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Contributed by Qifa Zhang, August 11, 2015 (sent for review July 2, 2015; reviewed by Roberto Tuberosa and Yunbi Xu)
Significance
Intensive rice breeding over the past 50 y has produced many high-performing cultivars, but our knowledge of the genomic changes associated with such improvement remains limited. By analyzing sequences of 1,479 rice accessions, this study identified genomic changes associated with breeding efforts, referred to as breeding signatures, involving 7.8% of the rice genome. Accumulation of selected regions is positively correlated with yield improvement. The number of selected regions in a line may be used for predicting agronomic potential, and the selected loci may provide useful targets for rice improvement.
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.
Footnotes
↵1W.X. and G.W. contributed equally to this work.
- ↵2To whom correspondence may be addressed. Email: qifazh{at}mail.hzau.edu.cn or xmlian{at}mail.hzau.edu.cn.
Author contributions: W.X. and Q.Z. designed research; W.X., G.W., M. Yuan, W.Y., K.L., and X. Lian performed research; M. Yuan, W.Y., H.Z., M. Yang, P.L., X.Z., J.Y., Q.W., F.L., H.D., L.Z., Xinglei Li, X.M., W.Z., L.X., Y.H., S.W., S.Y., C.X., J.L., Xianghua Li, and J.X. contributed new reagents/analytic tools; W.X. analyzed data; and W.X., G.W., X. Lian, and Q.Z. wrote the paper.
Reviewers: R.T., University of Bologna, Italy; Y.X., Chinese Academy of Agricultural Sciences.
The authors declare no conflict of interest.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1515919112/-/DCSupplemental.
Freely available online through the PNAS open access option.
Breeding signatures of rice improvement
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