QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Abstract

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F₂ and F₂-derived F₃ families) and late (F₆ and F₇, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F₂ and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F₂ mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

Keywords: F2; QTL; RILs; SNP markers; bread wheat; genetic map.

Figure 1

Principal component analysis (PCA) diagram showing the phenotypic variation and variable contribution in F₂ (A), F₃ (B), F₆ (C), and F₇ (D) generations. Black points correspond to genotypes, whereas the arrows represent the contribution of the variables to the total variation. HD, heading date; PH, plant height; GH, growth habit; TTN, total tiller number; FTN, fertile tiller number; contrib, contribution of variables to the principal axes expressed as a percentage (%).

Figure 2

Circle plot showing the collinearity between the 21 linkage groups generated by F₂ (blue lines, right side) and F₆ (red lines, left side) populations.

Figure 3

A graphical representation of the 2B and 4B linkage groups derived from the F₂ and F₆ maps and their comparison with the 90K consensus map. The distance between markers is in centimorgans (cM). The markers flanking the QTLs are colored in red (QHd-2B.1 and QPh-4B.1) and blue (QTtn-4B.1) in F₂, while in green for the QTLs (QHd-2B.2, QPh-4B.2, and QTtn-4B.2) in F₆. Solid lines connect the genetic loci in common between the F₂ and F₆ genetic maps and the 90K consensus map [60].