Bulk Segregant Analysis for Aluminium Toxicity Tolerance in F2:3 Population of Rice

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dc.contributor.advisorTyagi, Wricha
dc.contributor.authorSreeja, Akunuru
dc.date.accessioned2023-03-24T05:22:46Z
dc.date.available2023-03-24T05:22:46Z
dc.date.issued2022-01
dc.description.abstractSoil acidity is a key limiting factor for crop productivity around the world. Other than the frigid zones, thirty percent of the world's land is acidic, accounting for about half of all potentially arable land, and rice is grown on about 12 percent of the world's cultivated acidic soils. Aluminium toxicity is a quantitative trait in rice and therefore, genes/markers need to be identified for molecular breeding. The current study was conducted to screen and identify superior and inferior performing bulks in a set of 197 F2:3 progeny derived from JR-31 × CAUS-107 cross treated with aluminium (Al) in one round and low phosphorous (Pi) followed by Al in the other round of hydroponics and then, to determine the markers associated with tolerance. The phenotypic traits shoot length, root length, and visual observations in the first round and shoot length, longest root length, average root length, shoot fresh weight, root fresh weight, root spread, root area, and hematoxylin scoring on a scale of 1 to 5. The parents were surveyed for polymorphism using 76 SSR and 56 candidate gene-based (CG) markers which revealed 31 monomorphic and 23 polymorphic markers. Of which, four genic SSR and five CG markers were used for the genotyping of the extreme bulks of 76 progeny identified by two rounds of screening. According to ANOVA (CRD), all the phenotypic traits showed a significant variation in the progenies under both rounds of screening at 1% level of significance with values ranging from 3.48 (root weight (RW)) to 33.2 (average root length (ARL). Correlation coefficient analysis indicated that the shoot length (SL) significantly correlated with root length (RL) (0.263) in the first round of Al toxicity tolerance screening at 1% level of significance. In the second round of screening for both low Pi and Al toxicity tolerance, correlation coefficient analysis between the phenotypic traits at a 1% level of significance revealed that the SL significantly correlated with LRL (0.606), average root length (ARL) (0.866), shoot fresh weight (SFW)(0.729), root fresh weight (RFW) (0.393), root spread (RS) (0.899) and root area (RA) (0.916). The LRL significantly correlated with ARL (0.716), SFW (0.55), RFW (0.395), RS (0.686), and RA (0.691). The ARL significantly correlated with SFW (0.649), RFW (0.282), RS (0.949), and RA (0.949). The SFW significantly correlated with RFW (0.385), RS (0.654), and RA (0.683). The RFW significantly correlated with RS (0.334) and RA (0.359). The RS significantly correlated with and RA (0.981). While hematoxylin stain score negatively correlated with the LRL (0.261) at a 1% level of significance. When phenotypic traits of both the rounds of screening of hydroponics were compared, SL (Al) significantly correlated with the SL (Al+Pi) (0.317) at 1% level of significance, and with RS (Al+Pi) (0.234) and RA (Al+Pi) (0.25) at 5% level of significance. While the RL (Al), significantly correlated with SL (Al+Pi) (0.255), LRL (Al+Pi) (0.489), ARL (Al+Pi) (0.338), RA (Al+Pi) (0.339), positively at 1% level of significance and with hematoxylin stain score (Al+Pi) (0.227) negatively at 5% level of significance. When the yield traits were compared with phenotypic traits of hydroponics, where only Al toxicity tolerance was screened, SL (Al) positively correlated with the FGPP (0.142), and negatively with TN60 (0.147). Root length (Al) positively correlated with the FGPP (0.179) and SF% (0.141) at 5% level of significance. The yield traits did not correlate with phenotypic traits of hydroponics, where both low Pi and Al toxicity tolerances were screened. A polymorphic survey of parents with 76 SSR and 56 Candidate gene-based markers revealed 31 monomorphic and 23 polymorphic markers. From those polymorphic markers, 4 genic SSR and 5 Candidate gene-based markers were used for the genotyping of the bulks from the phenotyping screenings. Allele bands were scored and the marker-trait association was performed using simple t-test and chi-square analyses. The t-test revealed that the marker, HvSSR01-34 associated with the longest root length (Al+Pi) (-Log10P = 1.5); marker HvSSR02-14 with TN60 (-Log10P = 1.28), SL (Al) (-Log10P =1.89), RL (Al) (-Log10P = 1.21), overall score (Al) (-Log10P= 1.6), ARL (Al+Pi) ((-Log10P = 1.33), SFW (Al+Pi) (-Log10P = 1.11), RS (Al+Pi) (1.65), and RA (Al+Pi) (-Log10P = 1.42). The marker RM12557 associated with RL (Al) (-Log10P = 1.9), overall score (Al) (-Log10P= 1.84), and RS (Al+Pi) (-Log10P = 1.14); marker AR051-2 associated with PN (1.05), the FGPP (-Log10P = 1.1), root length (Al) (-Log10P = 1.39), overall score (Al) (-Log10P= 1.21), overall score (Al+Pi) (-Log10P= 0.99) and RW (Al+Pi) (-Log10P = 1.32). The marker AU01-3 associated with SFW (Al+Pi) (- Log10P= 1.29) and RA (Al+Pi) (-Log10P = 1.01); FR033-3 with the LRL (Al+Pi) (-Log10P= 1.01); PR026-3 with RL (Al) (1.01) and hematoxylin stain score (Al+Pi) (-Log10P= 1.17) and PR062-3 with TN60 (-Log10P= 1.19), PN (-Log10P= 1.69), SL (Al) (-Log10P= 1.36), overall score (Al+Pi) (-Log10P= 0.99) and RW (Al+Pi) (-Log10P= 1.32). Chi-Square analysis based on 30 superior and 30 inferior progenies revealed that the CAUS-107 allele significantly associated with three markers at 5% level of significance. Markers HvSSR01-34; HvSSR02- 14 and RM12557 associated with SF% (5.554); SL (Al) (5.684) and RL (Al) (χ2 = 5.225) and overall score (Al) (χ2 = 4.139), respectively. While JR-31 allele for marker HvSSR02-14 associated significantly with the overall score (Al) (χ2 = 4.669). Chi-Square analysis based on 20 superior and 20 inferior progenies revealed that four markers were significantly associated with the phenotypic traits at 5% level of significance. AR051-2 associated with overall score (Al) (χ2 = 4.916) and with RL (Al) (χ2 = 5.121), respectively. While the marker PR062-3 showed allelic distortion with 71% of progeny having JR-31 type allele. To summarise the bulks based on phenotypic data were significantly different and genotyping on a set of 76 progeny revealed that 7 markers viz. HvSSR01-34; RM12557; AR051-2; AU01-3; FR033-3; PR026-3 and PR062-3 associated with various traits under hydroponics conditions. Three markers viz, HvSSR01-34; AR051-2, and PR062-3 associated with better performance under lowland acidic soil conditions. These markers and traits can be used for MAS after further evaluation.en_US
dc.identifier.urihttps://krishikosh.egranth.ac.in/handle/1/5810195729
dc.keywordsBulk segregant analysis, rice, Al toxicity, low Pi, hydroponics, markersen_US
dc.language.isoEnglishen_US
dc.publisherCollege of Post Graduate Studies in Agricultural Sciences, CAU-Imphal, Umiamen_US
dc.subBiotechnology and molecular Biologyen_US
dc.themeAcademic Researchen_US
dc.these.typeM.Scen_US
dc.titleBulk Segregant Analysis for Aluminium Toxicity Tolerance in F2:3 Population of Riceen_US
dc.typeThesisen_US
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