Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers

Abstract

Background and aims: Weedy rice (Oryza sativa f. spontanea) is one of the most notorious weeds occurring in rice-planting areas worldwide. The objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from Liaoning Province in North-eastern China and to explore the possible origin of these weedy populations by comparing their genetic relationships with rice varieties (O. sativa) and wild rice (O. rufipogon) from different sources.

Methods: Simple sequence repeat (SSR) markers were used to estimate the genetic diversity of 30 weedy rice populations from Liaoning, each containing about 30 individuals, selected rice varieties and wild O. rufipogon. Genetic differentiation and the relationships of weedy rice populations were analysed using cluster analysis (UPGMA) and principle component analysis (PCA).

Key results: The overall genetic diversity of weedy rice populations from Liaoning was relatively high (H(e) = 0.313, I = 0.572), with about 35 % of the genetic variation found among regions. The Liaoning weedy rice populations were closely related to rice varieties from Liaoning and japonica varieties from other regions but distantly related to indica rice varieties and wild O. rufipogon.

Conclusions: Weedy rice populations from Liaoning are considerably variable genetically and most probably originated from Liaoning rice varieties by mutation and intervarietal hybrids. Recent changes in farming practices and cultivation methods along with less weed management may have promoted the re-emergence and divergence of weedy rice in North-eastern China.

Fig. 1

Sampling sites of weedy rice (Oryza sativa f. spontanea) populations in Liaoning Province of China.

Fig. 2

Linear correlation between genetic diversity (H_e) and the years when weedy rice was found in different localities of Liaoning Province.

Fig. 3

Dendrogram (UPGMA) constructed based on polymorphisms of 20 SSR loci in 30 weedy rice (Oryza sativa f. spontanea) populations, different groups of rice varieties (O. sativa) and wild rice (O. rufipogon), using Nei's unbiased genetic distance coefficients (Nei, 1978, see Table 6). Codes for the weedy rice populations, rice varieties and wild rice refer to those in Tables 1 and 2. The arrow in the dendrogram indicates the group of rice varieties from Liaoning Province.

Fig. 4

Scatter plot of the first and second principle components based on variation of 20 SSR loci for 949 individuals of weedy rice and cultivars from Liaoning Province and other regions (japonica) in China, showing a considerable area of overlap (shaded) of the Liaoning rice varieties with many weedy rice individuals. The letters dg, hc, ps, sjt, tl and zh in the top left corner denote the individuals of weedy rice from Donggang, Haicheng, Panshan, Sujiatun, Tieling and Zhuanghe regions, respectively; c-LN and jap-Ch denote rice varieties from Liaoning and other regions in China.