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Study on the mating systems of wild rice Oryza rufipogon and O. nivara and their effects on population genetic variation

Cite this dataset

Tang, Liang et al. (2024). Study on the mating systems of wild rice Oryza rufipogon and O. nivara and their effects on population genetic variation [Dataset]. Dryad. https://doi.org/10.5061/dryad.h70rxwdr6

Abstract

As the wild ancestors of Asian cultivated rice, Oryza rufipogon Griff. and O. nivara Sharma et Shastry serve as valuable germplasms for rice breeding. Mating systems are important in shaping the level and pattern of population genetic variation, and are crucial for germplasm conservation. We genotyped 12 simple sequence repeats (SSR) markers for a large number of maternal plants and seeds collected from O. rufipogon and O. nivara populations distributed in Southeast Aisa and South China. Based on the 12 SSR markers, we estimated the outcrossing rates and other parameters of the mixed-mating model for the two wild rice species. We also assessed the level of genetic diversity and population structure for parental populations of O. rufipogon and O. nivara. Our study could facilitate in situ and ex situ conservation, and the utilization of these valuable germplasm resources.

README: Study on the mating systems of wild rice Oryza rufipogon and O. nivara and their effects on population genetic variation

https://doi.org/10.5061/dryad.h70rxwdr6

Description of the data and file structure

This file contains SSR genotypes of the two wild rice species (Oryza rufipogon and O. nivara) and their progenies. There are three Microsoft Excel sheets in the file. The first sheet contains the SSR genotypes of the maternal parents, i.e. the maternal populations of O. rufipogon and O. nivara. The second sheet contains the SSR genotypes of progenies of O. rufipogon, and the third sheet contains the SSR genotypes of progenies of O. nivara.

Each cell contains one SSR allele, so two consecutive cells represent a SSR genotype. The missing data were coded as 0.

Methods

A total of 12 O. rufipogon populations were sampled, of which eight were collected from China, and the other four were collected from Cambodia (2), Nepal (1), and Vietnam (1). Four populations of O. nivara were collected from Laos (2), Cambodia (1), and Nepal (1). For each population, 11-31 maternal plants were collected with 5-20 seeds per plant. Leaves of maternal plants and seedings were dried using silica gel. The total genomic DNA was extracted using the CTAB method. Totally 12 SSR markers were selected from the 125 SSR primer pairs developed in the study by McCouch et al. (2002). Polymerase chain reactions (PCR) was carried out in a T-personal thermal cycler. The amplified products were subjected to fragment analysis on an ABI 3730XL analyzer (Applied Biosystems). SSR genotyping was conducted using the GeneMarker software (SoftGenetics, State College, Pennsylvania, USA).

Funding

Hainan Province Science and Technology Special Fund, Award: ZDYF2022XDNY260