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Acharya N G Ranga Agricultural University, Guntur

The Andhra Pradesh Agricultural University (APAU) was established on 12th June 1964 at Hyderabad. The University was formally inaugurated on 20th March 1965 by Late Shri. Lal Bahadur Shastri, the then Hon`ble Prime Minister of India. Another significant milestone was the inauguration of the building programme of the university by Late Smt. Indira Gandhi,the then Hon`ble Prime Minister of India on 23rd June 1966. The University was renamed as Acharya N. G. Ranga Agricultural University on 7th November 1996 in honour and memory of an outstanding parliamentarian Acharya Nayukulu Gogineni Ranga, who rendered remarkable selfless service for the cause of farmers and is regarded as an outstanding educationist, kisan leader and freedom fighter. HISTORICAL MILESTONE Acharya N. G. Ranga Agricultural University (ANGRAU) was established under the name of Andhra Pradesh Agricultural University (APAU) on the 12th of June 1964 through the APAU Act 1963. Later, it was renamed as Acharya N. G. Ranga Agricultural University on the 7th of November, 1996 in honour and memory of the noted Parliamentarian and Kisan Leader, Acharya N. G. Ranga. At the verge of completion of Golden Jubilee Year of the ANGRAU, it has given birth to a new State Agricultural University namely Prof. Jayashankar Telangana State Agricultural University with the bifurcation of the state of Andhra Pradesh as per the Andhra Pradesh Reorganization Act 2014. The ANGRAU at LAM, Guntur is serving the students and the farmers of 13 districts of new State of Andhra Pradesh with renewed interest and dedication. Genesis of ANGRAU in service of the farmers 1926: The Royal Commission emphasized the need for a strong research base for agricultural development in the country... 1949: The Radhakrishnan Commission (1949) on University Education led to the establishment of Rural Universities for the overall development of agriculture and rural life in the country... 1955: First Joint Indo-American Team studied the status and future needs of agricultural education in the country... 1960: Second Joint Indo-American Team (1960) headed by Dr. M. S. Randhawa, the then Vice-President of Indian Council of Agricultural Research recommended specifically the establishment of Farm Universities and spelt out the basic objectives of these Universities as Institutional Autonomy, inclusion of Agriculture, Veterinary / Animal Husbandry and Home Science, Integration of Teaching, Research and Extension... 1963: The Andhra Pradesh Agricultural University (APAU) Act enacted... June 12th 1964: Andhra Pradesh Agricultural University (APAU) was established at Hyderabad with Shri. O. Pulla Reddi, I.C.S. (Retired) was the first founder Vice-Chancellor of the University... June 1964: Re-affilitation of Colleges of Agriculture and Veterinary Science, Hyderabad (estt. in 1961, affiliated to Osmania University), Agricultural College, Bapatla (estt. in 1945, affiliated to Andhra University), Sri Venkateswara Agricultural College, Tirupati and Andhra Veterinary College, Tirupati (estt. in 1961, affiliated to Sri Venkateswara University)... 20th March 1965: Formal inauguration of APAU by Late Shri. Lal Bahadur Shastri, the then Hon`ble Prime Minister of India... 1964-66: The report of the Second National Education Commission headed by Dr. D.S. Kothari, Chairman of the University Grants Commission stressed the need for establishing at least one Agricultural University in each Indian State... 23, June 1966: Inauguration of the Administrative building of the university by Late Smt. Indira Gandhi, the then Hon`ble Prime Minister of India... July, 1966: Transfer of 41 Agricultural Research Stations, functioning under the Department of Agriculture... May, 1967: Transfer of Four Research Stations of the Animal Husbandry Department... 7th November 1996: Renaming of University as Acharya N. G. Ranga Agricultural University in honour and memory of an outstanding parliamentarian Acharya Nayukulu Gogineni Ranga... 15th July 2005: Establishment of Sri Venkateswara Veterinary University (SVVU) bifurcating ANGRAU by Act 18 of 2005... 26th June 2007: Establishment of Andhra Pradesh Horticultural University (APHU) bifurcating ANGRAU by the Act 30 of 2007... 2nd June 2014 As per the Andhra Pradesh Reorganization Act 2014, ANGRAU is now... serving the students and the farmers of 13 districts of new State of Andhra Pradesh with renewed interest and dedication...

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    ThesisItemOpen Access
    IDENTIFICATION OF DIFFERENTIALLY EXPRESSED TRANSCRIPTS IN GROUNDNUT CHALLENGED WITH Sclerotium rolfsii Sacc. CAUSING STEM ROT
    (Acharya N.G. Ranga Agricultural University, 2018) RAJASEKHAR, SRUNGARAPU; AMARAVATHI, Y
    Stem rot mainly a soil-borne disease caused by Sclerotium rolfsii, is one of the major constraints in groundnut production as it severely affects the yield and quality of the produce. The present investigation was aimed for histopathological, biochemical and identification of differentially expressed transcripts in response to stem rot caused by Sclerotium rolfsii in groundnut. A total of fifteen genotypes viz., ICGV 91114, ICGV 86590, ICGV 86031, ICGV 87160, ICGV 87157, ICGS 76, ICGS 44, ICGV 07132, ICGV 07072, CS19, Dharani, Kadiri 6, Rohini, TCGS 1157 and Narayani were selected and screened for stem rot resistance or tolerance in pot culture under artificial conditions. Among these fifteen genotypes, ICGV 86590 found to be highly tolerant as it has not shown any wilting symptoms even fifteen days after inoculation with S. rolfsii and in contrast, Narayani found to be highly susceptible with complete wilting and subsequent death of the plant. The pot culture experiments were carried out in the glass house of Regional Agricultural Research Station (RARS) and Molecular analysis at Genomics lab, Institute of Frontier Technology (IFT), RARS, Tirupati. The contrasting genotypes for stem rot viz., ICGV 86590 (tolerant) and Narayani xv (susceptible) were further analyzed for Scanning Electron Microscopy, Biochemical and Molecular parameters at 24 hrs interval upto 4 days. Scanning Electron Microscopy studies showed presence of distorted xylem vessels with fungal mycelial growth in susceptible genotype, Narayani at 72 HAI whereas in tolerant genotype, ICGV 86590 even at 72 HAI no mycelial growth were observed in xylem vessels. The accumulation of total phenol content was relatively increased by 2 folds in ICGV86950 at 96 hours after inoculation when compared to susceptible genotype Narayani. The elevated levels of total phenols play an important role in the resistance mechanism against infection with S.rolfsii in tolerant groundnut genotype. Chitinase activity was significantly increased 6 times more in ICGV86590 at 96 hrs after challenged with S. rolfsii whereas in Narayani it was almost constant throughout the sampling time in comparison with their respective controls. Peroxidase activity was induced as an early response to counter the fungal pathogen attack and the infected tissue showed a higher activity of the enzyme at 96 hrs after inoculation in tolerant genotype (1.87 min/gm/fresh weight) when compared with susceptible genotype (0.42 min/gm/fresh weight). β-1, 3-Glucanase activity was increased continuously at all sampling intervals in both stem rot tolerant and susceptible genotypes in comparison with their respective controls and was maximum in tolerant genotype ICGV 86590 at 96 hrs after S. rolfsii inoculation. Polyphenol oxidase increased significantly upto 72 hrs after inoculation in ICGV 86590 and slightly decreased at 96 hrs whereas in susceptible genotype the polyphenol activity was slight increased throughout sampling period. To unravel the molecular mechanisms conditioning stem rot tolerance, transcriptome was analyzed in groundnut subjected to S. rolfsii (0 to 96 hrs after inoculation). To identify differentially expressed transcripts, cDNARAPD analysis was carried out using total RNA collected from stem portion near collar region from both unchallenged (control) and challenged constrasting genotypes at 24 hrs interval upto 4 days. To identify differentially expressed transcripts the transcriptome was analyzed by cDNA-RAPD profiles in tolerant and susceptible groundnut genotypes subjected to S. rolfsii. A total of 3485 Transcript Derived Fragments (TDFs) were scored. Out of which 2137 TDFs were differentially expressed in both resistant and susceptible genotypes challenged with S. rolfsii at 24 hrs interval upto 4 days. Among the 2137 differentially expressed transcripts, 1471 transcripts exhibited qualitative difference and 666 transcripts displayed xvi quantitative differences in banding pattern of cDNA-RAPD profiles among the two groundnut genotypes. The transcriptome data analyzed by cDNA-RAPD profiles can serve as a valuable resource for gene discovery and the differentially expressed genes can be cloned and further sequenced to reveal the function. Thus the identified transcripts/genes can also be converted to functional markers and can be used in marker assisted selection for stem rot resistance breeding.
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    ThesisItemOpen Access
    MARKER ASSISTED INTROGRESSION OF BACTERIAL LEAF BLIGHT RESISTANCE GENES INTO AN ELITE RICE VARIETY, NELLORE MASHURI
    (Acharya N.G. Ranga Agricultural University, 2018) DIVYA, PAMMINA; ESWARA REDDY, N.P.
    Nellore Mahsuri (NLR34449) is a popular rice variety, and mostly adopted by many of the farmers by virtue of its fine grain appearance, short duration, non-lodging and high yielding characters. This variety is resistant to leaf blast but susceptible to bacterial leaf blight (BLB), the second most devastating disease in rice growing areas. The development of resistant varieties has been the most effective and economical strategy to control this disease. In the present investigation, an attempt was made to improve the NLR34449 for BLB resistance by introgressing three major resistant genes i.e., xa13, Xa21and xa5 from RPBio226 (improved samba Mahsuri) using marker-assisted backcross breeding. Phenotype screening of Nellore Mahsuri (NLR34449) and RPBio226 revealed that NLR34449 is found to be susceptible as it showed more lesion length in comparison to the RPBio226. Similarly, the genotyping of these two varieties using three gene specific markers namely pTA248, xa13 prom, xa5FS, linked to the BLB resistance genes viz., Xa21, xa13 and xa5, respectively revealed that the NLR34449 is devoid of these broad spectrum genes. Further, screening of the parents with 120 markers showed 30 polymorphic markers, which covered almost all rice chromosomes evenly. These polymorphic markers were used for background selection in BC1F1. The two parents were crossed to produce F1. True F1s were confirmed using gene-specific markers xa13prom (xa13), pTA248 (Xa21), xa5FS (xa5) and backcrossed with NLR34449 to generate 200 BC1F1. In all, 126 phenotypically superior BC1F1 plants were selected from the 200 BC1F1s plants, based xvi on the plant type similar to NLR34449 and further characterized for BLB resistance employing molecular and phenotypic studies The BC1F1 plants were screened with BLB gene-specific markers and 30 polymorphic markers for both foreground and background selection, respectively. Out of 126 BC1F1 plants selected, 21 were found to be positive for xa13, 18 were positive for Xa21, 32 were positive for xa5 gene, whereas, 16 were double positive for both Xa21 and xa13, 13 were double positive for both Xa21 and xa5, 15 were double positive for both xa13 and xa5. Interestingly, 9 BC1F1 plants with triple positive for Xa21, xa13 and xa5 genes were identified from foreground screening. Further 9 selected BC1F1 plants were subjected to the recombinant selection employing the closely located targeted 3 BLB genes to minimize the linkage drag from RPBio226 at these loci. In background selection the selected BC1F1 (three gene pyramid) plants were screened with 30 polymorphic markers. Recovery percentage of recurrent genome was 76.7 – 83.3 % and exhibited high levels of resistance against BLB. The BLB introgressed progeny BC1F1- 9 had showed significant yield increase (31.5) over NLR34449 apart from very low disease score (0.5-lesion length). However, BC1F1- 54 (20.6g); BC1F1- 79 (22.1); and BC1F- 82 (21.7) had recorded yield levels similar to donor parent. Hence, the BC1F1 plants that are having high yield levels along with BLB tolerance and almost all recurrent parent traits would be used to progress further generations to use as straight variety. In conciusion, in the present investigation NLR34449 high yielding fine grain variety susceptible to BLB disease and has been introgressed with three BLB genes from RPbio226.
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    ThesisItemOpen Access
    Validation of QTLs for Yellow Mosaic Virus Tolerance in Mungbean (Vigna radiata (L.) Wilczek)
    (Acharya N.G. Ranga Agricultural University, 2018) KEERTHI, ISSA; SRIVIDHYA, A
    Green gram (Vigna radiata (L.) Wilczek), is one of the important pulse crops mainly grown in developing countries. However, the yield level of the crop is very low due to many biotic and abiotic factors. Among biotic factors, yellow mosaic virus (YMV), which is transmitted by white fly (Bemisia tabaci) causes significant yield losses ranging from 10-100%. With this background, the present investigation was initiated to validate the reported markers linked to the YMV resistance in a F2 segregating population. The genotypes, TM-96-2 (Trombay Mungbean), susceptible to Yellow Mosaic Virus (YMV) and EC-396117 (Exotic Collection) tolerant to YMV were chosen as parents for development of F2 population. The parental DNA was screened with 206 markers which include microsatellites (203), RAPD (2) and SCAR (1) to detect the polymorphic markers. Out of these markers, 110 were amplified and 73 markers were not amplified. Of these 110 amplified markers, only 16 primers showed polymorphism (14.5%) between the parents, and the rest of the markers were found to be monomorphic. True F1 plants were selected after confirming their heterozygosity at molecular level using polymorphic microsatellite marker, CEDG305. These F1s were selfed to produce F2 population during Rabi, 2017-2018. As many as 150 F2 individuals along with the parents were evaluated for YMV tolerance at RARS, Tirupati during Summer, 2018 under natural field conditions. The DNA has been extracted from the parents and F2 population. All the 150 F2 plants were screened with the 16 polymorphic markers. Out of these markers, only 5 showed clear scorable bands in F2 xiv population. These 5 markers were CEDG245, CEDG149, CEDG305, DMBSSR125 and CEDG228. Single marker analysis of these five markers in the F2 population using MapDisto software v.2.0 revealed a significant association of CEDG228 marker with YMV tolerance. NCBI-BLAST analysis of primer sequence of CEDG228 hit an expressed gene, LOC106773961 of the greengram genome. In conclusion, the marker, CEDG228, which has shown association with the YMV tolerance in the present investigation, has the potential to use in marker-assisted breeding of the development of YMV tolerant green gram varieties. However, further validation of this marker in a diverse set of resistant and susceptible cultivars is warranted before being used in large scale marker-assisted selection programmes.
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    ThesisItemOpen Access
    MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF COTTON (Gossypium hirsutum L.)
    (Acharya N.G. Ranga Agricultural University, 2018) ANJANI, ALLURI; PADMA, V
    The present investigation was carried out during kharif 2017-18 at Regional Agricultural Research Station, Lam and APGC, Lam, Guntur to characterize 40 genotypes of cotton (G. hirsutum) using DUS characterstics of PPV & FRA and SSR markers and also to study the variability, heritability, genetic advance as per cent of mean, and genetic divergence of seed cotton yield per plant and yield component traits. The data were recorded on 20 descriptors viz., leaf colour, leaf hairiness, leaf appearance, gossypol glands, leaf nectaries, leaf petiole pigmentation, leaf shape, stem hairiness, stem pigmentation, bract type, petal colour, petal spot, stigma position, anther filament colouration, pollen colour, boll bearing habit, boll colour, boll shape, boll surface, prominence of boll tip and 14 quantitative characters viz., plant height (cm), days to 50 % flowering, number of monopodia per plant, number of sympodia per plant, number of bolls per plant, boll weight (g), seed index (g), lint index (g), ginning outturn (%), 2.5% span length (mm), uniformity ratio, micronaire value (10-6 g/inch), bundle strength (g/tex) and seed cotton yield per plant (g). The morphological descriptors indicated variability for eight characters (leaf petiole pigmentation, stem pigmentation, petal colour, stigma position, pollen colour, boll shape, boll surface, prominence of boll tip) out of twenty characters studied and these traits are helpful for the identification of the genotypes from one another and some of the characters like stem hairiness, can be exploited for breeding pest resistant genotypes. The genotypic coefficients of variation for all the characters studied were lesser than the phenotypic coefficients of variation indicating the masking effect of environment. Wide genetic variability was observed for the characters viz., plant height, number of sympodia per plant, number of bolls per plant, boll weight and seed cotton yield per plant. High heritability coupled with high genetic advance as per cent of mean was recorded for seed cotton yield per plant indicating the preponderance of additive gene action and hence further improvement may be done through simple selection procedures. The results of Mahalanobis D2 analysis indicated the presence of considerable genetic divergence among the 40 genotypes and the traits bundle strength, days to 50% flowering, number of monopodia per plant, 2.5% span length and boll weight contributed maximum towards genetic divergence. The 40 genotypes were grouped into 7 clusters using Tocher’s method indicating genetic diversity and geographical diversity were not related. The cluster I had the maximum number of genotypes while the intra-cluster distance was maximum in the cluster II. The clusters III, IV, V, VI, and VII were solitary clusters. The inter cluster distance was maximum between clusters II (SCS 1061, CCH 14-2, TSH 0533-1, RS 2767, SCS 1207, L 1008, CCH 14-1, GJHV 510, BS 26) and VI (BS 23) indicating the importance of genotypes present in these clusters in hybridization programme for the exploitation of heterosis. The cluster II recorded the highest mean values for the quality traits and seed cotton yield per plant and these genotypes can be effectively exploited in the breeding programmes. In the present study, 40 genotypes were also screened with 50 SSR primers out of which 19 showed polymorphism and the PIC values were also higher for 17 primers indicating their usefulness in characterization. The jaccard’s similarity coefficient values ranged from 0.03 to 0.80 indicating that the cultivars have a vast genetic base. The genotypes, RAH 1033 and L 788 showed least similarity coefficient value among the genotypes revealing their use in hybridization programme for generating variability and production of transgressive segregants in the future generations. The genotypes were grouped into seven clusters using UPGMA method. The cluster I had nine genotypes while the cluster III was the second largest cluster with 11 genotypes. The cluster IV was the largest with sixteen genotypes. The clusters II, V, VI and VII were solitary clusters.
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    ThesisItemOpen Access
    LINKAGE MAP CONSTRUCTION AND MAPPING QTLs FOR IMPORTANT AGRO-MORPHOLOGICAL TRAITS IN OIL PALM (Elaeis guineensis Jacq.)
    (Acharya N.G. Ranga Agricultural University, 2018) RANAJEETH VINAYAKA RAMARAJU, BAIP; RAMANA, J.V.
    The present investigation was carried out during 2017-18 at ICAR-IIOPR, Pedavegi, Andhra Pradesh, India. Two oil palm genotypes i.e. DURA 240D and DURA 281D which differ in yield and oil yield content were selected as parents which were developed at Regional Agricultural Research Station, Palode, Kerala. From this cross 70 F1 progenies were generated and raised at DURA block of IIOPR, Pedavegi, Andhra Pradesh. Morphological characters such as Bunch number, Bunch weight, Bunch index, Oil to dry mesocarp and Oil to wet mesocarp were recorded as per the standard procedures. The phenotypic and genotypic data of 70 palms were used for construction of linkage maps and QTL mapping. In Parental analysis study, a total of 400 SSR markers of Elaeis guineensis were used to screen two parental genotypes. Out of 400 SSR markers analyzed for polymorphism, 19 SSR markers (4.75%) were polymorphic and these 19 polymorphic SSRs were used to genotype the 70 F1 progenies of the 240D x 281D cross. Then the genotypic data was scored as ‘A’-homozygous allele to parent 240D, ‘B’-homozygous to parent 281D and ‘H’-which has both the alleles. In Linkage Mapping studies 70 F1 progenies of 240D x 281D cross genotypes were screened with the co-dominant subset of 19 putative polymorphic SSRs. Data for SSR markers was obtained in the form of A,B and H scoring which was then used for Linkage Map construction and QTL analysis. Linkage analysis and map construction were performed using Mapmanager software. Out of 19 SSRs, 13 SSRs were found linked with chromosome 1,6,8 and 15. Each chromosome was linked with 3 SSR markers, except the 8th chromosome which was linked with 4 markers. A total of 13 SSRs were mapped to 4 linkage groups (C1, C6, C8 and C15) of Elaeis guineensis genome. Map was drawn with the help of QTL Cartographer after determining the best possible order by Mapmanager. The map covered four linkage groups with 13 polymorphic SSR markers. In QTL mapping study three different methods were used i.e. Simple regression analysis, Simple interval mapping and Composite interval mapping for QTL detection. In Simple regression analysis (SRA) by WinQTL Cartographer 2.0 revealed two markers for bunch number on chromosome 1 and chromosome 8. Bunch weight, oil to dry mesocarp, oil to wet mesocarp and bunch index could not show any association with the QTL. In Simple Interval mapping (SIM) analysis by WinQTL Cartographer 2.0 revealed a total of 4 QTLs for various yield traits. Out of these identified QTLs, one QTL (qBN1.1) was for bunch number, two QTLs (qODM1.1, qODM1.2) for oil to dry mesocarp and one QTL (qOWM1.1) for oil to wet mesocarp in E.guineensis in the population under study. Bunch weight and Bunch index were not associated with any QTL. Composite Interval Mapping (CIM) analysis by WinQTL Cartographer 2.0 revealed a total of 5 QTLs for various yield traits. Out of these identified QTLs, one QTL (qBN1.1) was for bunch number, two QTLs (qODM1.1, qODM1.2) for oil to dry mesocarp and two QTLs (qOWM1.1, qOWM1.2) for oil to wet mesocarp. No QTLs were identified for bunch weight and bunch index. This study confirmed that QTLs can be detected in homozygous and heterogenous populations successfully in perennial crops like oil palm in limited time span by using SSR markers. At the same time linkage map studies in oil palm through morphological marker needs data for several years. However, this work provided valuable information and detected some important QTLs in oil palm, which can be used as parent material in oil palm breeding for yield improvement programmes as well as any intra-specific hybridization programme. Therefore the knowledge of QTLs in relation to yield and oil quality data would help in searching and pin-pointing palms as parent material. Therefore using the phenotypic data and genotyping it with various SSR Markers and performing QTLs analysis would be useful to link the phenotype to genotype for developing appropriate tools and methodologies for marker–assisted breeding. This knowledge will also provide a better understanding of the biological basis of various traits.
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    ThesisItemOpen Access
    ALLELE MINING AND ALLELIC DIVERSITY OF GENES GOVERNING GRAIN SIZE RELATED TRAITS IN RICE (Oryza sativa L.)
    (Acharya N.G. Ranga Agricultural University, 2017) SWARAJYA LAKSHMI NAIDU, B; LAKSHMI NARAYANA REDDY, V
    Mining elite alleles for grain size is one of the key aspects for the improvement of cultivated rice to suit diverse global consumer preferences. Thus with the goal of identification of novel and superior alleles from the genes governing the grain size related traits by exploring the natural variability present in the rice germplasm, the present study was conducted. In all, 124 rice genotypes were evaluated for different grain traits such as grain length (GL), grain width (GW), grain length to width ratio (GL/GW), and 1000-grain weight (TGW). The germplasm of 124 rice genotypes presented substantial variation for grain size traits. Significant correlations were detected among the grain size traits. All the four traits exhibited normal distribution in the germplasm indicating quantitative inheritance of these traits. In total, 32 molecular markers comprising of 8 grain size gene-specific markers and 24 SSR markers covering all 12 chromosomes were used in this study and all markers showed polymorphism and produced a total of 86 alleles among the 124 rice varieties. Number of alleles ranged from 2 to 4 with an average of 2.68 alleles per locus. The mean polymorphism information content (PIC) value was 0.34, with values ranging from 0.70 (RM 252) to 0.03 (RM 502). The screening of the 124 rice genotypes with eight gene-specific markers viz., GS3 specific marker revealed two alleles, GS5INDEL1 revealed two alleles, qSW5 specific marker revealed four alleles, qGRL7.1 specific marker revealed two alleles, GS2 specific marker revealed two alleles, qsgw7 specific marker revealed two alleles, SLG7 specific marker revealed two alleles and GLW7 specific marker revealed two alleles with substantial variation in the germplasm. For finding the allelic diversity a dendrogram consisting of 124 rice genotypes was drawn using unweighted pair group method using arithmetic averages (UPGMA) based on genotyping data using NTSY spc -2.02e software. The dendrogram revealed that 124 genotypes could be made into two groups, A and B. The group A exclusively includes the extra-long grain length basmati genotypes. However, the group B could be again divided into two groups i.e., B1 and B2. The group B1 includes mostly long grain genotypes. The group B2 comprising of all classes of grain length and size genotypes. Based on the population structure Q matrix data the 124 accessions are divided into four clusters/subpopulations, viz., from POP1 to POP4. POP1 subpopulation was grouped under extra-long grain type, POP2 was grouped under long grain type, POP3 and POP4 includes all the four grain size classes. Eight marker-trait associations were identified by screening 124 genotypes with grain size specific primers for GL, GW, L/B and TGW traits. One GS3 gene-specific marker, GS3RGS1 was found to be associated with GL, GW, L/B and TGW traits with their PVE as 15.2%, 16.9%, 10.3% and 7.8%, respectively. Earlier results by Fan et al., (2006), Lu et al., (2013) and Xu et al., (2016) also reported that the GS3 is the major gene governing the grain length and minor gene for grain width. Similarly, one SSR marker, RM505 was showed association with GL, GW, L/B and TGW traits with their PVE as 4.4%, 2.6%, 1.9% and 3.8%, respectively. The present investigation reinforce the fact that grain size is a complex trait regulated by many genes located on different chromosomes. However, the gene specific markers, for GL, GW, TGW and L/B traits, such as GS3RGS1 and RM505 have potential to be used as foreground markers in marker-assisted breeding. Mining of complete gene sequences and other genes governing grain size traits is warranted further investigation adding some more germplasm. However, harmonious pyramiding of superior and novel alleles from diverse germplasm facilitates the designing of rice varieties suitable to diverse consumers in the world
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    ThesisItemOpen Access
    GENE EXPRESSION AND SEQUENCE ANALYSIS OF KNOWN YIELD GENES IN HIGH YIELDING VARIETIES OF RICE (Oryza sativa L.)
    (Acharya N.G. Ranga Agricultural University, 2017) SURESH NAIK, E; LAKSMI NARAYANA REDDY, V
    Rice (Oryza sative. L) is one of the major food crops in the world. Half of the world's population depends on rice as their staple food. Rice yield is governed by mainly three major traits i.e., number of tillers per plant, grain number per panicle, grain size and are directly associated with rice grain productivity. Rice yield is a complexly inherited trait governed by many genes/QTLs. As of now more than 34 genes have been molecularly cloned and characterized, however, using donors from China and Japan only. However, their gene expression and sequence variation needs to be validated before directly using them in the rice breeding programmes. In the present investigation, an attempt has been made to validate the gene expression and sequence variation of the important cloned genes governing yield traits in known India donor varieties. In all, 21indica rice genotypes have been selected including 15 high yielding and 6 low yielding. The phenotypic data of the important yield and its component traits such as, plant height, culm height, number of tillers per plant, panicle length, number of grains per panicle, days to 50% flowering, filled grains, chaffy grains, spikelet fertility, grain weight, grain length, grain width, biological yield, harvest index, and economic yield have been recorded. The analysis of variance (ANOVA) for the 21 rice genotypes for all the agronomic traits revealed highly significant differences among the entries for all the characters except for panicle length, grain length, and grain width. The expression analysis was carried out with gene specific primers designed from key yield genes from the flag leaf and young panicles. The semi qRT PCR gene expression analysis in the selected rice genotypes revealed differential expression of all yield genes. The Gn1a gene expression analysis revealed that the known Indian high grain number donor varieties with low or nil gene expression such as, NLR33892, Ranjit, BPT2601, BPT5204 and Rasi can be used as donors for. The gene expression analysis of OsSPL14 revealed that the high grain number varieties with high gene expression can be used as donor varieties viz., MTU1064, Dee-geo-woo-gen, Rasi, BPT5204, and MTU1010 from Indian rice germplasm. The DEP1 gene expression revealed that the high expression varieties with high grain number could be value for marker assisted introgression of this trait into highly adaptable low grain number varieties. The GIF1 gene expression analysis revealed that the high gene expression varieties with high grain weight such as, BPT 2678 and Basmati370 are the potential donors for grain weight/grain filling trait. The GW8 gene expression analysis in all 21 rice genotypes revealed that the high grain weight varieties with high GW8 expression such as, MTU3626, IR-8, Dee-geo-woo-gen, MTU1010, MTU1001, and INRC10192 can be used as donors from Indian rice germplasm. The Ghd7 expression analysis revealed that the high grain number, tall plant, and late flowering varieties with high Ghd7 expression such as, NLR33892, BPT 2678, Ranjit are can be used a donors from Indian rice germplasm. Besides gene expression analysis, the DNA sequence variation of most differentially expressed yield genes such as Ghd7, DEP1 and Gn1a also analyzed in all high yielding and low yielding varieties. The whole genome DNA sequence of Ghd7 gene (3918 bp) was resequenced in all 21 rice genotypes. In all, 104 SNPs and 141 indels were detected. It was found that certain nucleotide variations are unique to high grain number varieties such as, MTU1121, MTU1010, and Dee-Geo-Woo-Gen. It was found that certain nucleotide variations are unique to tall (>95cm) varieties such as, INRC10192, Tetep, and MTU1001. It was found certain nucleotide variations are unique to late flowering (>105 days) varieties such as, MTU7029 (G/A) at 1426, MTU1001 (T/C) at 1425 bp positions of the gene. However, there is no nucleotide variations were found for their specific traits in all the varieties. The whole genome DNA sequence of DEP1 gene (4363 bp) was resequenced in all high yielding and low yielding rice genotypes. In all, 99 SNPs and 338 indels were detected in the 5732 base pair alignment and of these, three SNPs (IR-8) and 61 indels were detected in the promoter region of the gene. However, there are no nucleotide variations found specific to either low or high grain number varieties. The whole genomic DNA sequence of Gn1a gene (6476 base pair) was resequenced in all genotypes. In total, 97 SNPs and 121 indels were detected in the 4837 base pair alignment. Of these, one SNP (MTU1064) and 28 indels were detected in the promoter region. It was found certain nucleotide variations are unique to high grain number varieties such as, NLR33892, MTU1064, MTU1010 (G/G) and Dee-geo-woo-gen (A/T) having SNPs at 1426 base pair position of the gene. However, there are no nucleotide variations in specific to either low or high grain number varieties were observed. In short, an attempt was made to identify the Indian donor varieties comparison of important yield genes based on consistent gene expression and sequence analysis with reported donors. The shortlisted donors for the yield traits can be right away used in the rice breeding programmes.
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    ThesisItemOpen Access
    SELECTIVE LINE GENOTYPING FOR IDENTIFICATION OF MARKERS ASSOCIATED WITH HEAT TOLERANCE IN RICE (Oryza sativa L.)
    (Acharya N.G. Ranga Agricultural University, 2017) ARPITHA SHANKAR, BANDI; ESWARA REDDY, N.P.
    Due to global warming and quickening industrialization environment is changing day by day and heat stress has become a major challenge for sustained production of rice. Rice is highly sensitive to heat stress during all growth stages, which will reduce the yield and create great losses. Production levels are decreasing gradually due to high temperature conditions. Hence, the present investigation was carried out to identify rice genotypes which can withstand high temperature conditions by employing Selective Line Genotyping approach. A set of 74 genotypes were tested for heat tolerance under laboratory conditions employing Temperature Induction Response (TIR) technique with three temperature conditions viz. Control at room temperature, Sub-lethal gradual exposure to 38˚C -55˚C range and Lethal at 55˚C. Based on survival percentage (SP), relative root length, and relative shoot length measured under sub-lethal conditions over control, 14 genotypes were selected each under tolerant and sensitive classes. The genotypes under tolerant class fell between 80-100% survivability. Of 14 tolerant genotypes, two genotypes viz. FR13A and Swarna Sub1A showed 100% survivability and were highly out performed to check genotypes in relative root length (62.53% and 47.56%, respectively) and shoot length (106.20% and 40.74%, respectively), in comparison to known tolerant genotypes. Next to survival percentage, root length plays an important role for selecting genotypes. In our study Maximum root length fell in the range of 4.8 cm - 10.74 cm and maximum RRL was observed for BPT1235 (82.54%). Also when it comes to shoot length, highest shoot length was recorded in BPT1235 which is about 11.75cm. Based on the survival percentage (SP), RRL and RSL of genotypes, a total of 14 genotypes under each class viz. heat tolerant and heat sensitive classes were selected and used for molecular studies employing selective line genotyping approach (SLG). Under selective line genotyping approach, the selected tolerant and sensitive sets were genotyped with 51 SSR and genic markers. Out of all the 51 markers which were genotyped, the markers RM17270, RM16216, RM5687 and TTC/TTM gave polymorphic alleles, whereas 92% the markers couldn’t distinguish tolerant set from sensitive and as well among reported tolerant genotypes (N22, Dular and Nipponbare). In our study, the alleles generated by different polymorphic markers were not clearly distinguished the tolerant set from sensitive set of genotypes. Among the reported genotypes also the allele sizes were varied except for the marker TTC/TTM, as they are from different sub groups of rice. N22 and Dular comes under Aus group, whereas Nipponbare comes under japonica group. From the experiment, we have concluded that both heat stress tolerant genotypes FR13A and SwarnaSub1A can be used as donor sources for heat tolerance because these genotypes proved themselves to be good performers under sublethal conditions, also their amplification pattern with well reported loci RM17270 is similar to checks Dular and Nipponbare. Although, the other three markers are not much informative in the current study, to distinguish the tolerant group from sensitive group, they are reported to be linked to heat tolerance by different research groups. Thus, our study has unveiled valuable markers (regions) and genotypes in developing alternative donor sources in indica rice, rather original aus and japonica group, where they originally identified, to use them in heat tolerance breeding programmes for better yields. Put together the involvement of small set of phenotyping panel and use of extremely core set of genotyping panel for SLG that generated most relevant association of potent markers along with identified donors comparable to QTL mapping results. Further, the diverse allele pattern exhibited by genotypes alike large association panel, additional knowhow of the degree of association of a locus makes the SLG technique to be challenged as greatly powerful.
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    ThesisItemOpen Access
    IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES IN RESPONSE TO MID-SEASON DROUGHT IN GROUNDNUT (Arachis hypogaea L.)
    (Acharya N.G. Ranga Agricultural University, 2017) APARNA, ERAGAM; AMARAVATHI, Y
    Drought is one of the major constraints in groundnut and governed by many genes with small effects operating in a coordinating manner. The present investigation was aimed for identification of differentially expressed transcripts in response to midseason drought in groundnut. To this end, a total of eleven genotypes viz., ICGV 07132, ICGV 07070, TCGS 1398, TCGS 1157, TCGS 1073, TCGS 1173, MLTG 4, Narayani, Tirupati 1, Kadiri 9 and Kadiri 6 were screened in pot culture for moisture stress tolerance. Among the eleven genotypes, TCGS 1157 and MLTG 4 genotypes showed early recovery after reaching the permanent wilting point and were grouped into moisture stress tolerant group. In contrast, Narayani and Kadiri 6 were highly sensitive to moisture stress. The field experiments were carried out at the research farm of Regional Agricultural Research Station (RARS) and molecular analysis at Genomics lab, Institute of Frontier Technology (IFT), RARS, Tirupati. The contrasting genotypes for mid-season drought viz., MLTG 4 and TCGS 1157 (tolerant) and Narayani and Kadiri 6 (susceptible) were further analyzed for morphological, physiological, biochemical and molecular parameters submitted to midseason moisture stress (50-80 DAS) in the field conditions. xiv SPAD Chlorophyll Meter Reading (SCMR) and Specific Leaf Area (SLA) were considered as surrogate traits for drought tolerance. The SPAD Chlorophyll Meter Reading values were increased as moisture stress period was increased upto 30 days in both drought tolerant and susceptible groundnut genotypes studied. SCMR can be used as non-destructive measure to estimate chlorophyll density while screening groundnut genotypes for drought tolerance. SLA decreased significantly in drought tolerant genotypes than in drought susceptible genotypes. Based on the SLA values, groundnut genotypes can be clearly distinguished from the drought susceptible genotypes. The increased levels of proline under drought stress can be better considered as drought stress indicator in groundnut. The accumulation of proline was more as the moisture stress progressed up to 30 days in all groundnut genotypes under the study. The total chlorophyll content under moisture stress imposed in groundnut genotypes initially was increased up to 70 DAS and declined at 80 DAS except for TCGS 1157. This was most probably due to prolonged vegetative growth phase in TCGS 1157 (120 days duration) when compared to MLTG 4, Narayani and Kadiri 6. To protect the cell from Reactive Oxygen Species generated in photorespiration, both catalase and peroxidase activities were increased in all the genotypes submitted to prolonged moisture stress. To unravel the molecular mechanisms conditioning drought tolerance, transcriptome was analyzed in groundnut subjected to mid-season stress (50-80DAS). To identify differentially expressed transcripts, cDNARAPD analysis was carried out using total RNA collected from leaves under well watered (control) and moisture stress situations at 10 (60 Days After Sowing), 20 (70 Days After Sowing) and 30 (Days After Sowing) days. Transcriptome was analyzed by cDNA-RAPD to identify differentially expressed transcripts in groundnut subjected to mid-season stress. cDNA-RAPD profiles with 35 RAPD markers resulted in a total of 823 reproducible differentially expressed transcripts in three regimes of moisture stresses. Among the 823 differentially expressed transcripts, 523 transcripts exhibited qualitative difference while 300 transcripts displayed quantitative differences in banding pattern of cDNA-RAPD profiles among all the four genotypes.