Genetic diversity and population structure analysis of Asian and African aromatic rice (Oryza sativa L.) genotypes

Mishra, Anurag; Kumar, Pushpendra; Shamim,; Tiwari, Kapil K.; Fatima, Parveen; Srivastava, Deepti; Singh, Rajendra; Yadav, Prashant

doi:10.1007/s12041-019-1131-0

Cited by 17 publications

(12 citation statements)

References 46 publications

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“…Rice has been cultivated in Indonesia from the time between 2000 and 1400 B.C., while the production has considerably increased since 1925, thereby giving rise to a number of rice varieties. There are two groups of the grains based on their aroma (i.e., aromatic and non-aromatic) [2].…”

Section: Introductionmentioning

confidence: 99%

Key-Marker Volatile Compounds in Aromatic Rice (Oryza sativa) Grains: An HS-SPME Extraction Method Combined with GC×GC-TOFMS

et al. 2019

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The aroma of rice essentially contributes to the quality of rice grains. For some varieties, their aroma properties really drive consumer preferences. In this paper, using a dynamic headspace solid-phase microextraction (HS-SPME) system coupled to a two-dimensional gas chromatography (GC×GC) using a time-of-flight mass spectrometric detector (TOFMS) and multivariate analysis, the volatile compounds of aromatic and non-aromatic rice grains were contrasted to define some chemical markers. Fifty-one volatile compounds were selected for principal component analysis resulting in eight key-marker volatile compounds (i.e., pentanal, hexanal, 2-pentyl-furan, 2,4-nonadienal, pyridine, 1-octen-3-ol and (E)-2-octenal) as responsible for the differences between aromatic and non-aromatic rice varieties. The factors that are most likely to affect the HS-SPME efficiency for the aforementioned key-marker compounds were evaluated using a 2III5−2 fractional factorial design in conjunction with multi-response optimisation. The method precision values, expressed as % of coefficient of variation (CV), were ranging from 1.91% to 26.90% for repeatability (n = 9) and 7.32% to 37.36% for intermediate precision (n = 3 × 3). Furthermore, the method was successfully applied to evaluate the volatile compounds of rice varieties from some Asian countries.

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Section: Introductionmentioning

confidence: 99%

Key-Marker Volatile Compounds in Aromatic Rice (Oryza sativa) Grains: An HS-SPME Extraction Method Combined with GC×GC-TOFMS

et al. 2019

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“…As Pusa 1652 is an improved semi-dwarf version of a short-grain aromatic landrace, Kalanamak, obtained by crossing with Pusa 1176, the semi-dwarfism in Pusa 1652 (Pusa 1176/Kalanamak//Kalanamak*1) could be traced back to Pusa 1176 based on pedigree data ( Figure S4 ). Pusa 1176 is an aromatic semi-dwarf variety, but Kalanamak is a tall landrace [ 33 ]. Furthermore, Pusa 1176 has been developed from a cross between a mutant, Bindli Mutant 34 (BM34), and an aromatic landrace from Assam, IRGC16136.…”

Section: Discussionmentioning

confidence: 99%

Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection

Bhuvaneswari

Krishnan

Ellur

et al. 2020

Plants

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The semi-dwarfing allele, sd1-d, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), sd1-d, derived from a spontaneous mutation, has a 383-bp deletion in the SD1 gene. To date, as many as seven alleles of the SD1 gene have been identified and used in rice improvement, either with a functional single-nucleotide polymorphism (SNP), with insertion–deletions (InDels), or both. Here, we report discovery of a novel SNP in the SD1 gene from the rice genotype, Pusa 1652. Genetic analysis revealed that the inheritance of the semi-dwarfism in Pusa 1652 is monogenic and recessive, but it did not carry the sd1-d allele. However, response to exogenous gibberellic acid (GA3) application and the subsequent bulked segregant and linkage analyses confirmed that the SD1 gene is involved in the plant height reduction in Pusa 1652. Sequencing of the SD1 gene from Pusa 1652 revealed a novel transition in exon 3 (T/A) causing a nonsense mutation at the 300th codon. The stop codon leads to premature termination, resulting in a truncated protein of OsGA20ox2 obstructing the GA3 biosynthesis pathway. This novel recessive allele, named sd1-bm, is derived from Bindli Mutant 34 (BM34), a γ-ray induced mutant of a short-grain aromatic landrace, Bindli. BM34 is the parent of an aromatic semi-dwarf cultivar, Pusa 1176, from which Pusa 1652 is derived. The semi-dwarfing allele, sd1-bm, was further validated by developing a derived cleaved amplified polymorphic sequence (dCAPS) marker, AKS-sd1. This allele provides an alternative to the most widely used sd1-d in rice improvement programs and the functional dCAPS marker will facilitate marker-assisted introgression of the semi-dwarf trait into tall genotypes.

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“…Rice improvement efforts have thus been directed towards incorporating biotic and abiotic resistance to the cultivars and the physiological processes governing yield potential to optimize growth duration and improve grain quality of the cultivars [4,5]. The wide range of genetic diversity in Oryza species has been well documented [6][7][8][9][10]. In particular, the wild species closely related to cultivated rice have a valuable gene pool and play a pivotal role in rice breeding programs by contributing genes resistant to biotic stresses and tolerance to abiotic stresses [2,5,11].…”

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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Genetic diversity and population structure analysis of Asian and African aromatic rice (Oryza sativa L.) genotypes

Cited by 17 publications

References 46 publications

Key-Marker Volatile Compounds in Aromatic Rice (Oryza sativa) Grains: An HS-SPME Extraction Method Combined with GC×GC-TOFMS

Key-Marker Volatile Compounds in Aromatic Rice (Oryza sativa) Grains: An HS-SPME Extraction Method Combined with GC×GC-TOFMS

Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection

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

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