Increased novel single nucleotide polymorphisms in weedy rice populations associated with the change of farming styles: Implications in adaptive mutation and evolution

Abstract

Substantial genetic variation is found in weedy rice (Oryza sativa f. spontanea Roshev.) populations from different rice‐planting regions with the change of farming styles. To determine the association of such genetic variation with rice farming changes is critical for understanding the adaptive evolution of weedy rice. We studied weedy‐rice specific novel single nucleotide polymorphisms (SNPs) by genome‐wide comparison between DNA sequences of weedy and cultivated rice, in addition to polymerase chain reaction fingerprinting at 22 selected novel SNP loci in weedy rice populations. A great number of novel SNPs were identified across the weedy rice genome. High frequencies of the novel SNPs were determined at the 22 selected loci, although with considerable variation among weedy rice populations in different rice‐planting regions. The highest frequency (∼57%) of novel SNPs was identified in weedy rice populations from Jiangsu that experienced the most dramatic changes in rice farming styles, including the shift from transplanting to direct seeding, and from indica to japonica varieties. The lowest frequency (∼29%) was detected in weedy rice populations from Northeast China, where rice farming has undergone relatively less change. The association between frequencies of novel SNPs in weedy rice populations and the extent of changes in rice farming styles suggests the critical role of adaptive mutation and accumulation of the mutation influenced by human activities in the rapid evolution of weedy rice.

Enhanced genetic diversity of weedy rice populations associated with latitude decreases revealed by simple sequence repeat fingerprints

“…In addition, the close genetic relationship between SL WR and cultivated rice is probably due to the relatively few rice varieties with a similar genetic background to WR in this country (Xu et al, ). This is different from rice farming in China, where changes of rice varieties, even from indica to japonica varieties, are frequently taking place in many rice‐planting regions, particularly in JS province (Nai et al, ; Song et al, ). We therefore conclude that both geographical distribution and cultivar types have significantly influenced genetic differentiation of WR populations across the rice‐planting regions included in this study.…”

“…This result supports the multiple origins of the WR populations in JS province, most likely through introgression from cultivated rice (Xia et al, ; Sun et al, ), as well as dedomestication as suggested by Li et al () and Qiu et al (). The gradual transition from the traditional way of growing indica types of rice cultivars to the current cultivation of japonica types of cultivars over the past several decades (Nai et al, ; Song et al, ) might have promoted the change in the genetic diversity and structural patterns of WR in the JS region. Previous studies also documented such a change from the indica to japonica type of WR plants (Song et al, ), and increased single nucleotide polymorphisms in WR populations in JS province (Song et al, ).…”

“…In other words, WR individuals from the JS province showed transitional genetic characteristics between those from the GD (indica) and NE (japonica) rice-planting regions, suggesting evident indica-japonica differentiation of WR populations in JS, most likely influenced by crop-weed gene flow and introgression with different types of rice cultivars (Xia et al, 2011). The shift from indica to japonica rice cultivars in JS for the last several decades (Nai et al, 2012;Song et al, 2017) strongly supports this hypothesis. In addition, the close genetic relationship between SL WR and cultivated rice is probably due to the relatively few rice varieties with a similar genetic background to WR in this country (Xu et al, 2012).…”

“…The gradual transition from the traditional way of growing indica types of rice cultivars to the current cultivation of japonica types of cultivars over the past several decades (Nai et al, ; Song et al, ) might have promoted the change in the genetic diversity and structural patterns of WR in the JS region. Previous studies also documented such a change from the indica to japonica type of WR plants (Song et al, ), and increased single nucleotide polymorphisms in WR populations in JS province (Song et al, ). Furthermore, hybrid rice varieties are commonly grown in JS and GD provinces, which might also increase the heterogeneity (admixture) of WR if there exists recurrent crop‐to‐weed gene flow.…”

Spatial and temporal evolution of imidazolinone-resitant red rice in 'Clearfield' rice cultivations

“…However, a few seasons later, a large occurrence of escapees was observed again, which may be associated with the ALS alleles Ala122Thr and Ser653Asn carried by current CL rice cultivars. These results are related to the introgression among cultivated and red (Song et al, 2017) and wild rice , which is a challenge for the sustainability of technologies for herbicide-tolerance in rice crop.…”