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A major locus qS12, located in a duplicated segment of chromosome 12, causes spikelet sterility in an indica-japonica rice hybrid

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Abstract

Chromosome segment duplications are integral in genome evolution by providing a source for the origin of new genes. In the rice genome, besides an ancient polyploidy event known in the rice common ancestor, it had been identified that there was a special segmental duplication involving chromosomes 11 and 12, but the biological role of this duplication remains unknown. In this study, by using a set of chromosome segment substitution lines (CSSLs) and near isogenic lines (NILs) derived from the indica cultivar 9311 and japonica cultivar Nipponbare, a major QTL (qS12) resulting in hybrid male sterility was mapped within ~400 kb region adjacent to the special duplicated segment on the short arm of chromosome 12. Compared to the japonica cultivar Nipponbare, the two sides of the qS12 candidate region were inverted in the indica cultivar 9311. Among 47 of the 111 rice genotypes evaluated by molecular markers, the inverted sides were detected, and found completely homologous to indica cultivar 9311. These results suggested that the two inverted sides protect the sequence in the qS12 regions from recombination. On the short-arm of chromosome 12, two QTLs S-e and S25, in addition to qS12, were previously detected as a distinct segregation distortion and pollen semi-sterility loci. We propose these three hybrid sterility loci are the same locus, and the duplicated segment on chromosome 12 may play a prominent role in diversification, i.e., sub-speciation of cultivated rice.

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Abbreviations

CSSL:

Chromosome segment substitution line

CAPS:

Cleaved amplified polymorphic sequence

ICIM:

Inclusive composite interval mapping

ICIM-ADD:

ICIM of QTLs with additive effects

Mb:

Mega base pairs

MYA:

Million years ago

NIL:

Near isogenic line

PVE:

Phenotypic variation effect

SMA:

Single marker analysis

SSR:

Simple sequence repeat

STS:

Sequence-tagged site

WGD:

Whole genome duplication

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Acknowledgments

This work was supported in part by the National Basic Research Program (2007CB109005 and 2011CB100202), the National Special Program for Transgenic Research (2009ZX08009-008B), the National Natural Science Foundation (30521004 and 30971741), the Priority Academic Program Development from Jiangsu Government, and the Ministry of Education (307018 and NCET-07-0736) of China.

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Authors and Affiliations

  1. State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Developmental Biology of the Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China

    Hua Zhang, Wen Yu & Yang-Sheng Li

  2. Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China

    Chang-Quan Zhang, Zhi-Zhong Sun, Ming-Hong Gu & Qiao-Quan Liu

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  1. Hua Zhang
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  2. Chang-Quan Zhang
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Correspondence to Qiao-Quan Liu or Yang-Sheng Li.

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Communicated by A. Paterson.

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Zhang, H., Zhang, CQ., Sun, ZZ. et al. A major locus qS12, located in a duplicated segment of chromosome 12, causes spikelet sterility in an indica-japonica rice hybrid. Theor Appl Genet 123, 1247–1256 (2011). https://doi.org/10.1007/s00122-011-1663-z

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