Chromosome groups 5, 6 and 7 harbor major quantitative trait loci controlling root traits in bread wheat (Triticum aestivum L.)

Abstract

Identifying genomic regions for root traits in bread wheat can help breeders develop climate-resilient and high-yielding wheat varieties with desirable root traits. This study used the recombinant inbred line (RIL) population of Synthetic W7984 × Opata M85 to identify quantitative trait loci (QTL) for different root traits such as rooting depth (RD), root dry mass (RM), total root length (RL), root diameter (Rdia) and root surface areas (RSA1 for coarse roots and RSA2 for fine roots) under controlled conditions in a semi-hydroponic system. We detected 14 QTL for eight root traits on nine wheat chromosomes; we discovered three QTL each for RD and RSA1, two QTL each for RM and RSA2, and one QTL each for RL, Rdia, specific root length and nodal root number per plant. The detected QTL were concentrated on chromosome groups 5, 6 and 7. The QTL for shallow RD (Q.rd.uwa.7BL: Xbarc50) and high RM (Q.rm.uwa.6AS: Xgwm334) were validated in two independent F₂ populations of Synthetic W7984 × Chara and Opata M85 × Cascade, respectively. Genotypes containing negative alleles for Q.rd.uwa.7BL had 52% shallower RD than other Synthetic W7984 × Chara population lines. Genotypes with the positive alleles for Q.rm.uwa.6AS had 31.58% higher RM than other Opata M85 × Cascade population lines. Further, we identified 21 putative candidate genes for RD (Q.rd.uwa.7BL) and 13 for RM (Q.rm.uwa.6AS); TraesCS6A01G020400, TraesCS6A01G024400 and TraesCS6A01G021000 identified from Q.rm.uwa.6AS, and TraesCS7B01G404000, TraesCS7B01G254900 and TraesCS7B01G446200 identified from Q.rd.uwa.7BL encoded important proteins for root traits. We found germin-like protein encoding genes in both Q.rd.uwa.7BL and Q.rm.uwa.6AS regions. These genes may play an important role in RM and RD improvement. The identified QTL, especially the validated QTL and putative candidate genes are valuable genetic resources for future root trait improvement in wheat.

Keywords: QTL; candidate genes; genomic region; markers; phenotyping; recombinant inbred lines.

Figure 1

Distribution of (A) total root length (cm), (B) rooting depth (cm), (C) root dry mass (g), (D) root diameter (mm), (E) root surface area of fine roots (root diameter< 0.25 mm, cm²), (F) root surface area of coarse roots (root diameter > 0.25 mm, cm²), and (G) specific root length (cm g^-1) of 103 recombinant inbred lines and their parents, Synthetic W7984 and Opata 85. The green and red arrows indicate the phenotypic performance of Synthetic W7984 and Opata M85, respectively.

Figure 2

Mapping of important QTL for root traits in wheat in the Synthetic W7984 and Opata 85 RIL population (A) total root length (RL, cm), rooting depth (RD, cm), and nodal roots per plant (NNR) (B) rooting depth and root surface area of fine roots (root diameter < 0.25 mm, RSA2, cm²), (C) root dry mass (RM), and (D) rooting depth of recombinant inbred lines of Synthetic W7984 × Opata 85. Bars and caps indicate the QTL with LOD > 2.5. Red markers are flanking markers of different colours in individual chromosomes that represent the tightly linked marker of the respective QTL.

Figure 3

Quantitative trait loci (QTL) identified in this study and previous studies (Ibrahim et al., 2012; Ren et al., 2012; Liu et al., 2013; Xu et al., 2013; Atkinson et al., 2015; Ehdaie et al., 2016; Ayalew et al., 2017; Ren et al., 2017; Soriano and Alvaro, 2019; Li et al., 2020; Meng-jiao et al., 2020; Danakumara et al., 2021; Yang et al., 2021a) on chromosomes 5A, 5D, 6A, 6B, 6D, 7A and 7B. Previously discovered QTL for root traits and grain yield were depicted. The QTL identified in this study were labelled in red colour, and the previously studied QTL were represented by other colours (blue, yellow, green, green-cyan, magenta and blue-magenta). Blue circles represent the genomic regions of the validated QTL (Q.rm.uwa.6AS and Q.rd.uwa.7BL) positions from this study and their overlapping with other QTL from previous studies. Table 2 is referred to the detailed QTL identified in this study on different chromosomes; GY, grain yield; SA, surface area; RL, total root length; Rdia, root diameter; RV, root volume; NNR, number of nodal roots per plant; RSA2 root surface area of fine roots (root diameter < 0.25 mm); SRL, specific root length; RM, root dry mass; and RD, rooting depth.