Abstract
BackgroundRice is one of the most important crops, and it is essential to improve rice productivity to satisfy the future global food supply demands. Gn1a (OsCKX2), which encodes cytokinin oxidase/dehydrogenase, plays an important role in regulating rice grain yield.ResultsIn this study, we analyzed the genetic variation of Gn1a, which influences grain yield through controlling the number of spikelets in rice. The allelic variations in the promoter, 5’ untranslated region (UTR) and coding sequence (CDS) of Gn1a were investigated in 175 cultivars and 21 wild rice accessions. We found that Gn1a showed less sequence variation in the cultivars, but exhibited significant nucleotide diversity in wild rice. A total of 14 alleles, named AP1 to AP14, were identified in the cultivars based on the amino acid divergence of GN1A. Association analysis revealed that the number of spikelets and grain yield were significantly different between the different alleles. Phylogenetic analysis indicated that the three main alleles, AP3, AP8 and AP9, in the cultivars might originate from a common ancestor allele, AP1, in wild rice.ConclusionsOf these alleles in the cultivars, AP9 was suggested as the best allele in indica, as it has shown strong artificial selection in breeding high-yield rice in the past. It might be valuable to explore the high-yield-related alleles of Gn1a to develop high-yield rice cultivars in future breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0071-4) contains supplementary material, which is available to authorized users.
Highlights
Rice is one of the most important crops, and it is essential to improve rice productivity to satisfy the future global food supply demands
We found that the high-yield-related alleles of GN1A in the rice populations showed strong artificial selection during rice domestication, which indicated that Gn1a played an important role in rice improvements
Nucleotide Variations of Gn1a The Gn1a sequences were cloned and sequenced from the cultivar lines and wild rice accessions, which represented a diverse range of spikelet numbers
Summary
Rice is one of the most important crops, and it is essential to improve rice productivity to satisfy the future global food supply demands. Gn1a (OsCKX2), which encodes cytokinin oxidase/dehydrogenase, plays an important role in regulating rice grain yield. With the rapid decrease in the available farmland and increase in the global population, it is urgent to obtain enough grain production to meet the food supply demands (Weng et al 2008). Rice grain yield is controlled by four basic components, including number of panicles per plant, number of spikelets per panicle, the seed setting rate, and the grain weight, all of which are typical quantitative traits (Xing and Zhang 2010). The relationships between the alleles and rice yield components, including the number of spikelets, thousand-grain weight, seed setting rate and effective panicles per plant, were analyzed by association analysis. We found that the high-yield-related alleles of GN1A in the rice populations showed strong artificial selection during rice domestication, which indicated that Gn1a played an important role in rice improvements
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