Oryza nivara Sharma et Shastry

Guttikonda, Haritha; Malathi, S.; Balakrishnan, Divya; Swamy, B. P. Mallikarjuna; Mangrauthia, Satendra K.; Neelamraju, Sarla

doi:10.1007/978-3-319-71997-9_20

Cited by 14 publications

(9 citation statements)

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“…The current study sought the assistance of the wild annual progenitor species of cultivated rice, Oryza nivara. Wild species house tremendous allelic variation and have been utilized in the past for breeding of many economically important traits (Khush and Ling 1974;Tanksley and McCouch 1997;Thanh et al 2006;Kaladhar et al 2008;Swamy et al 2014;Haritha et al 2018). It could be possible to identify the donors in this rice germplasm that have lower straw silica content particularly in straw in such a way that does not hamper the plant growth and development.…”

Section: )mentioning

confidence: 99%

Genome wide association studies and candidate gene mining for understanding genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions

Gowda

Sharma

Gill

et al. 2023

Preprint

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Background Rice is a high silicon-accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crop plants. However, presence of high silica content is detrimental in rice straw and its management, hampering its use as animal feed and as raw material in multiple industries. Rice straw management is a serious concern in North-Western India and it is eventually burned in situ by the farmers contributing to air pollution. A practical solution to the said issue could lie in reducing the silica content in rice, while also attaining sound plant growth. Results A set of 258 Oryza nivara accessions along with 25 cultivated varieties were used to assess the variation for straw silica content using molybdenum blue colorimetry method. Large and continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08-16%, while it varied from 7.95–15.81% in the cultivated varieties. The O. nivara accessions containing 43–54% lower straw silica content than the currently prominent cultivated varieties in the region were identified. A set of 22,528 high-quality single nucleotide polymorphism (SNP) among the 258 O. nivara accessions were used for estimating population structure and genome wide association studies (GWAS). A weak population structure with 59% admixtures was identified among O. nivara accessions. Further, multi-locus GWAS revealed the presence of 14 marker trait associations (MTAs) for straw silica content, with six of them co-localizing with previously reported QTLs. Twelve out of the 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses among the QTL regions revealed the presence of promising candidate genes, including ABC transporter, Casparian thickening genes, multi-drug and toxin extrusion (MATE) protein, F-box domains, and MYB-transcription factor domains. Besides ortho-QTLs among rice and maize genomes were also identified which could open up ways for further genetic analysis of this trait. Conclusion The findings of the study could aid in further understanding and characterizing genes for Si transport and regulation in the plant body. The donors carrying the alleles for lower straw silica content can be used in further marker-assisted breeding programmes in order to develop rice varieties with lower silica content along with higher yield potential.

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Section: )mentioning

confidence: 99%

Genome wide association studies and candidate gene mining for understanding genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions

Gowda

Sharma

Gill

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…The current study sought the assistance of the wild annual progenitor species of cultivated rice, O. nivara. Wild species house tremendous allelic variation and have been utilized in the past for the breeding of many economically important traits ( Khush and Ling, 1974 ; Tanksley and McCouch, 1997 ; Thanh et al., 2006 ; Kaladhar et al., 2008 ; Swamy et al., 2014 ; Haritha et al., 2018 ). It could be possible to identify donors in this rice germplasm that have a lower straw silica content, particularly in straw, in such a way that it does not hamper the plant’s growth and development.…”

Section: Introductionmentioning

confidence: 99%

Genome wide association studies and candidate gene mining for understanding the genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions

et al. 2023

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Rice is a high-silica (SiO2·nH2O) accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crops. However, the presence of high silica content is detrimental to rice straw management, hampering its use as animal feed and as raw material in multiple industries. Rice straw management is a serious concern in north-western India, and it is eventually burned in situ by farmers, contributing to air pollution. A practical solution could lie in reducing the silica content in rice while also attaining sound plant growth. A set of 258 Oryza nivara accessions along with 25 cultivated varieties of Oryza sativa was used to assess the variation in straw silica content using the molybdenum blue colorimetry method. A large continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08% to 16%, while it varied from 6.18% to 15.81% in the cultivated varieties. The O. nivara accessions containing 43%–54% lower straw silica content than the currently prominent cultivated varieties in the region were identified. A set of 22,528 high-quality single nucleotide polymorphisms (SNPs) among 258 O. nivara accessions was used for estimating population structure and genome-wide association studies (GWAS). A weak population structure with 59% admixtures was identified among O. nivara accessions. Further, multi-locus GWAS revealed the presence of 14 marker-trait associations (MTAs) for straw silica content, with six of them co-localizing with previously reported quantitative trait loci (QTL). Twelve out of 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses revealed the presence of promising candidate genes, including those encoding the ATP-binding cassette (ABC) transporter, Casparian thickening, multi-drug and toxin extrusion (MATE) protein, F-box, and MYB-transcription factors. Besides, ortho-QTLs among rice and maize genomes were identified, which could open ways for further genetic analysis of this trait. The findings of the study could aid in further understanding and characterizing genes for Si transport and regulation in the plant body. The donors carrying the alleles for lower straw silica content can be used in further marker-assisted breeding programs to develop rice varieties with lower silica content and higher yield potential.

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“…These two species can readily hybridize with cultivated rice. Oryza nivara is the most closely related to O. sativa in terms of phenotypic and lifehistory traits and probably the direct progenitor of Asian rice [32,33]. Both species showed allopatric distribution in Sri Lanka, enhancing the potential of sharing genes with cultivated rice [34][35][36].…”

Section: Introductionmentioning

confidence: 99%

“…Both species showed allopatric distribution in Sri Lanka, enhancing the potential of sharing genes with cultivated rice [34][35][36]. The annual O. nivara is globally distributed in the tropics and subtropics of Asia [13] and Southern and Southeast Asia [32,33]. However, O. nivara found in South Asia is morphologically more differentiated than mainland Asia [37].…”

Section: Introductionmentioning

confidence: 99%

Phenotypic Characterization of Oryza nivara (Sharma et Shastry) Collected from Different Ecological Niches of Sri Lanka

Sandamal¹,

Tennakoon²,

Wijerathna³

et al. 2022

Phyton

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Information on the genetic diversity of wild rice species in Sri Lanka is relatively meagre, though it plays a key role in crop improvement programs of cultivated rice (Oryza sativa L.). The present study was carried out to identify the morphological variation pattern of the wild populations of O. nivara in Sri Lanka. Seven populations (P1 to P7) collected from different agro-ecological regions were characterized in a common garden based on nine morphological traits. The findings revealed a high level of phenotypic variation between populations when compared to within a population. The most variable traits were the flag leaf panicle neck length (FLPNL) and flag leaf angle (FLA), whereas the least variable trait was the flag leaf length (FLL). Box plots clearly illustrated the large differentiation of phenotypic traits in the entire distribution of wild rice populations. The cumulative values of the two principal components, i.e., FLPNL and FLA, explained 58.7% of the total variance. Populations from similar natural habitats clustered together. The P7 was adapted to intercept more sunlight by increasing flag leaf width (FLW) and FLA to compete with weeds and other shrubs. P2 and P5 were the most closely related populations representing approximately similar ecological conditions of the dry zone. The P3 population from the intermediate zone showed a vigorous plant growth with the highest plant height, culm girth and awn length (P < 0.05). Knowledge of such morphological diversity would facilitate designing conservation strategies and basic information for the proper utilization of wild resources in rice genetic improvement.

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Oryza nivara Sharma et Shastry

Cited by 14 publications

References 142 publications

Genome wide association studies and candidate gene mining for understanding genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions

Genome wide association studies and candidate gene mining for understanding genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions

Genome wide association studies and candidate gene mining for understanding the genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions

Phenotypic Characterization of Oryza nivara (Sharma et Shastry) Collected from Different Ecological Niches of Sri Lanka

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