Molecular diversity and genetic structure of wild rice accessions ( Oryza rufipogon Griff.) in Guangdong Province, China
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RESEARCH ARTICLE
Molecular diversity and genetic structure of wild rice accessions (Oryza rufipogon Griff.) in Guangdong Province, China, as revealed by SNP markers Jing Zhang . Bingrui Sun . Chen Li . Wenfeng Chen . Liqun Jiang . Shuwei Lv . Zhilan Fan . Dajian Pan
Received: 21 June 2020 / Accepted: 6 October 2020 Ó Springer Nature B.V. 2020
Abstract Common wild rice (Oryza rufipogon Griff.) is a valuable germplasm resource for rice genetic improvement. However, it is endangered due to habitat loss. Assessment of its genetic diversity is essential for germplasm characterization, utilization, and conservation. In the present study, we developed a 79,422-single-nucleotide polymorphism genomewide array by specific-locus amplified fragment sequencing (SLAF-seq) and used it to genotype 110 common wild rice accessions from different agroclimatic zones in Guangdong Province, China. The number of SNPs on each chromosome was consistent
Jing Zhang and Bingrui Sun contributed equally to this work.
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10722-020-01038-8) contains supplementary material, which is available to authorized users. J. Zhang B. Sun C. Li W. Chen L. Jiang S. Lv Z. Fan D. Pan Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China e-mail: [email protected] J. Zhang B. Sun C. Li W. Chen L. Jiang S. Lv Z. Fan (&) D. Pan (&) Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China e-mail: [email protected]
with the physical length of the chromosome, and the average marker density was approximately 4.83 kb/ SNP. The genome-wide linkage disequilibrium decayed to its half maximum within 0.52 kb for O. rufipogon. The common wild rice accessions were clustered into four subgroups, with some overlap in principal component analysis and a neighbor-joining tree that was also confirmed by model-based admixture. Analysis of molecular variance revealed significant genetic differentiation among individuals, accounting for 90.64% of the total molecular variance; however, the differences between the subgroups (Enping, Lufeng, Suixi and Fogang) were not significant. The significant genetic variations in resources collected in different years were observed in Enping and Suixi subgroups, but there was no significant genetic variation in Fogang subgroup. The pairwise fixation index (FST) suggested that the populations from Enping and Lufeng were most differentiated while those from Enping and Fogang were least differentiated. Our results illustrated clear genetic relationships among 110 common wild rice accessions, showing a potential molecular marker-based strategy for preserving the genetic diversity and accelerating the systematic utilization of these important wild rice resources. Keywords Genetic diversity Population structure SNP Common wild rice
D. Pan e-mail: [email protected]
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Genet Resour Crop Evol
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