QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat

Abstract

Leaf rolling is an important mechanism to mitigate the effects of moisture stress in several plant species. In the present study, a set of 92 wheat recombinant inbred lines derived from the cross between NI5439 × HD2012 were used to identify QTLs associated with leaf rolling under moisture stress condition. Linkage map was constructed using Axiom 35 K Breeder's SNP Array and microsatellite (SSR) markers. A linkage map with 3661 markers comprising 3589 SNP and 72 SSR markers spanning 22,275.01 cM in length across 21 wheat chromosomes was constructed. QTL analysis for leaf rolling trait under moisture stress condition revealed 12 QTLs on chromosomes 1B, 2A, 2B, 2D, 3A, 4A, 4B, 5D, and 6B. A stable QTL Qlr.nhv-5D.2 was identified on 5D chromosome flanked by SNP marker interval AX-94892575-AX-95124447 (5D:338665301-5D:410952987). Genetic and physical map integration in the confidence intervals of Qlr.nhv-5D.2 revealed 14 putative candidate genes for drought tolerance which was narrowed down to six genes based on in-silico analysis. Comparative study of leaf rolling genes in rice viz., NRL1, OsZHD1, Roc5, and OsHB3 on wheat genome revealed five genes on chromosome 5D. Out of the identified genes, TraesCS5D02G253100 falls exactly in the QTL Qlr.nhv-5D.2 interval and showed 96.9% identity with OsZHD1. Two genes similar to OsHB3 viz. TraesCS5D02G052300 and TraesCS5D02G385300 exhibiting 85.6% and 91.8% identity; one gene TraesCS5D02G320600 having 83.9% identity with Roc5 gene; and one gene TraesCS5D02G102600 showing 100% identity with NRL1 gene were also identified, however, these genes are located outside Qlr.nhv-5D.2 interval. Hence, TraesCS5D02G253100 could be the best potential candidate gene for leaf rolling and can be utilized for improving drought tolerance in wheat.

Figure 1

Linkage map constructed from SNP and SSR genotyping in a recombinant inbred population derived from a cross between NI5439 and HD2012.

Figure 2

(a) Scoring of leaf rolling trait ranging from 1 (no leaf rolling) to 5 (complete leaf rolling); (b) RILs of NI5439 × HD2012 mapping population showing difference in leaf rolling from no rolling of the leaf to complete rolling; (c) graphical illustration of QTLs detected in three environments for leaf rolling. Red, green and blue represent the three environments E17, E18 and E19.

Figure 3

Stable QTL (Qlr.nhv-5D.2) for leaf rolling on 5D chromosome during E17 (red), E18 (green) and E19 (blue). Genetic and physical map location of Qlr.nhv-5D.2 flanked by markers AX-94892575- AX-95124447.

Figure 4

(a) 3D protein structures of the predicted leaf rolling genes in wheat (left) along with the protein structure of corresponding gene in rice (right) and their superimposed (middle) 3D structure in red and grey color. Red color represents wheat protein whereas grey represents rice protein. (b) Expression profiles of predicted leaf rolling wheat genes in three different conditions (no stress control, drought stress and PEG 6000). The dark and light intensity of the blue color represents the higher and lower relative abundance of the transcript.