Genome-Wide Consistent Molecular Markers Associated with Phenology, Plant Production and Root Traits in Diverse Rice (&lt;i&gt;Oryza sativa&lt;/i&gt; L.) Accessions under Drought in Rainfed Target Populations of the Environment

Deshmukh, V. D.; Mankar, Sumeet; Muthukumar, C.; Divahar, P.; Bharathi, A.; Thomas, Helen Baby; Rajurkar, Ashish B.; Sellamuthu, Reena; Poornima, R.; Senthivel, S.; Babu, R. Chandra

doi:10.18520/cs/v114/i02/329-340

Cited by 9 publications

(4 citation statements)

References 53 publications

(59 reference statements)

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“…Thurber et al [ 112 ] studied 105 weedy rice accessions to map shattering loci to understand the influence of evolutionary pathway on rice domestication. In addition to the difficulty involved in root phenotyping approaches, researchers were successful in identifying genes associated with various root architectural traits in rice with 93 temperate [ 113 ] and field study with 49 [ 114 ] landrace accessions, in wheat which is very complex in contrast to rice genome composition and ploidy levels by using 91 genotypes [ 115 ] and with model plant, Arabidopsis (96 accessions) grown under nitrogen [ 116 ] and potassium nitrate [ 117 ] treatments respectively .…”

Section: Discussionmentioning

confidence: 99%

Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces

et al. 2021

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Background Asian cultivars were predominantly represented in global rice panel selected for sequencing and to identify novel alleles for drought tolerance. Diverse genetic resources adapted to Indian subcontinent were not represented much in spite harboring useful alleles that could improve agronomic traits, stress resilience and productivity. These rice accessions are valuable genetic resource in developing rice varieties suited to different rice ecosystem that experiences varying drought stress level, and at different crop stages. A core collection of rice germplasm adapted to Southwestern Indian peninsular genotyped using SSR markers and characterized by contrasting water regimes to associate genomic regions for physiological, root traits and yield related traits. Genotyping-By-Sequencing of selected accessions within the diverse panel revealed haplotype variation in genic content within genomic regions mapped for physiological, morphological and root traits. Results Diverse rice panel (99 accessions) were evaluated in field and measurements on plant physiological, root traits and yield related traits were made over five different seasons experiencing varying drought stress intensity at different crop stages. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Association mapping revealed genetic variation among accessions and revealed 14 genomic targets associated with different physiological, root and plant production traits. Certain accessions were found to have beneficial allele to improve traits, plant height, root length and spikelet fertility, that contribute to the grain yield under stress. Genomic characterization of eleven accessions revealed haplotype variation within key genomic targets on chromosomes 1, 4, 6 and 11 for potential use as molecular markers to combine drought avoidance and tolerance traits. Genes mined within the genomic QTL intervals identified were prioritized based on tissue specific expression level in publicly available rice transcriptome data. Conclusion The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars. Alleles associated with plant height, specific leaf area, root length from PTB8 and spikelet fertility and grain weight from PTB26 can be harnessed in future rice breeding program.

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Section: Discussionmentioning

confidence: 99%

Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces

et al. 2021

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“…Due to various factors such as climate change and irrigation malpractices, the soil salinity is predicted to increase by 16.2 million hectares by 2050 [47,48]. Among abiotic stresses, soil salinity is the second largest cause of crop loss in rice after drought [49,50]. Saline stress primarily affects rice during its seedling, early vegetative, and reproductive stages [49,51].…”

Section: Lysine Content In Ricementioning

confidence: 99%

Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice

et al. 2021

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Lysine is the first limiting essential amino acid in rice because it is present in the lowest quantity compared to all the other amino acids. Amino acids are the building block of proteins and play an essential role in maintaining the human body’s healthy functioning. Rice is a staple food for more than half of the global population; thus, increasing the lysine content in rice will help improve global health. In this paper, we studied the lysine biosynthesis pathway in rice (Oryza sativa) to identify the regulators of the lysine reporter gene LYSA (LOC_Os02g24354). Genetically intervening at the regulators has the potential to increase the overall lysine content in rice. We modeled the lysine biosynthesis pathway in rice seedlings under normal and saline (NaCl) stress conditions using Bayesian networks. We estimated the model parameters using experimental data and identified the gene DAPF(LOC_Os12g37960) as a positive regulator of the lysine reporter gene LYSA under both normal and saline stress conditions. Based on this analysis, we conclude that the gene DAPF is a potent candidate for genetic intervention. Upregulating DAPF using methods such as CRISPR-Cas9 gene editing strategy has the potential to upregulate the lysine reporter gene LYSA and increase the overall lysine content in rice.

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“…Due to various factors such as climate change and irrigation malpractices, the soil salinity is predicted to increase by 16.2 million hectares by 2050 [45,46]. Among abiotic stresses, soil salinity is the second largest cause of crop loss in rice after drought [47,48].Saline stress primarily affects rice during its seedling, early vegetative, and reproductive stages [47,49]. We have extensively studied and identified regulators of drought response in our previous works [42,43].…”

Section: Figurementioning

confidence: 99%

Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice

Lahiri¹,

Rastogi²,

Datta³

et al. 2021

Preprint

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Lysine is the first limiting essential amino acid in rice because it is present in the lowest quantity compared to all the other amino acids. Amino acids are the building block of proteins and play an essential role in maintaining the human body’s healthy functioning. Rice is a staple food for large proportion of the global population, thus increasing the lysine content in rice will improve its nutritional value. In this paper, we studied the lysine biosynthesis pathway in rice (Oryza Sativa) to identify the regulators of the lysine reporter gene LYSA (LOC_Os02g24354). Genetically intervening at the regulators has the potential to increase the overall lysine content in rice. We modeled the lysine biosynthesis pathway in rice seedlings under normal and saline (NaCl) stress conditions using Bayesian networks. We estimated the model parameters using experimental data and identified the gene DAPF(LOC_Os12g37960) as a positive regulator of the lysine reporter gene LYSA under both normal and saline stress conditions. Based on this analysis, we conclude that the gene DAPF is a potent candidate for genetic intervention. Upregulating DAPF using methods such as CRISPR-Cas9 has the potential to upregulate the lysine reporter gene LYSA and increase the overall lysine content in rice.

show abstract

Genome-Wide Consistent Molecular Markers Associated with Phenology, Plant Production and Root Traits in Diverse Rice (<i>Oryza sativa</i> L.) Accessions under Drought in Rainfed Target Populations of the Environment

Cited by 9 publications

References 53 publications

Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces

Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces

Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice

Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice

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