Genome-wide association mapping of leaf mass traits in a Vietnamese rice landrace panel

PLoS One. 2019 Jul 8;14(7):e0219274. doi: 10.1371/journal.pone.0219274. eCollection 2019.

Abstract

Leaf traits are often strongly correlated with yield, which poses a major challenge in rice breeding. In the present study, using a panel of Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers, a genome-wide association study (GWAS) was conducted for several leaf traits during the vegetative stage. Vietnamese landraces are often poorly represented in panels used for GWAS, even though they are adapted to contrasting agrosystems and can contain original, valuable genetic determinants. A panel of 180 rice varieties was grown in pots for four weeks with three replicates under nethouse conditions. Different leaf traits were measured on the second fully expanded leaf of the main tiller, which often plays a major role in determining the photosynthetic capacity of the plant. The leaf fresh weight, turgid weight and dry weight were measured; then, from these measurements, the relative tissue weight and leaf dry matter percentage were computed. The leaf dry matter percentage can be considered a proxy for the photosynthetic efficiency per unit leaf area, which contributes to yield. By a GWAS, thirteen QTLs associated with these leaf traits were identified. Eleven QTLs were identified for fresh weight, eleven for turgid weight, one for dry weight, one for relative tissue weight and one for leaf dry matter percentage. Eleven QTLs presented associations with several traits, suggesting that these traits share common genetic determinants, while one QTL was specific to leaf dry matter percentage and one QTL was specific to relative tissue weight. Interestingly, some of these QTLs colocalize with leaf- or yield-related QTLs previously identified using other material. Several genes within these QTLs with a known function in leaf development or physiology are reviewed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping / methods
  • Chromosomes, Plant / genetics
  • Edible Grain / genetics
  • Genome-Wide Association Study
  • Genotype
  • Oryza / genetics*
  • Phenotype
  • Plant Leaves / genetics*
  • Polymorphism, Single Nucleotide / genetics
  • Quantitative Trait Loci / genetics
  • Vietnam

Grants and funding

In addition to institutional funding, this work was supported by the French Ministry of Foreign Affairs and International Development, the Ministry of Science and Technology of Vietnam as part of the project “Application of functional genomics and association genetics to characterize genes involved in abiotic stresses tolerance in rice”, and the CGIAR Research Program (CRP) on Rice Agri-food Systems (RICE, 2017-2022). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.