Identification of quantitative trait loci for zinc deficiency tolerance in finger millet (Eleusine coracana (L.) Gaertn) by linkage mapping and in silico analysis of candidate genes

Abstract

Finger millet (Eleusine coracana (L.) Gaertn) is a nutrient-rich cereal crop widely cultivated in many low- and middle-income countries of Asia and Africa. Zinc (Zn) deficiency is the most common problem in worldwide agricultural soils. Zn is one of the important soil micronutrients limiting crop productivity. The objective of this study was to identify quantitative trait loci (QTL) conditioning phenotypic traits, photosynthetic pigment, and Zn content of 100 F2:3 populations of finger millet grown under Zn deficient (ZnD, 0.05 mu M) and Zn sufficient (ZnS, 1.0 mu M) conditions using 101 simple sequence repeats (SSR) markers by linkage mapping. The ZnD influenced the growth, biomass, photosynthetic pigment, and Zn content in the leaf and root tissues in 100 F2:3 populations of finger millet in this study. A total of 36 QTL were identified under the ZnS condition, and 63 QTL were identified under the ZnD condition. Four SSR markers (UGEP16, UGEP95, UGEP101, and UGEP104) were mostly flanked with several QTL for various traits under ZnS and ZnD conditions. Several abiotic stress-responsive genes were found to be linked with QTL markers identified in this study. This study provides information on the effects of Zn deficiency in finger millet and QTL and candidate genes related to Zn deficiency tolerance. The identified QTL and genes from the present study might help to develop ZnD-tolerant or Zn use-efficient finger millet varieties through marker-assisted breeding. The findings from this study might guide finger millet researchers involved in Zn deficiency-tolerance improvement and genetic analysis.