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Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.


ABSTRACT: Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement.

SUBMITTER: Xie W 

PROVIDER: S-EPMC4593105 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Xie Weibo W   Wang Gongwei G   Yuan Meng M   Yao Wen W   Lyu Kai K   Zhao Hu H   Yang Meng M   Li Pingbo P   Zhang Xing X   Yuan Jing J   Wang Quanxiu Q   Liu Fang F   Dong Huaxia H   Zhang Lejing L   Li Xinglei X   Meng Xiangzhou X   Zhang Wan W   Xiong Lizhong L   He Yuqing Y   Wang Shiping S   Yu Sibin S   Xu Caiguo C   Luo Jie J   Li Xianghua X   Xiao Jinghua J   Lian Xingming X   Zhang Qifa Q  

Proceedings of the National Academy of Sciences of the United States of America 20150910 39


Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative he  ...[more]

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