SNP-based mixed model association of growth- and yield-related traits in popcorn

PLoS One. 2019 Jun 25;14(6):e0218552. doi: 10.1371/journal.pone.0218552. eCollection 2019.

Abstract

The identification of the genes responsible for complex traits is highly promising to accelerate crop breeding, but such information is still limited for popcorn. Thus, in the present study, a mixed linear model-based association analysis (MLMA) was applied for six important popcorn traits: plant and ear height, 100-grain weight, popping expansion, grain yield and expanded popcorn volume per hectare. To this end, 196 plants of the open-pollinated popcorn population UENF-14 were sampled, selfed (S1), and then genotyped with a panel of 10,507 single nucleotide polymorphisms (SNPs) markers distributed throughout the genome. The six traits were studied under two environments [Campos dos Goytacazes-RJ (ENV1) and Itaocara-RJ (ENV2)] in an incomplete block design. Based on the phenotypic data of the S1 progenies and on the genetic characteristics of the parents, the MLMA was performed. Thereafter, genes annotated in the MaizeGDB platform were screened for potential linkage disequilibrium with the SNPs associated to the six evaluated traits. Overall, seven and eight genes were identified as associated with the traits in ENV1 and ENV2, respectively, and proteins encoded by these genes were evaluated for their function. The results obtained here contribute to increase knowledge on the genetic architecture of the six evaluated traits and might be used for marker-assisted selection in breeding programs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Edible Grain / genetics*
  • Linkage Disequilibrium
  • Polymorphism, Single Nucleotide*
  • Quantitative Trait, Heritable
  • Zea mays / genetics*

Grant support

This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001 to JSS, VJdL, SHK, YPdS, IAS, TdOS and RBB. Funding was also provided by Rio de Janeiro State Research Support Foundation (FAPERJ), with the project E26/200.585/2016 to GSM and E26/202.310/2017 to ATdAJ, and Bayer for providing support in the form of salary to the author JEdAF, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.