Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India

Abstract

The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the world. The efforts for conservation of rice germplasm in NE India should consider saving rice varieties representing different types with specific emphasis given to sali and jum types. The protection against the loss of vast genetic diversity found in indigenous rice varieties in NE India is crucial for maintaining future food security in the changing world.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-2-228) contains supplementary material, which is available to authorized users.

Alteration in the expression of MGMT and RUNX3 due to non-CpG promoter methylation and their correlation with different risk factors in esophageal cancer patients

“…30 NE region of India has the highest incidence of EC when compared to other regions of the country with an increasing trend. 31,32 In our study, we evaluated the promoter methylation status of MGMT and RUNX3 promoter in EC cases and controls by NGS and correlated with quantitative estimation of mRNA expression.…”

Identifikasi Gen Ketahanan terhadap (Xanthomonasoryzae pv. Oryzae), penyebab Penyakit Hawar Daun Bakteri padaPlasma Nutfah Padi Lokal Sulawesi Selatan

“…Alel ketahanan HDB pada aksesi Ase Pulut Jawa hanya terdeteksi pada empat lokus dari total tujuh lokus yang dianalisis, dengan rerata satu alel per lokusnya. Minimnya jumlah alel ini mengindikasikan adanya kemungkinan proses seleksi telah terjadi secara intensif selama musim tanam sehingga hanya alel superior saja yang masih bertahan dan terdeteksi (Choudhury et al, 2013;Sutoro et al, 2015).…”

“…Adanya keragaman alel menunjukkan peran penting petani lokal dalam konservasi indigenous plasma nutfah padi sebagai sumber genetik. Oleh karena itu, penerapan konservasi yang mengedepankan kearifan petani lokal sangat diperlukan dalam budi daya kultivar padi lokal (Brush dan Meng, 1998;Choudhury et al, 2013).…”

Genetic Diversity of Upland Rice Landraces From Java Island as Revealed by SSR Markers

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“…The pretty high diversity of upland rice in Java reflects the importance of traditional knowledge in conservation of indigenous rice genetic resources. Therefore, appropriate conservation measures should be taken to promote the cultivation of local varieties with local knowledge (Brush and Meng 1998;Choudhury et al 2013).…”