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Letter

Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice

¹ State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; ² Department of Plant Genetics and Breeding and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China; ³ Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China; ⁴ Beijing Key Laboratory of Crop Genetic Improvement, Beijing 100094, China; ⁵ Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing 100094, China.

By constructing nearly isogenic lines (NILs) that differ only at a single quantitative trait locus (QTL), we fine-mapped the yield-improving QTL qGY2–1 to a 102.9-kb region on rice chromosome 2. Comparison analysis of the genomic sequences in the mapped QTL region between the donor (Dongxiang wild rice, Oryza rufipogon Griff.) and recurrent (Guichao2, Oryza sativa ssp. indica) parents used for the development of NILs identified the haplotypes of a leucine-rich repeat receptor kinase gene cluster, which showed extensive allelic variation. The sequences between genes in the cluster had a very high rate of divergence. More importantly, the genes themselves also differed between two haplotypes: Only 92% identity was observed for one allele, and another allele was found to have completely lost its allelic counterpart in Guichao2. The other six shared genes all showed >98% identity, and four of these exhibited obvious regulatory variation. The same haplotype segments also differed in length (43.9-kb in Guichao2 vs. 52.6-kb in Dongxiang wild rice). Such extensive sequence variation was also observed between orthologous regions of indica (cv. 93–11) and japonica (cv. Nipponbare) subspecies of Oryza sativa. Different rates of sequence divergence within the cluster have resulted in haplotype variability in 13 rice accessions. We also detected allelic expression variation in this gene cluster, in which some genes gave unequal expression of alleles in hybrids. These allelic variations in structure and expression suggest that the leucine-rich repeat receptor kinase gene cluster identified in our study should be a particularly good candidate for the source of the yield QTL.

⁷ Corresponding authors.

E-mail suncq{at}cau.edu.cn; fax 86-10-62731811.

E-mail jsyang{at}fudan.edu.cn; fax 86-21-65648376.

[Supplemental material is available online at www.genome.org.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.4814006

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