Morphological characterization and genetic identity of crop wild relatives of rice (Oryza sativa L.) collected from different ecological niches of India

Crop wild relatives of rice ( Oryza sativa L.) are an important reservoir of genes for broadening the genetic base of commercial varieties. India is the centre of genetic diversity of some of the wild as-well-as the cultivated rice species. In order to collect genetic diversity, explorations were un...

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Veröffentlicht in:	Genetic resources and crop evolution Jg. 67; H. 8; S. 2037 - 2055
Hauptverfasser:	Tiwari, Shailesh, Yadav, Mahesh C., Dikshit, Nilamani, Yadav, Vijay K., Pani, Dipti R., Latha, M.
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	Dordrecht Springer Netherlands 01.12.2020 Springer Nature B.V
Schlagworte:	Agriculture Biomedical and Life Sciences Cluster analysis color Cultivation Deoxyribonucleic acid DNA DNA sequencing Ecological niches Ecology Flowering genes genetic background Genetic diversity genetic improvement genetic variation Genomes Germplasm Grain cultivation India internal transcribed spacers Life Sciences Morphology Niches Oryza nivara Oryza officinalis Oryza rufipogon Oryza sativa panicles peduncle phenotypic variation Phenotypic variations Phylogeny Plant Genetics and Genomics plant height Plant Physiology Plant Sciences Plant Systematics/Taxonomy/Biogeography Research Article Rice Species wild rice Wild type India ITS region sequencing Morphological characterization Wild rice species AA-genome
ISSN:	0925-9864, 1573-5109
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Abstract	Crop wild relatives of rice ( Oryza sativa L.) are an important reservoir of genes for broadening the genetic base of commercial varieties. India is the centre of genetic diversity of some of the wild as-well-as the cultivated rice species. In order to collect genetic diversity, explorations were undertaken in six states located in different agro-ecological zones of India. Forty-four accessions belonging to four wild species ( Oryza rufipogon Griff., Oryza nivara Sharma et Shastry, Oryza officinalis Wall. ex Watt and Oryza sativa L. f. spontanea Roshev.) including two accessions of cultivated rice ( Oryza sativa L. subsp. indica Kato) were collected from different ecological niches. The rice accessions were characterized using 28 morphological descriptors, which included 15 qualitative and 13 quantitative traits. Wild rice accessions displayed a broad range of phenotypic variation for plant height, main heading days, days to 50% flowering, flag-leaf length and width, panicle shape and size, peduncle length, awning pattern, awn length and colour, seed length and width, seed length/width ratio and 100-seed weight. Cluster analysis based on Jaccard’s similarity coefficients derived from 28 morphological traits grouped 44 accessions into three clades. DNA sequencing revealed that internal transcribed spacer (ITS) region of 18S–5.8S–28S nuclear ribosomal cistron varied from 574 to 577 bp with mean of 576.1 bp in AA-genome species. GC content was high in ITS region, which varied from 69.57 to 70.36% with mean value of 69.99%. Neighbour-joining phylogenetic tree distinguished Oryza sativa – nivara – rufipogon complex from other species of AA-genome. The wild germplasm characterized in this study could be utilized in the genetic enhancement of cultivated rice.
AbstractList	Crop wild relatives of rice (Oryza sativa L.) are an important reservoir of genes for broadening the genetic base of commercial varieties. India is the centre of genetic diversity of some of the wild as-well-as the cultivated rice species. In order to collect genetic diversity, explorations were undertaken in six states located in different agro-ecological zones of India. Forty-four accessions belonging to four wild species (Oryza rufipogon Griff., Oryza nivara Sharma et Shastry, Oryza officinalis Wall. ex Watt and Oryza sativa L. f. spontanea Roshev.) including two accessions of cultivated rice (Oryza sativa L. subsp. indica Kato) were collected from different ecological niches. The rice accessions were characterized using 28 morphological descriptors, which included 15 qualitative and 13 quantitative traits. Wild rice accessions displayed a broad range of phenotypic variation for plant height, main heading days, days to 50% flowering, flag-leaf length and width, panicle shape and size, peduncle length, awning pattern, awn length and colour, seed length and width, seed length/width ratio and 100-seed weight. Cluster analysis based on Jaccard’s similarity coefficients derived from 28 morphological traits grouped 44 accessions into three clades. DNA sequencing revealed that internal transcribed spacer (ITS) region of 18S–5.8S–28S nuclear ribosomal cistron varied from 574 to 577 bp with mean of 576.1 bp in AA-genome species. GC content was high in ITS region, which varied from 69.57 to 70.36% with mean value of 69.99%. Neighbour-joining phylogenetic tree distinguished Oryza sativa–nivara–rufipogon complex from other species of AA-genome. The wild germplasm characterized in this study could be utilized in the genetic enhancement of cultivated rice. Crop wild relatives of rice ( Oryza sativa L.) are an important reservoir of genes for broadening the genetic base of commercial varieties. India is the centre of genetic diversity of some of the wild as-well-as the cultivated rice species. In order to collect genetic diversity, explorations were undertaken in six states located in different agro-ecological zones of India. Forty-four accessions belonging to four wild species ( Oryza rufipogon Griff., Oryza nivara Sharma et Shastry, Oryza officinalis Wall. ex Watt and Oryza sativa L. f. spontanea Roshev.) including two accessions of cultivated rice ( Oryza sativa L. subsp. indica Kato) were collected from different ecological niches. The rice accessions were characterized using 28 morphological descriptors, which included 15 qualitative and 13 quantitative traits. Wild rice accessions displayed a broad range of phenotypic variation for plant height, main heading days, days to 50% flowering, flag-leaf length and width, panicle shape and size, peduncle length, awning pattern, awn length and colour, seed length and width, seed length/width ratio and 100-seed weight. Cluster analysis based on Jaccard’s similarity coefficients derived from 28 morphological traits grouped 44 accessions into three clades. DNA sequencing revealed that internal transcribed spacer (ITS) region of 18S–5.8S–28S nuclear ribosomal cistron varied from 574 to 577 bp with mean of 576.1 bp in AA-genome species. GC content was high in ITS region, which varied from 69.57 to 70.36% with mean value of 69.99%. Neighbour-joining phylogenetic tree distinguished Oryza sativa – nivara – rufipogon complex from other species of AA-genome. The wild germplasm characterized in this study could be utilized in the genetic enhancement of cultivated rice.
Author	Pani, Dipti R. Yadav, Vijay K. Latha, M. Tiwari, Shailesh Yadav, Mahesh C. Dikshit, Nilamani
Author_xml	– sequence: 1 givenname: Shailesh surname: Tiwari fullname: Tiwari, Shailesh organization: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR) – sequence: 2 givenname: Mahesh C. orcidid: 0000-0002-7607-6875 surname: Yadav fullname: Yadav, Mahesh C. email: mahesh.yadav1@icar.gov.in organization: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR) – sequence: 3 givenname: Nilamani surname: Dikshit fullname: Dikshit, Nilamani organization: NBPGR Regional Station – sequence: 4 givenname: Vijay K. surname: Yadav fullname: Yadav, Vijay K. organization: Department of Genetics and Plant Breeding, C.S. Azad University of Agriculture and Technology – sequence: 5 givenname: Dipti R. surname: Pani fullname: Pani, Dipti R. organization: NBPGR Regional Station – sequence: 6 givenname: M. surname: Latha fullname: Latha, M. organization: NBPGR Regional Station
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Copyright	Springer Nature B.V. 2020 Springer Nature B.V. 2020.
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Keywords	ITS region sequencing Morphological characterization Wild rice species AA-genome
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Snippet	Crop wild relatives of rice ( Oryza sativa L.) are an important reservoir of genes for broadening the genetic base of commercial varieties. India is the centre... Crop wild relatives of rice (Oryza sativa L.) are an important reservoir of genes for broadening the genetic base of commercial varieties. India is the centre...
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SubjectTerms	Agriculture Biomedical and Life Sciences Cluster analysis color Cultivation Deoxyribonucleic acid DNA DNA sequencing Ecological niches Ecology Flowering genes genetic background Genetic diversity genetic improvement genetic variation Genomes Germplasm Grain cultivation India internal transcribed spacers Life Sciences Morphology Niches Oryza nivara Oryza officinalis Oryza rufipogon Oryza sativa panicles peduncle phenotypic variation Phenotypic variations Phylogeny Plant Genetics and Genomics plant height Plant Physiology Plant Sciences Plant Systematics/Taxonomy/Biogeography Research Article Rice Species wild rice Wild type
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Title	Morphological characterization and genetic identity of crop wild relatives of rice (Oryza sativa L.) collected from different ecological niches of India
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