Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding

Author:

Wang Yulong1,Jiang Conghui12,Zhang Xingtan34ORCID,Yan Huimin5,Yin Zhigang1,Sun Xingming1,Gao Fenghua1,Zhao Yan1,Liu Wei1,Han Shichen1,Zhang Jingjing1,Zhang Yage6,Zhang Zhanying1ORCID,Zhang Hongliang1ORCID,Li Jinjie1ORCID,Xie Xianzhi2,Zhao Quanzhi5,Wang Xiaoning6,Ye Guoyou47ORCID,Li Junzhou5,Ming Ray3,Li Zichao16ORCID

Affiliation:

1. Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology China Agricultural University Beijing China

2. Institute of Wetland Agriculture and Ecology Shandong Academy of Agricultural Sciences Jinan Shandong China

3. Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education Fujian Agriculture and Forestry University Fuzhou Fujian China

4. Agricultural Genomics Institute in Shenzhen Chinese Academy of Agricultural Sciences Shenzhen Guangdong China

5. Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Biology Henan Agricultural University Zhengzhou Henan China

6. Sanya Institute of Hainan Academy of Agricultural Sciences Sanya Hainan China

7. Institution International Rice Research Institute Los Baños Laguna Philippines

Abstract

SummaryUpland rice is a distinctive drought‐aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought‐aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high‐quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought‐resistant rice and the “blue revolution” in agriculture.

Funder

National Natural Science Foundation of China

Publisher

Wiley

Subject

Plant Science,Agronomy and Crop Science,Biotechnology

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