Open Access Research article

A genomic perspective on the important genetic mechanisms of upland adaptation of rice

Jun Lyu1*, Baoye Li2, Weiming He3, Shilai Zhang2, Zhiheng Gou1, Jing Zhang2, Liyun Meng4, Xin Li5, Dayun Tao2, Wangqi Huang2, Fengyi Hu2* and Wen Wang1*

Author Affiliations

1 CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China

2 Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China

3 BGI-Shenzhen, Shenzhen 518083, China

4 Inner Mongolia Agricultural University, Hohhot 010018, China

5 Center for Epigenetics, Johns Hopkins University School of Medicine Baltimore, MD, Baltimore 21205, USA

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BMC Plant Biology 2014, 14:160  doi:10.1186/1471-2229-14-160

Published: 11 June 2014



Cultivated rice consists of two important ecotypes, upland and irrigated, that have respectively adapted to either dry land or irrigated cultivation. Upland rice, widely adopted in rainfed upland areas in virtue of its little water requirement, contains abundant untapped genetic resources, such as genes for drought adaptation. With water shortage exacerbated and population expanding, the need for breeding crop varieties with drought adaptation becomes more and more urgent. However, a previous oversight in upland rice research reveals little information regarding its genetic mechanisms for upland adaption, greatly hindering progress in harnessing its genetic resources for breeding and cultivation.


In this study, we selected 84 upland and 82 irrigated accessions from all over the world, phenotyped them under both irrigated and dry land environments, and investigated the phylogenetic relations and population structure of the upland ecotype using whole genome variation data. Further comparative analysis yields a list of differentiated genes that may account for the phenotypic and physiological differences between upland and irrigated rice.


This study represents the first genomic investigation in a large sample of upland rice, providing valuable gene list for understanding upland rice adaptation, especially drought-related adaptation, and its subsequent utilization in modern agriculture.

Upland rice; Upland adaptation; Genetic mechanisms; Phylogenetics; Population structure; Artificial selection