title: Artificial Selection of Gn1a Plays an Important role in Improving Rice Yields Across Different Ecological Regions.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  Of 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.
authors.affiliation: State Key Laboratory of Hybrid Rice; Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Science, Wuhan University, Wuhan, 430072, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Hybrid Rice; Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Science, Wuhan University, Wuhan, 430072, China.
authors.forename: Huaxue
authors.initials: H
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Hybrid Rice; Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Science, Wuhan University, Wuhan, 430072, China.
authors.forename: Nengwu
authors.initials: N
authors.lastname: Li
authors.affiliation: State Key Laboratory of Hybrid Rice; Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Science, Wuhan University, Wuhan, 430072, China.
authors.forename: Fengfeng
authors.initials: F
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Hybrid Rice; Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Science, Wuhan University, Wuhan, 430072, China.
authors.forename: Liuting
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Hybrid Rice; Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Science, Wuhan University, Wuhan, 430072, China.
authors.forename: Yingguo
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Hybrid Rice; Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Science, Wuhan University, Wuhan, 430072, China. shaoqingli@whu.edu.cn.
authors.forename: Shaoqing
authors.initials: S
authors.lastname: Li
keywords: Allele; Artificial selection; Association analysis; Gn1a; Rice