Genetic Identity Based on Whole-Genome SNP Array Data of Weedy Rice in Nagano, Japan

Wenjing Bi,Tohru Tominaga,Zhengjin Xu,Nagao Sakai,Jian Sun,Jun Hosoi,Tomio Itani,Masaharu Aoki

doi:10.3390/agronomy9080472

Abstract

The rice production system in Japan is changing due to the aging of rice farmers, shortage of labor, mechanization, and increase of large-scale rice fields and increased application of direct sowing, all of which contribute to the lack of sophisticated weed management practices. Because the changing production system has not improved and likely worsened weed management practices, weedy rice (Oryza sativa L.) has become a serious threat to rice production in Japan. We analyzed weedy rice accessions from Nagano, the central part of Japan, and other rice accessions to elucidate the origin of this weedy rice using a whole-genome single nucleotide polymorphism (SNP) array. For developing sustainable weedy rice management practices, the elucidation of the origin of re-emerging weedy rice is crucial. Population genetic analysis indicated that weedy rice in Nagano was phylogenetically independent from the local red rice cultivar with low genetic diversity. Past and recently re-emerging weedy rice ecotypes in Nagano shared a similar genetic background which implies the evolution of weedy rice by severe natural selection. Window-based FST and selection sweep analysis revealed the divergence of some of the known key domestication-related genes, such as shattering gene sh4 and qsh1, of weedy rice from domesticated rice cultivars.

Highlights

IntroductionWeeds are typically controlled by the application of herbicides. In modern agriculture, selective herbicides are used in crop production to more effectively reduce weed populations.Herbicide selectivity between crops and weeds is conferred by the differences in growth stage, growth characteristics, and physiological properties between the crop and weed
In crop production, weeds are typically controlled by the application of herbicides
quality control (QC) > 0.82 and calling rate >0.92, resulting in a total population of 50,281 single nucleotide polymorphism (SNP) obtained for the following analysis

Summary

Introduction

Weeds are typically controlled by the application of herbicides. In modern agriculture, selective herbicides are used in crop production to more effectively reduce weed populations.Herbicide selectivity between crops and weeds is conferred by the differences in growth stage, growth characteristics, and physiological properties between the crop and weed. Weeds are typically controlled by the application of herbicides. Selective herbicides are used in crop production to more effectively reduce weed populations. Herbicide selectivity between crops and weeds is conferred by the differences in growth stage, growth characteristics, and physiological properties between the crop and weed. This weed-control strategy is undermined when weeds are too closely related to the crop. Weedy rice belongs to the same species as cultivated rice and, is problematic in almost all rice-producing countries. A major difficulty to control weedy rice is the scarcity of effective selective herbicides against weedy rice that will not harm cultivated rice

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Discussion

Conclusion