize inbred lines for high plant density amenable traits(Punjab Agricultural University, 2024) Meena, Tarun Kumar; Dr Gagandeep SinghIn temperate maize, breeding for stress tolerance including a higher number of plants per unit area has been extensively used for productivity enhancement in commercial hybrids but this strategy has not been exploited in tropical maize. The increase in the number of plants per unit area through the adoption of high density planting (HDP) is one of the alternative strategies to achieve high productivity in tropical/subtropical maize. Narrow leaf angle, shorter anthesis silking interval, and moderate plant height were delineated as major architectural traits for tolerance to HDP in parental lines. The lines harboring these traits coupled with high grain yield potential under HDP were identified and recommended to use as parents for the HDP breeding program. These are following inbred lines identified for HPD traits CML 451, 221520, EML108, EML113, EML129, PML1112, PML115, PML1194, PML1239, PML133, PML162, PML163, PML164, PML18, PML2, PML80, PML81, SN485145 and VL174449.The inheritance study of leaf angle resulted as the expected number of intermediate, broad leaf angle and narrow leaf angle plants for 9:6:1 was 405, 250 and 607, respectively, giving a chi-square value of 1.097 (< 5.991) hence giving a perfect fit to 9:6:1. Thus, Chi-square analysis revealed that the narrow leaf angle is controlled by two recessive gene. A cross between broad leaf angle (PML1126) and narrow leaf angle (CML451) inbred line was used to raise an F2 mapping population for the construction of two contrasting bulks namely, broad leaf angle (BLA) and narrow leaf angle (NLA). These bulks along with both the parents were sequenced using whole genome resequencing and analysed using the SNP-index method for identifying the narrow leaf angle associated region. Identification of QTLs associated with narrow leaf angle in the material under study based on sequence based bulked segregant analysis and use of QTLseqr software was done. It was observed that the ∆SNP-index values in the region 48.72mb to 55.13mb on chr 6, 44.63mb to 45.74mb; 46.21mb to 50.86mb on chromosome 7, 48.22mb to 54.56mb on chromosome 9 lied outside the statistically calculated confidence interval at 99% level of significance. The findings of the present study will facilitate in genetic dissection of candidate gene(s) responsible for the narrow leaf angle gene. This study will also help in the development of SNP-based markers which would facilitate marker-assisted transfer of narrow leaf angle gene in maize inbred line.ThesisItem Restricted Genetic and biochemical characterization among diverse set of Linseed (Linum usitatissimum L.) germplasm(Punjab Agricultural University, 2024) Alka; Dr. Arvinder Kaur ToorThe present study involved the evaluation of sixty linseed genotypes at two locations. Two experiments were conducted, focusing on agro-morphological and biochemical traits. The agromorphological assessment included traits like branches, capsules, seed yield, and maturity duration. Genotype BAU-2019-13 excelled in seed yield at Ludhiana, while LCK-2134 performed best at Gurdaspur. Descriptive statistics indicated minimal environmental impact on most of the traits, suggesting potential for improvement through direct phenotypic selection. Traits like primary branches and seed yield per plant showed high heritability and genetic advance, indicating suitability for improvement through phenotypic selection. Genotype × environment interaction was observed, and GGE biplot analysis highlighted superior performances of LCK-2134 in Gurdaspur and BAU-2019-13 in Ludhiana. Positive correlations were identified between morphological traits and seed yield per plot. Dendrograms revealed six clusters at each location, by grouping genotypes with similar features. These clusters are crucial for breeding programs and for suggesting potential for heterosis. The agro-morphological characterization demonstrated significant genotype variation. The second experiment focused on biochemical traits, including crude protein, oil percentage, and fatty acids. Genotypes with high oil percentage and low anti-nutritional factors were identified as valuable for both human and livestock feeding. The top genotypes for oil percentage and crude protein were Surbhi × LC 2023 and BAU-2021-08, respectively. Genetic variability was confirmed by significant mean sum of squares in the analysis of variance. G × E interaction was significant for tannins and crude protein, while other traits showed non-significant interaction. Dendrograms for biochemical traits classified genotypes based on homogeneity and heterogeneity. The study's comprehensive characterization identified promising genotypes with exceptional performance in both agro-morphological and biochemical traits. This information is valuable for future linseed breeding programs.ThesisItem Restricted Genome wide association studies for sorghum shoot fly and red leaf spot resistance(Punjab Agricultural University, 2024) Jasneet Kaur; Dr. R.S. SohuThe present study was conducted for the assessment of shoot fly and red leaf spot resistance and discovery of markers and candidate genes associated with target traits in Sorghum bicolor across years and locations. A diversity set of 121 germplasm lines, acquired from ICRISAT and IIMR, was evaluated under two environments (two locations – Ludhiana (2020-21 and 2021-22) and Faridkot (2021-22)) for shoot fly whereas at Ludhiana for two years kharif 2020-21 and 2021-22 for red leaf spot disease. The germplasm lines were evaluated for nine morphological traits for shoot fly representing- per cent dead heart formation (DH), glossiness(GL), leaf sheath pigmentation (LSP), plants infested with eggs (PWE), number of eggs per plant (PPE), seedling vigour (SV), seedling height (SDH), plant height (PH) and number of tillers (TL). Significant genetic and genotype x environment interaction variance was observed for all test traits. Ten genotypes viz., IC 288122, IS 7657, IS 7663, IS 7745, IS 8155, IS 8282, IS 8256, IS 8348, IS 8230 and SSV 17 were found resistant and gave stable performance across all environments. Resistant genotype IS 8348 was selected for generation of bi-parental cross with susceptible genotype IS 7017. Similarly, disease score and area under disease progressive curve was used for assessment of red leaf spot disease. Significant genetic variance and genotype x environment interaction variance was observed for disease score under both the environments. Four lines viz., IS 7017, IS 8015, IS 8256 and SCL 4 were free from infection, indicating resistance to red leaf spot. Best linear unbiased predictors values (BLUP) of traits were used for genome-wide association study (GWAS) using 42678 SNPs. Linkage disequilibrium decay in population was estimated to be ~50kb. A large number of significant marker-trait associations were identified for all test traits. The genomic regions identified on chromosomes 1, 2, 4, 7 and 10 were previously reported to be associated with shoot fly resistance for trait DH and GL. Annotations helped to predict candidate genes in the genomic regions associated with the significant SNPs. Important candidate genes involved were receptor kinases (LRR, serine/threonine protein kinases, hydrolases and transferases), stress signalling pathways (ethylene, abscisic acid and jasmonic) for shoot fly and (RLP, WRKY, F-box protein, CDP, zinc finger and putative disease resistance protein) for red leaf spot disease. Associative SNPs were converted into KASP markers and S1_15319241 KASP marker associated with DH was validated in the F2 population of cross IS 8348 x IS 7017.ThesisItem Embargo Genome wide association studies and genomic prediction for maydis leaf blight resistance in tropical maize (Zea mays L.)(Punjab Agricultural University, 2023) Wajhat-Un-Nisa; Sandhu, SurinderThe present study was undertaken to identify marker-trait associations (MTA) and candidate genes associated with maydis leaf blight (MLB) in maize (Zea mays L.). A diverse panel of 359 genotypes, known as the CIMMYT Asia Associated Mapping Panel (CAAM), was used in this study. The evaluation of MLB resistance was conducted through artificial inoculation across four different environments (two years and two locations). Disease severity was measured on the scale of 1-9. Significant variation was observed for genotypes. Heritability was high (>70%) for the trait. GGE-biplot depicted the stability and performance with lower disease score. A set of 10 genotypes was reported as resistant across environments with average disease score of 3.0. Best linear unbiased predictor (BLUPs) values were used for GWAS with 128,490 SNPs. Linkage disequilibrium (LD) decay in panel was estimated to be ~ 0.9 kb at r2 =0.1. Based on cumulative analysis of data, a total of 26 significant SNPs, distributed across all ten chromosomes were associated with MLB resistance. Notably, the highest number (6) of SNPs was reported on chromosome 8, 5 SNPs within bin 8.06 and 1 SNP in bin 8.01. This suggests that chromosome 8 plays a crucial role in MLB resistance. Seven novel SNPs were reported from chromosomal bins viz., 9.06, 6.05, 5.01, 1.04, 7.04, 9.01, and 4.06. Gene mining and in silico expression analysis led to the identification of 22 putative candidate genes (on the basis of significant SNPs) with the functional relevance for resistance against necrotrophic pathogen. The expression values were above 2 fragments per kilobase of transcript per million mapped reads (FPKM). The important candidate genes were protein suppressor of PHYA-105 1/SPA, ATP-dependent helicase, MYB DNA-Binding domain, PR5-like receptor kinase, bZIP transcription factor 23, Aspartic proteinase nepenthesin-2, Cdpk7, acetyltransferase NAGS1, Ubiquitin protein ligase binding, B3 domain containing protein, and ABC transporter B family member 4. These genes play pivotal roles in promoting basal defence and effector-triggered immunity (ETI) within the plant through phyto-hormone signaling, oxidative burst, hypersensitivity cell death response, transport of secondary metabolites, mitogen activated protein kinase (MAPK) mechanism, and serine/threonine protein kinase activity against necrotrophic fungi. The co-expression and physical interaction among candidate genes were 88.70%, and 8.98%, respectively. All the candidate genes were co-expressing, indicating potential functional relationships. However, physical interaction was observed between the genes SPA1/ GRMZM2G061602 and ABI3/GRMZM2G313737, associated with single SNP (S8_155841067). The sub-cellular localization predicted signals in nucleus, chloroplast, vacuole, extracellular space, and cell membrane for candidate genes. Genomic Prediction (GP) was performed using a subset of 9223 SNPs including the significant markers with genomic-BLUP model, as five-fold cross-validation. Prediction accuracy of 0.35 was observed across four environments with the training and testing set from the CAAM panel in the ratio of 90:10. The accuracy depicted higher genetic diversity in association mapping panel and potential use of GP strategies to enhance selection efficiency. The study enriched allelic diversity, along with the understanding of underlying resistance mechanism against MLB in maize.ThesisItem Embargo Phenotypic and molecular evaluation of advanced backcross lines of chickpea (Cicer arietinum L.)(Punjab Agricultural University, 2023) Gopal Krishan; Bindra, ShaylaThe present study entitled “Phenotypic and molecular evaluation of advanced backcross lines of chickpea (Cicer arietinum L.)” was conducted to incorporate the genes for FW resistance from WR315 in PBG7 and for AB resistance from ILC3279 in L552. A set of 35 lines and 20 lines from Cross I (PBG7 × WR315) and Cross II (L552 × ILC3279) respectively, were phenotyped during rabi 2021-22 and 2022-23 along with their molecular evaluation. Analysis of variance, evinced significant difference for all the traits among the backcross derived lines. The PCV values were observed to be slightly greater than the corresponding GCV values for all the characters studied in both the crosses, indicating the influence of the environment for the expressions of the traits. In both the crosses PCV and GCV values were recorded to be maximum for seed yield per plant. High heritability coupled with moderate genetic advance was observed for seed yield per plant in Cross I while in Cross II, it was for seed yield per plant, aerial biomass and number of pods per plant. Correlation studies revealed positive and highly significant correlation of seed yield per plant with harvest index and aerial biomass, both for Cross I and Cross II. In Cross I highest positive direct effect of harvest index was for seed yield per plant whereas, for aerial biomass in cross II. Based on screening for disease resistance, a total of eight lines of Cross I for FW and four lines of Cross II for AB were found to be resistant. A total of six linked markers (GA16, TAA60, TA194, TS82, TA110 and TR19) for FW and eight (GA16, TS82, TA194, TR58, GAA47, SCY17, TA130 and TA2) for AB were used for foreground selection. To estimate background genome recovery, a total of 40 and 45 SSR markers were used for Cross I and Cross II, respectively. The GGT analysis for Cross I revealed the RPG recovery as high as 93.75% while in Cross II with 98.88%. Overall, two lines each of Cross I (GLMFW02 and GLMFW10) and Cross II (GLMAB06 and GLMAB07) with maximum RPG recovery were found to be promising for yield and related traits under study.
