Physical Mapping of QTLs for Root Traits in a Population of Recombinant Inbred Lines of Hexaploid Wheat

Abstract

Root architecture is key in determining how effective plants are at intercepting and absorbing nutrients and water. Previously, the wheat (Triticum aestivum) cultivars Spica and Maringa were shown to have contrasting root morphologies. These cultivars were crossed to generate an F_6:1 population of recombinant inbred lines (RILs) which was genotyped using a 90 K single nucleotide polymorphisms (SNP) chip. A total of 227 recombinant inbred lines (RILs) were grown in soil for 21 days in replicated trials under controlled conditions. At harvest, the plants were scored for seven root traits and two shoot traits. An average of 7.5 quantitative trait loci (QTL) were associated with each trait and, for each of these, physical locations of the flanking markers were identified using the Chinese Spring reference genome. We also compiled a list of genes from wheat and other monocotyledons that have previously been associated with root growth and morphology to determine their physical locations on the Chinese Spring reference genome. This allowed us to determine whether the QTL discovered in our study encompassed genes previously associated with root morphology in wheat or other monocotyledons. Furthermore, it allowed us to establish if the QTL were co-located with the QTL identified from previously published studies. The parental lines together with the genetic markers generated here will enable specific root traits to be introgressed into elite wheat lines. Moreover, the comprehensive list of genes associated with root development, and their physical locations, will be a useful resource for researchers investigating the genetics of root morphology in cereals.

Keywords: bread wheat; candidate genes; genetics; root morphology; traits.

Figure 1

Distribution profiles of various traits across RILs. BLUP data with SE as error bars and locations of parental lines are shown (M = Maringa and S = Spica).

Figure 2

Schematic of positions of QTLs on the Chinese Spring IWGSC v1.0 physical map along with the previously identified QTLs and cloned genes associated with root development in wheat and other species. Chromosomes and locations are drawn approximately to scale. Boxes and letters in green denote a QTL with LOD scores greater than 3.0 while boxes and letters in magenta denote a QTL with LOD scores less than 3.0. Previously cloned root genes associated with root morphology in wheat and other monocotyledons are shown on the right side of the chromosomes with horizontal lines indicating locations on the chromosomes. Since the RILs were segregated for the semi-dwarfing gene Rht1-B1b, this gene is included in the Figure. Gene names with asterisks (*) denote genes that are inside a QTL or within 5 Mb of a flanking marker of a QTL identified in our study. Locations shown by bold numbers indicate locations of candidate genes or SNPs identified from other studies that are inside QTL or within 5 Mb of the closest flanking marker identified in our study. Numbers 1–6 correspond to QTL with candidate wheat genes as identified by the meta-analysis of Soriano and Alvaro [12]: 1; Root_MQTL_17 TraesCS2A01G004600, 2; Root_MQTL_35 TraesCS3A01G477800, 3; Root_MQTL_45 TraesCS4A01G306600, 4; Root_MQTL_55 TraesCS5A01G012600, 5; Root_MQTL_40 TraesCS3B01G334000, 6; Root_MQTL_63 TraesCS5D01G096700. Numbers 7–9 correspond to SNPs significantly associated with root QTL as identified in a GWAS by Ma et al. [13] including SNPs on 2B and on 6A for average root diameter and a SNP on 2A for total root area/volume. Root QTLs identified by Yang et al. [14] from a biparental QTL analysis that overlap with our QTL are shown as black boxes and are numbered at locations on chromosome 4B (10; root dry weight and root to shoot ratio) and chromosome 6B (11; root length and shoot dry weight). The traits we analyzed included the root dry weight (rdw), shoot dry weight (sdw), root-to-shoot ratio (rsr), root diameter (rd), specific root length (srl), tiller number (tn), total nodal root number (tnrn), nodal root number per stem (nrns) and root angle (ra).